answer
stringlengths 17
10.2M
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package mobi.cangol.mobile.security;
import android.test.InstrumentationTestCase;
public class AESUtilsTest extends InstrumentationTestCase {
public void testEncrypt() throws Exception {
assertNotNull(AESUtils.encrypt("12345678", "test"));
}
public void testDecrypt() throws Exception {
//assertEquals(AESUtils.decrypt("12345678", AESUtils.encrypt("12345678", "test")), "test");
}
public void testToByte() throws Exception {
}
public void testToHex() throws Exception {
}
}
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package prodocswing.forms;
import java.awt.Font;
import java.awt.Image;
import java.io.File;
import java.io.PrintWriter;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.Date;
import java.util.HashSet;
import java.util.Iterator;
import javax.swing.ImageIcon;
import javax.swing.JFileChooser;
import javax.swing.filechooser.FileNameExtensionFilter;
import javax.swing.text.DefaultFormatterFactory;
import javax.swing.tree.DefaultMutableTreeNode;
import javax.swing.tree.DefaultTreeModel;
import javax.swing.tree.TreeModel;
import javax.swing.tree.TreePath;
import prodoc.*;
import prodocswing.PDTableModel;
import prodocswing.TreeFolder;
/**
*
* @author jhierrot
*/
public class MainWin extends javax.swing.JFrame
{
static private Font MenuFont=null;
static private Font TreeFont=null;
static private Font ListFont=null;
static private Font DialogFont=null;
private static DriverGeneric Session=null;
static private DefaultTreeModel FoldTreeModel=null;
private static SimpleDateFormat formatterTS = null;
private static SimpleDateFormat formatterDate = null;
private static DefaultFormatterFactory formFacTS = null;
private static DefaultFormatterFactory formFacDate = null;
static private String ActFolderId=PDFolders.ROOTFOLDER;
static private PDTableModel DocsContained;
static private int ExpFolds=0;
static private int ExpDocs=0;
private PDFolders FoldAct=null;
static private String List=PDFolders.fACL+"/"+PDFolders.fFOLDTYPE+"/"+PDFolders.fPARENTID+"/"+PDFolders.fPDID+"/"+PDFolders.fTITLE+"/"+PDFolders.fPDAUTOR+"/"+PDFolders.fPDDATE;
static private HashSet ExecFiles=new HashSet();
static private java.awt.Cursor DefCur=new java.awt.Cursor(java.awt.Cursor.DEFAULT_CURSOR);
static private final java.awt.Cursor WaitCur=new java.awt.Cursor(java.awt.Cursor.WAIT_CURSOR);
/**
* @return the Session
*/
public static DriverGeneric getSession()
{
return Session;
}
/** Creates new form MainWin */
public MainWin()
{
initComponents();
TreeFolder.setPreferredSize(null);
DocsTable.setAutoCreateRowSorter(true);
DocsTable.setAutoCreateColumnsFromModel(true);
SetMenu();
}
/** This method is called from within the constructor to
* initialize the form.
* WARNING: Do NOT modify this code. The content of this method is
* always regenerated by the Form Editor.
*/
@SuppressWarnings("unchecked")
// <editor-fold defaultstate="collapsed" desc="Generated Code">//GEN-BEGIN:initComponents
private void initComponents() {
jSplitPane1 = new javax.swing.JSplitPane();
jScrollPane1 = new javax.swing.JScrollPane();
TreeFolder = new javax.swing.JTree();
jSplitPane2 = new javax.swing.JSplitPane();
jScrollPane2 = new javax.swing.JScrollPane();
SelFolderDesc = new javax.swing.JLabel();
jScrollPane3 = new javax.swing.JScrollPane();
DocsTable = new javax.swing.JTable();
menuBar = new javax.swing.JMenuBar();
FolderMenu = new javax.swing.JMenu();
AddFold = new javax.swing.JMenuItem();
DelFold = new javax.swing.JMenuItem();
ModFold = new javax.swing.JMenuItem();
jSeparator2 = new javax.swing.JPopupMenu.Separator();
AddFoldAdvanced = new javax.swing.JMenuItem();
ModFoldAdvanced = new javax.swing.JMenuItem();
RefreshFold = new javax.swing.JMenuItem();
SearchFold = new javax.swing.JMenuItem();
jSeparator6 = new javax.swing.JPopupMenu.Separator();
ExportFold = new javax.swing.JMenuItem();
ImportFold = new javax.swing.JMenuItem();
ImportExtFold = new javax.swing.JMenuItem();
jSeparator5 = new javax.swing.JPopupMenu.Separator();
exitMenuItem = new javax.swing.JMenuItem();
DocMenu = new javax.swing.JMenu();
AddDoc = new javax.swing.JMenuItem();
DelDoc = new javax.swing.JMenuItem();
jSeparator3 = new javax.swing.JPopupMenu.Separator();
AddDocAdvanced = new javax.swing.JMenuItem();
ModDocAdvanced = new javax.swing.JMenuItem();
ViewMetadata = new javax.swing.JMenuItem();
RefreshDocs = new javax.swing.JMenuItem();
jSeparator4 = new javax.swing.JPopupMenu.Separator();
CheckOut = new javax.swing.JMenuItem();
CheckIn = new javax.swing.JMenuItem();
CancelCheckout = new javax.swing.JMenuItem();
ListVersions = new javax.swing.JMenuItem();
jSeparator1 = new javax.swing.JPopupMenu.Separator();
SearchDocs = new javax.swing.JMenuItem();
ExportDoc = new javax.swing.JMenuItem();
ImportDoc = new javax.swing.JMenuItem();
OtherMenu = new javax.swing.JMenu();
PaperBin = new javax.swing.JMenuItem();
ChangePass = new javax.swing.JMenuItem();
AdminMenu = new javax.swing.JMenu();
ACLMenuItem = new javax.swing.JMenuItem();
GroupMenuItem = new javax.swing.JMenuItem();
UserMenuItem = new javax.swing.JMenuItem();
RolMenuItem = new javax.swing.JMenuItem();
MimeTypeMenuItem = new javax.swing.JMenuItem();
ReposMenuItem = new javax.swing.JMenuItem();
ObjDefMenuItem = new javax.swing.JMenuItem();
AuthentMenuItem = new javax.swing.JMenuItem();
CustomMenuItem = new javax.swing.JMenuItem();
helpMenu = new javax.swing.JMenu();
contentsMenuItem1 = new javax.swing.JMenuItem();
aboutMenuItem1 = new javax.swing.JMenuItem();
ReportBugs = new javax.swing.JMenuItem();
setDefaultCloseOperation(javax.swing.WindowConstants.EXIT_ON_CLOSE);
setTitle("OpenProdoc "+getVersion());
setIconImage(getIcon());
addWindowListener(new java.awt.event.WindowAdapter() {
public void windowClosing(java.awt.event.WindowEvent evt) {
formWindowClosing(evt);
}
});
jSplitPane1.setDividerLocation(180);
jSplitPane1.setDividerSize(4);
TreeFolder.setFont(getFontTree());
TreeFolder.setModel(getTreeModel());
TreeFolder.setAlignmentX(0.3F);
TreeFolder.setAutoscrolls(true);
TreeFolder.setComponentPopupMenu(FolderMenu.getComponentPopupMenu());
TreeFolder.setMaximumSize(new java.awt.Dimension(400, 76));
TreeFolder.setMinimumSize(new java.awt.Dimension(200, 60));
TreeFolder.setPreferredSize(new java.awt.Dimension(200, 76));
TreeFolder.addTreeExpansionListener(new javax.swing.event.TreeExpansionListener() {
public void treeCollapsed(javax.swing.event.TreeExpansionEvent evt) {
}
public void treeExpanded(javax.swing.event.TreeExpansionEvent evt) {
TreeFolderTreeExpanded(evt);
}
});
TreeFolder.addTreeSelectionListener(new javax.swing.event.TreeSelectionListener() {
public void valueChanged(javax.swing.event.TreeSelectionEvent evt) {
TreeFolderValueChanged(evt);
}
});
jScrollPane1.setViewportView(TreeFolder);
jSplitPane1.setLeftComponent(jScrollPane1);
jSplitPane2.setDividerLocation(160);
jSplitPane2.setDividerSize(4);
jSplitPane2.setOrientation(javax.swing.JSplitPane.VERTICAL_SPLIT);
jScrollPane2.setMinimumSize(new java.awt.Dimension(24, 48));
SelFolderDesc.setFont(getFontMenu());
SelFolderDesc.setVerticalAlignment(javax.swing.SwingConstants.TOP);
jScrollPane2.setViewportView(SelFolderDesc);
jSplitPane2.setTopComponent(jScrollPane2);
DocsTable.setFont(getFontList());
DocsTable.setModel(new javax.swing.table.DefaultTableModel(
new Object [][] {
},
new String [] {
}
));
DocsTable.addMouseListener(new java.awt.event.MouseAdapter() {
public void mouseClicked(java.awt.event.MouseEvent evt) {
DocsTableMouseClicked(evt);
}
});
jScrollPane3.setViewportView(DocsTable);
jSplitPane2.setRightComponent(jScrollPane3);
jSplitPane1.setRightComponent(jSplitPane2);
menuBar.setFont(getFontMenu());
FolderMenu.setText(TT("Folders"));
FolderMenu.setFont(getFontMenu());
AddFold.setFont(getFontMenu());
AddFold.setIcon(new javax.swing.ImageIcon(getClass().getResource("/resources/add.png"))); // NOI18N
AddFold.setText(TT("Add"));
AddFold.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
AddFoldActionPerformed(evt);
}
});
FolderMenu.add(AddFold);
DelFold.setFont(getFontMenu());
DelFold.setIcon(new javax.swing.ImageIcon(getClass().getResource("/resources/del.png"))); // NOI18N
DelFold.setText(TT("Delete"));
DelFold.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
DelFoldActionPerformed(evt);
}
});
FolderMenu.add(DelFold);
ModFold.setFont(getFontMenu());
ModFold.setText(TT("Update"));
ModFold.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
ModFoldActionPerformed(evt);
}
});
FolderMenu.add(ModFold);
FolderMenu.add(jSeparator2);
AddFoldAdvanced.setFont(getFontMenu());
AddFoldAdvanced.setText(TT("Extended_Add"));
AddFoldAdvanced.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
AddFoldAdvancedActionPerformed(evt);
}
});
FolderMenu.add(AddFoldAdvanced);
ModFoldAdvanced.setFont(getFontMenu());
ModFoldAdvanced.setIcon(new javax.swing.ImageIcon(getClass().getResource("/resources/edit.png"))); // NOI18N
ModFoldAdvanced.setText(TT("Update_Extended"));
ModFoldAdvanced.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
ModFoldAdvancedActionPerformed(evt);
}
});
FolderMenu.add(ModFoldAdvanced);
RefreshFold.setFont(getFontMenu());
RefreshFold.setText(TT("Refresh"));
RefreshFold.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
RefreshFoldActionPerformed(evt);
}
});
FolderMenu.add(RefreshFold);
SearchFold.setFont(getFontMenu());
SearchFold.setText(TT("Search_Folders"));
SearchFold.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
SearchFoldActionPerformed(evt);
}
});
FolderMenu.add(SearchFold);
FolderMenu.add(jSeparator6);
ExportFold.setFont(getFontMenu());
ExportFold.setText(TT("Export_Folders"));
ExportFold.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
ExportFoldActionPerformed(evt);
}
});
FolderMenu.add(ExportFold);
ImportFold.setFont(getFontMenu());
ImportFold.setText(TT("Import_Folders"));
ImportFold.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
ImportFoldActionPerformed(evt);
}
});
FolderMenu.add(ImportFold);
ImportExtFold.setFont(getFontMenu());
ImportExtFold.setText(TT("Import_Ext_Systems"));
ImportExtFold.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
ImportExtFoldActionPerformed(evt);
}
});
FolderMenu.add(ImportExtFold);
FolderMenu.add(jSeparator5);
exitMenuItem.setFont(getFontMenu());
exitMenuItem.setText(TT("Exit"));
exitMenuItem.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
exitMenuItemActionPerformed(evt);
}
});
FolderMenu.add(exitMenuItem);
menuBar.add(FolderMenu);
DocMenu.setText(TT("Documents"));
DocMenu.setFont(getFontMenu());
AddDoc.setFont(getFontMenu());
AddDoc.setIcon(new javax.swing.ImageIcon(getClass().getResource("/resources/add.png"))); // NOI18N
AddDoc.setText(TT("Add"));
AddDoc.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
AddDocActionPerformed(evt);
}
});
DocMenu.add(AddDoc);
DelDoc.setFont(getFontMenu());
DelDoc.setIcon(new javax.swing.ImageIcon(getClass().getResource("/resources/del.png"))); // NOI18N
DelDoc.setText(TT("Delete"));
DelDoc.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
DelDocActionPerformed(evt);
}
});
DocMenu.add(DelDoc);
DocMenu.add(jSeparator3);
AddDocAdvanced.setFont(getFontMenu());
AddDocAdvanced.setText(TT("Extended_Add"));
AddDocAdvanced.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
AddDocAdvancedActionPerformed(evt);
}
});
DocMenu.add(AddDocAdvanced);
ModDocAdvanced.setFont(getFontMenu());
ModDocAdvanced.setIcon(new javax.swing.ImageIcon(getClass().getResource("/resources/edit.png"))); // NOI18N
ModDocAdvanced.setText(TT("Update_Extended"));
ModDocAdvanced.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
ModDocAdvancedActionPerformed(evt);
}
});
DocMenu.add(ModDocAdvanced);
ViewMetadata.setFont(getFontMenu());
ViewMetadata.setText(TT("Document_Attributes"));
ViewMetadata.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
ViewMetadataActionPerformed(evt);
}
});
DocMenu.add(ViewMetadata);
RefreshDocs.setFont(getFontMenu());
RefreshDocs.setText(TT("Refresh"));
RefreshDocs.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
RefreshDocsActionPerformed(evt);
}
});
DocMenu.add(RefreshDocs);
DocMenu.add(jSeparator4);
CheckOut.setFont(getFontMenu());
CheckOut.setIcon(new javax.swing.ImageIcon(getClass().getResource("/resources/checkout.png"))); // NOI18N
CheckOut.setText("CheckOut");
CheckOut.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
CheckOutActionPerformed(evt);
}
});
DocMenu.add(CheckOut);
CheckIn.setFont(getFontMenu());
CheckIn.setIcon(new javax.swing.ImageIcon(getClass().getResource("/resources/checkin.png"))); // NOI18N
CheckIn.setText("CheckIn");
CheckIn.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
CheckInActionPerformed(evt);
}
});
DocMenu.add(CheckIn);
CancelCheckout.setFont(getFontMenu());
CancelCheckout.setIcon(new javax.swing.ImageIcon(getClass().getResource("/resources/cancelcheckout.png"))); // NOI18N
CancelCheckout.setText("CancelCheckout");
CancelCheckout.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
CancelCheckoutActionPerformed(evt);
}
});
DocMenu.add(CancelCheckout);
ListVersions.setFont(getFontMenu());
ListVersions.setText(TT("List_of_Versions"));
ListVersions.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
ListVersionsActionPerformed(evt);
}
});
DocMenu.add(ListVersions);
DocMenu.add(jSeparator1);
SearchDocs.setFont(getFontMenu());
SearchDocs.setText(TT("Search_Documents"));
SearchDocs.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
SearchDocsActionPerformed(evt);
}
});
DocMenu.add(SearchDocs);
ExportDoc.setFont(getFontMenu());
ExportDoc.setText(TT("Export_Doc"));
ExportDoc.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
ExportDocActionPerformed(evt);
}
});
DocMenu.add(ExportDoc);
ImportDoc.setFont(getFontMenu());
ImportDoc.setText(TT("Import_Doc"));
ImportDoc.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
ImportDocActionPerformed(evt);
}
});
DocMenu.add(ImportDoc);
menuBar.add(DocMenu);
OtherMenu.setText(TT("Other_Tasks"));
OtherMenu.setFont(getFontMenu());
PaperBin.setFont(getFontMenu());
PaperBin.setIcon(new javax.swing.ImageIcon(getClass().getResource("/resources/undel.png"))); // NOI18N
PaperBin.setText(MainWin.TT("Trash_bin"));
PaperBin.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
PaperBinActionPerformed(evt);
}
});
OtherMenu.add(PaperBin);
ChangePass.setFont(getFontMenu());
ChangePass.setText(MainWin.TT("Password_change"));
ChangePass.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
ChangePassActionPerformed(evt);
}
});
OtherMenu.add(ChangePass);
menuBar.add(OtherMenu);
AdminMenu.setText(TT("Administration"));
AdminMenu.setFont(getFontMenu());
ACLMenuItem.setFont(getFontMenu());
ACLMenuItem.setText("ACL");
ACLMenuItem.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
ACLMenuItemActionPerformed(evt);
}
});
AdminMenu.add(ACLMenuItem);
GroupMenuItem.setFont(getFontMenu());
GroupMenuItem.setText(TT("Groups"));
GroupMenuItem.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
GroupMenuItemActionPerformed(evt);
}
});
AdminMenu.add(GroupMenuItem);
UserMenuItem.setFont(getFontMenu());
UserMenuItem.setText(TT("Users"));
UserMenuItem.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
UserMenuItemActionPerformed(evt);
}
});
AdminMenu.add(UserMenuItem);
RolMenuItem.setFont(getFontMenu());
RolMenuItem.setText(TT("Roles"));
RolMenuItem.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
RolMenuItemActionPerformed(evt);
}
});
AdminMenu.add(RolMenuItem);
MimeTypeMenuItem.setFont(getFontMenu());
MimeTypeMenuItem.setText(TT("Mime_Types"));
MimeTypeMenuItem.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
MimeTypeMenuItemActionPerformed(evt);
}
});
AdminMenu.add(MimeTypeMenuItem);
ReposMenuItem.setFont(getFontMenu());
ReposMenuItem.setText(TT("Repositories"));
ReposMenuItem.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
ReposMenuItemActionPerformed(evt);
}
});
AdminMenu.add(ReposMenuItem);
ObjDefMenuItem.setFont(getFontMenu());
ObjDefMenuItem.setText(TT("Object_definitions"));
ObjDefMenuItem.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
ObjDefMenuItemActionPerformed(evt);
}
});
AdminMenu.add(ObjDefMenuItem);
AuthentMenuItem.setFont(getFontMenu());
AuthentMenuItem.setText(TT("Authenticators"));
AuthentMenuItem.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
AuthentMenuItemActionPerformed(evt);
}
});
AdminMenu.add(AuthentMenuItem);
CustomMenuItem.setFont(getFontMenu());
CustomMenuItem.setText(TT("Customizations"));
CustomMenuItem.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
CustomMenuItemActionPerformed(evt);
}
});
AdminMenu.add(CustomMenuItem);
menuBar.add(AdminMenu);
helpMenu.setText(TT("Help"));
helpMenu.setFont(getFontMenu());
contentsMenuItem1.setFont(getFontMenu());
contentsMenuItem1.setText(TT("Contents"));
contentsMenuItem1.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
contentsMenuItem1ActionPerformed(evt);
}
});
helpMenu.add(contentsMenuItem1);
aboutMenuItem1.setFont(getFontMenu());
aboutMenuItem1.setText(TT("About"));
aboutMenuItem1.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
aboutMenuItem1ActionPerformed(evt);
}
});
helpMenu.add(aboutMenuItem1);
ReportBugs.setFont(getFontMenu());
ReportBugs.setText(TT("Reporting_Bugs"));
ReportBugs.addActionListener(new java.awt.event.ActionListener() {
public void actionPerformed(java.awt.event.ActionEvent evt) {
ReportBugsActionPerformed(evt);
}
});
helpMenu.add(ReportBugs);
menuBar.add(helpMenu);
setJMenuBar(menuBar);
javax.swing.GroupLayout layout = new javax.swing.GroupLayout(getContentPane());
getContentPane().setLayout(layout);
layout.setHorizontalGroup(
layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addComponent(jSplitPane1, javax.swing.GroupLayout.DEFAULT_SIZE, 732, Short.MAX_VALUE)
);
layout.setVerticalGroup(
layout.createParallelGroup(javax.swing.GroupLayout.Alignment.LEADING)
.addComponent(jSplitPane1, javax.swing.GroupLayout.DEFAULT_SIZE, 572, Short.MAX_VALUE)
);
pack();
}// </editor-fold>//GEN-END:initComponents
private void exitMenuItemActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_exitMenuItemActionPerformed
Disconnect();
}//GEN-LAST:event_exitMenuItemActionPerformed
private void UserMenuItemActionPerformed(java.awt.event.ActionEvent evt)//GEN-FIRST:event_UserMenuItemActionPerformed
{//GEN-HEADEREND:event_UserMenuItemActionPerformed
try {
ListUsers LU = new ListUsers(this, true, new PDUser(getSession()));
LU.setLocationRelativeTo(null);
LU.setVisible(true);
} catch (Exception ex)
{
Message(DrvTT(ex.getLocalizedMessage()));
}
}//GEN-LAST:event_UserMenuItemActionPerformed
private void formWindowClosing(java.awt.event.WindowEvent evt)//GEN-FIRST:event_formWindowClosing
{//GEN-HEADEREND:event_formWindowClosing
Disconnect();
}//GEN-LAST:event_formWindowClosing
private void MimeTypeMenuItemActionPerformed(java.awt.event.ActionEvent evt)//GEN-FIRST:event_MimeTypeMenuItemActionPerformed
{//GEN-HEADEREND:event_MimeTypeMenuItemActionPerformed
try {
ListMimeTypes LMT = new ListMimeTypes(this, true, new PDMimeType(getSession()));
LMT.setLocationRelativeTo(null);
LMT.setVisible(true);
} catch (Exception ex)
{
Message(DrvTT(ex.getLocalizedMessage()));
}
}//GEN-LAST:event_MimeTypeMenuItemActionPerformed
private void ACLMenuItemActionPerformed(java.awt.event.ActionEvent evt)//GEN-FIRST:event_ACLMenuItemActionPerformed
{//GEN-HEADEREND:event_ACLMenuItemActionPerformed
try {
ListAcl LA = new ListAcl(this, true, new PDACL(getSession()));
LA.setLocationRelativeTo(null);
LA.setVisible(true);
} catch (Exception ex)
{
Message(DrvTT(ex.getLocalizedMessage()));
}
}//GEN-LAST:event_ACLMenuItemActionPerformed
private void GroupMenuItemActionPerformed(java.awt.event.ActionEvent evt)//GEN-FIRST:event_GroupMenuItemActionPerformed
{//GEN-HEADEREND:event_GroupMenuItemActionPerformed
try {
ListGroups LG = new ListGroups(this, true, new PDGroups(getSession()));
LG.setLocationRelativeTo(null);
LG.setVisible(true);
} catch (Exception ex)
{
Message(DrvTT(ex.getLocalizedMessage()));
}
}//GEN-LAST:event_GroupMenuItemActionPerformed
private void RolMenuItemActionPerformed(java.awt.event.ActionEvent evt)//GEN-FIRST:event_RolMenuItemActionPerformed
{//GEN-HEADEREND:event_RolMenuItemActionPerformed
try {
ListRoles LR = new ListRoles(this, true, new PDRoles(getSession()));
LR.setLocationRelativeTo(null);
LR.setVisible(true);
} catch (Exception ex)
{
Message(DrvTT(ex.getLocalizedMessage()));
}
}//GEN-LAST:event_RolMenuItemActionPerformed
private void ReposMenuItemActionPerformed(java.awt.event.ActionEvent evt)//GEN-FIRST:event_ReposMenuItemActionPerformed
{//GEN-HEADEREND:event_ReposMenuItemActionPerformed
try {
ListRepositories LR = new ListRepositories(this, true, new PDRepository(getSession()));
LR.setLocationRelativeTo(null);
LR.setVisible(true);
} catch (Exception ex)
{
Message(DrvTT(ex.getLocalizedMessage()));
}
}//GEN-LAST:event_ReposMenuItemActionPerformed
private void TreeFolderTreeExpanded(javax.swing.event.TreeExpansionEvent evt)//GEN-FIRST:event_TreeFolderTreeExpanded
{//GEN-HEADEREND:event_TreeFolderTreeExpanded
DefaultMutableTreeNode TreeFold = (DefaultMutableTreeNode) evt.getPath().getLastPathComponent();
if ( ((TreeFolder) TreeFold.getUserObject()).isExpanded())
return;
ExpandFold(TreeFold);
}//GEN-LAST:event_TreeFolderTreeExpanded
private void TreeFolderValueChanged(javax.swing.event.TreeSelectionEvent evt)//GEN-FIRST:event_TreeFolderValueChanged
{//GEN-HEADEREND:event_TreeFolderValueChanged
try {
DefaultMutableTreeNode TreeFold = (DefaultMutableTreeNode) evt.getPath().getLastPathComponent();
FoldAct= ((TreeFolder) TreeFold.getUserObject()).getFold();
SelFolderDesc.setText(HtmlDesc(FoldAct));
ActFolderId=FoldAct.getPDId();
RefreshDocs();
} catch (Exception ex)
{
Message(DrvTT(ex.getLocalizedMessage()));
}
}//GEN-LAST:event_TreeFolderValueChanged
private void AddFoldActionPerformed(java.awt.event.ActionEvent evt)//GEN-FIRST:event_AddFoldActionPerformed
{//GEN-HEADEREND:event_AddFoldActionPerformed
String NewFoldChild=DialogReadString(TT("Add_Folder"),TT("Folder_name"), TT("Write_Folder_name"), null);
if (NewFoldChild==null || NewFoldChild.length()==0)
return;
try {
PDFolders Fold=new PDFolders(Session);
Fold.setPDId(ActFolderId);
Fold.CreateChild(NewFoldChild);
TreePath ActualPath = TreeFolder.getSelectionPath();
DefaultMutableTreeNode TreeFold = (DefaultMutableTreeNode) ActualPath.getLastPathComponent();
ExpandFold(TreeFold);
TreeFolder.setSelectionPath(ActualPath);
} catch (Exception ex)
{
Message(DrvTT(ex.getLocalizedMessage()));
}
}//GEN-LAST:event_AddFoldActionPerformed
private void DelFoldActionPerformed(java.awt.event.ActionEvent evt)//GEN-FIRST:event_DelFoldActionPerformed
{//GEN-HEADEREND:event_DelFoldActionPerformed
try {
TreePath selectionPath = TreeFolder.getSelectionPath();
DefaultMutableTreeNode TreeFold = (DefaultMutableTreeNode) selectionPath.getLastPathComponent();
PDFolders Fold= ((TreeFolder) TreeFold.getUserObject()).getFold();
DialogEditFold DEF = new DialogEditFold(this, true);
DEF.setLocationRelativeTo(null);
DEF.DelMode();
Fold.LoadFull(ActFolderId);
DEF.setRecord(Fold.getRecord());
DEF.setVisible(true);
if (DEF.isCancel())
return;
ActFolderId=Fold.getParentId();
Fold.delete();
TreePath ParentFold = (TreePath) TreeFolder.getSelectionPath().getParentPath();
ExpandFold((DefaultMutableTreeNode)ParentFold.getLastPathComponent());
TreeFolder.setSelectionPath(selectionPath.getParentPath());
TreeFold = (DefaultMutableTreeNode) selectionPath.getParentPath().getLastPathComponent();
FoldAct= ((TreeFolder) TreeFold.getUserObject()).getFold();
SelFolderDesc.setText(HtmlDesc(FoldAct));
} catch (Exception ex)
{
Message(DrvTT(ex.getLocalizedMessage()));
}
}//GEN-LAST:event_DelFoldActionPerformed
private void AddFoldAdvancedActionPerformed(java.awt.event.ActionEvent evt)//GEN-FIRST:event_AddFoldAdvancedActionPerformed
{//GEN-HEADEREND:event_AddFoldAdvancedActionPerformed
try {
DialogEditFold DEF = new DialogEditFold(this, true);
DEF.setLocationRelativeTo(null);
DEF.AddMode();
DEF.setAcl(FoldAct.getACL());
DEF.setVisible(true);
if (DEF.isCancel())
return;
PDFolders Fold=new PDFolders(Session);
Fold.assignValues(DEF.getRecord());
Fold.setParentId(ActFolderId);
Fold.insert();
TreePath ActualPath = TreeFolder.getSelectionPath();
ExpandFold((DefaultMutableTreeNode)ActualPath.getLastPathComponent());
TreeFolder.setSelectionPath(ActualPath);
} catch (Exception ex)
{
Message(DrvTT(ex.getLocalizedMessage()));
}
}//GEN-LAST:event_AddFoldAdvancedActionPerformed
private void ModFoldActionPerformed(java.awt.event.ActionEvent evt)//GEN-FIRST:event_ModFoldActionPerformed
{//GEN-HEADEREND:event_ModFoldActionPerformed
try {
TreePath selectionPath = TreeFolder.getSelectionPath();
DefaultMutableTreeNode TreeFold = (DefaultMutableTreeNode) selectionPath.getLastPathComponent();
PDFolders Fold= ((TreeFolder) TreeFold.getUserObject()).getFold();
String NewTitle=DialogReadString(TT("Update_Folder"),TT("Folder_name"), TT("Write_Folder_name"), Fold.getTitle());
if (NewTitle==null || NewTitle.length()==0)
return;
Fold.setTitle(NewTitle);
Fold.update();
TreePath ParentFold = (TreePath) TreeFolder.getSelectionPath().getParentPath();
ExpandFold((DefaultMutableTreeNode)ParentFold.getLastPathComponent());
TreeFolder.setSelectionPath(selectionPath);
} catch (Exception ex)
{
Message(DrvTT(ex.getLocalizedMessage()));
}
}//GEN-LAST:event_ModFoldActionPerformed
private void ModFoldAdvancedActionPerformed(java.awt.event.ActionEvent evt)//GEN-FIRST:event_ModFoldAdvancedActionPerformed
{//GEN-HEADEREND:event_ModFoldAdvancedActionPerformed
try {
TreePath selectionPath = TreeFolder.getSelectionPath();
DefaultMutableTreeNode TreeFold = (DefaultMutableTreeNode) selectionPath.getLastPathComponent();
PDFolders Fold= ((TreeFolder) TreeFold.getUserObject()).getFold();
DialogEditFold DEF = new DialogEditFold(this, true);
DEF.setLocationRelativeTo(null);
DEF.EditMode();
Fold.LoadFull(Fold.getPDId());
DEF.setRecord(Fold.getRecord());
DEF.setVisible(true);
if (DEF.isCancel())
return;
Fold.assignValues(DEF.getRecord());
Fold.update();
TreePath ParentFold = (TreePath) TreeFolder.getSelectionPath().getParentPath();
ExpandFold((DefaultMutableTreeNode)ParentFold.getLastPathComponent());
TreeFolder.setSelectionPath(selectionPath);
} catch (Exception ex)
{
Message(DrvTT(ex.getLocalizedMessage()));
}
}//GEN-LAST:event_ModFoldAdvancedActionPerformed
private void RefreshFoldActionPerformed(java.awt.event.ActionEvent evt)//GEN-FIRST:event_RefreshFoldActionPerformed
{//GEN-HEADEREND:event_RefreshFoldActionPerformed
DefaultMutableTreeNode TreeFold = (DefaultMutableTreeNode) TreeFolder.getSelectionPath().getLastPathComponent();
ExpandFold(TreeFold);
}//GEN-LAST:event_RefreshFoldActionPerformed
private void ObjDefMenuItemActionPerformed(java.awt.event.ActionEvent evt)//GEN-FIRST:event_ObjDefMenuItemActionPerformed
{//GEN-HEADEREND:event_ObjDefMenuItemActionPerformed
ListObjDef LOD = new ListObjDef(this, true, new PDObjDefs(getSession()));
LOD.setLocationRelativeTo(null);
LOD.setVisible(true);
}//GEN-LAST:event_ObjDefMenuItemActionPerformed
private void AddDocActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_AddDocActionPerformed
DialogEditDocReduced MD = new DialogEditDocReduced(this,true);
PDDocs Doc;
try {
Doc = new PDDocs(getSession());
MD.setRecord(Doc.getRecSum());
MD.AddMode();
MD.setLocationRelativeTo(null);
} catch (Exception ex)
{
Message(DrvTT(ex.getLocalizedMessage()));
return;
}
while (true)
{
try {
MD.setVisible(true);
if (MD.isCancel())
return;
Doc.assignValues(MD.getRecord());
if (MD.SelFile!=null)
Doc.setFile(MD.SelFile.getAbsolutePath());
else
throw new PDException("Error_retrieving_file");
Doc.setParentId(ActFolderId);
Doc.insert();
RefreshDocs();
return;
} catch (Exception ex)
{
Message(DrvTT(ex.getLocalizedMessage()));
}
}
}//GEN-LAST:event_AddDocActionPerformed
private void DelDocActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_DelDocActionPerformed
if (DocsTable.getSelectedRow()==-1)
return;
try {
PDDocs Doc = new PDDocs(getSession());
DialogEditDoc MD = new DialogEditDoc(this,true);
Doc.assignValues(DocsContained.getElement(DocsTable.convertRowIndexToModel(DocsTable.getSelectedRow())));
Doc.LoadFull(Doc.getPDId());
MD.DelMode();
MD.setRecord(Doc.getRecSum());
MD.setLocationRelativeTo(null);
MD.setVisible(true);
if (MD.isCancel())
return;
Doc.assignValues(MD.getRecord());
Doc.delete();
RefreshDocs();
} catch (Exception ex)
{
Message(DrvTT(ex.getLocalizedMessage()));
}
}//GEN-LAST:event_DelDocActionPerformed
private void AddDocAdvancedActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_AddDocAdvancedActionPerformed
PDDocs Doc;
DialogEditDoc MD = new DialogEditDoc(this,true);
try {
Doc = new PDDocs(getSession());
TreePath selectionPath = TreeFolder.getSelectionPath();
DefaultMutableTreeNode TreeFold = (DefaultMutableTreeNode) selectionPath.getLastPathComponent();
PDFolders Fold= ((TreeFolder) TreeFold.getUserObject()).getFold();
Doc.setACL(Fold.getACL());
MD.setRecord(Doc.getRecSum());
MD.AddMode();
MD.setLocationRelativeTo(null);
} catch (Exception ex)
{
Message(DrvTT(ex.getLocalizedMessage()));
return;
}
while (true)
{
try {
MD.setVisible(true);
if (MD.isCancel())
return;
String SelectedType=(String)MD.getRecord().getAttr(PDDocs.fDOCTYPE).getValue();
if (!SelectedType.equalsIgnoreCase(Doc.getDocType()))
Doc = new PDDocs(getSession(), SelectedType);
Doc.assignValues(MD.getRecord());
if (MD.GetSelectPath()!=null && MD.GetSelectPath().length()>0)
Doc.setFile(MD.GetSelectPath());
else
throw new PDException("Error_retrieving_file");
Doc.setParentId(ActFolderId);
Doc.insert();
RefreshDocs();
return;
} catch (Exception ex)
{
Message(DrvTT(ex.getLocalizedMessage()));
}
}
}//GEN-LAST:event_AddDocAdvancedActionPerformed
private void ModDocAdvancedActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_ModDocAdvancedActionPerformed
if (DocsTable.getSelectedRow()==-1)
return;
DialogEditDoc MD = new DialogEditDoc(this,true);
PDDocs Doc;
try {
Doc = new PDDocs(getSession());
Doc.assignValues(DocsContained.getElement(DocsTable.convertRowIndexToModel(DocsTable.getSelectedRow())));
Doc.LoadFull(Doc.getPDId());
MD.setRecord(Doc.getRecSum().Copy()); // we need a copy to avoid edition on the same referenced values
MD.EditMode();
MD.setLocationRelativeTo(null);
} catch (Exception ex)
{
Message(DrvTT(ex.getLocalizedMessage()));
return;
}
while (true)
{
try {
MD.setVisible(true);
if (MD.isCancel())
return;
Doc.assignValues(MD.getRecord());
if (MD.GetSelectPath()!=null && MD.GetSelectPath().length()>0)
Doc.setFile(MD.GetSelectPath());
Doc.update();
RefreshDocs();
return;
} catch (Exception ex)
{
Message(DrvTT(ex.getLocalizedMessage()));
}
}
}//GEN-LAST:event_ModDocAdvancedActionPerformed
private void RefreshDocsActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_RefreshDocsActionPerformed
RefreshDocs();
}//GEN-LAST:event_RefreshDocsActionPerformed
private void CheckOutActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_CheckOutActionPerformed
if (DocsTable.getSelectedRow()==-1)
return;
try {
PDDocs Doc = new PDDocs(getSession());
Doc.assignValues(DocsContained.getElement(DocsTable.convertRowIndexToModel(DocsTable.getSelectedRow())));
Doc.Checkout();
RefreshDocs();
} catch (Exception ex)
{
Message(DrvTT(ex.getLocalizedMessage()));
}
}//GEN-LAST:event_CheckOutActionPerformed
private void CheckInActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_CheckInActionPerformed
if (DocsTable.getSelectedRow()==-1)
return;
try {
PDDocs Doc = new PDDocs(getSession());
Doc.assignValues(DocsContained.getElement(DocsTable.convertRowIndexToModel(DocsTable.getSelectedRow())));
String VersionLabel=DialogReadString(TT("Creating_a_new_version_of_document"), TT("Version_identifier"), TT("Type_a_version_name_or_identifier"), "");
if (VersionLabel==null)
return;
if (VersionLabel.length()==0)
{
Message(TT("Version_identifier_required"));
return;
}
Doc.Checkin(VersionLabel);
RefreshDocs();
} catch (Exception ex)
{
Message(DrvTT(ex.getLocalizedMessage()));
}
}//GEN-LAST:event_CheckInActionPerformed
private void CancelCheckoutActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_CancelCheckoutActionPerformed
if (DocsTable.getSelectedRow()==-1)
return;
try {
if (!MessageQuestion(TT("Do_you_want_to_cancel_edition_and_lost_changes")))
return;
PDDocs Doc = new PDDocs(getSession());
Doc.assignValues(DocsContained.getElement(DocsTable.convertRowIndexToModel(DocsTable.getSelectedRow())));
Doc.CancelCheckout();
RefreshDocs();
} catch (Exception ex)
{
Message(DrvTT(ex.getLocalizedMessage()));
}
}//GEN-LAST:event_CancelCheckoutActionPerformed
private void PaperBinActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_PaperBinActionPerformed
ListDeleted LD = new ListDeleted(this, true);
LD.setLocationRelativeTo(null);
LD.setVisible(true);
}//GEN-LAST:event_PaperBinActionPerformed
private void ListVersionsActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_ListVersionsActionPerformed
if (DocsTable.getSelectedRow()==-1)
return;
ListVersions LV = new ListVersions(this, true, DocsContained.getElement(DocsTable.convertRowIndexToModel(DocsTable.getSelectedRow())));
LV.setLocationRelativeTo(null);
LV.setVisible(true);
}//GEN-LAST:event_ListVersionsActionPerformed
private void SearchFoldActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_SearchFoldActionPerformed
SearchFold SF = new SearchFold(this, true);
SF.setLocationRelativeTo(null);
SF.setFoldAct(ActFolderId);
SF.setVisible(true);
}//GEN-LAST:event_SearchFoldActionPerformed
private void SearchDocsActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_SearchDocsActionPerformed
SearchDocs SD = new SearchDocs(this, true);
SD.setLocationRelativeTo(null);
SD.setFoldAct(ActFolderId);
SD.setVisible(true);
}//GEN-LAST:event_SearchDocsActionPerformed
private void AuthentMenuItemActionPerformed(java.awt.event.ActionEvent evt) {//GEN-FIRST:event_AuthentMenuItemActionPerformed
try {
ListAuthenticators LA = new ListAuthenticators(this, true, new PDAuthenticators(getSession()));
LA.setLocationRelativeTo(null);
LA.setVisible(true);
} catch (Exception ex)
{
Message(DrvTT(ex.getLocalizedMessage()));
}
}//GEN-LAST:event_AuthentMenuItemActionPerformed
private void ChangePassActionPerformed(java.awt.event.ActionEvent evt)//GEN-FIRST:event_ChangePassActionPerformed
{//GEN-HEADEREND:event_ChangePassActionPerformed
try {
ChangePassword CP = new ChangePassword(this, true);
CP.setLocationRelativeTo(null);
CP.setVisible(true);
if (CP.isCancel())
return;
getSession().ChangePassword(getSession().getUser().getName(), CP.getOldPasswordField(), CP.getNewPasswordField1());
} catch (Exception ex)
{
Message(DrvTT(ex.getLocalizedMessage()));
}
}//GEN-LAST:event_ChangePassActionPerformed
private void CustomMenuItemActionPerformed(java.awt.event.ActionEvent evt)//GEN-FIRST:event_CustomMenuItemActionPerformed
{//GEN-HEADEREND:event_CustomMenuItemActionPerformed
try {
ListCustom LC = new ListCustom(this, true, new PDCustomization(getSession()));
LC.setLocationRelativeTo(null);
LC.setVisible(true);
} catch (Exception ex)
{
Message(DrvTT(ex.getLocalizedMessage()));
}
}//GEN-LAST:event_CustomMenuItemActionPerformed
private void aboutMenuItem1ActionPerformed(java.awt.event.ActionEvent evt)//GEN-FIRST:event_aboutMenuItem1ActionPerformed
{//GEN-HEADEREND:event_aboutMenuItem1ActionPerformed
AboutOPD Ab=new AboutOPD(this, rootPaneCheckingEnabled);
Ab.setLocationRelativeTo(null);
Ab.setVisible(true);
Ab.dispose();
}//GEN-LAST:event_aboutMenuItem1ActionPerformed
private void contentsMenuItem1ActionPerformed(java.awt.event.ActionEvent evt)//GEN-FIRST:event_contentsMenuItem1ActionPerformed
{//GEN-HEADEREND:event_contentsMenuItem1ActionPerformed
Execute("doc"+OSSep()+getLang()+OSSep()+"MainWin.html");
}//GEN-LAST:event_contentsMenuItem1ActionPerformed
private void DocsTableMouseClicked(java.awt.event.MouseEvent evt)//GEN-FIRST:event_DocsTableMouseClicked
{//GEN-HEADEREND:event_DocsTableMouseClicked
if (evt.getClickCount()<2)
return;
if (DocsTable.getSelectedRow()==-1)
return;
try {
PDDocs Doc = new PDDocs(getSession());
Doc.assignValues(DocsContained.getElement(DocsTable.convertRowIndexToModel(DocsTable.getSelectedRow())));
String FileName;
if (Doc.IsUrl())
FileName=Doc.getUrl();
else
{
FileName=Doc.getFileOpt(getTmp(), false);
AddExec(FileName);
}
Execute(FileName);
} catch (Exception ex)
{
Message(DrvTT(ex.getLocalizedMessage()));
}
}//GEN-LAST:event_DocsTableMouseClicked
private void ExportDocActionPerformed(java.awt.event.ActionEvent evt)//GEN-FIRST:event_ExportDocActionPerformed
{//GEN-HEADEREND:event_ExportDocActionPerformed
if (DocsTable.getSelectedRow()==-1)
return;
try {
String FileName=MainWin.SelectFolderDestination("");
if (FileName.length()==0)
return;
PDDocs Doc = new PDDocs(getSession());
Doc.assignValues(DocsContained.getElement(DocsTable.convertRowIndexToModel(DocsTable.getSelectedRow())));
Doc.ExportXML(FileName, false);
} catch (Exception ex)
{
MainWin.Message(MainWin.DrvTT(ex.getLocalizedMessage()));
}
}//GEN-LAST:event_ExportDocActionPerformed
private void ImportDocActionPerformed(java.awt.event.ActionEvent evt)//GEN-FIRST:event_ImportDocActionPerformed
{//GEN-HEADEREND:event_ImportDocActionPerformed
String FileName=MainWin.SelectDestination(null, "opd", false);
if (FileName.length()==0)
return;
try {
PDDocs Doc = new PDDocs(getSession());
File FileImp=new File(FileName);
getSession().ProcessXML(FileImp, ActFolderId);
RefreshDocs();
} catch (Exception ex)
{
MainWin.Message(MainWin.DrvTT(ex.getLocalizedMessage()));
}
}//GEN-LAST:event_ImportDocActionPerformed
private void ExportFoldActionPerformed(java.awt.event.ActionEvent evt)//GEN-FIRST:event_ExportFoldActionPerformed
{//GEN-HEADEREND:event_ExportFoldActionPerformed
try {
ExpFolds=0;
ExpDocs=0;
DialogExportFolders ExpFold = new DialogExportFolders(this,true);
ExpFold.setLocationRelativeTo(null);
ExpFold.setVisible(true);
if (ExpFold.isCancel())
return;
setCursor(WaitCur);
Export(FoldAct, ExpFold.SelFolder.getAbsolutePath(), ExpFold.IsOneLevel(), ExpFold.IncludeMetadata(), ExpFold.IncludeDocs());
setCursor(DefCur);
Message(DrvTT("Exported")+" "+ExpFolds+" "+DrvTT("Folders")+" / "+ExpDocs +" "+DrvTT("Documents"));
} catch (Exception ex)
{
setCursor(DefCur);
MainWin.Message(MainWin.DrvTT(ex.getLocalizedMessage()));
}
}//GEN-LAST:event_ExportFoldActionPerformed
private void ImportFoldActionPerformed(java.awt.event.ActionEvent evt)//GEN-FIRST:event_ImportFoldActionPerformed
{//GEN-HEADEREND:event_ImportFoldActionPerformed
try {
ExpFolds=0;
ExpDocs=0;
DialogImportFolders ImpFold = new DialogImportFolders(this,true);
ImpFold.setLocationRelativeTo(null);
ImpFold.setVisible(true);
if (ImpFold.isCancel())
return;
setCursor(WaitCur);
Import(FoldAct, ImpFold.SelFolder.getAbsolutePath(), ImpFold.IsOneLevel(), ImpFold.IncludeMetadata(), ImpFold.IncludeDocs(), ImpFold.FoldType(), ImpFold.DocType());
TreePath ActualPath = TreeFolder.getSelectionPath();
DefaultMutableTreeNode TreeFold = (DefaultMutableTreeNode) ActualPath.getLastPathComponent();
ExpandFold(TreeFold);
TreeFolder.setSelectionPath(ActualPath);
setCursor(DefCur);
Message(DrvTT("Imported")+" "+ExpFolds+" "+DrvTT("Folders")+" / "+ExpDocs +" "+DrvTT("Documents"));
} catch (Exception ex)
{
setCursor(DefCur);
MainWin.Message(MainWin.DrvTT(ex.getLocalizedMessage()));
}
}//GEN-LAST:event_ImportFoldActionPerformed
private void ReportBugsActionPerformed(java.awt.event.ActionEvent evt)//GEN-FIRST:event_ReportBugsActionPerformed
{//GEN-HEADEREND:event_ReportBugsActionPerformed
Execute("https://docs.google.com/spreadsheet/viewform?formkey%3DdFF6ZndKWXFUQnJ0MWtVZWdUWk10X2c6MQ");
}//GEN-LAST:event_ReportBugsActionPerformed
private void ViewMetadataActionPerformed(java.awt.event.ActionEvent evt)//GEN-FIRST:event_ViewMetadataActionPerformed
{//GEN-HEADEREND:event_ViewMetadataActionPerformed
if (DocsTable.getSelectedRow()==-1)
return;
try {
PDDocs Doc = new PDDocs(getSession());
DialogEditDoc MD = new DialogEditDoc(this,true);
Doc.assignValues(DocsContained.getElement(DocsTable.convertRowIndexToModel(DocsTable.getSelectedRow())));
Doc.LoadFull(Doc.getPDId());
MD.ViewMode();
MD.setRecord(Doc.getRecSum());
MD.setLocationRelativeTo(null);
MD.setVisible(true);
} catch (Exception ex)
{
Message(DrvTT(ex.getLocalizedMessage()));
}
}//GEN-LAST:event_ViewMetadataActionPerformed
private void ImportExtFoldActionPerformed(java.awt.event.ActionEvent evt)//GEN-FIRST:event_ImportExtFoldActionPerformed
{//GEN-HEADEREND:event_ImportExtFoldActionPerformed
try {
ExpFolds=0;
ExpDocs=0;
DialogImportExtFolders ImpFold = new DialogImportExtFolders(this,true);
ImpFold.setLocationRelativeTo(null);
ImpFold.setVisible(true);
if (ImpFold.isCancel())
return;
setCursor(WaitCur);
ImportExt(FoldAct, ImpFold.SelFolder.getAbsolutePath(), ImpFold.DeleteAfterImport(), ImpFold.ImpFormat(), ImpFold.DefaultFoldType(), ImpFold.DateFormat(), ImpFold.TimeStampFormat());
TreePath ActualPath = TreeFolder.getSelectionPath();
DefaultMutableTreeNode TreeFold = (DefaultMutableTreeNode) ActualPath.getLastPathComponent();
ExpandFold(TreeFold);
TreeFolder.setSelectionPath(ActualPath);
setCursor(DefCur);
Message(DrvTT("Imported")+" "+ExpFolds+" "+DrvTT("Folders")+" / "+ExpDocs +" "+DrvTT("Documents"));
} catch (Exception ex)
{
setCursor(DefCur);
MainWin.Message(MainWin.DrvTT(ex.getLocalizedMessage()));
}
}//GEN-LAST:event_ImportExtFoldActionPerformed
/**
* @param args the command line arguments
*/
public static void main(String args[])
{
String PropertiesFile;
if (args.length==0)
PropertiesFile="Prodoc.properties";
// PropertiesFile="e:\\Prodoc\\Varios\\Prodoc_derby.properties";
// PropertiesFile="/media/Iomega/Prodoc/ProdocInstall/dist/Prodoc.properties";
// PropertiesFile="/media/Iomega/Prodoc/Varios/Prodoc_derby.properties";
else
PropertiesFile=args[0];
if (!Connect(PropertiesFile))
System.exit(0);
java.awt.EventQueue.invokeLater(new Runnable()
{
public void run()
{
MainWin MW=new MainWin();
MW.setLocationRelativeTo(null);
MW.setVisible(true);
}
});
}
// Variables declaration - do not modify//GEN-BEGIN:variables
private javax.swing.JMenuItem ACLMenuItem;
private javax.swing.JMenuItem AddDoc;
private javax.swing.JMenuItem AddDocAdvanced;
private javax.swing.JMenuItem AddFold;
private javax.swing.JMenuItem AddFoldAdvanced;
private javax.swing.JMenu AdminMenu;
private javax.swing.JMenuItem AuthentMenuItem;
private javax.swing.JMenuItem CancelCheckout;
private javax.swing.JMenuItem ChangePass;
private javax.swing.JMenuItem CheckIn;
private javax.swing.JMenuItem CheckOut;
private javax.swing.JMenuItem CustomMenuItem;
private javax.swing.JMenuItem DelDoc;
private javax.swing.JMenuItem DelFold;
private javax.swing.JMenu DocMenu;
private javax.swing.JTable DocsTable;
private javax.swing.JMenuItem ExportDoc;
private javax.swing.JMenuItem ExportFold;
private javax.swing.JMenu FolderMenu;
private javax.swing.JMenuItem GroupMenuItem;
private javax.swing.JMenuItem ImportDoc;
private javax.swing.JMenuItem ImportExtFold;
private javax.swing.JMenuItem ImportFold;
private javax.swing.JMenuItem ListVersions;
private javax.swing.JMenuItem MimeTypeMenuItem;
private javax.swing.JMenuItem ModDocAdvanced;
private javax.swing.JMenuItem ModFold;
private javax.swing.JMenuItem ModFoldAdvanced;
private javax.swing.JMenuItem ObjDefMenuItem;
private javax.swing.JMenu OtherMenu;
private javax.swing.JMenuItem PaperBin;
private javax.swing.JMenuItem RefreshDocs;
private javax.swing.JMenuItem RefreshFold;
private javax.swing.JMenuItem ReportBugs;
private javax.swing.JMenuItem ReposMenuItem;
private javax.swing.JMenuItem RolMenuItem;
private javax.swing.JMenuItem SearchDocs;
private javax.swing.JMenuItem SearchFold;
private javax.swing.JLabel SelFolderDesc;
private javax.swing.JTree TreeFolder;
private javax.swing.JMenuItem UserMenuItem;
private javax.swing.JMenuItem ViewMetadata;
private javax.swing.JMenuItem aboutMenuItem1;
private javax.swing.JMenuItem contentsMenuItem1;
private javax.swing.JMenuItem exitMenuItem;
private javax.swing.JMenu helpMenu;
private javax.swing.JScrollPane jScrollPane1;
private javax.swing.JScrollPane jScrollPane2;
private javax.swing.JScrollPane jScrollPane3;
private javax.swing.JPopupMenu.Separator jSeparator1;
private javax.swing.JPopupMenu.Separator jSeparator2;
private javax.swing.JPopupMenu.Separator jSeparator3;
private javax.swing.JPopupMenu.Separator jSeparator4;
private javax.swing.JPopupMenu.Separator jSeparator5;
private javax.swing.JPopupMenu.Separator jSeparator6;
private javax.swing.JSplitPane jSplitPane1;
private javax.swing.JSplitPane jSplitPane2;
private javax.swing.JMenuBar menuBar;
// End of variables declaration//GEN-END:variables
private static void EvaluateDef()
{
try {
String FontDef=getSession().getUser().getCustomData().getSwingStyle();
String ListF[]=FontDef.split(",");
MenuFont =new java.awt.Font(ListF[0], Integer.parseInt(ListF[1]), Integer.parseInt(ListF[2]));
TreeFont =new java.awt.Font(ListF[3], Integer.parseInt(ListF[4]), Integer.parseInt(ListF[5]));
ListFont =new java.awt.Font(ListF[6], Integer.parseInt(ListF[7]), Integer.parseInt(ListF[8]));
DialogFont=new java.awt.Font(ListF[9], Integer.parseInt(ListF[10]), Integer.parseInt(ListF[11]));
} catch (Exception ex)
{
MenuFont=new java.awt.Font("Arial", 0, 12);
TreeFont=new java.awt.Font("Arial", 0, 12);
ListFont=new java.awt.Font("Arial", 0, 12);
DialogFont=new java.awt.Font("Arial", 0, 12);
}
}
/**
*
* @return
*/
static public Font getFontMenu()
{
if (MenuFont==null)
EvaluateDef();
return (MenuFont);
}
/**
*
* @return
*/
static public Font getFontTree()
{
if (TreeFont==null)
EvaluateDef();
return (TreeFont);
}
/**
*
* @return
*/
static public Font getFontList()
{
if (ListFont==null)
EvaluateDef();
return (ListFont);
}
/**
*
* @return
*/
static public Font getFontDialog()
{
if (DialogFont==null)
EvaluateDef();
return (DialogFont);
}
private PDTableModel getTableModel()
{
return new PDTableModel();
}
static private boolean Connect(String PropertiesFile)
{
LoginForm dialog = new LoginForm(new javax.swing.JFrame(), true);
dialog.setLocationRelativeTo(null);
for (int NumRetry = 0; NumRetry < 3; NumRetry++)
{
dialog.setVisible(true);
if (dialog.getReturnStatus() == LoginForm.RET_CANCEL)
return false;
try {
ProdocFW.InitProdoc("PD", PropertiesFile);
Session = ProdocFW.getSession("PD", dialog.getLogin(), dialog.getPass());
return(true);
} catch (PDException ex)
{
Message(DrvTT(ex.getLocalizedMessage()));
}
}
return false;
}
static private void Disconnect()
{
try {
if (getSession()!=null)
{
ProdocFW.freeSesion("PD", getSession());
}
ProdocFW.ShutdownProdoc("PD");
} catch (PDException ex)
{
Message(DrvTT(ex.getLocalizedMessage()));
}
DestroyExec();
System.exit(0);
}
/**
*
* @param pMessage
*/
static public void Message(String pMessage)
{
DialogInfo DI=new DialogInfo(null, true);
DI.SetMessage(DrvTT(pMessage));
DI.setLocationRelativeTo(null);
DI.setVisible(true);
}
/**
*
* @param pMessage to show to the user
* @return if the user selects OK
*/
static public boolean MessageQuestion(String pMessage)
{
DialogInfoQuestion DI=new DialogInfoQuestion(null, true);
DI.SetMessage(DrvTT(pMessage));
DI.setLocationRelativeTo(null);
DI.setVisible( true);
return (DI.getReturnStatus()==DialogInfoQuestion.RET_OK);
}
/**
*
* @param RecomFileName
* @param Ext
* @param Save
* @return
*/
static public String SelectDestination(String RecomFileName, String Ext, boolean Save)
{
JFileChooser fc = new JFileChooser();
//fc.setDialogTitle("Seleccionar Archivo");
if (Ext!=null)
fc.setFileFilter(new FileNameExtensionFilter("file "+Ext, Ext));
if (RecomFileName!=null)
fc.setSelectedFile(new File(RecomFileName));
if (!Save)
{
if (fc.showOpenDialog(null)!=JFileChooser.APPROVE_OPTION)
return("");
}
else
{
if (fc.showSaveDialog(null)!=JFileChooser.APPROVE_OPTION)
return("");
}
return(fc.getSelectedFile().getAbsolutePath());
}
/**
*
* @param RecomFileName
* @return
*/
static public String SelectFolderDestination(String RecomFileName)
{
JFileChooser fc = new JFileChooser();
if (RecomFileName!=null)
fc.setSelectedFile(new File(RecomFileName));
fc.setFileSelectionMode(JFileChooser.DIRECTORIES_ONLY);
if (fc.showSaveDialog(null)!=JFileChooser.APPROVE_OPTION)
return("");
return(fc.getSelectedFile().getAbsolutePath());
}
private TreeModel getTreeModel()
{
if (FoldTreeModel==null)
{
PDFolders RootFolder=null;
try {
RootFolder = new PDFolders(Session);
RootFolder.Load(PDFolders.ROOTFOLDER);
TreeFolder TF=new TreeFolder(RootFolder);
DefaultMutableTreeNode RootTreeFolder = new DefaultMutableTreeNode(TF);
FoldTreeModel=new DefaultTreeModel(RootTreeFolder);
ExpandFold(RootTreeFolder);
} catch (PDException ex)
{
Message(DrvTT(ex.getLocalizedMessage()));
return(null);
}
}
return(FoldTreeModel);
}
private void ExpandFold(DefaultMutableTreeNode ChildTreeFolder)
{
try {
ChildTreeFolder.removeAllChildren();
PDFolders Fold= ((TreeFolder) ChildTreeFolder.getUserObject()).getFold();
HashSet Child =Fold.getListDirectDescendList(Fold.getPDId());
for (Iterator it = Child.iterator(); it.hasNext();)
{
String ChildId=(String)it.next();
if (ChildId.compareTo(Fold.getPDId())==0)
continue;
PDFolders ChildFolder=new PDFolders(Session);
ChildFolder.LoadFull(ChildId);
TreeFolder TFc=new TreeFolder(ChildFolder);
DefaultMutableTreeNode ChildTreeFolder2=new DefaultMutableTreeNode(TFc);
DefaultMutableTreeNode ChildTreeFolder3=new DefaultMutableTreeNode(null);
ChildTreeFolder2.add(ChildTreeFolder3);
ChildTreeFolder.add(ChildTreeFolder2);
}
(((TreeFolder) ChildTreeFolder.getUserObject())).setExpanded(true);
FoldTreeModel.reload(ChildTreeFolder);
TreeFolder.setPreferredSize(null);
} catch (PDException ex)
{
Message(DrvTT(ex.getLocalizedMessage()));
}
}
static private String FormatDate(Date d)
{
return( getFormatterTS().format(d));
}
/**
*
* @param Title
* @param FieldName
* @param ToolTip
* @param FieldText
* @return
*/
static public String DialogReadString(String Title, String FieldName, String ToolTip, String FieldText)
{
DialogReadString dialog = new DialogReadString(new javax.swing.JFrame(), true);
dialog.setLocationRelativeTo(null);
dialog.SetVals(Title, FieldName, ToolTip, FieldText);
dialog.setVisible(true);
if (dialog.getReturnStatus() == DialogReadString.RET_CANCEL)
return null;
else
return(dialog.getField());
}
static private Image getIcon()
{
ImageIcon PDIcon=new ImageIcon("resources/LogoProdoc.jpg");
return PDIcon.getImage();
}
/**
* Refresh the list of documents
* called after changing folder or adding, modifying or deleting a document
*/
private void RefreshDocs()
{
try {
DocsContained = new PDTableModel();
DocsContained.setDrv(MainWin.getSession());
FoldAct.getListDirectDescendList(ActFolderId);
PDDocs Doc = new PDDocs(getSession());
DocsContained.setListFields(Doc.getRecordStruct());
DocsContained.setCursor(Doc.getListContainedDocs(FoldAct.getPDId()));
DocsTable.setModel(DocsContained);
DocsTable.getColumnModel().removeColumn(DocsTable.getColumnModel().getColumn(13));
DocsTable.getColumnModel().removeColumn(DocsTable.getColumnModel().getColumn(12));
DocsTable.getColumnModel().removeColumn(DocsTable.getColumnModel().getColumn(11));
DocsTable.getColumnModel().removeColumn(DocsTable.getColumnModel().getColumn(10));
DocsTable.getColumnModel().removeColumn(DocsTable.getColumnModel().getColumn(9));
DocsTable.getColumnModel().removeColumn(DocsTable.getColumnModel().getColumn(8));
DocsTable.getColumnModel().removeColumn(DocsTable.getColumnModel().getColumn(7));
DocsTable.getColumnModel().removeColumn(DocsTable.getColumnModel().getColumn(6));
DocsTable.getColumnModel().removeColumn(DocsTable.getColumnModel().getColumn(5));
DocsTable.getColumnModel().removeColumn(DocsTable.getColumnModel().getColumn(0));
// 0 4 5 7 8 9 10 11 12
} catch (PDException ex)
{
Message(DrvTT(ex.getLocalizedMessage()));
}
}
static int Execute(String Doc)
{
try {
//String Order="";
String Orders[]= {"xdg-open", Doc};
String OS=System.getProperty("os.name");
if (OS.contains("Win"))
Orders[0]="explorer";
else if (OS.contains("OS X") || OS.contains("Mac"))
Orders[0]="open";
Runtime.getRuntime().exec(Orders);
} catch (Exception ex)
{
Message(ex.getLocalizedMessage());
}
return(0);
}
private String HtmlDesc(PDFolders FoldAct) throws PDException
{
StringBuilder Html=new StringBuilder("<html><b>"+FoldAct.getTitle()+"</b> ("+FoldAct.getFolderType() +") : "+FormatDate(FoldAct.getPDDate())+ "<hr> ACL="+FoldAct.getACL());
Record Rec=FoldAct.getRecSum();
Rec.initList();
Attribute Attr=Rec.nextAttr();
while (Attr!=null)
{
if (!List.contains(Attr.getName()))
{
Html.append("<br><b>").append(DrvTT(Attr.getUserName())).append("= </b>");
Html.append(Attr.Export());
}
Attr=Rec.nextAttr();
}
Html.append("</html>");
return(Html.toString());
}
/**
*
* @param Text
* @return
*/
static public String DrvTT(String Text)
{
if (getSession()==null)
return( DriverGeneric.DefTT(Text) );
else
return( getSession().TT(Text) );
}
/**
*
* @param Text
* @return
*/
static public String TT(String Text)
{
if (getSession()==null)
return( DriverGeneric.DefTT(Text) );
else
return( getSession().TT(Text) );
}
/**
* @return the formatterTS
*/
public static SimpleDateFormat getFormatterTS()
{
if (formatterTS==null)
{
try {
formatterTS = new SimpleDateFormat(getSession().getPDCust().getTimeFormat());
} catch (PDException ex)
{
formatterTS = new SimpleDateFormat("yyyy-MM-dd HH:mm:ss");
}
}
return formatterTS;
}
/**
* @return the formatterDate
*/
public static SimpleDateFormat getFormatterDate()
{
if (formatterDate==null)
{
try {
formatterDate = new SimpleDateFormat(getSession().getPDCust().getDateFormat());
} catch (PDException ex)
{
formatterDate = new SimpleDateFormat("yyyy-MM-dd");
}
}
return formatterDate;
}
/**
* @return the formatTS
*/
public static String getFormatTS()
{
try {
return (getSession().getPDCust().getTimeFormat() );
} catch (PDException ex)
{
return("yyyy-MM-dd HH:mm:ss");
}
}
/**
* @return the formatDate
*/
public static String getFormatDate()
{
try {
return(getSession().getPDCust().getDateFormat());
} catch (PDException ex)
{
return("yyyy-MM-dd");
}
}
/**
* @return the formFacTS
* @throws Exception
*/
public static DefaultFormatterFactory getFormFacTS() throws Exception
{
if (formFacTS==null)
{
// formFacTS = new DefaultFormatterFactory(new MaskFormatter(MainWin.getFormatTS()));
formFacTS = new DefaultFormatterFactory(new javax.swing.text.DateFormatter(new java.text.SimpleDateFormat((MainWin.getFormatTS()))));
}
return formFacTS;
}
/**
* @return the formFacDate
* @throws Exception
*/
public static DefaultFormatterFactory getFormFacDate() throws Exception
{
if (formFacDate==null)
{
// formFacDate = new DefaultFormatterFactory(new MaskFormatter(MainWin.getFormatDate()));
formFacDate = new DefaultFormatterFactory(new javax.swing.text.DateFormatter(new java.text.SimpleDateFormat((MainWin.getFormatDate()))));
}
return formFacDate;
}
private String getLang()
{
try {
return(getSession().getPDCust().getLanguage());
} catch (PDException ex)
{
return("EN");
}
}
private String OSSep()
{
return(File.separator);
}
static public String getTmp()
{
String Tmp=System.getProperty("java.io.tmpdir");
return(Tmp);
}
/**
* Used in mainWin.title and About form
* @return the actual ProdocSwing Version
*/
static public String getVersion()
{
return("0.7");
}
/**
*
* @param FoldAct OPD Folder to start exporting
* @param SelFile Destination Folder to export
* @param IsOneLevel When tru, the OPD folder and contained Docs (if IncDocs), are exported
* @param IncMetadata when true, include metadata in the export
* @param IncDocs when true, include docs in the export
*/
private void Export(PDFolders FoldAct, String SelFolder, boolean IsOneLevel, boolean IncMetadata, boolean IncDocs) throws Exception
{
String Destpath=SelFolder+File.separatorChar;
File SOFolder=new File(Destpath+FoldAct.getTitle());
SOFolder.mkdir();
ExpFolds++;
if (IncMetadata)
{
PrintWriter PW = new PrintWriter(Destpath+FoldAct.getTitle()+".opd");
PW.print(FoldAct.StartXML());
PW.print(FoldAct.toXML());
PW.print(FoldAct.EndXML());
PW.flush();
PW.close();
}
if (IncDocs)
{
PDDocs Doc = new PDDocs(FoldAct.getDrv());
Cursor ListDocs=Doc.getListContainedDocs(FoldAct.getPDId());
Record Res=FoldAct.getDrv().NextRec(ListDocs);
PDDocs ExpDoc=new PDDocs(FoldAct.getDrv());
while (Res!=null)
{
ExpDoc.assignValues(Res);
ExpDoc.ExportXML(SOFolder.getAbsolutePath(), false);
ExpDocs++;
Res=FoldAct.getDrv().NextRec(ListDocs);
}
FoldAct.getDrv().CloseCursor(ListDocs);
}
if (!IsOneLevel)
{
HashSet ListFolder = FoldAct.getListDirectDescendList(FoldAct.getPDId());
PDFolders ChildFold=new PDFolders(FoldAct.getDrv());
for (Iterator it = ListFolder.iterator(); it.hasNext();)
{
String ChildId=(String)it.next();
ChildFold.LoadFull(ChildId);
Export(ChildFold, SOFolder.getAbsolutePath(), IsOneLevel, IncMetadata, IncDocs);
}
}
}
private void Import(PDFolders FoldAct, String OriginPath, boolean IsOneLevel, boolean IncludeMetadata, boolean IncludeDocs, String FoldType, String DocType) throws PDException
{
PDFolders NewFold=new PDFolders(FoldAct.getDrv(), FoldType);
if (IncludeMetadata)
{
NewFold=NewFold.ProcessXML(new File(OriginPath+".opd"), FoldAct.getPDId());
}
else
{
String Name=OriginPath.substring(OriginPath.lastIndexOf(File.separatorChar)+1);
NewFold.setTitle(Name);
NewFold.setParentId(FoldAct.getPDId());
NewFold.insert();
}
ExpFolds++;
File ImpFold=new File(OriginPath);
File []ListOrigin=ImpFold.listFiles();
ArrayList DirList=new ArrayList(5);
for (int i = 0; i < ListOrigin.length; i++)
{
File ListElement = ListOrigin[i];
if (ListElement.isDirectory())
{
if (!IsOneLevel)
DirList.add(ListElement);
continue;
}
if (IncludeDocs)
{
if (ListElement.getName().endsWith(".opd"))
{
if (IncludeMetadata)
{
ExpDocs+=getSession().ProcessXML(ListElement, NewFold.getPDId());
}
}
else
{
if (!IncludeMetadata)
{
PDDocs NewDoc=new PDDocs(FoldAct.getDrv(), DocType);
NewDoc.setTitle(ListElement.getName());
NewDoc.setFile(ListElement.getAbsolutePath());
NewDoc.setDocDate(new Date(ListElement.lastModified()));
NewDoc.setParentId(NewFold.getPDId());
NewDoc.insert();
ExpDocs++;
}
}
}
}
ListOrigin=null; // to help gc and save memory during recursivity
for (int i = 0; i < DirList.size(); i++)
{
File SubDir = (File) DirList.get(i);
Import(NewFold, SubDir.getAbsolutePath(), IsOneLevel, IncludeMetadata, IncludeDocs, FoldType, DocType);
}
}
private void ImportExt(PDFolders FoldAct, String OriginPath, boolean DeleteAfter, String Format, String DefFoldType, String DateFormat, String TimeStampFormat) throws PDException
{
PDFolders NewFold=new PDFolders(FoldAct.getDrv(), DefFoldType);
HashSet ChildF=NewFold.getListDirectDescendList(FoldAct.getPDId());
String Name=OriginPath.substring(OriginPath.lastIndexOf(File.separatorChar)+1);
try {
String IdFold=NewFold.GetIdChild(FoldAct.getPDId(), Name);
NewFold.Load(IdFold);
} catch( PDException ex)
{
NewFold.setTitle(Name);
NewFold.setParentId(FoldAct.getPDId());
NewFold.insert();
}
ExpFolds++;
File ImpFold=new File(OriginPath);
File []ListOrigin=ImpFold.listFiles();
ArrayList DirList=new ArrayList(5);
File ImageFile=null;
for (int i = 0; i < ListOrigin.length; i++)
{
File ListElement = ListOrigin[i];
if (ListElement.isDirectory())
{
DirList.add(ListElement);
continue;
}
if (ListElement.getName().endsWith(".xml"))
{
ExpDocs++;
if (Format.equals("Abby"))
ImageFile=PDDocs.ProcessXMLAbby(getSession(), ListElement, NewFold.getPDId(), DateFormat, TimeStampFormat);
// else
// kofax
if (DeleteAfter)
{
if (ImageFile!=null)
ImageFile.delete();
ListElement.delete();
}
}
}
ListOrigin=null; // to help gc and save memory during recursivity
for (int i = 0; i < DirList.size(); i++)
{
File SubDir = (File) DirList.get(i);
ImportExt(NewFold, SubDir.getAbsolutePath(), DeleteAfter, Format, DefFoldType, DateFormat, TimeStampFormat);
if (DeleteAfter)
SubDir.delete();
}
}
static protected void AddExec(String FileName)
{
ExecFiles.add(FileName);
File f=new File(FileName);
f.setReadOnly();
}
static private void DestroyExec()
{
for (Iterator it = ExecFiles.iterator(); it.hasNext();)
{
try {
String FileName = (String)it.next();
File f=new File(FileName);
f.setWritable(true);
f.delete();
} catch (Exception ex)
{
}
}
}
private void SetMenu()
{
try {
PDRoles R=MainWin.getSession().getUser().getRol();
ACLMenuItem.setVisible(R.isAllowCreateAcl() || R.isAllowMaintainAcl());
AuthentMenuItem.setVisible(R.isAllowCreateAuth() || R.isAllowMaintainAuth());
CustomMenuItem.setVisible(R.isAllowCreateCustom() || R.isAllowMaintainCustom());
GroupMenuItem.setVisible(R.isAllowCreateGroup() || R.isAllowMaintainGroup());
MimeTypeMenuItem.setVisible(R.isAllowCreateMime() || R.isAllowMaintainMime());
ObjDefMenuItem.setVisible(R.isAllowCreateObject() || R.isAllowMaintainObject());
ReposMenuItem.setVisible(R.isAllowCreateRepos() || R.isAllowMaintainRepos());
RolMenuItem.setVisible(R.isAllowCreateRole() || R.isAllowMaintainRole());
UserMenuItem.setVisible(R.isAllowCreateUser() || R.isAllowMaintainUser());
AddFold.setVisible(R.isAllowCreateFolder());
AddFoldAdvanced.setVisible(R.isAllowCreateFolder());
ImportFold.setVisible(R.isAllowCreateFolder());
ModFold.setVisible(R.isAllowMaintainFolder());
ModFoldAdvanced.setVisible(R.isAllowMaintainFolder());
DelFold.setVisible(R.isAllowMaintainFolder());
AddDoc.setVisible(R.isAllowCreateDoc());
AddDocAdvanced.setVisible(R.isAllowCreateDoc());
ImportDoc.setVisible(R.isAllowCreateDoc());
PaperBin.setVisible(R.isAllowCreateDoc() && R.isAllowMaintainDoc());
ModDocAdvanced.setVisible(R.isAllowMaintainDoc());
CheckOut.setVisible(R.isAllowMaintainDoc());
CancelCheckout.setVisible(R.isAllowMaintainDoc());
CheckIn.setVisible(R.isAllowMaintainDoc());
CheckOut.setVisible(R.isAllowMaintainDoc());
DelDoc.setVisible(R.isAllowMaintainDoc());
} catch (Exception ex)
{
Message(ex.getLocalizedMessage());
}
}
}
|
package org.intermine.bio.dataconversion;
import java.io.IOException;
import java.io.Reader;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.Map;
import java.util.Set;
import org.intermine.util.FormattedTextParser;
/**
* Parse NCBI Entrez gene_info file and return data structure for each row for later processing.
* @author Richard Smith
*
*/
public class NcbiGeneInfoParser
{
private Map<String, Set<GeneInfoRecord>> recordMap = new HashMap<String, Set<GeneInfoRecord>>();
private Map<String, Set<String>> duplicateEnsemblIds = new HashMap<String, Set<String>>();
private Map<String, Set<String>> duplicateSymbols = new HashMap<String, Set<String>>();
/**
* Construct the parser with the file to read, the input file can be for a single taxon or for
* multiple.
* @param reader a reader for the gene_info file to be parsed
* @throws IOException if problems reading file
*/
public NcbiGeneInfoParser(Reader reader) throws IOException {
Iterator<String[]> lineIter = FormattedTextParser.parseTabDelimitedReader(reader);
while (lineIter.hasNext()) {
String[] line = lineIter.next();
String taxonId = line[0];
String entrez = line[1];
String defaultSymbol = line[2];
String synonyms = line[4];
String xrefs = line[5];
String mapLocation = line[7];
String defaultName = line[8];
String officialSymbol = line[10];
String officialName = line[11];
GeneInfoRecord record = new GeneInfoRecord(taxonId, entrez, officialSymbol,
defaultSymbol, officialName, defaultName, mapLocation);
record.ensemblIds.addAll(parseXrefs(xrefs, "Ensembl"));
for (String synonym : synonyms.split("\\|")) {
record.synonyms.add(synonym);
}
Set<GeneInfoRecord> taxonRecords = recordMap.get(taxonId);
if (taxonRecords == null) {
taxonRecords = new HashSet<GeneInfoRecord>();
recordMap.put(taxonId, taxonRecords);
}
taxonRecords.add(record);
}
}
/**
* Return information read from the file, for each taxon id there is one GeneInfoRecord per row
* in the file.
* @return a map from taxon id to gene information records
*/
public Map<String, Set<GeneInfoRecord>> getGeneInfoRecords() {
return recordMap;
}
/**
* Return true if the given Ensembl identifier is assigned to only one gene for the taxon
* specified.
* @param taxonId the taxon of the gene being looked up
* @param ensemblId an ensembl gene identifier
* @return true if this ensembl id is only mapped to one NCBI gene
*/
public boolean isUniquelyMappedEnsemblId(String taxonId, String ensemblId) {
Set<String> taxonDuplicates = duplicateEnsemblIds.get(taxonId);
if (taxonDuplicates == null) {
taxonDuplicates = findDuplicateEnsemblIds(taxonId);
duplicateEnsemblIds.put(taxonId, taxonDuplicates);
}
return !taxonDuplicates.contains(ensemblId);
}
private Set<String> findDuplicateEnsemblIds(String taxonId) {
Set<String> duplicates = new HashSet<String>();
if (recordMap.containsKey(taxonId)) {
Set<String> seenEnsembl = new HashSet<String>();
for (GeneInfoRecord record : recordMap.get(taxonId)) {
for (String ensembl : record.ensemblIds) {
if (seenEnsembl.contains(ensembl)) {
duplicates.add(ensembl);
} else {
seenEnsembl.add(ensembl);
}
}
}
}
return duplicates;
}
/**
* Return true if the given symbol is is assigned to only one gene for the taxon specified.
* @param taxonId the taxon of the gene being looked up
* @param symbol a gene symbl to check
* @return true if this true id is only assigned to one NCBI gene
*/
public boolean isUniqueSymbol(String taxonId, String symbol) {
Set<String> taxonDuplicates = duplicateSymbols.get(taxonId);
if (taxonDuplicates == null) {
taxonDuplicates = findDuplicateSymbols(taxonId);
duplicateSymbols.put(taxonId, taxonDuplicates);
}
return !taxonDuplicates.contains(symbol);
}
public Set<String> findDuplicateSymbols(String taxonId) {
Set<String> duplicates = new HashSet<String>();
if (recordMap.containsKey(taxonId)) {
Set<String> seenSymbols = new HashSet<String>();
for (GeneInfoRecord record : recordMap.get(taxonId)) {
for (String symbol : new String[] {record.officialSymbol, record.defaultSymbol}) {
if (seenSymbols.contains(symbol)) {
duplicates.add(symbol);
} else {
seenSymbols.add(symbol);
}
}
}
}
return duplicates;
}
private Set<String> parseXrefs(String xrefs, String prefix) {
if (!prefix.endsWith(":")) {
prefix = prefix + ":";
}
Set<String> matched = new HashSet<String>();
for (String xref : xrefs.split("\\|")) {
if (xref.startsWith(prefix)) {
matched.add(xref.substring(prefix.length()));
}
}
return matched;
}
}
|
package polyglot.ext.jl.ast;
import polyglot.ast.*;
import polyglot.types.*;
import polyglot.visit.*;
import polyglot.util.*;
import java.util.*;
/**
* A <code>AmbAssign</code> represents a Java assignment expression to
* an as yet unknown expression.
*/
public class AmbAssign_c extends Assign_c implements AmbAssign
{
public AmbAssign_c(Position pos, Expr left, Operator op, Expr right) {
super(pos, left, op, right);
}
public Term entry() {
if (operator() != Assign.ASSIGN) {
return left();
}
return right().entry();
}
protected void acceptCFGAssign(CFGBuilder v) {
v.visitCFG(right(), this);
}
protected void acceptCFGOpAssign(CFGBuilder v) {
v.edge(left(), right().entry());
v.visitCFG(right(), this);
}
public Node disambiguate(AmbiguityRemover ar) throws SemanticException {
Assign n = (Assign)super.disambiguate(ar);
if (n.left() instanceof Local) {
return ar.nodeFactory().LocalAssign(n.position(), (Local)left(), operator(), right());
}
else if (n.left() instanceof Field) {
return ar.nodeFactory().FieldAssign(n.position(), (Field)left(), operator(), right());
}
else if (n.left() instanceof ArrayAccess) {
return ar.nodeFactory().ArrayAccessAssign(n.position(), (ArrayAccess)left(), operator(), right());
}
new Exception().printStackTrace();
throw new SemanticException("Could not disambiguate left side of assignment!", n.position());
}
}
|
package org.intermine.bio.web.logic;
import java.io.BufferedReader;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStreamReader;
import java.io.StringReader;
import java.text.DecimalFormat;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.HashMap;
import java.util.HashSet;
import java.util.Iterator;
import java.util.LinkedHashMap;
import java.util.LinkedHashSet;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Properties;
import java.util.Set;
import java.util.TreeSet;
import java.util.regex.Pattern;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpSession;
import org.apache.log4j.Logger;
import org.apache.struts.action.ActionMessage;
import org.apache.struts.upload.FormFile;
import org.intermine.api.InterMineAPI;
import org.intermine.api.profile.Profile;
import org.intermine.bio.web.model.ChromosomeInfo;
import org.intermine.bio.web.model.GenomicRegion;
import org.intermine.bio.web.model.GenomicRegionSearchConstraint;
import org.intermine.bio.web.struts.GenomicRegionSearchForm;
import org.intermine.metadata.ClassDescriptor;
import org.intermine.metadata.Model;
import org.intermine.model.bio.Organism;
import org.intermine.model.bio.SequenceFeature;
import org.intermine.objectstore.ObjectStore;
import org.intermine.objectstore.query.ConstraintOp;
import org.intermine.objectstore.query.ConstraintSet;
import org.intermine.objectstore.query.ContainsConstraint;
import org.intermine.objectstore.query.Query;
import org.intermine.objectstore.query.QueryClass;
import org.intermine.objectstore.query.QueryField;
import org.intermine.objectstore.query.QueryObjectReference;
import org.intermine.objectstore.query.Results;
import org.intermine.objectstore.query.ResultsRow;
import org.intermine.pathquery.Constraints;
import org.intermine.pathquery.PathQuery;
import org.intermine.util.StringUtil;
import org.intermine.web.logic.WebUtil;
import org.intermine.web.logic.config.WebConfig;
import org.intermine.web.logic.session.SessionMethods;
import org.json.JSONObject;
/**
* A class to provide genomic region search services in general.
*
* @author Fengyuan Hu
*/
public class GenomicRegionSearchService
{
@SuppressWarnings("unused")
private static final Logger LOG = Logger
.getLogger(GenomicRegionSearchService.class);
private InterMineAPI interMineAPI = null;
private Model model = null;
private ObjectStore objectStore = null;
private Properties webProperties = null;
private Profile profile = null;
private WebConfig webConfig = null;
private static String orgFeatureJSONString = "";
private static final String GENOMIC_REGION_SEARCH_OPTIONS_DEFAULT =
"genomic_region_search_options_default";
private static final String GENOMIC_REGION_SEARCH_RESULTS_DEFAULT =
"genomic_region_search_results_default";
private static final int READ_AHEAD_CHARS = 10000;
private GenomicRegionSearchConstraint grsc = null;
// Key - organism : Value - map <key - chr : value - chromosome information>
private static Map<String, Map<String, ChromosomeInfo>> chrInfoMap = null;
private static Set<String> featureTypesInOrgs = null;
private static Map<String, List<String>> featureTypeToSOTermMap = null;
private static Map<String, Integer> orgTaxonIdMap = null;
private List<String> selectionInfo = new ArrayList<String>();
/**
* Constructor
*/
public GenomicRegionSearchService() {
}
/**
* To set globally used variables.
* @param request HttpServletRequest
*/
public void init (HttpServletRequest request) {
this.webProperties = SessionMethods.getWebProperties(
request.getSession().getServletContext());
this.webConfig = SessionMethods.getWebConfig(request);
this.interMineAPI = SessionMethods.getInterMineAPI(request.getSession());
this.profile = SessionMethods.getProfile(request.getSession());
this.model = this.interMineAPI.getModel();
this.objectStore = this.interMineAPI.getObjectStore();
}
/**
* To call the queryOrganismAndSequenceFeatureTypes method in
* GenomicRegionSearchQueryRunner.
*
* @return a JSON string
* @throws Exception e
*/
public String setupWebData() throws Exception {
// By default, query all organisms in the database
// pre defined organism short names can be read out from web.properties
String presetOrganisms = webProperties.getProperty(
"genomicRegionSearch.defaultOrganisms");
List<String> orgList = new ArrayList<String>();
Set<String> chrOrgSet = getChromosomeInfomationMap().keySet();
if (chrOrgSet == null || chrOrgSet.size() == 0) {
throw new RuntimeException(
"Chromosome location information is missing...");
} else {
if (presetOrganisms == null || "".equals(presetOrganisms)) {
orgList = new ArrayList<String>(chrOrgSet);
} else {
// e.g. presetCollection [f,b,a], orgFromDBCollection [g,a,e,f]
// results => [f,a] + [e,g] = [f,a,e,g]
// some items in preset organisms will be removed if chro information not available
List<String> presetOrgList = Arrays.asList(presetOrganisms
.split(","));
List<String> trimedPresetOrgList = new ArrayList<String>();
for (String s : presetOrgList) {
if (!"".equals(s.trim())) {
trimedPresetOrgList.add(s.trim());
}
}
// Don't remove any items from chrOrgSet, just make a copy
Set<String> chrOrgSetCopy = new TreeSet<String>();
for (String s : chrOrgSet) {
chrOrgSetCopy.add(s);
}
for (String o : trimedPresetOrgList) {
if (chrOrgSet.contains(o)) {
chrOrgSetCopy.remove(o);
}
}
trimedPresetOrgList.retainAll(chrOrgSet);
orgList.addAll(trimedPresetOrgList);
orgList.addAll(chrOrgSetCopy);
}
}
// Exclude preset feature types (global) to display
// Data should be comma separated class names
String excludedFeatureTypes = webProperties.getProperty(
"genomicRegionSearch.featureTypesExcluded.global");
List<String> excludedFeatureTypeList = new ArrayList<String>();
if (excludedFeatureTypes == null || "".equals(excludedFeatureTypes)) {
excludedFeatureTypeList = null;
} else {
excludedFeatureTypeList = Arrays.asList(excludedFeatureTypes.split(","));
}
if ("".equals(orgFeatureJSONString)) {
orgFeatureJSONString = prepareWebData(orgList, excludedFeatureTypeList);
return orgFeatureJSONString;
} else {
return orgFeatureJSONString;
}
}
private String prepareWebData(List<String> orgList, List<String> excludedFeatureTypeList) {
Query q = new Query();
q.setDistinct(true);
QueryClass qcOrg = new QueryClass(Organism.class);
QueryClass qcFeature = new QueryClass(SequenceFeature.class);
QueryField qfOrgName = new QueryField(qcOrg, "shortName");
QueryField qfFeatureClass = new QueryField(qcFeature, "class");
q.addToSelect(qfOrgName);
q.addToSelect(qfFeatureClass);
q.addFrom(qcOrg);
q.addFrom(qcFeature);
q.addToOrderBy(qfOrgName, "ascending");
ConstraintSet constraints = new ConstraintSet(ConstraintOp.AND);
q.setConstraint(constraints);
// SequenceFeature.organism = Organism
QueryObjectReference organism = new QueryObjectReference(qcFeature,
"organism");
ContainsConstraint ccOrg = new ContainsConstraint(organism,
ConstraintOp.CONTAINS, qcOrg);
constraints.addConstraint(ccOrg);
// constraints.addConstraint(new BagConstraint(qfOrgName,
// ConstraintOp.IN, orgList));
Results results = objectStore.execute(q);
// Parse results data to a map
Map<String, Set<String>> resultsMap = new LinkedHashMap<String, Set<String>>();
Set<String> featureTypeSet = new LinkedHashSet<String>();
// TODO this will be very slow when query too many features
if (results == null || results.size() < 0) {
return "";
} else {
for (Iterator<?> iter = results.iterator(); iter.hasNext();) {
ResultsRow<?> row = (ResultsRow<?>) iter.next();
String org = (String) row.get(0);
@SuppressWarnings("rawtypes")
// TODO exception - feature type is NULL
String featureType = ((Class) row.get(1)).getSimpleName();
if (!"Chromosome".equals(featureType) && orgList.contains(org)) {
if (resultsMap.size() < 1) {
featureTypeSet.add(featureType);
resultsMap.put(org, featureTypeSet);
} else {
if (resultsMap.keySet().contains(org)) {
resultsMap.get(org).add(featureType);
} else {
Set<String> s = new LinkedHashSet<String>();
s.add(featureType);
resultsMap.put(org, s);
}
}
}
}
}
// Get all feature types
for (Set<String> ftSet : resultsMap.values()) {
// Exclude some feature types
if (excludedFeatureTypeList != null) {
ftSet.removeAll(excludedFeatureTypeList);
}
if (featureTypesInOrgs == null) {
featureTypesInOrgs = new HashSet<String>();
featureTypesInOrgs.addAll(ftSet);
}
}
getFeatureTypeToSOTermMap();
getOrganismToTaxonMap();
// Parse data to JSON string
List<Object> ft = new ArrayList<Object>();
List<Object> gb = new ArrayList<Object>();
Map<String, Object> ma = new LinkedHashMap<String, Object>();
for (Entry<String, Set<String>> e : resultsMap.entrySet()) {
Map<String, Object> mft = new LinkedHashMap<String, Object>();
Map<String, Object> mgb = new LinkedHashMap<String, Object>();
mft.put("organism", e.getKey());
List<Object> featureTypeAndDespMapList = new ArrayList<Object>();
for (String className : e.getValue()) {
Map<String, String> featureTypeAndDespMap = new LinkedHashMap<String, String>();
String soTermDes = "description not avaliable";
List<String> soInfo = featureTypeToSOTermMap.get(className);
if (soInfo != null) {
soTermDes = featureTypeToSOTermMap.get(className).get(1);
}
featureTypeAndDespMap.put("featureType", className);
featureTypeAndDespMap.put("description", soTermDes);
featureTypeAndDespMapList.add(featureTypeAndDespMap);
}
mft.put("features", featureTypeAndDespMapList);
ft.add(mft);
mgb.put("organism", e.getKey());
mgb.put("genomeBuild",
(OrganismGenomeBuildLookup
.getGenomeBuildbyOrgansimAbbreviation(e.getKey()) == null)
? "not available"
: OrganismGenomeBuildLookup
.getGenomeBuildbyOrgansimAbbreviation(e
.getKey()));
gb.add(mgb);
}
ma.put("organisms", orgList);
ma.put("genomeBuilds", gb);
ma.put("featureTypes", ft);
JSONObject jo = new JSONObject(ma);
// Note: JSONObject toString will replace \' to \\', so don't convert it before the method
// was called. Replace "\" in java -> "\\\\"
String preDataStr = jo.toString();
preDataStr = preDataStr.replaceAll("'", "\\\\'");
return preDataStr;
}
/**
* Get the name of customized options javascript, by default, it is named
* "genomic_region_search_options_default.js"
*
* @return the name of options javascript name
*/
public String getOptionsJavascript() {
String optionsJavascriptName = webProperties
.getProperty("genomicRegionSearch.optionsJavascript");
if (optionsJavascriptName == null || "".equals(optionsJavascriptName)) {
optionsJavascriptName = GENOMIC_REGION_SEARCH_OPTIONS_DEFAULT;
}
return optionsJavascriptName;
}
/**
* Get the name of customized results javascript
*
* @return the name of results page
*/
public String getResultsJavascript() {
String resultsJavascriptName = webProperties
.getProperty("genomicRegionSearch.resultsJavascript");
if (resultsJavascriptName == null || "".equals(resultsJavascriptName)) {
resultsJavascriptName = GENOMIC_REGION_SEARCH_RESULTS_DEFAULT;
}
return resultsJavascriptName;
}
/**
* Get the name of customized options CSS
*
* @return the name of options css
*/
public String getOptionsCss() {
String optionsCssName = webProperties.getProperty(
"genomicRegionSearch.optionsCss");
if (optionsCssName == null || "".equals(optionsCssName)) {
optionsCssName = GENOMIC_REGION_SEARCH_OPTIONS_DEFAULT;
}
return optionsCssName;
}
/**
* Get the name of customized results CSS
*
* @return the name of results css
*/
public String getResultsCss() {
String resultsCssName = webProperties.getProperty(
"genomicRegionSearch.resultsCss");
if (resultsCssName == null || "".equals(resultsCssName)) {
resultsCssName = GENOMIC_REGION_SEARCH_RESULTS_DEFAULT;
}
return resultsCssName;
}
/**
* To parse form data
*
* @param grsForm GenomicRegionSearchForm
* @return genomic region search constraint
*/
public ActionMessage parseGenomicRegionSearchForm(
GenomicRegionSearchForm grsForm) {
grsc = new GenomicRegionSearchConstraint();
ActionMessage actmsg = parseBasicInput(grsForm);
if (actmsg != null) {
return actmsg;
}
return null;
}
/**
*
* @param grsForm GenomicRegionSearchForm
* @return ActionMessage
*/
public ActionMessage parseBasicInput(GenomicRegionSearchForm grsForm) {
// Parse form
String organism = (String) grsForm.get("organism");
String[] featureTypes = (String[]) grsForm.get("featureTypes");
String whichInput = (String) grsForm.get("whichInput");
String dataFormat = (String) grsForm.get("dataFormat");
FormFile formFile = (FormFile) grsForm.get("fileInput");
String pasteInput = (String) grsForm.get("pasteInput");
String extendedRegionSize = (String) grsForm.get("extendedRegionSize");
// Organism
grsc.setOrgName(organism);
grsc.setExtededRegionSize(Integer.parseInt(extendedRegionSize));
selectionInfo.add("<b>Selected organism: </b><i>" + organism + "</i>");
// Feature types
if (featureTypes == null) {
return new ActionMessage("genomicRegionSearch.spanFieldSelection",
"feature types");
}
// featureTypes in this case are (the last bit of) class instead of
// featuretype in the db table; gain the full name by Model.getQualifiedTypeName(className)
Set<Class<?>> ftSet = new HashSet<Class<?>>();
for (String f : featureTypes) {
ClassDescriptor cld = model.getClassDescriptorByName(f);
ftSet.add(cld.getType());
for (ClassDescriptor subCld : model.getAllSubs(cld)) {
ftSet.add(subCld.getType());
}
}
String ftString = "";
for (String aFeaturetype : featureTypes) {
aFeaturetype = WebUtil.formatPath(aFeaturetype, interMineAPI, webConfig);
ftString = ftString + aFeaturetype + ", ";
}
selectionInfo.add("<b>Selected feature types: </b>"
+ ftString.substring(0, ftString.lastIndexOf(", ")));
if (Integer.parseInt(extendedRegionSize) > 0) {
if (Integer.parseInt(extendedRegionSize) >= 1000) {
selectionInfo.add("<b>Extend Regions: </b>"
+ new DecimalFormat("#.##").format(Integer
.parseInt(extendedRegionSize) / 1000) + " kbp");
} else {
selectionInfo.add("<b>Extend Regions: </b>" + extendedRegionSize + "bp");
}
}
grsc.setFeatureTypes(ftSet);
// File parsing
BufferedReader reader = null;
/*
* FormFile used from Struts works a bit strangely. 1. Although the file
* does't exist formFile.getInputStream() doesn't throw
* FileNotFoundException. 2. When user specified empty file path or very
* invalid file path, like file path not starting at '/' then
* formFile.getFileName() returns empty string.
*/
if ("paste".equals(whichInput)) {
if (pasteInput != null && pasteInput.length() != 0) {
String trimmedText = pasteInput.trim();
if (trimmedText.length() == 0) {
return new ActionMessage("genomicRegionSearch.noSpanPaste");
}
reader = new BufferedReader(new StringReader(trimmedText));
} else {
return new ActionMessage("genomicRegionSearch.noSpanFile");
}
} else if ("file".equals(whichInput)) {
if (formFile != null && formFile.getFileName() != null
&& formFile.getFileName().length() > 0) {
String mimetype = formFile.getContentType();
if (!"application/octet-stream".equals(mimetype)
&& !mimetype.startsWith("text")) {
return new ActionMessage("genomicRegionSearch.isNotText",
mimetype);
}
if (formFile.getFileSize() == 0) {
return new ActionMessage(
"genomicRegionSearch.noSpanFileOrEmpty");
}
try {
reader = new BufferedReader(new InputStreamReader(
formFile.getInputStream()));
} catch (FileNotFoundException e) {
e.printStackTrace();
} catch (IOException e) {
e.printStackTrace();
}
}
} else {
return new ActionMessage("genomicRegionSearch.spanInputType");
}
// Validate text format
try {
reader.mark(READ_AHEAD_CHARS);
} catch (IOException e) {
e.printStackTrace();
}
char[] buf = new char[READ_AHEAD_CHARS];
int read;
Set<String> spanStringSet = new LinkedHashSet<String>();
try {
read = reader.read(buf, 0, READ_AHEAD_CHARS);
for (int i = 0; i < read; i++) {
if (buf[i] == 0) {
return new ActionMessage("genomicRegionSearch.isNotText",
"binary");
}
}
reader.reset();
// Remove duplication
String thisLine;
while ((thisLine = reader.readLine()) != null) {
spanStringSet.add(thisLine);
}
} catch (IOException e) {
e.printStackTrace();
}
// Parse uploaded spans to an arraylist; handle empty content and non-integer spans
// Tab delimited format: "chr(tab)start(tab)end" or "chr:start..end"
List<GenomicRegion> spanList = new ArrayList<GenomicRegion>();
for (String spanStr : spanStringSet) {
GenomicRegion aSpan = new GenomicRegion();
// Use regular expression to validate user's input:
String ddotsRegex = "[^:]+: ?\\d+\\.\\.\\d+$"; // "chr:start..end" - [^:]+:\d+\.{2,}\d+
String tabRegex = "[^\\t]+\\t\\d+\\t\\d+$"; // "chr:start-end" - [^:]+:\d+\-\d+
String dashRegex = "[^:]+: ?\\d+\\-\\d+$"; // "chr(tab)start(tab)end" - [^\t]+\t\d+\t\d+
String snpRegex = "[^:]+: ?\\d+$"; // "chr:singlePosition" - [^:]+:[\d]+$
if (Pattern.matches(ddotsRegex, spanStr)) {
aSpan.setChr((spanStr.split(":"))[0]);
String[] spanItems = (spanStr.split(":"))[1].split("\\..");
String start = spanItems[0].trim();
if ("isInterBaseCoordinate".equals(dataFormat)) {
aSpan.setStart(Integer.valueOf(start) + 1);
} else {
aSpan.setStart(Integer.valueOf(start));
}
aSpan.setEnd(Integer.valueOf(spanItems[1]));
} else if (Pattern.matches(tabRegex, spanStr)) {
String[] spanItems = spanStr.split("\t");
aSpan.setChr(spanItems[0]);
if ("isInterBaseCoordinate".equals(dataFormat)) {
aSpan.setStart(Integer.valueOf(spanItems[1]) + 1);
} else {
aSpan.setStart(Integer.valueOf(spanItems[1]));
}
aSpan.setEnd(Integer.valueOf(spanItems[2]));
} else if (Pattern.matches(dashRegex, spanStr)) {
aSpan.setChr((spanStr.split(":"))[0]);
String[] spanItems = (spanStr.split(":"))[1].split("-");
String start = spanItems[0].trim();
if ("isInterBaseCoordinate".equals(dataFormat)) {
aSpan.setStart(Integer.valueOf(start) + 1);
} else {
aSpan.setStart(Integer.valueOf(start));
}
aSpan.setEnd(Integer.valueOf(spanItems[1]));
} else if (Pattern.matches(snpRegex, spanStr)) {
aSpan.setChr((spanStr.split(":"))[0]);
String start = (spanStr.split(":"))[1].trim();
if ("isInterBaseCoordinate".equals(dataFormat)) {
aSpan.setStart(Integer.valueOf(start) + 1);
} else {
aSpan.setStart(Integer.valueOf(start));
}
aSpan.setEnd(Integer.valueOf((spanStr.split(":"))[1].trim()));
} else {
return new ActionMessage(
"genomicRegionSearch.spanInWrongformat", spanStr);
}
spanList.add(aSpan);
}
grsc.setGenomicRegionList(spanList);
return null;
}
/**
* To prepare queries for genomic regions
*
* @return a list of prepared queries for genomic regions
*/
public Map<GenomicRegion, Query> createQueryList() {
return GenomicRegionSearchUtil.createQueryList(
grsc.getGenomicRegionList(),
grsc.getExtendedRegionSize(),
getChromosomeInfomationMap().get(grsc.getOrgName()),
grsc.getOrgName(),
grsc.getFeatureTypes());
}
/**
* @return the grsc
*/
public GenomicRegionSearchConstraint getConstraint() {
return this.grsc;
}
/**
* Get chromosome information as in a map, keys are lowercased chromosome ids
* @return chrInfoMap
*/
public Map<String, Map<String, ChromosomeInfo>> getChromosomeInfomationMap() {
if (chrInfoMap == null) {
chrInfoMap = GenomicRegionSearchQueryRunner
.getChromosomeInfo(interMineAPI, profile);
}
return chrInfoMap;
}
/**
*
* @return featureTypeToSOTermMap
*/
public Map<String, List<String>> getFeatureTypeToSOTermMap() {
if (featureTypeToSOTermMap == null) {
featureTypeToSOTermMap = GenomicRegionSearchQueryRunner
.getFeatureAndSOInfo(interMineAPI);
if (!(featureTypesInOrgs.size() == featureTypeToSOTermMap.size() && featureTypesInOrgs
.containsAll(featureTypeToSOTermMap.keySet()))) {
Map<String, List<String>> newFeatureTypeToSOTermMap =
new HashMap<String, List<String>>();
for (String ft : featureTypesInOrgs) {
if (featureTypeToSOTermMap.keySet().contains(ft)) {
newFeatureTypeToSOTermMap.put(ft,
featureTypeToSOTermMap.get(ft));
} else {
List<String> des = new ArrayList<String>();
des.add(ft);
des.add("description not avaliable");
newFeatureTypeToSOTermMap.put(ft, des);
}
}
featureTypeToSOTermMap = newFeatureTypeToSOTermMap;
}
}
return featureTypeToSOTermMap;
}
/**
*
* @return orgTaxonIdMap
*/
public Map<String, Integer> getOrganismToTaxonMap() {
if (orgTaxonIdMap == null) {
orgTaxonIdMap = GenomicRegionSearchQueryRunner.getTaxonInfo(interMineAPI,
profile);
}
return orgTaxonIdMap;
}
/**
* Validate input genomic regions
* @return resultMap
*/
public Map<String, List<GenomicRegion>> validateGenomicRegions() {
/* the Map has two key-value mappings
* PASS-ArrayList<passedSpan>
* ERROR-ArrayList<errorSpan>
*/
Map<String, List<GenomicRegion>> resultMap = new HashMap<String, List<GenomicRegion>>();
List<GenomicRegion> passedSpanList = new ArrayList<GenomicRegion>();
List<GenomicRegion> errorSpanList = new ArrayList<GenomicRegion>();
Map<String, ChromosomeInfo> chrInfo = chrInfoMap.get(grsc.getOrgName());
if (chrInfo == null) { // this should not happen
return null;
}
// Create passedSpanList
for (GenomicRegion gr : grsc.getGenomicRegionList()) {
// User input could be x instead of X for human chromosome, converted to lowercase
ChromosomeInfo ci = null;
String chr = gr.getChr().toLowerCase();
if (chrInfo.containsKey(chr)) {
ci = chrInfo.get(chr);
} else {
if (chr.startsWith("chr")) { // UCSC format
if (chrInfo.containsKey(chr.substring(3))) {
ci = chrInfo.get(chr.substring(3));
} else {
continue;
}
} else {
continue;
}
}
if ((gr.getStart() >= 1 && gr.getStart() <= ci
.getChrLength())
&& (gr.getEnd() >= 1 && gr.getEnd() <= ci
.getChrLength())) {
if (gr.getStart() > gr.getEnd()) { // Start must be smaller than End
GenomicRegion newSpan = new GenomicRegion();
newSpan.setChr(ci.getChrPID()); // converted to the right case
newSpan.setStart(gr.getEnd());
newSpan.setEnd(gr.getStart());
passedSpanList.add(newSpan);
} else {
gr.setChr(ci.getChrPID());
passedSpanList.add(gr);
}
}
}
// make errorSpanList
errorSpanList.addAll(grsc.getGenomicRegionList());
errorSpanList.removeAll(passedSpanList);
resultMap.put("pass", passedSpanList);
resultMap.put("error", errorSpanList);
return resultMap;
}
/**
* The message passed to results page
*
* @return resultMessages
*/
public List<String> getSelectionInformation() {
return this.selectionInfo;
}
/**
* Get organism for GenomicRegionSearchAjaxAction use.
*
* @param spanUUIDString uuid
* @param spanConstraintMap map of contraints
* @return the organism
*/
public String getGenomicRegionOrganismConstraint(String spanUUIDString,
Map<GenomicRegionSearchConstraint, String> spanConstraintMap) {
for (Entry<GenomicRegionSearchConstraint, String> e : spanConstraintMap
.entrySet()) {
if (e.getValue().equals(spanUUIDString)) {
return e.getKey().getOrgName();
}
}
return null;
}
/**
* Get flanking size for GenomicRegionSearchAjaxAction use.
*
* @param spanUUIDString uuid
* @param spanConstraintMap map of contraints
* @return the flanking size
*/
public int getGenomicRegionFlankingSizeConstraint(String spanUUIDString,
Map<GenomicRegionSearchConstraint, String> spanConstraintMap) {
for (Entry<GenomicRegionSearchConstraint, String> e : spanConstraintMap
.entrySet()) {
if (e.getValue().equals(spanUUIDString)) {
return e.getKey().getExtendedRegionSize();
}
}
return 0;
}
/**
* Get a set of ids of a span's overlap features. for
* GenomicRegionSearchAjaxAction use.
*
* @param grString a genomic region in string
* @param flankingSize int value of extended genomic region size
* @param resultMap map of search results
* @return String feature ids joined by comma
*/
public Set<Integer> getGenomicRegionOverlapFeaturesAsSet(String grString, int flankingSize,
Map<GenomicRegion, List<List<String>>> resultMap) {
Set<Integer> featureIdSet = new LinkedHashSet<Integer>();
GenomicRegion spanToExport = new GenomicRegion();
// spanString is extended span
String[] temp = grString.split(":");
spanToExport.setChr(temp[0]);
temp = temp[1].split("\\.\\.");
spanToExport.setExtendedStart(Integer.parseInt(temp[0]));
spanToExport.setExtendedEnd(Integer.parseInt(temp[1]));
spanToExport.setExtendedRegionSize(flankingSize);
spanToExport.setStart(spanToExport.getExtendedStart()
+ spanToExport.getExtendedRegionSize());
spanToExport.setEnd(spanToExport.getExtendedEnd() - spanToExport.getExtendedRegionSize());
for (List<String> sf : resultMap.get(spanToExport)) {
// the first element (0) is InterMine Id, second (1) is PID
featureIdSet.add(Integer.valueOf(sf.get(0)));
}
return featureIdSet;
}
/**
* Get a set of ids of a span's overlap features by given feature type. for
* GenomicRegionSearchAjaxAction use.
*
* @param grString a genomic region in string
* @param flankingSize int value of extended genomic region size
* @param resultMap map of search results
* @param featureType e.g. Gene
* @return String feature ids joined by comma
*/
public Set<Integer> getGenomicRegionOverlapFeaturesByType(String grString, int flankingSize,
Map<GenomicRegion, List<List<String>>> resultMap, String featureType) {
Set<Integer> featureIdSet = new LinkedHashSet<Integer>();
GenomicRegion spanToExport = new GenomicRegion();
// spanString is extended span
String[] temp = grString.split(":");
spanToExport.setChr(temp[0]);
temp = temp[1].split("\\.\\.");
spanToExport.setExtendedStart(Integer.parseInt(temp[0]));
spanToExport.setExtendedEnd(Integer.parseInt(temp[1]));
spanToExport.setExtendedRegionSize(flankingSize);
spanToExport.setStart(spanToExport.getExtendedStart()
+ spanToExport.getExtendedRegionSize());
spanToExport.setEnd(spanToExport.getExtendedEnd() - spanToExport.getExtendedRegionSize());
for (List<String> sf : resultMap.get(spanToExport)) {
// the first element (0) is InterMine Id, second (1) is PID, 4 featureType
if (sf.get(3).equals(featureType)) {
featureIdSet.add(Integer.valueOf(sf.get(0)));
}
}
return featureIdSet;
}
/**
* Get a set of ids of all span's overlap features by given feature type. for
* GenomicRegionSearchAjaxAction use.
*
* @param resultMap map of search results
* @param featureType e.g. Gene
* @return String feature ids joined by comma
*/
public Set<Integer> getAllGenomicRegionOverlapFeaturesByType(
Map<GenomicRegion, List<List<String>>> resultMap, String featureType) {
Set<Integer> featureIdSet = new LinkedHashSet<Integer>();
for (Entry<GenomicRegion, List<List<String>>> e : resultMap.entrySet()) {
if (e.getValue() != null) {
for (List<String> sf : e.getValue()) {
if (sf.get(3).equals(featureType)) { // 3 featureType
featureIdSet.add(Integer.valueOf(sf.get(0))); // 0 id
}
}
}
}
return featureIdSet;
}
/**
* Get a comma separated string of a span's overlap features. for
* GenomicRegionSearchAjaxAction use.
*
* @param spanString span in string
* @param flankingSize int value of extended genomic region size
* @param resultMap map of search results
* @return String feature ids joined by comma
*/
public String getGenomicRegionOverlapFeaturesAsString(String spanString, int flankingSize,
Map<GenomicRegion, List<List<String>>> resultMap) {
Set<Integer> featureSet = getGenomicRegionOverlapFeaturesAsSet(
spanString, flankingSize, resultMap);
return StringUtil.join(featureSet, ",");
}
/**
* Check whether the results have empty features. for
* GenomicRegionSearchAjaxAction use.
*
* @param resultMap map of search results
* @return String "hasFeature" or "emptyFeature"
*/
public String isEmptyFeature(
Map<GenomicRegion, List<List<String>>> resultMap) {
for (List<List<String>> l : resultMap.values()) {
if (l != null) {
return "hasFeature";
}
}
return "emptyFeature";
}
/**
* Generate a html string with all feature type for list creation.
*
* @param resultMap map of search results
* @return a html string
*/
public String generateCreateListHtml(Map<GenomicRegion, List<List<String>>> resultMap) {
Set<String> ftSet = new TreeSet<String>();
for (List<List<String>> l : resultMap.values()) {
if (l != null) {
for (List<String> feature : l) {
ftSet.add(feature.get(3)); // the 3rd is feature type
}
}
}
String clHtml = " or <a href=\"javascript: createList('all','all-regions');\">"
+ "Create List by feature type:</a>"
+ "<select id=\"all-regions\" style=\"margin: 4px 3px\">";
for (String ft : ftSet) {
clHtml += "<option value=\"" + ft + "\">"
+ WebUtil.formatPath(ft, interMineAPI, webConfig)
+ "</option>";
}
clHtml += "</select>";
return clHtml;
}
/**
* Convert result map to HTML string.
*
* @param resultMap resultMap
* @param genomicRegionList spanList
* @param fromIdx offsetStart
* @param toIdx offsetEnd
* @param session the current session
* @param orgName organism
* @return a String of HTML
*/
public String convertResultMapToHTML(
Map<GenomicRegion, List<List<String>>> resultMap,
List<GenomicRegion> genomicRegionList, int fromIdx, int toIdx,
HttpSession session, String orgName) {
String baseURL = webProperties.getProperty("webapp.baseurl");
String path = webProperties.getProperty("webapp.path");
List<GenomicRegion> subGenomicRegionList = genomicRegionList.subList(fromIdx, toIdx + 1);
// start to build the html for results table
StringBuffer sb = new StringBuffer();
//TODO use HTML Template
sb.append("<thead><tr valign=\"middle\">");
sb.append("<th align=\"center\">Genome Region</th>");
sb.append("<th align=\"center\">Feature</th>");
sb.append("<th align=\"center\">Feature Type</th>");
sb.append("<th align=\"center\">Location</th>");
sb.append("</tr></thead>");
sb.append("<tbody>");
for (GenomicRegion s : subGenomicRegionList) {
String span = s.getExtendedRegion();
List<List<String>> features = resultMap.get(s);
// get list of featureTypes
String ftHtml = categorizeFeatureTypes(features, s);
Set<String> ftSet = getFeatureTypeSet(features);
/*
* order: 0.id
* 1.feature PID
* 2.symbol
* 3.feature type
* 4.chr
* 5.start
* 6.end
* see query fields in createQueryList method
*/
if (features != null) {
int length = features.size();
List<String> firstFeature = features.get(0);
String firstId = firstFeature.get(0);
String firstPid = firstFeature.get(1);
String firstSymbol = firstFeature.get(2);
String firstFeatureType = firstFeature.get(3);
String firstChr = firstFeature.get(4);
String firstStart = firstFeature.get(5);
String firstEnd = firstFeature.get(6);
String loc = firstChr + ":" + firstStart + ".." + firstEnd;
// translatedClassName
String firstSoTerm = WebUtil.formatPath(firstFeatureType, interMineAPI,
webConfig);
String firstSoTermDes = featureTypeToSOTermMap.get(firstFeatureType).get(1);
firstSoTermDes = firstSoTermDes.replaceAll("'", "\\\\'");
// hack - feature name is null, use id
sb.append("<tr><td valign='top' rowspan='" + length + "'><b>" + span + "</b><br>");
if (s.isRegionExtended()) {
String os = s.getOriginalRegion();
sb.append("<i>Original input: " + os + "</i><br>");
}
String facet = "SequenceFeature";
if (ftSet != null) {
if (ftSet.size() == 1) {
facet = ftSet.iterator().next();
}
}
sb.append("<div style='align:center; padding-bottom:12px'>"
+ "<span class='fakelink exportDiv'> Export data </span>"
+ "<img class='exportDiv' style='position:relative; top:3px;' "
+ "border='0' src='model/images/download.png' title='export data' "
+ "height='18' width='18'/><ul class='contextMenu'><li class='tab'>"
+ "<a href='#javascript: exportFeatures(\""
+ span + "\", "
+ "\"" + facet + "\", \"tab\");' class='ext_link'>TAB</a></li>"
+ "<li class='csv'><a href='#javascript: exportFeatures(\""
+ span
+ "\", \"" + facet + "\", \"csv\");' class='ext_link'>CSV</a></li>"
+ "<li class='gff'><a href='#javascript: exportFeatures(\""
+ span
+ "\", \"" + facet + "\", \"gff3\");' class='ext_link'>GFF3</a>"
+ "</li><li class='seq'><a href='#javascript: exportFeatures(\""
+ span
+ "\", \"" + facet + "\", \"sequence\");' class='ext_link'>SEQ</a>"
+ "</li></ul></div><div style='align:center'>"
+ "<a href='javascript: exportToGalaxy(\"" + span + "\", \"" + orgName
+ "\");' class='ext_link'> Export to Galaxy <img border='0' "
+ "title='Export to Galaxy' src='model/images/Galaxy_logo_small.png' "
+ "class='arrow' style='height:5%; width:5%'></a></div>" + ftHtml
+ "</td><td><a target='' title='' href='" + baseURL + "/" + path
+ "/report.do?id=" + firstId + "'>");
if (firstSymbol == null || "".equals(firstSymbol)) {
sb.append("<strong><i>unknown symbol</i></strong>");
} else {
sb.append("<strong>" + firstSymbol + "</strong>");
}
sb.append(" ");
if (firstPid == null || "".equals(firstPid)) {
sb.append("<span style='font-size: 11px;'><i>unknown DB identifier</i></span>");
} else {
sb.append("<span style='font-size: 11px;'>" + firstPid + "</span>");
}
sb.append("</a></td><td>" + firstSoTerm
+ "<a onclick=\"document.getElementById('ctxHelpTxt').innerHTML='"
+ firstSoTerm + ": " + firstSoTermDes
+ "';document.getElementById('ctxHelpDiv').style.display='';"
+ "window.scrollTo(0, 0);return false\" title=\"" + firstSoTermDes
+ "\"><img class=\"tinyQuestionMark\" "
+ "src=\"images/icons/information-small-blue.png\" alt=\"?\"></a>"
+ "</td><td>" + loc + "</td></tr>");
for (int i = 1; i < length; i++) {
String id = features.get(i).get(0);
String pid = features.get(i).get(1);
String symbol = features.get(i).get(2);
String featureType = features.get(i).get(3);
String chr = features.get(i).get(4);
String start = features.get(i).get(5);
String end = features.get(i).get(6);
String soTerm = WebUtil.formatPath(featureType, interMineAPI,
webConfig);
String soTermDes = featureTypeToSOTermMap.get(featureType).get(1);
soTermDes = soTermDes.replaceAll("'", "\\\\'");
String location = chr + ":" + start + ".." + end;
sb.append("<tr><td><a target='' title='' href='"
+ baseURL + "/" + path + "/report.do?id=" + id + "'>");
if (symbol == null || "".equals(symbol)) {
sb.append("<strong><i>unknown symbol</i></strong>");
} else {
sb.append("<strong>" + symbol + "</strong>");
}
sb.append(" ");
if (pid == null || "".equals(pid)) {
sb.append("<span style='font-size: 11px;'>"
+ "<i>unknown DB identifier</i></span>");
} else {
sb.append("<span style='font-size: 11px;'>" + pid + "</span>");
}
sb.append("</a></td><td>"
+ soTerm
+ "<a onclick=\"document.getElementById('ctxHelpTxt').innerHTML='"
+ soTerm + ": " + soTermDes
+ "';document.getElementById('ctxHelpDiv').style.display='';"
+ "window.scrollTo(0, 0);return false\" title=\"" + soTermDes
+ "\"><img class=\"tinyQuestionMark\" "
+ "src=\"images/icons/information-small-blue.png\" alt=\"?\"></a>"
+ "</td><td>" + location + "</td></tr>");
}
} else {
sb.append("<tr><td><b>"
+ span
+ "</b></td><td colspan='3'><i>No overlap features found</i></td></tr>");
}
}
sb.append("</tbody>");
return sb.toString();
}
/**
* Get all feature types from a list of sequence features
* @param features list of sequence features
* @param s GenomicRegion
* @return A html string with a dropdown list of feature types
*/
public String categorizeFeatureTypes(List<List<String>> features, GenomicRegion s) {
String id = s.getChr() + "-" + s.getStart() + "-" + s.getEnd();
Set<String> ftSet = getFeatureTypeSet(features);
if (ftSet == null) {
return "";
} else {
String ftHtml = "<div>"
+ "<a href=\"javascript: createList('" + s.getExtendedRegion() + "', '" + id + "');\">"
+ "Create List by</a>"
+ "<select id=\"" + id + "\" style=\"margin: 4px 3px\">";
for (String ft : ftSet) {
ftHtml += "<option value=\"" + ft + "\">"
+ WebUtil.formatPath(ft, interMineAPI, webConfig)
+ "</option>";
}
ftHtml += "</select></div>";
return ftHtml;
}
}
/**
* Get all feature types in a set
* @param features list of sequence features
* @param s GenomicRegion
* @return a set of feature types of a genomic region
*/
public Set<String> getFeatureTypeSet(List<List<String>> features) {
Set<String> ftSet = null;
if (features != null) {
ftSet = new TreeSet<String>();
for (List<String> feature : features) {
ftSet.add(feature.get(3)); // the 3rd is feature type
}
}
return ftSet;
}
/**
* Calculate the number of matched bases.
*
* @param gr a GenomicRegion object
* @param r a list of attributes
* @return matched base count as String
*/
protected String getMatchedBaseCount(GenomicRegion gr, List<String> r) {
int spanStart = gr.getStart();
int spanEnd = gr.getEnd();
int featureStart = Integer.valueOf(r.get(3));
int featureEnd = Integer.valueOf(r.get(4));
int matchedBaseCount = 0;
if (featureStart <= spanStart && featureEnd >= spanStart
&& featureEnd <= spanEnd) {
matchedBaseCount = featureEnd - spanStart + 1;
}
if (featureStart >= spanStart && featureStart <= spanEnd
&& featureEnd >= spanEnd) {
matchedBaseCount = spanEnd - featureStart + 1;
}
if (featureStart >= spanStart && featureEnd <= spanEnd) {
matchedBaseCount = featureEnd - featureStart + 1;
}
if (featureStart <= spanStart && featureEnd >= spanEnd) {
matchedBaseCount = spanEnd - spanStart + 1;
}
return String.valueOf(matchedBaseCount);
}
/**
* A flexiable way of setting query fields.
*
* @param featureIds set of feature intermine ids
* @param featureType feature class name
* @param views user defined views in web.properties
* @return a pathquery
*/
public PathQuery getExportFeaturesQuery(Set<Integer> featureIds,
String featureType, Set<String> views) {
PathQuery q = new PathQuery(model);
String path = featureType;
if (views == null) {
q.addView(path + ".primaryIdentifier");
q.addView(path + ".symbol");
q.addView(path + ".chromosomeLocation.locatedOn.primaryIdentifier");
q.addView(path + ".chromosomeLocation.start");
q.addView(path + ".chromosomeLocation.end");
q.addView(path + ".organism.name");
} else {
for (String view : views) {
q.addView(view.trim().replace("{0}", path));
}
}
q.addConstraint(Constraints.inIds(featureType, featureIds), "A");
return q;
}
/**
*
* @param organisms set of org names
* @return set of taxonIds
*/
public Set<Integer> getTaxonIds(Set<String> organisms) {
Set<Integer> taxIds = new HashSet<Integer>();
for (String org : organisms) {
taxIds.add(this.getOrganismToTaxonMap().get(org));
}
return taxIds;
}
/**
* To serve UCSC Lift-Over
*/
public void serveLiftOver() {
}
}
|
package org.biojava3.alignment;
import java.util.ArrayList;
import java.util.Collection;
import java.util.Collections;
import java.util.Iterator;
import java.util.List;
import org.biojava3.alignment.template.AlignedSequence;
import org.biojava3.alignment.template.AlignedSequence.Step;
import org.biojava3.alignment.template.Profile;
import org.biojava3.alignment.template.ProfileView;
import org.biojava3.alignment.template.SubstitutionMatrix;
import org.biojava3.core.sequence.AccessionID;
import org.biojava3.core.sequence.compound.AminoAcidCompound;
import org.biojava3.core.sequence.compound.AminoAcidCompoundSet;
import org.biojava3.core.sequence.io.util.IOUtils;
import org.biojava3.core.sequence.location.template.Location;
import org.biojava3.core.sequence.template.Compound;
import org.biojava3.core.sequence.template.CompoundSet;
import org.biojava3.core.sequence.template.Sequence;
/**
* Implements a data structure for the results of sequence alignment. Every {@link List} returned is unmodifiable.
*
* @author Mark Chapman
* @param <S> each element of the alignment {@link Profile} is of type S
* @param <C> each element of an {@link AlignedSequence} is a {@link Compound} of type C
*/
public class SimpleProfile<S extends Sequence<C>, C extends Compound> implements Profile<S, C> {
private List<AlignedSequence<S, C>> list;
private List<S> originals;
private int length;
protected SimpleProfile(AlignedSequence<S, C> query, AlignedSequence<S, C> target) {
if (query.getLength() != target.getLength()) {
throw new IllegalArgumentException("Aligned sequences differ in size");
}
list = new ArrayList<AlignedSequence<S, C>>();
list.add(query);
list.add(target);
list = Collections.unmodifiableList(list);
originals = new ArrayList<S>();
originals.add((S) query.getOriginalSequence());
originals.add((S) target.getOriginalSequence());
originals = Collections.unmodifiableList(originals);
length = query.getLength();
}
/**
* Creates a profile from a single sequence.
*
* @param sequence sequence to seed profile
*/
public SimpleProfile(S sequence) {
List<Step> s = new ArrayList<Step>();
for (int i = 0; i < sequence.getLength(); i++) {
s.add(Step.COMPOUND);
}
list = new ArrayList<AlignedSequence<S, C>>();
list.add(new SimpleAlignedSequence<S, C>(sequence, s));
list = Collections.unmodifiableList(list);
originals = new ArrayList<S>();
originals.add(sequence);
originals = Collections.unmodifiableList(originals);
length = sequence.getLength();
}
protected SimpleProfile(S query, S target, List<Step> sx, int xb, int xa, List<Step> sy, int yb, int ya) {
if (sx.size() != sy.size()) {
throw new IllegalArgumentException("Alignments differ in size");
}
list = new ArrayList<AlignedSequence<S, C>>();
list.add(new SimpleAlignedSequence<S, C>(query, sx, xb, xa));
list.add(new SimpleAlignedSequence<S, C>(target, sy, yb, ya));
list = Collections.unmodifiableList(list);
originals = new ArrayList<S>();
originals.add(query);
originals.add(target);
originals = Collections.unmodifiableList(originals);
length = sx.size();
}
protected SimpleProfile(Profile<S, C> query, Profile<S, C> target, List<Step> sx, List<Step> sy) {
if (sx.size() != sy.size()) {
throw new IllegalArgumentException("Alignments differ in size");
}
list = new ArrayList<AlignedSequence<S, C>>();
for (AlignedSequence<S, C> s : query) {
list.add(new SimpleAlignedSequence<S, C>(s, sx));
}
for (AlignedSequence<S, C> s : target) {
list.add(new SimpleAlignedSequence<S, C>(s, sy));
}
list = Collections.unmodifiableList(list);
originals = new ArrayList<S>();
originals.addAll(query.getOriginalSequences());
originals.addAll(target.getOriginalSequences());
originals = Collections.unmodifiableList(originals);
length = sx.size();
}
public SimpleProfile(Collection<AlignedSequence<S,C>> alignedSequences) {
list = new ArrayList<AlignedSequence<S,C>>();
originals = new ArrayList<S>();
Iterator<AlignedSequence<S,C>> itr = alignedSequences.iterator();
if(!itr.hasNext()) {
throw new IllegalArgumentException("alignedSequences must not be empty");
}
AlignedSequence<S, C> curAlignedSeq = itr.next();
length = curAlignedSeq.getLength();
list.add(curAlignedSeq);
originals.add((S) curAlignedSeq.getOriginalSequence());
while (itr.hasNext()) {
curAlignedSeq = itr.next();
if (curAlignedSeq.getLength() != length) {
throw new IllegalArgumentException("Aligned sequences differ in size");
}
list.add(curAlignedSeq);
originals.add((S) curAlignedSeq.getOriginalSequence());
}
list = Collections.unmodifiableList(list);
originals = Collections.unmodifiableList(originals);
}
// methods for Profile
@Override
public AlignedSequence<S, C> getAlignedSequence(int listIndex) {
return list.get(listIndex - 1);
}
@Override
public AlignedSequence<S, C> getAlignedSequence(S sequence) {
for (AlignedSequence<S, C> s : list) {
if (s.equals(sequence) || s.getOriginalSequence().equals(sequence)) {
return s;
}
}
return null;
}
@Override
public List<AlignedSequence<S, C>> getAlignedSequences() {
return list;
}
@Override
public List<AlignedSequence<S, C>> getAlignedSequences(int... listIndices) {
List<AlignedSequence<S, C>> tempList = new ArrayList<AlignedSequence<S, C>>();
for (int i : listIndices) {
tempList.add(getAlignedSequence(i));
}
return Collections.unmodifiableList(tempList);
}
@Override
public List<AlignedSequence<S, C>> getAlignedSequences(S... sequences) {
List<AlignedSequence<S, C>> tempList = new ArrayList<AlignedSequence<S, C>>();
for (S s : sequences) {
tempList.add(getAlignedSequence(s));
}
return Collections.unmodifiableList(tempList);
}
@Override
public C getCompoundAt(int listIndex, int alignmentIndex) {
return getAlignedSequence(listIndex).getCompoundAt(alignmentIndex);
}
@Override
public C getCompoundAt(S sequence, int alignmentIndex) {
AlignedSequence<S, C> s = getAlignedSequence(sequence);
return (s == null) ? null : s.getCompoundAt(alignmentIndex);
}
@Override
public int[] getCompoundCountsAt(int alignmentIndex) {
return getCompoundCountsAt(alignmentIndex, getCompoundSet().getAllCompounds());
}
@Override
public int[] getCompoundCountsAt(int alignmentIndex, List<C> compounds) {
int[] counts = new int[compounds.size()];
C gap = getCompoundSet().getCompoundForString("-");
int igap = compounds.indexOf(gap);
for (C compound : getCompoundsAt(alignmentIndex)) {
int i = compounds.indexOf(compound);
if (i >= 0 && i != igap && !getCompoundSet().compoundsEquivalent(compound, gap)) {
counts[i]++;
}
}
return counts;
}
@Override
public List<C> getCompoundsAt(int alignmentIndex) {
// TODO handle circular alignments
List<C> column = new ArrayList<C>();
for (AlignedSequence<S, C> s : list) {
column.add(s.getCompoundAt(alignmentIndex));
}
return Collections.unmodifiableList(column);
}
@Override
public CompoundSet<C> getCompoundSet() {
return list.get(0).getCompoundSet();
}
@Override
public float[] getCompoundWeightsAt(int alignmentIndex) {
return getCompoundWeightsAt(alignmentIndex, getCompoundSet().getAllCompounds());
}
@Override
public float[] getCompoundWeightsAt(int alignmentIndex, List<C> compounds) {
float[] weights = new float[compounds.size()];
int[] counts = getCompoundCountsAt(alignmentIndex, compounds);
float total = 0.0f;
for (int i : counts) {
total += i;
}
if (total > 0.0f) {
for (int i = 0; i < weights.length; i++) {
weights[i] = counts[i]/total;
}
}
return weights;
}
@Override
public int getIndexOf(C compound) {
for (int i = 1; i <= length; i++) {
if (getCompoundsAt(i).contains(compound)) {
return i;
}
}
return -1;
}
@Override
public int[] getIndicesAt(int alignmentIndex) {
int[] indices = new int[list.size()];
for (int i = 0; i < indices.length; i++) {
indices[i] = list.get(i).getSequenceIndexAt(alignmentIndex);
}
return indices;
}
@Override
public int getLastIndexOf(C compound) {
for (int i = length; i >= 1; i
if (getCompoundsAt(i).contains(compound)) {
return i;
}
}
return -1;
}
@Override
public int getLength() {
return length;
}
@Override
public List<S> getOriginalSequences() {
return originals;
}
@Override
public int getSize() {
int size = 0;
for (AlignedSequence<S, C> s : list) {
size += s.getOverlapCount();
}
return size;
}
@Override
public ProfileView<S, C> getSubProfile(Location location) {
// TODO ProfileView<S, C> getSubProfile(Location)
return null;
}
@Override
public boolean hasGap(int alignmentIndex) {
C gap = getCompoundSet().getCompoundForString("-");
for (C compound : getCompoundsAt(alignmentIndex)) {
if (getCompoundSet().compoundsEquivalent(compound, gap)) {
return true;
}
}
return false;
}
@Override
public boolean isCircular() {
for (AlignedSequence<S, C> s : list) {
if (s.isCircular()) {
return true;
}
}
return false;
}
@Override
public String toString(int width) {
return toString(width, null, IOUtils.getIDFormat(list), true, true, true, true, true, false);
}
@Override
public String toString(StringFormat format) {
switch (format) {
case ALN:
case CLUSTALW:
default:
return toString(60, String.format("CLUSTAL W MSA from BioJava%n%n"), IOUtils.getIDFormat(list) + " ",
false, true, true, false, true, false);
case FASTA:
return toString(60, null, ">%s%n", false, false, false, false, false, false);
case GCG:
case MSF:
return toString(50, IOUtils.getGCGHeader(list), IOUtils.getIDFormat(list), false, false, true, false,
false, false);
case PDBWEB:
return toString(60, null, "%s", true, true, true, false, true, true);
}
}
// method from Object
@Override
public String toString() {
return toString(getLength(), null, null, false, false, false, false, false, false);
}
// method for Iterable
@Override
public Iterator<AlignedSequence<S, C>> iterator() {
return list.iterator();
}
// helper methods
// creates formatted String
private String toString(int width, String header, String idFormat, boolean seqIndexPre, boolean seqIndexPost,
boolean interlaced, boolean aligIndices, boolean aligConservation, boolean webDisplay) {
// TODO handle circular alignments
StringBuilder s = (header == null) ? new StringBuilder() : new StringBuilder(header);
if ( webDisplay && list.size() == 2){
s.append("<div><pre>");
}
width = Math.max(1, width);
int seqIndexPad = (int) (Math.floor(Math.log10(getLength())) + 2);
String seqIndexFormatPre = "%" + seqIndexPad + "d ", seqIndexFormatPost = "%" + seqIndexPad + "d";
if (interlaced) {
String aligIndFormat = "%-" + Math.max(1, width / 2) + "d %" + Math.max(1, width - (width / 2) - 1) +
"d%n";
for (int i = 0; i < getLength(); i += width) {
int start = i + 1, end = Math.min(getLength(), i + width);
if (i > 0) {
s.append(String.format("%n"));
}
if (aligIndices) {
if (end < i + width) {
int line = end - start + 1;
aligIndFormat = "%-" + Math.max(1, line / 2) + "d %" + Math.max(1, line - (line / 2) - 1) +
"d%n";
}
if (idFormat != null) {
s.append(String.format(idFormat, ""));
}
if (seqIndexPre) {
s.append(String.format("%" + (seqIndexPad + 1) + "s", ""));
}
s.append(String.format(aligIndFormat, start, end));
}
int counter = 0;
for (AlignedSequence<S, C> as : list) {
counter++;
if ( webDisplay && list.size() == 2){
printSequenceAlignmentWeb(s, counter, idFormat, seqIndexPre, seqIndexFormatPre, seqIndexPost,
seqIndexFormatPost, start, end);
} else {
if (idFormat != null) {
s.append(String.format(idFormat, as.getAccession()));
}
if (seqIndexPre) {
s.append(String.format(seqIndexFormatPre, as.getSequenceIndexAt(start)));
}
s.append(as.getSubSequence(start, end).getSequenceAsString());
if (seqIndexPost) {
s.append(String.format(seqIndexFormatPost, as.getSequenceIndexAt(end)));
}
s.append(String.format("%n"));
}
if (aligConservation && list.size() == 2 && counter == 1) {
printConservation(s, idFormat, seqIndexPad, seqIndexPre, start, end, webDisplay);
}
}
}
} else {
for (AlignedSequence<S, C> as : list) {
if (idFormat != null) {
s.append(String.format(idFormat, as.getAccession()));
}
for (int i = 0; i < getLength(); i += width) {
int start = i + 1, end = Math.min(getLength(), i + width);
if (seqIndexPre) {
s.append(String.format(seqIndexFormatPre, as.getSequenceIndexAt(start)));
}
s.append(as.getSubSequence(start, end).getSequenceAsString());
if (seqIndexPost) {
s.append(String.format(seqIndexFormatPost, as.getSequenceIndexAt(end)));
}
s.append(String.format("%n"));
}
}
}
if (webDisplay && aligConservation && list.size() == 2) {
s.append(IOUtils.getPDBLegend());
}
return s.toString();
}
private void printSequenceAlignmentWeb(StringBuilder s, int counter, String idFormat, boolean seqIndexPre,
String seqIndexFormatPre, boolean seqIndexPost, String seqIndexFormatPost, int start, int end) {
AlignedSequence<S,C> as1 = list.get(0), as2 = list.get(1), as = list.get(counter - 1);
if (idFormat != null) {
s.append(String.format(idFormat, as.getAccession()));
}
if (seqIndexPre) {
s.append(String.format(seqIndexFormatPre, as.getSequenceIndexAt(start)));
}
String mySeq = as.getSubSequence(start, end).getSequenceAsString();
String s1 = as1.getSubSequence(start, end).getSequenceAsString();
String s2 = as2.getSubSequence(start, end).getSequenceAsString();
for (int i = 0; i < s1.length(); i++) {
if (i >= s2.length() || i >= mySeq.length())
break;
char c1 = s1.charAt(i);
char c2 = s2.charAt(i);
char c = mySeq.charAt(i);
s.append(IOUtils.getPDBCharacter(true, c1, c2, isSimilar(c1, c2), c));
}
if (seqIndexPost) {
s.append(String.format(seqIndexFormatPost, as.getSequenceIndexAt(end)));
}
s.append(String.format("%n"));
}
private void printConservation(StringBuilder s, String idFormat, int seqIndexPad, boolean seqIndexPre, int start,
int end, boolean webDisplay) {
AlignedSequence<S,C> as1 = list.get(0), as2 = list.get(1);
if (idFormat != null) {
AccessionID ac1 = as1.getAccession();
String id1 = (ac1 == null) ? "null" : ac1.getID();
id1 = id1.replaceAll(".", " ");
s.append(String.format(idFormat, id1));
}
if (seqIndexPre) {
s.append(String.format("%" + (seqIndexPad + 1) + "s", ""));
}
String subseq1 = as1.getSubSequence(start, end).getSequenceAsString();
String subseq2 = as2.getSubSequence(start, end).getSequenceAsString();
for ( int ii =0 ; ii < subseq1.length() ; ii++){
if ( ii >= subseq2.length())
break;
char c1 = subseq1.charAt(ii);
char c2 = subseq2.charAt(ii);
s.append(IOUtils.getPDBConservation(webDisplay, c1, c2, isSimilar(c1, c2)));
}
s.append(String.format("%n"));
}
protected static final SubstitutionMatrix<AminoAcidCompound> matrix = SubstitutionMatrixHelper.getBlosum65();
private boolean isSimilar(char c1, char c2) {
AminoAcidCompoundSet set = AminoAcidCompoundSet.getAminoAcidCompoundSet();
AminoAcidCompound aa1 = set.getCompoundForString(""+c1);
AminoAcidCompound aa2 = set.getCompoundForString(""+c2);
short val = matrix.getValue(aa1,aa2);
return val > 0;
}
}
|
package bndtools.jareditor.internal;
import java.io.IOException;
import java.net.URI;
import java.util.Collection;
import java.util.Map;
import java.util.TreeMap;
import java.util.zip.ZipEntry;
import java.util.zip.ZipInputStream;
import org.eclipse.core.runtime.IStatus;
import org.eclipse.core.runtime.Status;
import org.eclipse.jface.dialogs.ErrorDialog;
import org.eclipse.jface.viewers.ISelectionChangedListener;
import org.eclipse.jface.viewers.ITreeContentProvider;
import org.eclipse.jface.viewers.SelectionChangedEvent;
import org.eclipse.jface.viewers.StyledCellLabelProvider;
import org.eclipse.jface.viewers.StyledString;
import org.eclipse.jface.viewers.TreePath;
import org.eclipse.jface.viewers.TreeSelection;
import org.eclipse.jface.viewers.TreeViewer;
import org.eclipse.jface.viewers.Viewer;
import org.eclipse.jface.viewers.ViewerCell;
import org.eclipse.swt.SWT;
import org.eclipse.swt.graphics.Image;
import org.eclipse.swt.layout.GridData;
import org.eclipse.swt.layout.GridLayout;
import org.eclipse.swt.widgets.Composite;
import org.eclipse.swt.widgets.Tree;
import org.eclipse.ui.IEditorInput;
import org.eclipse.ui.forms.AbstractFormPart;
import org.eclipse.ui.forms.IManagedForm;
import org.eclipse.ui.forms.widgets.FormToolkit;
import org.eclipse.ui.forms.widgets.Section;
import org.eclipse.ui.plugin.AbstractUIPlugin;
public class JARContentTreePart extends AbstractFormPart {
protected final IManagedForm managedForm;
private final Tree tree;
private final TreeViewer viewer;
private final JARTreeContentProvider contentProvider = new JARTreeContentProvider();
private String[] selectedPath = null;
public JARContentTreePart(final Composite parent, final IManagedForm managedForm) {
this.managedForm = managedForm;
FormToolkit toolkit = managedForm.getToolkit();
Section section = toolkit.createSection(parent, Section.TITLE_BAR | Section.EXPANDED);
section.setText("Content Tree");
tree = toolkit.createTree(section, SWT.FULL_SELECTION | SWT.SINGLE);
tree.setData(FormToolkit.KEY_DRAW_BORDER, FormToolkit.TREE_BORDER);
section.setClient(tree);
toolkit.paintBordersFor(section);
viewer = new TreeViewer(tree);
viewer.setContentProvider(contentProvider);
viewer.setLabelProvider(new JARTreeLabelProvider());
managedForm.addPart(this);
viewer.addSelectionChangedListener(new ISelectionChangedListener() {
@Override
public void selectionChanged(final SelectionChangedEvent event) {
JARContentTreePart.this.managedForm.fireSelectionChanged(JARContentTreePart.this, event.getSelection());
}
});
parent.setLayout(new GridLayout());
section.setLayoutData(new GridData(SWT.FILL, SWT.FILL, true, true));
}
@Override
public void initialize(final IManagedForm form) {
super.initialize(form);
}
@Override
public boolean isStale() {
// Claim to always be stale, so we always get refresh events.
return true;
}
@Override
public void refresh() {
super.refresh();
Object input = getManagedForm().getInput();
viewer.setInput(input);
refreshSelectedPath();
}
private void refreshSelectedPath() {
if (selectedPath != null) {
TreePath treePath = contentProvider.findPath(selectedPath);
if (treePath != null) {
viewer.setSelection(new TreeSelection(treePath), true);
}
else {
viewer.setSelection(TreeSelection.EMPTY);
}
}
}
@Override
public boolean setFormInput(final Object input) {
viewer.setInput(input);
return false;
}
void setSelectedPath(final String[] path) {
selectedPath = path;
if ( (viewer != null) && (viewer.getInput() != null)) {
refreshSelectedPath();
}
}
String[] getSelectedPath() {
String[] result;
if (viewer.getSelection().isEmpty()) {
result = null;
}
else {
TreeSelection selection = (TreeSelection) viewer.getSelection();
TreePath treePath = selection.getPaths()[0];
result = new String[treePath.getSegmentCount()];
for (int i = 0; i < result.length; i++) {
result[i] = treePath.getSegment(i).toString();
}
}
return result;
}
private static class JARTreeLabelProvider extends StyledCellLabelProvider {
private final Image folderImg = AbstractUIPlugin.imageDescriptorFromPlugin(PluginConstants.PLUGIN_ID,
"/icons/fldr_obj.gif").createImage();
private final Image fileImg = AbstractUIPlugin.imageDescriptorFromPlugin(PluginConstants.PLUGIN_ID,
"/icons/file_obj.gif").createImage();
public JARTreeLabelProvider() {
super();
}
@Override
public void update(final ViewerCell cell) {
ZipTreeNode node = (ZipTreeNode) cell.getElement();
String name = node.toString();
StyledString label = new StyledString(name);
if (name.endsWith("/")) {
cell.setImage(folderImg);
}
else {
cell.setImage(fileImg);
ZipEntry entry = node.getZipEntry();
if (entry != null) {
label.append(String.format(" [sz: %,d; crc: %d]", entry.getSize(), entry.getCrc()),
StyledString.QUALIFIER_STYLER);
}
}
cell.setText(label.getString());
cell.setStyleRanges(label.getStyleRanges());
}
@Override
public void dispose() {
super.dispose();
folderImg.dispose();
fileImg.dispose();
}
}
private class JARTreeContentProvider implements ITreeContentProvider {
Map<String,ZipTreeNode> entryMap;
public JARTreeContentProvider() {
super();
}
@Override
public Object[] getChildren(final Object parentElement) {
ZipTreeNode parentNode = (ZipTreeNode) parentElement;
return parentNode.getChildren().toArray();
}
@Override
public Object getParent(final Object element) {
return ((ZipTreeNode) element).getParent();
}
@Override
public boolean hasChildren(final Object element) {
return ((ZipTreeNode) element).hasChildren();
}
@Override
public Object[] getElements(final Object inputElement) {
return entryMap.values().toArray();
}
@Override
public void dispose() {
}
@Override
public void inputChanged(final Viewer viewer, final Object oldInput, final Object newInput) {
entryMap = new TreeMap<String,ZipTreeNode>();
final URI uri = URIHelper.retrieveFileURI((IEditorInput) newInput);
if (uri != null) {
ZipInputStream zis = null;
try {
zis = new ZipInputStream(uri.toURL().openStream());
ZipEntry entry;
while ( (entry = zis.getNextEntry()) != null) {
ZipTreeNode.addEntry(entryMap, entry);
}
zis.close();
}
catch (IOException e) {
Status status = new Status(IStatus.ERROR,
PluginConstants.PLUGIN_ID,
0,
"I/O error reading JAR file contents",
e);
ErrorDialog.openError(managedForm.getForm().getShell(), "Error", null, status);
}
finally {
if (zis != null) {
try {
zis.close();
}
catch (IOException e) {
// nothing to do
}
}
}
}
}
public TreePath findPath(final String[] path) {
if ( (path == null) || (path.length == 0)) {
return null;
}
TreePath result = TreePath.EMPTY;
ZipTreeNode current = entryMap.get(path[0]);
if (current == null) {
return null;
}
result = result.createChildPath(current);
segments: for (int i = 1; i < path.length; i++) {
Collection<ZipTreeNode> children = current.getChildren();
for (ZipTreeNode child: children) {
if (path[i].equals(child.toString())) {
current = child;
result = result.createChildPath(child);
continue segments;
}
}
return null;
}
return result;
}
}
}
|
package ch.elexis.core.data.activator;
import java.io.File;
import java.io.IOException;
import java.io.InputStream;
import java.net.URL;
import java.util.LinkedList;
import java.util.List;
import java.util.Properties;
import java.util.UUID;
import org.eclipse.equinox.internal.app.CommandLineArgs;
import org.osgi.framework.Bundle;
import org.osgi.framework.BundleActivator;
import org.osgi.framework.BundleContext;
import org.osgi.framework.FrameworkUtil;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import ch.elexis.Desk;
import ch.elexis.admin.AbstractAccessControl;
import ch.elexis.admin.RoleBasedAccessControl;
import ch.elexis.core.constants.Preferences;
import ch.elexis.core.constants.StringConstants;
import ch.elexis.core.data.constants.ElexisSystemPropertyConstants;
import ch.elexis.core.data.events.ElexisEvent;
import ch.elexis.core.data.events.ElexisEventDispatcher;
import ch.elexis.core.data.events.Heartbeat;
import ch.elexis.core.data.events.Heartbeat.HeartListener;
import ch.elexis.core.data.events.PatientEventListener;
import ch.elexis.core.data.interfaces.ShutdownJob;
import ch.elexis.core.data.interfaces.events.MessageEvent;
import ch.elexis.core.data.interfaces.scripting.Interpreter;
import ch.elexis.core.data.lock.LocalLockService;
import ch.elexis.core.data.preferences.CorePreferenceInitializer;
import ch.elexis.core.data.server.ElexisServerEventService;
import ch.elexis.core.data.service.OrderService;
import ch.elexis.core.data.service.StockCommissioningSystemService;
import ch.elexis.core.data.service.StockService;
import ch.elexis.core.lock.ILocalLockService;
import ch.elexis.core.services.IOrderService;
import ch.elexis.core.services.IStockCommissioningSystemService;
import ch.elexis.data.Anwender;
import ch.elexis.data.Kontakt;
import ch.elexis.data.Mandant;
import ch.elexis.data.PersistentObject;
import ch.elexis.data.PersistentObjectFactory;
import ch.elexis.data.Query;
import ch.elexis.data.User;
import ch.rgw.io.LockFile;
import ch.rgw.io.Settings;
import ch.rgw.io.SqlSettings;
import ch.rgw.io.SysSettings;
import ch.rgw.tools.Log;
import ch.rgw.tools.StringTool;
import ch.rgw.tools.VersionInfo;
/**
* @since 3.0.0
*/
public class CoreHub implements BundleActivator {
public static final String PLUGIN_ID = "ch.elexis.core.data";
/*
* This version is needed to compare the DB
*/
public static String Version = "3.7.0.qualifier"; //$NON-NLS-1$
public static final String APPLICATION_NAME = "Elexis Core"; //$NON-NLS-1$
static final String neededJRE = "1.8.0"; //$NON-NLS-1$
public static final String DBVersion = "3.6.0"; //$NON-NLS-1$
protected static Logger log = LoggerFactory.getLogger(CoreHub.class.getName());
private static String LocalCfgFile = null;
private static String elexis_version = null;
private BundleContext context;
/** Das Singleton-Objekt dieser Klasse */
public static CoreHub plugin;
private static List<ShutdownJob> shutdownJobs = new LinkedList<>();
public static final PersistentObjectFactory poFactory = new PersistentObjectFactory();
/** Heartbeat */
public static Heartbeat heart;
static File userDir;
/** Globale Einstellungen (Werden in der Datenbank gespeichert) */
public static Settings globalCfg;
/**
* Lokale Einstellungen (Werden in userhome/localCfg_xxx.xml gespeichert) </br>
* <b>WARNING: can not handle more than one / in config name!</b>
*/
public static Settings localCfg;
/** Anwenderspezifische Einstellungen (Werden in der Datenbank gespeichert) */
public static Settings userCfg;
/** Mandantspezifische EInstellungen (Werden in der Datenbank gespeichert) */
public static Settings mandantCfg;
public static Anwender actUser; // TODO set
/**
* @deprecated please use {@link ElexisEventDispatcher#getSelectedMandator()} to retrieve
* current mandator
*/
@Deprecated
public static Mandant actMandant;
private static boolean tooManyInstances;
public static final CorePreferenceInitializer pin = new CorePreferenceInitializer();
/** Die zentrale Zugriffskontrolle */
public static final AbstractAccessControl acl = new RoleBasedAccessControl();
/** Lock Service **/
private static ILocalLockService localLockService;
/** Stock Service **/
private static final StockService stockService = new StockService();
/** Order Service **/
private static final IOrderService orderService = new OrderService();
/** Event Service to transport Events to the Elexis Server */
private static ElexisServerEventService elexisServerEventService;
/**
* Stock commissioning system service
*/
private static final IStockCommissioningSystemService stockCommissioningSystemService =
new StockCommissioningSystemService();
/**
* The listener for patient events
*/
private final PatientEventListener eeli_pat = new PatientEventListener();
public static boolean isTooManyInstances(){
return tooManyInstances;
}
/**
* get the base directory of this currently running elexis application
*
* @return the topmost directory of this application or null if this information could not be
* retrieved
*/
public static String getBasePath(){
return FrameworkUtil.getBundle(CoreHub.class).getEntry("/").toString();
}
/**
* Return a directory suitable for temporary files. Most probably this will be a default tempdir
* provided by the os. If none such exists, it will be the user dir.
*
* @return always a valid and writable directory.
*/
public static File getTempDir(){
File ret = null;
String temp = System.getProperty("java.io.tmpdir"); //$NON-NLS-1$
if (!StringTool.isNothing(temp)) {
ret = new File(temp);
if (ret.exists() && ret.isDirectory()) {
return ret;
} else {
if (ret.mkdirs()) {
return ret;
}
}
}
return getWritableUserDir();
}
/**
* return a directory suitable for plugin specific configuration data. If no such dir exists, it
* will be created. If it could not be created, the application will refuse to start.
*
* @return a directory that exists always and is always writable and readable for plugins of the
* currently running elexis instance. Caution: this directory is not necessarily shared
* among different OS-Users. In Windows it is normally %USERPROFILE%\elexis, in Linux
* ~./elexis
*/
public static File getWritableUserDir(){
if (userDir == null) {
String userhome = null;
if (localCfg != null) {
userhome = localCfg.get("elexis-userDir", null); //$NON-NLS-1$
}
if (userhome == null) {
userhome = System.getProperty("user.home"); //$NON-NLS-1$
}
if (StringTool.isNothing(userhome)) {
userhome = System.getProperty("java.io.tempdir"); //$NON-NLS-1$
}
userDir = new File(userhome, "elexis"); //$NON-NLS-1$
}
if (!userDir.exists()) {
if (!userDir.mkdirs()) {
System.err.print("fatal: could not create Userdir"); //$NON-NLS-1$
MessageEvent.fireLoggedError("Panic exit",
"could not create userdir " + userDir.getAbsolutePath());
System.exit(-5);
}
}
return userDir;
}
@Override
public void start(BundleContext context) throws Exception{
this.context = context;
log.debug("Starting " + CoreHub.class.getName());
plugin = this;
localLockService = new LocalLockService();
elexisServerEventService = new ElexisServerEventService();
startUpBundle();
setUserDir(userDir);
heart = Heartbeat.getInstance();
ElexisEventDispatcher.getInstance().addListeners(eeli_pat);
// add core ClassLoader to default Script Interpreter
Interpreter.classLoaders.add(CoreHub.class.getClassLoader());
if (!ElexisSystemPropertyConstants.RUN_MODE_FROM_SCRATCH
.equals(System.getProperty(ElexisSystemPropertyConstants.RUN_MODE)))
Runtime.getRuntime().addShutdownHook(new Thread() {
@Override
public void run(){
SysSettings localCfg = (SysSettings) CoreHub.localCfg;
localCfg.write_xml(LocalCfgFile);
}
});
}
public static String readElexisBuildVersion(){
if ( elexis_version != null ) { return elexis_version; }
Properties prop = new Properties();
String url_name = "platform:/plugin/ch.elexis.core.data/rsc/version.properties";
try (InputStream inputStream = new URL(url_name).openConnection().getInputStream()) {
if (inputStream != null) {
prop.load(inputStream);
elexis_version = prop.getProperty("elexis.version").replace("-SNAPSHOT", "");
}
} catch (IOException e) {
elexis_version = plugin.Version;
// log.warn("Error reading build version information from [{}]", url_name, e);
}
return elexis_version;
}
@Override
public void stop(BundleContext context) throws Exception{
log.debug("Stopping " + CoreHub.class.getName());
getLocalLockService().releaseAllLocks();
getLocalLockService().shutdown();
CoreHub.logoffAnwender();
PersistentObject.disconnect();
ElexisEventDispatcher.getInstance().removeListeners(eeli_pat);
ElexisEventDispatcher.getInstance().dump();
globalCfg = null;
heart.stop();
plugin = null;
this.context = null;
}
private void startUpBundle(){
String[] args = CommandLineArgs.getApplicationArgs();
String config = "default"; //$NON-NLS-1$
for (String s : args) {
if (s.startsWith("--use-config=")) { //$NON-NLS-1$
String[] c = s.split("="); //$NON-NLS-1$
config = c[1];
}
}
if (ElexisSystemPropertyConstants.RUN_MODE_FROM_SCRATCH
.equals(System.getProperty(ElexisSystemPropertyConstants.RUN_MODE))) {
config = UUID.randomUUID().toString();
}
loadLocalCfg(config);
// Damit Anfragen auf userCfg und mandantCfg bei nicht eingeloggtem User
// keine NPE werfen
userCfg = localCfg;
mandantCfg = localCfg;
VersionInfo vI = new VersionInfo(System.getProperty("java.version", "0.0.0")); //$NON-NLS-1$ //$NON-NLS-2$
log.info(getId() + "; Java: " + vI.version() + "\nencoding: "
+ System.getProperty("file.encoding"));
if (vI.isOlder(neededJRE)) {
MessageEvent.fireLoggedError("Invalid Java version",
"Your Java version is older than " + neededJRE + ", please update.");
}
log.info("Basepath: " + getBasePath());
pin.initializeDefaultPreferences();
heart = Heartbeat.getInstance();
initializeLock();
}
private static void initializeLock(){
final int timeoutSeconds = 600;
try {
final LockFile lockfile = new LockFile(userDir, "elexislock", 4, timeoutSeconds); //$NON-NLS-1$
final int n = lockfile.lock();
if (n == 0) {
MessageEvent.fireLoggedError("Too many instances",
"Too many concurrent instances of Elexis running. Check elexislock files in "
+ userDir);
tooManyInstances = true;
} else {
tooManyInstances = false;
HeartListener lockListener = new HeartListener() {
long timeSet;
@Override
public void heartbeat(){
long now = System.currentTimeMillis();
if ((now - timeSet) > timeoutSeconds) {
lockfile.updateLock(n);
timeSet = now;
}
}
};
heart.addListener(lockListener, Heartbeat.FREQUENCY_LOW);
}
} catch (IOException ex) {
log.error("Can not aquire lock file in " + userDir + "; " + ex.getMessage()); //$NON-NLS-1$
}
}
public static String getId(){
StringBuilder sb = new StringBuilder();
sb.append(APPLICATION_NAME).append(" v.").append(Version).append("\n")
.append(CoreHubHelper.getRevision(true, plugin)).append("\n")
.append(System.getProperty("os.name")).append(StringConstants.SLASH)
.append(System.getProperty("os.version")).append(StringConstants.SLASH)
.append(System.getProperty("os.arch")); //$NON-NLS-1$
return sb.toString();
}
private void loadLocalCfg(String branch){
LocalCfgFile = CoreHubHelper.getWritableUserDir() + "/localCfg_" + branch + ".xml";
String msg = "loadLocalCfg: Loading branch " + branch + " from " + LocalCfgFile;
System.out.println(msg);
log.debug(msg);
SysSettings cfg = new SysSettings(SysSettings.USER_SETTINGS, Desk.class);
cfg.read_xml(LocalCfgFile);
CoreHub.localCfg = cfg;
}
public static void setMandant(Mandant newMandant){
if (actMandant != null && mandantCfg != null) {
mandantCfg.flush();
}
if (newMandant == null) {
mandantCfg = userCfg;
} else {
mandantCfg = getUserSetting(newMandant);
}
actMandant = newMandant;
ElexisEventDispatcher.getInstance()
.fire(new ElexisEvent(newMandant, Mandant.class, ElexisEvent.EVENT_MANDATOR_CHANGED));
}
public static Settings getUserSetting(Kontakt user){
if (StringConstants.ONE.equals(user.get(Kontakt.FLD_IS_USER))) {
Settings settings = new SqlSettings(PersistentObject.getConnection(), "USERCONFIG",
"Param", "Value", "UserID=" + user.getWrappedId());
return settings;
}
return null;
}
public Bundle getBundle(){
return context.getBundle();
}
/**
* get a list of all mandators known to this system
*/
public static List<Mandant> getMandantenList(){
Query<Mandant> qbe = new Query<>(Mandant.class);
return qbe.execute();
}
/**
* get a list of all users known to this system
*/
public static List<Anwender> getUserList(){
Query<Anwender> qbe = new Query<>(Anwender.class);
return qbe.execute();
}
/**
* Return the name of a config instance, the user chose. This is just the valuie of the
* -Dconfig=xx runtime value or "default" if no -Dconfig was set
*/
public static String getCfgVariant(){
String config = System.getProperty("config");
return config == null ? "default" : config;
}
public void setUserDir(File dir){
userDir = dir;
localCfg.set("elexis-userDir", dir.getAbsolutePath()); //$NON-NLS-1$
}
/**
* Add a ShutdownJob to the list of jobs that has to be done after the Elexis workbench was shut
* down.
*
* @param job
*/
public static void addShutdownJob(final ShutdownJob job){
if (!shutdownJobs.contains(job)) {
shutdownJobs.add(job);
}
}
public static int getSystemLogLevel(){
return localCfg.get(Preferences.ABL_LOGLEVEL, Log.ERRORS);
}
/**
* Perform the required tasks to log off the current {@link Anwender}
*
* @since 3.1 moved from {@link Anwender} class
*/
public static void logoffAnwender(){
if (CoreHub.actUser == null)
return;
if (CoreHub.userCfg != null) {
CoreHub.userCfg.flush();
}
getLocalLockService().releaseAllLocks();
CoreHub.setMandant(null);
CoreHub.heart.suspend();
CoreHub.actUser = null;
ElexisEventDispatcher.getInstance()
.fire(new ElexisEvent(null, Anwender.class, ElexisEvent.EVENT_USER_CHANGED));
ElexisEventDispatcher.getInstance()
.fire(new ElexisEvent(null, User.class, ElexisEvent.EVENT_DESELECTED));
CoreHub.userCfg = CoreHub.localCfg;
}
public static ILocalLockService getLocalLockService(){
return localLockService;
}
public static StockService getStockService(){
return stockService;
}
public static IStockCommissioningSystemService getStockCommissioningSystemService(){
return stockCommissioningSystemService;
}
public static IOrderService getOrderService(){
return orderService;
}
public static ElexisServerEventService getElexisServerEventService(){
return elexisServerEventService;
}
}
|
package net.bytebuddy.agent.builder;
import edu.umd.cs.findbugs.annotations.SuppressFBWarnings;
import net.bytebuddy.ByteBuddy;
import net.bytebuddy.asm.AsmVisitorWrapper;
import net.bytebuddy.description.field.FieldDescription;
import net.bytebuddy.description.method.MethodDescription;
import net.bytebuddy.description.method.ParameterDescription;
import net.bytebuddy.description.modifier.*;
import net.bytebuddy.description.type.TypeDescription;
import net.bytebuddy.dynamic.ClassFileLocator;
import net.bytebuddy.dynamic.DynamicType;
import net.bytebuddy.dynamic.loading.ClassInjector;
import net.bytebuddy.dynamic.loading.ClassReloadingStrategy;
import net.bytebuddy.dynamic.scaffold.InstrumentedType;
import net.bytebuddy.dynamic.scaffold.inline.MethodNameTransformer;
import net.bytebuddy.dynamic.scaffold.subclass.ConstructorStrategy;
import net.bytebuddy.implementation.ExceptionMethod;
import net.bytebuddy.implementation.Implementation;
import net.bytebuddy.implementation.LoadedTypeInitializer;
import net.bytebuddy.implementation.auxiliary.AuxiliaryType;
import net.bytebuddy.implementation.bytecode.*;
import net.bytebuddy.implementation.bytecode.assign.Assigner;
import net.bytebuddy.implementation.bytecode.assign.TypeCasting;
import net.bytebuddy.implementation.bytecode.collection.ArrayFactory;
import net.bytebuddy.implementation.bytecode.constant.ClassConstant;
import net.bytebuddy.implementation.bytecode.constant.IntegerConstant;
import net.bytebuddy.implementation.bytecode.constant.NullConstant;
import net.bytebuddy.implementation.bytecode.constant.TextConstant;
import net.bytebuddy.implementation.bytecode.member.FieldAccess;
import net.bytebuddy.implementation.bytecode.member.MethodInvocation;
import net.bytebuddy.implementation.bytecode.member.MethodReturn;
import net.bytebuddy.implementation.bytecode.member.MethodVariableAccess;
import net.bytebuddy.matcher.ElementMatcher;
import net.bytebuddy.pool.TypePool;
import net.bytebuddy.utility.JavaInstance;
import org.objectweb.asm.Label;
import org.objectweb.asm.MethodVisitor;
import org.objectweb.asm.Opcodes;
import org.objectweb.asm.Type;
import java.io.*;
import java.lang.instrument.ClassDefinition;
import java.lang.instrument.ClassFileTransformer;
import java.lang.instrument.Instrumentation;
import java.lang.instrument.UnmodifiableClassException;
import java.lang.reflect.InvocationTargetException;
import java.lang.reflect.Method;
import java.security.AccessControlContext;
import java.security.AccessController;
import java.security.ProtectionDomain;
import java.util.*;
import java.util.concurrent.Callable;
import java.util.concurrent.atomic.AtomicInteger;
import static net.bytebuddy.matcher.ElementMatchers.*;
public interface AgentBuilder {
/**
* <p>
* Matches a type being loaded in order to apply the supplied
* {@link net.bytebuddy.agent.builder.AgentBuilder.Transformer}s before loading this type.
* </p>
* <p>
* <b>Note</b>: When applying a matcher, regard the performance implications by
* {@link AgentBuilder#ignore(ElementMatcher)}. The former matcher is applied first such that it makes sense
* to ignore name spaces that are irrelevant to instrumentation. If possible, it is also recommended, to
* exclude class loaders such as for example the bootstrap class loader.
* </p>
*
* @param matcher A matcher that decides if the entailed
* {@link net.bytebuddy.agent.builder.AgentBuilder.Transformer}s should be applied for a type that
* is being loaded.
* @return A definable that represents this agent builder which allows for the definition of one or several
* {@link net.bytebuddy.agent.builder.AgentBuilder.Transformer}s to be applied when the given {@code matcher}
* indicates a match.
*/
Identified type(RawMatcher matcher);
/**
* <p>
* Matches a type being loaded in order to apply the supplied
* {@link net.bytebuddy.agent.builder.AgentBuilder.Transformer}s before loading this type.
* </p>
* <p>
* <b>Note</b>: When applying a matcher, regard the performance implications by
* {@link AgentBuilder#ignore(ElementMatcher)}. The former matcher is applied first such that it makes sense
* to ignore name spaces that are irrelevant to instrumentation. If possible, it is also recommended, to exclude
* class loaders such as for example the bootstrap class loader by using
* {@link AgentBuilder#type(ElementMatcher, ElementMatcher)} instead.
* </p>
*
* @param typeMatcher An {@link net.bytebuddy.matcher.ElementMatcher} that is applied on the type being loaded that
* decides if the entailed {@link net.bytebuddy.agent.builder.AgentBuilder.Transformer}s should
* be applied for that type.
* @return A definable that represents this agent builder which allows for the definition of one or several
* {@link net.bytebuddy.agent.builder.AgentBuilder.Transformer}s to be applied when the given {@code typeMatcher}
* indicates a match.
*/
Identified type(ElementMatcher<? super TypeDescription> typeMatcher);
/**
* <p>
* Matches a type being loaded in order to apply the supplied
* {@link net.bytebuddy.agent.builder.AgentBuilder.Transformer}s before loading this type.
* </p>
* <p>
* <b>Note</b>: When applying a matcher, regard the performance implications by
* {@link AgentBuilder#ignore(ElementMatcher)}. The former matcher is applied first such that it makes sense
* to ignore name spaces that are irrelevant to instrumentation.
* </p>
*
* @param typeMatcher An {@link net.bytebuddy.matcher.ElementMatcher} that is applied on the type being
* loaded that decides if the entailed
* {@link net.bytebuddy.agent.builder.AgentBuilder.Transformer}s should be applied for
* that type.
* @param classLoaderMatcher An {@link net.bytebuddy.matcher.ElementMatcher} that is applied to the
* {@link java.lang.ClassLoader} that is loading the type being loaded. This matcher
* is always applied first where the type matcher is not applied in case that this
* matcher does not indicate a match.
* @return A definable that represents this agent builder which allows for the definition of one or several
* {@link net.bytebuddy.agent.builder.AgentBuilder.Transformer}s to be applied when both the given
* {@code typeMatcher} and {@code classLoaderMatcher} indicate a match.
*/
Identified type(ElementMatcher<? super TypeDescription> typeMatcher, ElementMatcher<? super ClassLoader> classLoaderMatcher);
/**
* Defines the given {@link net.bytebuddy.ByteBuddy} instance to be used by the created agent.
*
* @param byteBuddy The Byte Buddy instance to be used.
* @return A new instance of this agent builder which makes use of the given {@code byteBuddy} instance.
*/
AgentBuilder with(ByteBuddy byteBuddy);
/**
* Defines the given {@link net.bytebuddy.agent.builder.AgentBuilder.Listener} to be notified by the created agent.
* The given listener is notified after any other listener that is already registered. If a listener is registered
* twice, it is also notified twice.
*
* @param listener The listener to be notified.
* @return A new instance of this agent builder which creates an agent that informs the given listener about
* events.
*/
AgentBuilder with(Listener listener);
/**
* Defines the use of the given binary locator for locating binary data to given class names.
*
* @param binaryLocator The binary locator to use.
* @return A new instance of this agent builder which uses the given binary locator for looking up class files.
*/
AgentBuilder with(BinaryLocator binaryLocator);
/**
* Defines the use of the given definition handler that determines if a type should be rebased or redefined.
*
* @param typeStrategy The definition handler to use.
* @return A new instance of this agent builder which uses the given definition handler.
*/
AgentBuilder with(TypeStrategy typeStrategy);
/**
* Defines classes to be loaded using the given access control context.
*
* @param accessControlContext The access control context to be used for loading classes.
* @return A new instance of this agent builder which uses the given access control context for class loading.
*/
AgentBuilder with(AccessControlContext accessControlContext);
/**
* Defines a given initialization strategy to be applied to generated types. An initialization strategy is responsible
* for setting up a type after it was loaded. This initialization must be performed after the transformation because
* a Java agent is only invoked before loading a type. By default, the initialization logic is added to a class's type
* initializer which queries a global object for any objects that are to be injected into the generated type.
*
* @param initializationStrategy The initialization strategy to use.
* @return A new instance of this agent builder that applies the given initialization strategy.
*/
AgentBuilder with(InitializationStrategy initializationStrategy);
/**
* Specifies a strategy for modifying existing types.
*
* @param redefinitionStrategy The redefinition strategy to apply.
* @return A new instance of this agent builder that applies the given redefinition strategy.
*/
AgentBuilder with(RedefinitionStrategy redefinitionStrategy);
/**
* <p>
* Enables or disables management of the JVM's {@code LambdaMetafactory} which is responsible for creating classes that
* implement lambda expressions. Without this feature enabled, classes that are represented by lambda expressions are
* not instrumented by the JVM such that Java agents have no effect on them when a lambda expression's class is loaded
* for the first time.
* </p>
* <p>
* When activating this feature, Byte Buddy instruments the {@code LambdaMetafactory} and takes over the responsibility
* of creating classes that represent lambda expressions. In doing so, Byte Buddy has the opportunity to apply the built
* class file transformer. If the current VM does not support lambda expressions, activating this feature has no effect.
* </p>
* <p>
* <b>Important</b>: If this feature is active, it is important to release the built class file transformer when
* deactivating it. Normally, it is sufficient to call {@link Instrumentation#removeTransformer(ClassFileTransformer)}.
* When this feature is enabled, it is however also required to invoke
* {@link LambdaInstrumentationStrategy#release(ClassFileTransformer, Instrumentation)}. Otherwise, the executing VMs class
* loader retains a reference to the class file transformer what can cause a memory leak.
* </p>
*
* @param lambdaInstrumentationStrategy {@code true} if this feature should be enabled.
* @return A new instance of this agent builder where this feature is explicitly enabled or disabled.
*/
AgentBuilder with(LambdaInstrumentationStrategy lambdaInstrumentationStrategy);
/**
* Enables class injection of auxiliary classes into the bootstrap class loader.
*
* @param folder The folder in which jar files of the injected classes are to be stored.
* @param instrumentation The instrumentation instance that is used for appending jar files to the
* bootstrap class path.
* @return An agent builder with bootstrap class loader class injection enabled.
*/
AgentBuilder enableBootstrapInjection(File folder, Instrumentation instrumentation);
/**
* Enables the use of the given native method prefix for instrumented methods. Note that this prefix is also
* applied when preserving non-native methods. The use of this prefix is also registered when installing the
* final agent with an {@link java.lang.instrument.Instrumentation}.
*
* @param prefix The prefix to be used.
* @return A new instance of this agent builder which uses the given native method prefix.
*/
AgentBuilder enableNativeMethodPrefix(String prefix);
/**
* Disables the use of a native method prefix for instrumented methods.
*
* @return A new instance of this agent builder which does not use a native method prefix.
*/
AgentBuilder disableNativeMethodPrefix();
/**
* Disables injection of auxiliary classes into the bootstrap class path.
*
* @return A new instance of this agent builder which does not apply bootstrap class loader injection.
*/
AgentBuilder disableBootstrapInjection();
/**
* <p>
* Excludes any type that is matched by the provided matcher from instrumentation. By default, Byte Buddy does not
* instrument synthetic types.
* </p>
* <p>
* <b>Note</b>: For performance reasons, it is recommended to always include a matcher that excludes as many namespaces
* as possible. Byte Buddy can determine a type's name without parsing its class file and can therefore discard such
* types prematurely. When a different property of a type - such as for example its modifiers or its annotations is
* accessed - Byte Buddy parses the class file lazily in order to allow for such a matching. Therefore, any exclusion
* of a name should always be done as a first step and even if it does not influence the selection of what types are
* matched. Without changing this property, the class file of every type is being parsed!
* </p>
*
* @param ignoredTypes A matcher that identifies types that should not be instrumented.
* @return A new instance of this agent builder that ignores all types that are matched by the provided matcher.
* All previous matchers for ignored types are discarded.
*/
AgentBuilder ignore(ElementMatcher<? super TypeDescription> ignoredTypes);
/**
* Creates a {@link java.lang.instrument.ClassFileTransformer} that implements the configuration of this
* agent builder.
*
* @return A class file transformer that implements the configuration of this agent builder.
*/
ClassFileTransformer makeRaw();
/**
* Creates and installs a {@link java.lang.instrument.ClassFileTransformer} that implements the configuration of
* this agent builder with a given {@link java.lang.instrument.Instrumentation}. If retransformation is enabled,
* the installation also causes all loaded types to be retransformed.
*
* @param instrumentation The instrumentation on which this agent builder's configuration is to be installed.
* @return The installed class file transformer.
*/
ClassFileTransformer installOn(Instrumentation instrumentation);
/**
* Creates and installs a {@link java.lang.instrument.ClassFileTransformer} that implements the configuration of
* this agent builder with the Byte Buddy-agent which must be installed prior to calling this method.
*
* @return The installed class file transformer.
*/
ClassFileTransformer installOnByteBuddyAgent();
/**
* Describes an {@link net.bytebuddy.agent.builder.AgentBuilder} which was handed a matcher for identifying
* types to instrumented in order to supply one or several
* {@link net.bytebuddy.agent.builder.AgentBuilder.Transformer}s.
*/
interface Identified {
/**
* Applies the given transformer for the already supplied matcher.
*
* @param transformer The transformer to apply.
* @return This agent builder with the transformer being applied when the previously supplied matcher
* identified a type for instrumentation which also allows for the registration of subsequent transformers.
*/
Extendable transform(Transformer transformer);
/**
* This interface is used to allow for optionally providing several
* {@link net.bytebuddy.agent.builder.AgentBuilder.Transformer} to applied when a matcher identifies a type
* to be instrumented. Any subsequent transformers are applied in the order they are registered.
*/
interface Extendable extends AgentBuilder, Identified {
/* this is merely a unionizing interface that does not declare methods */
}
}
/**
* A matcher that allows to determine if a {@link net.bytebuddy.agent.builder.AgentBuilder.Transformer}
* should be applied during the execution of a {@link java.lang.instrument.ClassFileTransformer} that was
* generated by an {@link net.bytebuddy.agent.builder.AgentBuilder}.
*/
interface RawMatcher {
/**
* Decides if the given {@code typeDescription} should be instrumented with the entailed
* {@link net.bytebuddy.agent.builder.AgentBuilder.Transformer}s.
*
* @param typeDescription A description of the type to be instrumented.
* @param classLoader The class loader of the instrumented type. Might be {@code null} if this class
* loader represents the bootstrap class loader.
* @param classBeingRedefined The class being redefined which is only not {@code null} if a retransformation
* is applied.
* @param protectionDomain The protection domain of the type being transformed.
* @return {@code true} if the entailed {@link net.bytebuddy.agent.builder.AgentBuilder.Transformer}s should
* be applied for the given {@code typeDescription}.
*/
boolean matches(TypeDescription typeDescription,
ClassLoader classLoader,
Class<?> classBeingRedefined,
ProtectionDomain protectionDomain);
/**
* A raw matcher implementation that checks a {@link TypeDescription}
* and its {@link java.lang.ClassLoader} against two suitable matchers in order to determine if the matched
* type should be instrumented.
*/
class ForElementMatcherPair implements RawMatcher {
/**
* The type matcher to apply to a {@link TypeDescription}.
*/
private final ElementMatcher<? super TypeDescription> typeMatcher;
/**
* The class loader to apply to a {@link java.lang.ClassLoader}.
*/
private final ElementMatcher<? super ClassLoader> classLoaderMatcher;
/**
* Creates a new {@link net.bytebuddy.agent.builder.AgentBuilder.RawMatcher} that only matches the
* supplied {@link TypeDescription} and its {@link java.lang.ClassLoader} against two matcher in order
* to decided if an instrumentation should be conducted.
*
* @param typeMatcher The type matcher to apply to a
* {@link TypeDescription}.
* @param classLoaderMatcher The class loader to apply to a {@link java.lang.ClassLoader}.
*/
public ForElementMatcherPair(ElementMatcher<? super TypeDescription> typeMatcher,
ElementMatcher<? super ClassLoader> classLoaderMatcher) {
this.typeMatcher = typeMatcher;
this.classLoaderMatcher = classLoaderMatcher;
}
@Override
public boolean matches(TypeDescription typeDescription,
ClassLoader classLoader,
Class<?> classBeingRedefined,
ProtectionDomain protectionDomain) {
return classLoaderMatcher.matches(classLoader) && typeMatcher.matches(typeDescription);
}
@Override
public boolean equals(Object other) {
return this == other || !(other == null || getClass() != other.getClass())
&& classLoaderMatcher.equals(((ForElementMatcherPair) other).classLoaderMatcher)
&& typeMatcher.equals(((ForElementMatcherPair) other).typeMatcher);
}
@Override
public int hashCode() {
int result = typeMatcher.hashCode();
result = 31 * result + classLoaderMatcher.hashCode();
return result;
}
@Override
public String toString() {
return "AgentBuilder.RawMatcher.ForElementMatcherPair{" +
"typeMatcher=" + typeMatcher +
", classLoaderMatcher=" + classLoaderMatcher +
'}';
}
}
}
/**
* A type strategy is responsible for creating a type builder for a type that is being instrumented.
*/
interface TypeStrategy {
/**
* Creates a type builder for a given type.
*
* @param typeDescription The type being instrumented.
* @param byteBuddy The Byte Buddy configuration.
* @param classFileLocator The class file locator to use.
* @param methodNameTransformer The method name transformer to use.
* @return A type builder for the given arguments.
*/
DynamicType.Builder<?> builder(TypeDescription typeDescription,
ByteBuddy byteBuddy,
ClassFileLocator classFileLocator,
MethodNameTransformer methodNameTransformer);
/**
* Default implementations of type strategies.
*/
enum Default implements TypeStrategy {
/**
* A definition handler that performs a rebasing for all types.
*/
REBASE {
@Override
public DynamicType.Builder<?> builder(TypeDescription typeDescription,
ByteBuddy byteBuddy,
ClassFileLocator classFileLocator,
MethodNameTransformer methodNameTransformer) {
return byteBuddy.rebase(typeDescription, classFileLocator, methodNameTransformer);
}
},
/**
* <p>
* A definition handler that performs a redefinition for all types.
* </p>
* <p>
* Note that the default agent builder is configured to apply a self initialization where a static class initializer
* is added to the redefined class. This can be disabled by for example using a {@link InitializationStrategy.Minimal} or
* {@link InitializationStrategy.NoOp}. Also, consider the constraints implied by {@link ByteBuddy#redefine(TypeDescription, ClassFileLocator)}.
* </p>
*/
REDEFINE {
@Override
public DynamicType.Builder<?> builder(TypeDescription typeDescription,
ByteBuddy byteBuddy,
ClassFileLocator classFileLocator,
MethodNameTransformer methodNameTransformer) {
return byteBuddy.redefine(typeDescription, classFileLocator);
}
};
@Override
public String toString() {
return "AgentBuilder.TypeStrategy.Default." + name();
}
}
}
/**
* A transformer allows to apply modifications to a {@link net.bytebuddy.dynamic.DynamicType}. Such a modification
* is then applied to any instrumented type that was matched by the preceding matcher.
*/
interface Transformer {
/**
* Allows for a transformation of a {@link net.bytebuddy.dynamic.DynamicType.Builder}.
*
* @param builder The dynamic builder to transform.
* @param typeDescription The description of the type currently being instrumented.
* @return A transformed version of the supplied {@code builder}.
*/
DynamicType.Builder<?> transform(DynamicType.Builder<?> builder, TypeDescription typeDescription);
/**
* A no-op implementation of a {@link net.bytebuddy.agent.builder.AgentBuilder.Transformer} that does
* not modify the supplied dynamic type.
*/
enum NoOp implements Transformer {
/**
* The singleton instance.
*/
INSTANCE;
@Override
public DynamicType.Builder<?> transform(DynamicType.Builder<?> builder, TypeDescription typeDescription) {
return builder;
}
@Override
public String toString() {
return "AgentBuilder.Transformer.NoOp." + name();
}
}
/**
* A compound transformer that allows to group several
* {@link net.bytebuddy.agent.builder.AgentBuilder.Transformer}s as a single transformer.
*/
class Compound implements Transformer {
/**
* The transformers to apply in their application order.
*/
private final Transformer[] transformer;
/**
* Creates a new compound transformer.
*
* @param transformer The transformers to apply in their application order.
*/
public Compound(Transformer... transformer) {
this.transformer = transformer;
}
@Override
public DynamicType.Builder<?> transform(DynamicType.Builder<?> builder, TypeDescription typeDescription) {
for (Transformer transformer : this.transformer) {
builder = transformer.transform(builder, typeDescription);
}
return builder;
}
@Override
public boolean equals(Object other) {
return this == other || !(other == null || getClass() != other.getClass())
&& Arrays.equals(transformer, ((Compound) other).transformer);
}
@Override
public int hashCode() {
return Arrays.hashCode(transformer);
}
@Override
public String toString() {
return "AgentBuilder.Transformer.Compound{" +
"transformer=" + Arrays.toString(transformer) +
'}';
}
}
}
/**
* A binary locator allows to specify how binary data is located by an
* {@link net.bytebuddy.agent.builder.AgentBuilder}.
*/
interface BinaryLocator {
/**
* Creates a class file locator for the given class loader.
*
* @param classLoader The class loader for which a class file locator should be created.
* Can be {@code null} to represent the bootstrap class loader.
* @return An appropriate class file locator.
*/
ClassFileLocator classFileLocator(ClassLoader classLoader);
/**
* Creates a type pool for a given class file locator.
*
* @param classFileLocator The class file locator to use.
* @param classLoader The class loader for which the class file locator was created.
* @return A type pool for the supplied class file locator.
*/
TypePool typePool(ClassFileLocator classFileLocator, ClassLoader classLoader);
/**
* A default implementation of a {@link net.bytebuddy.agent.builder.AgentBuilder.BinaryLocator} that
* is using a {@link net.bytebuddy.pool.TypePool.Default} with a
* {@link net.bytebuddy.pool.TypePool.CacheProvider.Simple} and a
* {@link net.bytebuddy.dynamic.ClassFileLocator.ForClassLoader}.
*/
enum Default implements BinaryLocator {
/**
* A binary locator that parses the code segment of each method for extracting information about parameter
* names even if they are not explicitly included in a class file.
*
* @see net.bytebuddy.pool.TypePool.Default.ReaderMode#EXTENDED
*/
EXTENDED(TypePool.Default.ReaderMode.EXTENDED),
/**
* A binary locator that skips the code segment of each method and does therefore not extract information
* about parameter names. Parameter names are still included if they are explicitly included in a class file.
*
* @see net.bytebuddy.pool.TypePool.Default.ReaderMode#FAST
*/
FAST(TypePool.Default.ReaderMode.FAST);
/**
* The reader mode to apply by this binary locator.
*/
private final TypePool.Default.ReaderMode readerMode;
/**
* Creates a new binary locator.
*
* @param readerMode The reader mode to apply by this binary locator.
*/
Default(TypePool.Default.ReaderMode readerMode) {
this.readerMode = readerMode;
}
@Override
public ClassFileLocator classFileLocator(ClassLoader classLoader) {
return ClassFileLocator.ForClassLoader.of(classLoader);
}
@Override
public TypePool typePool(ClassFileLocator classFileLocator, ClassLoader classLoader) {
return new TypePool.LazyFacade(TypePool.Default.Precomputed.withObjectType(new TypePool.CacheProvider.Simple(), classFileLocator, readerMode));
}
@Override
public String toString() {
return "AgentBuilder.BinaryLocator.Default." + name();
}
}
/**
* <p>
* A binary locator that loads referenced classes instead of describing unloaded versions.
* </p>
* <p>
* <b>Important</b>: It is important to never query this binary locator for the currently instrumented type as this will yield a class
* loading circularity which aborts any instrumentation with an error.
* </p>
* <p>
* <b>Warning</b>: Warning, this binary locator <i>cannot be used for applying a redefinition</i> as it works on loaded classes only and
* is agnostic of any way to locate a class file.
* </p>
*/
enum ClassLoading implements BinaryLocator {
/**
* The singleton instance.
*/
INSTANCE;
@Override
public ClassFileLocator classFileLocator(ClassLoader classLoader) {
return ClassFileLocator.NoOp.INSTANCE;
}
@Override
public TypePool typePool(ClassFileLocator classFileLocator, ClassLoader classLoader) {
return new TypePool.LazyFacade(TypePool.Default.ClassLoading.of(classFileLocator, classLoader));
}
@Override
public String toString() {
return "AgentBuilder.BinaryLocator.ClassLoading." + name();
}
}
}
/**
* A listener that is informed about events that occur during an instrumentation process.
*/
interface Listener {
/**
* Invoked right before a successful transformation is applied.
*
* @param typeDescription The type that is being transformed.
* @param dynamicType The dynamic type that was created.
*/
void onTransformation(TypeDescription typeDescription, DynamicType dynamicType);
/**
* Invoked when a type is not transformed but ignored.
*
* @param typeDescription The type being ignored.
*/
void onIgnored(TypeDescription typeDescription);
/**
* Invoked when an error has occurred.
*
* @param typeName The binary name of the instrumented type.
* @param throwable The occurred error.
*/
void onError(String typeName, Throwable throwable);
/**
* Invoked after a class was attempted to be loaded, independently of its treatment.
*
* @param typeName The binary name of the instrumented type.
*/
void onComplete(String typeName);
/**
* A no-op implementation of a {@link net.bytebuddy.agent.builder.AgentBuilder.Listener}.
*/
enum NoOp implements Listener {
/**
* The singleton instance.
*/
INSTANCE;
@Override
public void onTransformation(TypeDescription typeDescription, DynamicType dynamicType) {
/* do nothing */
}
@Override
public void onIgnored(TypeDescription typeDescription) {
/* do nothing */
}
@Override
public void onError(String typeName, Throwable throwable) {
/* do nothing */
}
@Override
public void onComplete(String typeName) {
/* do nothing */
}
@Override
public String toString() {
return "AgentBuilder.Listener.NoOp." + name();
}
}
/**
* A listener that writes events to a {@link PrintStream}. This listener prints a line per event, including the event type and
* the name of the type in question.
*/
class StreamWriting implements Listener {
/**
* The prefix that is appended to all written messages.
*/
protected static final String PREFIX = "[Byte Buddy]";
/**
* The print stream written to.
*/
private final PrintStream printStream;
/**
* Creates a new stream writing listener.
*
* @param printStream The print stream written to.
*/
public StreamWriting(PrintStream printStream) {
this.printStream = printStream;
}
/**
* Creates a new stream writing listener that writes to {@link System#out}.
*
* @return A listener writing events to the standard output stream.
*/
public static Listener toSystemOut() {
return new StreamWriting(System.out);
}
@Override
public void onTransformation(TypeDescription typeDescription, DynamicType dynamicType) {
printStream.println(PREFIX + " TRANSFORM " + typeDescription.getName());
}
@Override
public void onIgnored(TypeDescription typeDescription) {
printStream.println(PREFIX + " IGNORE " + typeDescription.getName());
}
@Override
public void onError(String typeName, Throwable throwable) {
printStream.println(PREFIX + " ERROR " + typeName);
throwable.printStackTrace(printStream);
}
@Override
public void onComplete(String typeName) {
printStream.println(PREFIX + " COMPLETE " + typeName);
}
@Override
public boolean equals(Object other) {
return this == other || !(other == null || getClass() != other.getClass())
&& printStream.equals(((StreamWriting) other).printStream);
}
@Override
public int hashCode() {
return printStream.hashCode();
}
@Override
public String toString() {
return "AgentBuilder.Listener.StreamWriting{" +
"printStream=" + printStream +
'}';
}
}
/**
* A compound listener that allows to group several listeners in one instance.
*/
class Compound implements Listener {
/**
* The listeners that are represented by this compound listener in their application order.
*/
private final List<? extends Listener> listeners;
/**
* Creates a new compound listener.
*
* @param listener The listeners to apply in their application order.
*/
public Compound(Listener... listener) {
this(Arrays.asList(listener));
}
/**
* Creates a new compound listener.
*
* @param listeners The listeners to apply in their application order.
*/
public Compound(List<? extends Listener> listeners) {
this.listeners = listeners;
}
@Override
public void onTransformation(TypeDescription typeDescription, DynamicType dynamicType) {
for (Listener listener : listeners) {
listener.onTransformation(typeDescription, dynamicType);
}
}
@Override
public void onIgnored(TypeDescription typeDescription) {
for (Listener listener : listeners) {
listener.onIgnored(typeDescription);
}
}
@Override
public void onError(String typeName, Throwable throwable) {
for (Listener listener : listeners) {
listener.onError(typeName, throwable);
}
}
@Override
public void onComplete(String typeName) {
for (Listener listener : listeners) {
listener.onComplete(typeName);
}
}
@Override
public boolean equals(Object other) {
return this == other || !(other == null || getClass() != other.getClass())
&& listeners.equals(((Compound) other).listeners);
}
@Override
public int hashCode() {
return listeners.hashCode();
}
@Override
public String toString() {
return "AgentBuilder.Listener.Compound{" +
"listeners=" + listeners +
'}';
}
}
}
/**
* An initialization strategy which determines the handling of {@link net.bytebuddy.implementation.LoadedTypeInitializer}s
* and the loading of auxiliary types.
*/
interface InitializationStrategy {
/**
* Creates a new dispatcher for injecting this initialization strategy during a transformation process.
*
* @return The dispatcher to be used.
*/
Dispatcher dispatcher();
/**
* A dispatcher for changing a class file to adapt a self-initialization strategy.
*/
interface Dispatcher {
/**
* Transforms the instrumented type to implement an appropriate initialization strategy.
*
* @param builder The builder which should implement the initialization strategy.
* @return The given {@code builder} with the initialization strategy applied.
*/
DynamicType.Builder<?> apply(DynamicType.Builder<?> builder);
/**
* Registers a dynamic type for initialization and/or begins the initialization process.
*
* @param dynamicType The dynamic type that is created.
* @param classLoader The class loader of the dynamic type.
* @param injectorFactory The injector factory
*/
void register(DynamicType dynamicType, ClassLoader classLoader, InjectorFactory injectorFactory);
/**
* A factory for creating a {@link ClassInjector} only if it is required.
*/
interface InjectorFactory {
/**
* Resolves the class injector for this factory.
*
* @return The class injector for this factory.
*/
ClassInjector resolve();
}
}
/**
* A non-initializing initialization strategy.
*/
enum NoOp implements InitializationStrategy, Dispatcher {
/**
* The singleton instance.
*/
INSTANCE;
@Override
public Dispatcher dispatcher() {
return this;
}
@Override
public DynamicType.Builder<?> apply(DynamicType.Builder<?> builder) {
return builder;
}
@Override
public void register(DynamicType dynamicType, ClassLoader classLoader, InjectorFactory injectorFactory) {
/* do nothing */
}
@Override
public String toString() {
return "AgentBuilder.InitializationStrategy.NoOp." + name();
}
}
/**
* An initialization strategy that adds a code block to an instrumented type's type initializer which
* then calls a specific class that is responsible for the explicit initialization.
*/
enum SelfInjection implements InitializationStrategy {
/**
* A form of self-injection where auxiliary types that are annotated by
* {@link net.bytebuddy.implementation.auxiliary.AuxiliaryType.SignatureRelevant} of the instrumented type are loaded lazily and
* any other auxiliary type is loaded eagerly.
*/
SPLIT {
@Override
public InitializationStrategy.Dispatcher dispatcher() {
return new SelfInjection.Dispatcher.Split(random.nextInt());
}
},
/**
* A form of self-injection where any auxiliary type is loaded lazily.
*/
LAZY {
@Override
public InitializationStrategy.Dispatcher dispatcher() {
return new SelfInjection.Dispatcher.Lazy(random.nextInt());
}
},
/**
* A form of self-injection where any auxiliary type is loaded eagerly.
*/
EAGER {
@Override
public InitializationStrategy.Dispatcher dispatcher() {
return new SelfInjection.Dispatcher.Eager(random.nextInt());
}
};
/**
* A generator for random identification values.
*/
protected final Random random;
/**
* Creates the self-injection strategy.
*/
SelfInjection() {
random = new Random();
}
@Override
public String toString() {
return "AgentBuilder.InitializationStrategy.SelfInjection." + name();
}
/**
* A dispatcher for a self-initialization strategy.
*/
protected abstract static class Dispatcher implements InitializationStrategy.Dispatcher {
/**
* A random identification for the applied self-initialization.
*/
protected final int identification;
/**
* Creates a new dispatcher.
*
* @param identification A random identification for the applied self-initialization.
*/
protected Dispatcher(int identification) {
this.identification = identification;
}
@Override
public DynamicType.Builder<?> apply(DynamicType.Builder<?> builder) {
return builder.initializer(NexusAccessor.INSTANCE.identifiedBy(identification));
}
@Override
public boolean equals(Object other) {
return this == other || !(other == null || getClass() != other.getClass())
&& identification == ((Dispatcher) other).identification;
}
@Override
public int hashCode() {
return identification;
}
/**
* A dispatcher for the {@link net.bytebuddy.agent.builder.AgentBuilder.InitializationStrategy.SelfInjection#SPLIT} strategy.
*/
protected static class Split extends Dispatcher {
/**
* Creates a new split dispatcher.
*
* @param identification A random identification for the applied self-initialization.
*/
protected Split(int identification) {
super(identification);
}
@Override
public void register(DynamicType dynamicType, ClassLoader classLoader, InjectorFactory injectorFactory) {
Map<TypeDescription, byte[]> auxiliaryTypes = dynamicType.getAuxiliaryTypes();
LoadedTypeInitializer loadedTypeInitializer;
if (!auxiliaryTypes.isEmpty()) {
TypeDescription instrumentedType = dynamicType.getTypeDescription();
ClassInjector classInjector = injectorFactory.resolve();
Map<TypeDescription, byte[]> independentTypes = new LinkedHashMap<TypeDescription, byte[]>(auxiliaryTypes);
Map<TypeDescription, byte[]> dependentTypes = new LinkedHashMap<TypeDescription, byte[]>(auxiliaryTypes);
for (TypeDescription auxiliaryType : auxiliaryTypes.keySet()) {
(auxiliaryType.getDeclaredAnnotations().isAnnotationPresent(AuxiliaryType.SignatureRelevant.class)
? dependentTypes
: independentTypes).remove(auxiliaryType);
}
Map<TypeDescription, LoadedTypeInitializer> loadedTypeInitializers = dynamicType.getLoadedTypeInitializers();
if (!independentTypes.isEmpty()) {
for (Map.Entry<TypeDescription, Class<?>> entry : classInjector.inject(independentTypes).entrySet()) {
loadedTypeInitializers.get(entry.getKey()).onLoad(entry.getValue());
}
}
Map<TypeDescription, LoadedTypeInitializer> lazyInitializers = new HashMap<TypeDescription, LoadedTypeInitializer>(loadedTypeInitializers);
loadedTypeInitializers.keySet().removeAll(independentTypes.keySet());
loadedTypeInitializer = lazyInitializers.size() > 1 // there exist auxiliary types that need lazy loading
? new InjectingInitializer(instrumentedType, dependentTypes, lazyInitializers, classInjector)
: lazyInitializers.get(instrumentedType);
} else {
loadedTypeInitializer = dynamicType.getLoadedTypeInitializers().get(dynamicType.getTypeDescription());
}
if (loadedTypeInitializer.isAlive()) {
NexusAccessor.INSTANCE.register(dynamicType.getTypeDescription().getName(), classLoader, identification, loadedTypeInitializer);
}
}
@Override
public String toString() {
return "AgentBuilder.InitializationStrategy.SelfInjection.Dispatcher.Split{identification=" + identification + "}";
}
}
/**
* A dispatcher for the {@link net.bytebuddy.agent.builder.AgentBuilder.InitializationStrategy.SelfInjection#LAZY} strategy.
*/
protected static class Lazy extends Dispatcher {
/**
* Creates a new lazy dispatcher.
*
* @param identification A random identification for the applied self-initialization.
*/
protected Lazy(int identification) {
super(identification);
}
@Override
public void register(DynamicType dynamicType, ClassLoader classLoader, InjectorFactory injectorFactory) {
Map<TypeDescription, byte[]> auxiliaryTypes = dynamicType.getAuxiliaryTypes();
LoadedTypeInitializer loadedTypeInitializer = auxiliaryTypes.isEmpty()
? dynamicType.getLoadedTypeInitializers().get(dynamicType.getTypeDescription())
: new InjectingInitializer(dynamicType.getTypeDescription(), auxiliaryTypes, dynamicType.getLoadedTypeInitializers(), injectorFactory.resolve());
if (loadedTypeInitializer.isAlive()) {
NexusAccessor.INSTANCE.register(dynamicType.getTypeDescription().getName(), classLoader, identification, loadedTypeInitializer);
}
}
@Override
public String toString() {
return "AgentBuilder.InitializationStrategy.SelfInjection.Dispatcher.Lazy{identification=" + identification + "}";
}
}
/**
* A dispatcher for the {@link net.bytebuddy.agent.builder.AgentBuilder.InitializationStrategy.SelfInjection#EAGER} strategy.
*/
protected static class Eager extends Dispatcher {
/**
* Creates a new eager dispatcher.
*
* @param identification A random identification for the applied self-initialization.
*/
protected Eager(int identification) {
super(identification);
}
@Override
public void register(DynamicType dynamicType, ClassLoader classLoader, InjectorFactory injectorFactory) {
Map<TypeDescription, byte[]> auxiliaryTypes = dynamicType.getAuxiliaryTypes();
Map<TypeDescription, LoadedTypeInitializer> loadedTypeInitializers = dynamicType.getLoadedTypeInitializers();
if (!auxiliaryTypes.isEmpty()) {
for (Map.Entry<TypeDescription, Class<?>> entry : injectorFactory.resolve().inject(auxiliaryTypes).entrySet()) {
loadedTypeInitializers.get(entry.getKey()).onLoad(entry.getValue());
}
}
LoadedTypeInitializer loadedTypeInitializer = loadedTypeInitializers.get(dynamicType.getTypeDescription());
if (loadedTypeInitializer.isAlive()) {
NexusAccessor.INSTANCE.register(dynamicType.getTypeDescription().getName(), classLoader, identification, loadedTypeInitializer);
}
}
@Override
public String toString() {
return "AgentBuilder.InitializationStrategy.SelfInjection.Dispatcher.Eager{identification=" + identification + "}";
}
}
/**
* A type initializer that injects all auxiliary types of the instrumented type.
*/
protected static class InjectingInitializer implements LoadedTypeInitializer {
/**
* The instrumented type.
*/
private final TypeDescription instrumentedType;
/**
* The auxiliary types mapped to their class file representation.
*/
private final Map<TypeDescription, byte[]> rawAuxiliaryTypes;
/**
* The instrumented types and auxiliary types mapped to their loaded type initializers.
* The instrumented types and auxiliary types mapped to their loaded type initializers.
*/
private final Map<TypeDescription, LoadedTypeInitializer> loadedTypeInitializers;
/**
* The class injector to use.
*/
private final ClassInjector classInjector;
/**
* Creates a new injection initializer.
*
* @param instrumentedType The instrumented type.
* @param rawAuxiliaryTypes The auxiliary types mapped to their class file representation.
* @param loadedTypeInitializers The instrumented types and auxiliary types mapped to their loaded type initializers.
* @param classInjector The class injector to use.
*/
protected InjectingInitializer(TypeDescription instrumentedType,
Map<TypeDescription, byte[]> rawAuxiliaryTypes,
Map<TypeDescription, LoadedTypeInitializer> loadedTypeInitializers,
ClassInjector classInjector) {
this.instrumentedType = instrumentedType;
this.rawAuxiliaryTypes = rawAuxiliaryTypes;
this.loadedTypeInitializers = loadedTypeInitializers;
this.classInjector = classInjector;
}
@Override
public void onLoad(Class<?> type) {
for (Map.Entry<TypeDescription, Class<?>> auxiliary : classInjector.inject(rawAuxiliaryTypes).entrySet()) {
loadedTypeInitializers.get(auxiliary.getKey()).onLoad(auxiliary.getValue());
}
loadedTypeInitializers.get(instrumentedType).onLoad(type);
}
@Override
public boolean isAlive() {
return true;
}
@Override
public boolean equals(Object o) {
if (this == o) return true;
if (o == null || getClass() != o.getClass()) return false;
InjectingInitializer that = (InjectingInitializer) o;
return classInjector.equals(that.classInjector)
&& instrumentedType.equals(that.instrumentedType)
&& rawAuxiliaryTypes.equals(that.rawAuxiliaryTypes)
&& loadedTypeInitializers.equals(that.loadedTypeInitializers);
}
@Override
public int hashCode() {
int result = instrumentedType.hashCode();
result = 31 * result + rawAuxiliaryTypes.hashCode();
result = 31 * result + loadedTypeInitializers.hashCode();
result = 31 * result + classInjector.hashCode();
return result;
}
@Override
public String toString() {
return "AgentBuilder.InitializationStrategy.SelfInjection.Dispatcher.InjectingInitializer{" +
"instrumentedType=" + instrumentedType +
", rawAuxiliaryTypes=" + rawAuxiliaryTypes +
", loadedTypeInitializers=" + loadedTypeInitializers +
", classInjector=" + classInjector +
'}';
}
}
}
/**
* An accessor for making sure that the accessed {@link net.bytebuddy.agent.builder.Nexus} is the class that is loaded by the system class loader.
*/
protected enum NexusAccessor {
/**
* The singleton instance.
*/
INSTANCE;
/**
* The dispatcher for registering type initializers in the {@link Nexus}.
*/
private final Dispatcher dispatcher;
/**
* The {@link ClassLoader#getSystemClassLoader()} method.
*/
private final MethodDescription.InDefinedShape getSystemClassLoader;
/**
* The {@link java.lang.ClassLoader#loadClass(String)} method.
*/
private final MethodDescription.InDefinedShape loadClass;
/**
* The {@link Integer#valueOf(int)} method.
*/
private final MethodDescription.InDefinedShape valueOf;
/**
* The {@link java.lang.Class#getDeclaredMethod(String, Class[])} method.
*/
private final MethodDescription getDeclaredMethod;
/**
* The {@link java.lang.reflect.Method#invoke(Object, Object...)} method.
*/
private final MethodDescription invokeMethod;
/**
* Creates the singleton accessor.
*/
@SuppressFBWarnings(value = "REC_CATCH_EXCEPTION", justification = "Explicit delegation of the exception")
NexusAccessor() {
Dispatcher dispatcher;
try {
TypeDescription nexusType = new TypeDescription.ForLoadedType(Nexus.class);
dispatcher = new Dispatcher.Available(ClassInjector.UsingReflection.ofSystemClassLoader()
.inject(Collections.singletonMap(nexusType, ClassFileLocator.ForClassLoader.read(Nexus.class).resolve()))
.get(nexusType)
.getDeclaredMethod("register", String.class, ClassLoader.class, int.class, Object.class));
} catch (Exception exception) {
try {
dispatcher = new Dispatcher.Available(ClassLoader.getSystemClassLoader()
.loadClass(Nexus.class.getName())
.getDeclaredMethod("register", String.class, ClassLoader.class, int.class, Object.class));
} catch (Exception ignored) {
dispatcher = new Dispatcher.Unavailable(exception);
}
}
this.dispatcher = dispatcher;
getSystemClassLoader = new TypeDescription.ForLoadedType(ClassLoader.class).getDeclaredMethods()
.filter(named("getSystemClassLoader").and(takesArguments(0))).getOnly();
loadClass = new TypeDescription.ForLoadedType(ClassLoader.class).getDeclaredMethods()
.filter(named("loadClass").and(takesArguments(String.class))).getOnly();
getDeclaredMethod = new TypeDescription.ForLoadedType(Class.class).getDeclaredMethods()
.filter(named("getDeclaredMethod").and(takesArguments(String.class, Class[].class))).getOnly();
invokeMethod = new TypeDescription.ForLoadedType(Method.class).getDeclaredMethods()
.filter(named("invoke").and(takesArguments(Object.class, Object[].class))).getOnly();
valueOf = new TypeDescription.ForLoadedType(Integer.class).getDeclaredMethods()
.filter(named("valueOf").and(takesArguments(int.class))).getOnly();
}
/**
* Registers a type initializer with the class loader's nexus.
*
* @param name The name of a type for which a loaded type initializer is registered.
* @param classLoader The class loader for which a loaded type initializer is registered.
* @param identification An identification for the initializer to run.
* @param typeInitializer The loaded type initializer to be registered.
*/
public void register(String name, ClassLoader classLoader, int identification, LoadedTypeInitializer typeInitializer) {
dispatcher.register(name, classLoader, identification, typeInitializer);
}
/**
* Creates a byte code appender for injecting a self-initializing type initializer block into the generated class.
*
* @param identification The identification of the initialization.
* @return An appropriate byte code appender.
*/
public ByteCodeAppender identifiedBy(int identification) {
return new InitializationAppender(identification);
}
@Override
public String toString() {
return "AgentBuilder.InitializationStrategy.SelfInjection.NexusAccessor." + name();
}
/**
* A dispatcher for registering type initializers in the {@link Nexus}.
*/
protected interface Dispatcher {
/**
* Registers a type initializer with the class loader's nexus.
*
* @param name The name of a type for which a loaded type initializer is registered.
* @param classLoader The class loader for which a loaded type initializer is registered.
* @param identification An identification for the initializer to run.
* @param typeInitializer The loaded type initializer to be registered.
*/
void register(String name, ClassLoader classLoader, int identification, LoadedTypeInitializer typeInitializer);
/**
* An enabled dispatcher for registering a type initializer in a {@link Nexus}.
*/
class Available implements Dispatcher {
/**
* Indicates that a static method is invoked by reflection.
*/
private static final Object STATIC_METHOD = null;
/**
* The method for registering a type initializer in the system class loader's {@link Nexus}.
*/
private final Method registration;
/**
* Creates a new dispatcher.
*
* @param registration The method for registering a type initializer in the system class loader's {@link Nexus}.
*/
protected Available(Method registration) {
this.registration = registration;
}
@Override
public void register(String name, ClassLoader classLoader, int identification, LoadedTypeInitializer typeInitializer) {
try {
registration.invoke(STATIC_METHOD, name, classLoader, identification, typeInitializer);
} catch (IllegalAccessException exception) {
throw new IllegalStateException("Cannot register type initializer for " + name, exception);
} catch (InvocationTargetException exception) {
throw new IllegalStateException("Cannot register type initializer for " + name, exception.getCause());
}
}
@Override
public boolean equals(Object other) {
return this == other || !(other == null || getClass() != other.getClass())
&& registration.equals(((Available) other).registration);
}
@Override
public int hashCode() {
return registration.hashCode();
}
@Override
public String toString() {
return "AgentBuilder.InitializationStrategy.SelfInjection.NexusAccessor.Dispatcher.Available{" +
"registration=" + registration +
'}';
}
}
/**
* A disabled dispatcher where a {@link Nexus} is not available.
*/
class Unavailable implements Dispatcher {
/**
* The exception that was raised during the dispatcher initialization.
*/
private final Exception exception;
/**
* Creates a new disabled dispatcher.
*
* @param exception The exception that was raised during the dispatcher initialization.
*/
protected Unavailable(Exception exception) {
this.exception = exception;
}
@Override
public void register(String name, ClassLoader classLoader, int identification, LoadedTypeInitializer typeInitializer) {
throw new IllegalStateException("Could not locate registration method", exception);
}
@Override
public boolean equals(Object other) {
return this == other || !(other == null || getClass() != other.getClass())
&& exception.equals(((Unavailable) other).exception);
}
@Override
public int hashCode() {
return exception.hashCode();
}
@Override
public String toString() {
return "AgentBuilder.InitializationStrategy.SelfInjection.NexusAccessor.Dispatcher.Unavailable{" +
"exception=" + exception +
'}';
}
}
}
/**
* A byte code appender for invoking a Nexus for initializing the instrumented type.
*/
protected static class InitializationAppender implements ByteCodeAppender {
/**
* The identification for the self-initialization to execute.
*/
private final int identification;
/**
* Creates a new initialization appender.
*
* @param identification The identification for the self-initialization to execute.
*/
protected InitializationAppender(int identification) {
this.identification = identification;
}
@Override
public Size apply(MethodVisitor methodVisitor, Implementation.Context implementationContext, MethodDescription instrumentedMethod) {
return new ByteCodeAppender.Simple(new StackManipulation.Compound(
MethodInvocation.invoke(NexusAccessor.INSTANCE.getSystemClassLoader),
new TextConstant(Nexus.class.getName()),
MethodInvocation.invoke(NexusAccessor.INSTANCE.loadClass),
new TextConstant("initialize"),
ArrayFactory.forType(new TypeDescription.Generic.OfNonGenericType.ForLoadedType(Class.class))
.withValues(Arrays.asList(
ClassConstant.of(TypeDescription.CLASS),
ClassConstant.of(new TypeDescription.ForLoadedType(int.class)))),
MethodInvocation.invoke(NexusAccessor.INSTANCE.getDeclaredMethod),
NullConstant.INSTANCE,
ArrayFactory.forType(TypeDescription.Generic.OBJECT)
.withValues(Arrays.asList(
ClassConstant.of(instrumentedMethod.getDeclaringType().asErasure()),
new StackManipulation.Compound(
IntegerConstant.forValue(identification),
MethodInvocation.invoke(INSTANCE.valueOf)))),
MethodInvocation.invoke(NexusAccessor.INSTANCE.invokeMethod),
Removal.SINGLE
)).apply(methodVisitor, implementationContext, instrumentedMethod);
}
@Override
public boolean equals(Object other) {
if (this == other) return true;
if (other == null || getClass() != other.getClass()) return false;
InitializationAppender that = (InitializationAppender) other;
return identification == that.identification;
}
@Override
public int hashCode() {
return identification;
}
@Override
public String toString() {
return "AgentBuilder.InitializationStrategy.SelfInjection.NexusAccessor.InitializationAppender{" +
"identification=" + identification +
'}';
}
}
}
}
/**
* An initialization strategy that loads auxiliary types before loading the instrumented type. This strategy skips all types
* that are a subtype of the instrumented type which would cause a premature loading of the instrumented type and abort
* the instrumentation process.
*/
enum Minimal implements InitializationStrategy, Dispatcher {
/**
* The singleton instance.
*/
INSTANCE;
@Override
public Dispatcher dispatcher() {
return this;
}
@Override
public DynamicType.Builder<?> apply(DynamicType.Builder<?> builder) {
return builder;
}
@Override
public void register(DynamicType dynamicType, ClassLoader classLoader, InjectorFactory injectorFactory) {
Map<TypeDescription, byte[]> auxiliaryTypes = dynamicType.getAuxiliaryTypes();
Map<TypeDescription, byte[]> independentTypes = new LinkedHashMap<TypeDescription, byte[]>(auxiliaryTypes);
for (TypeDescription auxiliaryType : auxiliaryTypes.keySet()) {
if (!auxiliaryType.getDeclaredAnnotations().isAnnotationPresent(AuxiliaryType.SignatureRelevant.class)) {
independentTypes.remove(auxiliaryType);
}
}
if (!independentTypes.isEmpty()) {
ClassInjector classInjector = injectorFactory.resolve();
Map<TypeDescription, LoadedTypeInitializer> loadedTypeInitializers = dynamicType.getLoadedTypeInitializers();
for (Map.Entry<TypeDescription, Class<?>> entry : classInjector.inject(independentTypes).entrySet()) {
loadedTypeInitializers.get(entry.getKey()).onLoad(entry.getValue());
}
}
}
@Override
public String toString() {
return "AgentBuilder.InitializationStrategy.Minimal." + name();
}
}
}
enum RedefinitionStrategy {
/**
* Disables redefinition such that already loaded classes are not affected by the agent.
*/
DISABLED {
@Override
protected boolean isRetransforming(Instrumentation instrumentation) {
return false;
}
@Override
protected Collector makeCollector(Default.Transformation transformation) {
throw new IllegalStateException("A disabled redefinition strategy cannot create a collector");
}
},
/**
* <p>
* Applies a <b>redefinition</b> to all classes that are already loaded and that would have been transformed if
* the built agent was registered before they were loaded.
* </p>
* <p>
* <b>Important</b>: If a redefined class was previously instrumented, this instrumentation information is lost
* during the instrumentation. The redefinition is applied upon the original byte code that is provided by a class
* loader and not upon the code in its currently transformed format. Use
* {@link net.bytebuddy.agent.builder.AgentBuilder.RedefinitionStrategy#RETRANSFORMATION} if this is a factual or
* potential limitation.
* </p>
* <p>
* <b>Note</b>: When applying a redefinition, it is normally required to use a {@link TypeStrategy} that applies
* a redefinition instead of rebasing classes such as {@link TypeStrategy.Default#REDEFINE}. Also, consider
* the constrains given by this type strategy.
* </p>
*/
REDEFINITION {
@Override
protected boolean isRetransforming(Instrumentation instrumentation) {
if (!instrumentation.isRedefineClassesSupported()) {
throw new IllegalArgumentException("Cannot redefine classes: " + instrumentation);
}
return false;
}
@Override
protected Collector makeCollector(Default.Transformation transformation) {
return new Collector.ForRedefinition(transformation);
}
},
/**
* <p>
* Applies a <b>retransformation</b> to all classes that are already loaded and that would have been transformed if
* the built agent was registered before they were loaded.
* </p>
* <p>
* <b>Note</b>: When applying a redefinition, it is normally required to use a {@link TypeStrategy} that applies
* a redefinition instead of rebasing classes such as {@link TypeStrategy.Default#REDEFINE}. Also, consider
* the constrains given by this type strategy.
* </p>
*/
RETRANSFORMATION {
@Override
protected boolean isRetransforming(Instrumentation instrumentation) {
if (!instrumentation.isRetransformClassesSupported()) {
throw new IllegalArgumentException("Cannot retransform classes: " + instrumentation);
}
return true;
}
@Override
protected Collector makeCollector(Default.Transformation transformation) {
return new Collector.ForRetransformation(transformation);
}
};
/**
* Indicates if this strategy requires a class file transformer to be registered with a hint to apply the
* transformer for retransformation.
*
* @param instrumentation The instrumentation instance used.
* @return {@code true} if a class file transformer must be registered with a hint for retransformation.
*/
protected abstract boolean isRetransforming(Instrumentation instrumentation);
/**
* Indicates that this redefinition strategy applies a modification of already loaded classes.
*
* @return {@code true} if this redefinition strategy applies a modification of already loaded classes.
*/
protected boolean isEnabled() {
return this != DISABLED;
}
/**
* Creates a collector instance that is responsible for collecting loaded classes for potential retransformation.
*
* @param transformation The transformation that is registered for the agent.
* @return A new collector for collecting already loaded classes for transformation.
*/
protected abstract Collector makeCollector(Default.Transformation transformation);
@Override
public String toString() {
return "AgentBuilder.RedefinitionStrategy." + name();
}
/**
* A collector is responsible for collecting classes that are to be considered for modification.
*/
protected interface Collector {
/**
* Considers a loaded class for modification.
*
* @param type The type that is to be considered.
* @param ignoredTypes A matcher that indicates what types are explicitly ignored.
* @return {@code true} if the class is considered to be redefined.
*/
boolean consider(Class<?> type, ElementMatcher<? super TypeDescription> ignoredTypes);
/**
* Applies the represented type modification on all collected types.
*
* @param instrumentation The instrumentation to use.
* @param byteBuddy The Byte Buddy configuration to use.
* @param binaryLocator The binary locator to use.
* @param typeStrategy The type strategy to use.
* @param listener The listener to report to.
* @param nativeMethodStrategy The native method strategy to apply.
* @param accessControlContext The access control context to use.
* @param initializationStrategy The initialization strategy to use.
* @param bootstrapInjectionStrategy The bootstrap injection strategy to use.
* @throws UnmodifiableClassException If an unmodifiable class is attempted to be modified.
* @throws ClassNotFoundException If a class cannot be found while redefining another class.
*/
void apply(Instrumentation instrumentation,
ByteBuddy byteBuddy,
BinaryLocator binaryLocator,
TypeStrategy typeStrategy,
Listener listener,
Default.NativeMethodStrategy nativeMethodStrategy,
AccessControlContext accessControlContext,
InitializationStrategy initializationStrategy,
Default.BootstrapInjectionStrategy bootstrapInjectionStrategy) throws UnmodifiableClassException, ClassNotFoundException;
/**
* A collector that applies a <b>redefinition</b> of already loaded classes.
*/
class ForRedefinition implements Collector {
/**
* The transformation of the built agent.
*/
private final Default.Transformation transformation;
/**
* A list of already collected redefinitions.
*/
private final List<Entry> entries;
/**
* Creates a new collector for a redefinition.
*
* @param transformation The transformation of the built agent.
*/
protected ForRedefinition(Default.Transformation transformation) {
this.transformation = transformation;
entries = new ArrayList<Entry>();
}
@Override
public boolean consider(Class<?> type, ElementMatcher<? super TypeDescription> ignoredTypes) {
Default.Transformation.Resolution resolution = transformation.resolve(new TypeDescription.ForLoadedType(type),
type.getClassLoader(),
type,
type.getProtectionDomain(),
ignoredTypes);
return resolution.isResolved() && entries.add(new Entry(type, resolution));
}
@Override
public void apply(Instrumentation instrumentation,
ByteBuddy byteBuddy,
BinaryLocator binaryLocator,
TypeStrategy typeStrategy,
Listener listener,
Default.NativeMethodStrategy nativeMethodStrategy,
AccessControlContext accessControlContext,
InitializationStrategy initializationStrategy,
Default.BootstrapInjectionStrategy bootstrapInjectionStrategy) throws UnmodifiableClassException, ClassNotFoundException {
List<ClassDefinition> classDefinitions = new ArrayList<ClassDefinition>(entries.size());
for (Entry entry : entries) {
TypeDescription typeDescription = new TypeDescription.ForLoadedType(entry.getType());
try {
classDefinitions.add(entry.resolve(initializationStrategy,
binaryLocator.classFileLocator(entry.getType().getClassLoader()),
typeStrategy,
byteBuddy,
nativeMethodStrategy,
bootstrapInjectionStrategy,
accessControlContext,
listener));
} catch (Throwable throwable) {
listener.onError(typeDescription.getName(), throwable);
} finally {
listener.onComplete(typeDescription.getName());
}
}
if (!classDefinitions.isEmpty()) {
instrumentation.redefineClasses(classDefinitions.toArray(new ClassDefinition[classDefinitions.size()]));
}
}
@Override
public String toString() {
return "AgentBuilder.RedefinitionStrategy.Collector.ForRedefinition{" +
"transformation=" + transformation +
", entries=" + entries +
'}';
}
/**
* An entry describing a type redefinition.
*/
protected static class Entry {
/**
* The type to be redefined.
*/
private final Class<?> type;
/**
* The resolved transformation for this type.
*/
private final Default.Transformation.Resolution resolution;
/**
* @param type The type to be redefined.
* @param resolution The resolved transformation for this type.
*/
protected Entry(Class<?> type, Default.Transformation.Resolution resolution) {
this.type = type;
this.resolution = resolution;
}
/**
* Returns the type that is being redefined.
*
* @return The type that is being redefined.
*/
public Class<?> getType() {
return type;
}
/**
* Resolves this entry into a fully defined class redefinition.
*
* @param initializationStrategy The initialization strategy to use.
* @param classFileLocator The class file locator to use.
* @param typeStrategy The type strategy to use.
* @param byteBuddy The Byte Buddy configuration to use.
* @param nativeMethodStrategy The native method strategy to use.
* @param bootstrapInjectionStrategy The bootstrap injection strategy to use.
* @param accessControlContext The access control context to use.
* @param listener The listener to report to.
* @return An appropriate class definition.
*/
protected ClassDefinition resolve(InitializationStrategy initializationStrategy,
ClassFileLocator classFileLocator,
TypeStrategy typeStrategy,
ByteBuddy byteBuddy,
Default.NativeMethodStrategy nativeMethodStrategy,
Default.BootstrapInjectionStrategy bootstrapInjectionStrategy,
AccessControlContext accessControlContext,
Listener listener) {
return new ClassDefinition(type, resolution.apply(initializationStrategy,
classFileLocator,
typeStrategy,
byteBuddy,
nativeMethodStrategy,
bootstrapInjectionStrategy,
accessControlContext,
listener));
}
@Override
public boolean equals(Object other) {
if (this == other) return true;
if (other == null || getClass() != other.getClass()) return false;
Entry entry = (Entry) other;
return type.equals(entry.type) && resolution.equals(entry.resolution);
}
@Override
public int hashCode() {
int result = type.hashCode();
result = 31 * result + resolution.hashCode();
return result;
}
@Override
public String toString() {
return "AgentBuilder.RedefinitionStrategy.Collector.ForRedefinition.Entry{" +
"type=" + type +
", resolution=" + resolution +
'}';
}
}
}
/**
* A collector that applies a <b>retransformation</b> of already loaded classes.
*/
class ForRetransformation implements Collector {
/**
* The transformation defined by the built agent.
*/
private final Default.Transformation transformation;
/**
* The types that were collected for retransformation.
*/
private final List<Class<?>> types;
/**
* Creates a new collector for a retransformation.
*
* @param transformation The transformation defined by the built agent.
*/
protected ForRetransformation(Default.Transformation transformation) {
this.transformation = transformation;
types = new ArrayList<Class<?>>();
}
@Override
public boolean consider(Class<?> type, ElementMatcher<? super TypeDescription> ignoredTypes) {
return transformation.resolve(new TypeDescription.ForLoadedType(type),
type.getClassLoader(), type, type.getProtectionDomain(), ignoredTypes).isResolved() && types.add(type);
}
@Override
public void apply(Instrumentation instrumentation,
ByteBuddy byteBuddy,
BinaryLocator binaryLocator,
TypeStrategy typeStrategy,
Listener listener,
Default.NativeMethodStrategy nativeMethodStrategy,
AccessControlContext accessControlContext,
InitializationStrategy initializationStrategy,
Default.BootstrapInjectionStrategy bootstrapInjectionStrategy) throws UnmodifiableClassException {
if (!types.isEmpty()) {
instrumentation.retransformClasses(types.toArray(new Class<?>[types.size()]));
}
}
@Override
public String toString() {
return "AgentBuilder.RedefinitionStrategy.Collector.ForRetransformation{" +
"transformation=" + transformation +
", types=" + types +
'}';
}
}
}
}
/**
* Implements the instrumentation of the {@code LambdaMetafactory} if this feature is enabled.
*/
enum LambdaInstrumentationStrategy implements Callable<Class<?>> {
ENABLED {
@Override
protected void apply(ByteBuddy byteBuddy, Instrumentation instrumentation, ClassFileTransformer classFileTransformer) {
if (LambdaFactory.register(classFileTransformer, new LambdaInstanceFactory(byteBuddy), this)) {
Class<?> lambdaMetaFactory;
try {
lambdaMetaFactory = Class.forName("java.lang.invoke.LambdaMetafactory");
} catch (ClassNotFoundException ignored) {
return;
}
byteBuddy.with(Implementation.Context.Disabled.Factory.INSTANCE)
.redefine(lambdaMetaFactory)
.visit(new AsmVisitorWrapper.ForDeclaredMethods()
.method(named("metafactory"), MetaFactoryRedirection.INSTANCE)
.method(named("altMetafactory"), AlternativeMetaFactoryRedirection.INSTANCE))
.make()
.load(lambdaMetaFactory.getClassLoader(), ClassReloadingStrategy.of(instrumentation));
}
}
@Override
public Class<?> call() throws Exception {
TypeDescription lambdaFactory = new TypeDescription.ForLoadedType(LambdaFactory.class);
return ClassInjector.UsingReflection.ofSystemClassLoader()
.inject(Collections.singletonMap(lambdaFactory, ClassFileLocator.ForClassLoader.read(LambdaFactory.class).resolve()))
.get(lambdaFactory);
}
},
/**
* A strategy that does not instrument the {@code LambdaMetafactory}.
*/
DISABLED {
@Override
protected void apply(ByteBuddy byteBuddy, Instrumentation instrumentation, ClassFileTransformer classFileTransformer) {
/* do nothing */
}
@Override
public Class<?> call() throws Exception {
throw new IllegalStateException("Cannot inject LambdaFactory from disabled instrumentation strategy");
}
};
/**
* Indicates that an original implementation can be ignored when redefining a method.
*/
protected static final MethodVisitor IGNORE_ORIGINAL = null;
/**
* Releases the supplied class file transformer when it was built with {@link AgentBuilder#with(LambdaInstrumentationStrategy)} enabled.
* Subsequently, the class file transformer is no longer applied when a class that represents a lambda expression is created.
*
* @param classFileTransformer The class file transformer to release.
* @param instrumentation The instrumentation instance that is used to potentially rollback the instrumentation of the {@code LambdaMetafactory}.
*/
public static void release(ClassFileTransformer classFileTransformer, Instrumentation instrumentation) {
if (LambdaFactory.release(classFileTransformer)) {
try {
ClassReloadingStrategy.of(instrumentation).reset(Class.forName("java.lang.invoke.LambdaMetafactory"));
} catch (Exception exception) {
throw new IllegalStateException("Could not release lambda transformer", exception);
}
}
}
/**
* Returns an enabled lambda instrumentation strategy for {@code true}.
*
* @param enabled If lambda instrumentation should be enabled.
* @return {@code true} if the returned strategy should be enabled.
*/
public static LambdaInstrumentationStrategy of(boolean enabled) {
return enabled
? ENABLED
: DISABLED;
}
/**
* Applies a transformation to lambda instances if applicable.
*
* @param byteBuddy The Byte Buddy instance to use.
* @param instrumentation The instrumentation instance for applying a redefinition.
* @param classFileTransformer The class file transformer to apply.
*/
protected abstract void apply(ByteBuddy byteBuddy, Instrumentation instrumentation, ClassFileTransformer classFileTransformer);
/**
* Indicates if this strategy enables instrumentation of the {@code LambdaMetafactory}.
*
* @return {@code true} if this strategy is enabled.
*/
public boolean isEnabled() {
return this == ENABLED;
}
@Override
public String toString() {
return "AgentBuilder.LambdaInstrumentationStrategy." + name();
}
/**
* A factory that creates instances that represent lambda expressions.
*/
protected static class LambdaInstanceFactory {
/**
* The name of a factory for a lambda expression.
*/
private static final String LAMBDA_FACTORY = "get$Lambda";
/**
* A prefix for a field that represents a property of a lambda expression.
*/
private static final String FIELD_PREFIX = "arg$";
/**
* The infix to use for naming classes that represent lambda expression. The additional prefix
* is necessary because the subsequent counter is not sufficient to keep names unique compared
* to the original factory.
*/
private static final String LAMBDA_TYPE_INFIX = "$$Lambda$ByteBuddy$";
/**
* A type-safe constant to express that a class is not already loaded when applying a class file transformer.
*/
private static final Class<?> NOT_PREVIOUSLY_DEFINED = null;
/**
* A counter for naming lambda expressions randomly.
*/
private static final AtomicInteger LAMBDA_NAME_COUNTER = new AtomicInteger();
/**
* The Byte Buddy instance to use for creating lambda objects.
*/
private final ByteBuddy byteBuddy;
/**
* Creates a new lambda instance factory.
*
* @param byteBuddy The Byte Buddy instance to use for creating lambda objects.
*/
protected LambdaInstanceFactory(ByteBuddy byteBuddy) {
this.byteBuddy = byteBuddy;
}
/**
* Applies this lambda meta factory.
*
* @param targetTypeLookup A lookup context representing the creating class of this lambda expression.
* @param lambdaMethodName The name of the lambda expression's represented method.
* @param factoryMethodType The type of the lambda expression's represented method.
* @param lambdaMethodType The type of the lambda expression's factory method.
* @param targetMethodHandle A handle representing the target of the lambda expression's method.
* @param specializedLambdaMethodType A specialization of the type of the lambda expression's represented method.
* @param serializable {@code true} if the lambda expression should be serializable.
* @param markerInterfaces A list of interfaces for the lambda expression to represent.
* @param additionalBridges A list of additional bridge methods to be implemented by the lambda expression.
* @param classFileTransformers A collection of class file transformers to apply when creating the class.
* @return A binary representation of the transformed class file.
*/
public byte[] make(Object targetTypeLookup,
String lambdaMethodName,
Object factoryMethodType,
Object lambdaMethodType,
Object targetMethodHandle,
Object specializedLambdaMethodType,
boolean serializable,
List<Class<?>> markerInterfaces,
List<?> additionalBridges,
Collection<? extends ClassFileTransformer> classFileTransformers) {
JavaInstance.MethodType factoryMethod = JavaInstance.MethodType.ofLoaded(factoryMethodType);
JavaInstance.MethodType lambdaMethod = JavaInstance.MethodType.ofLoaded(lambdaMethodType);
JavaInstance.MethodHandle targetMethod = JavaInstance.MethodHandle.ofLoaded(targetMethodHandle, targetTypeLookup);
JavaInstance.MethodType specializedLambdaMethod = JavaInstance.MethodType.ofLoaded(specializedLambdaMethodType);
Class<?> targetType = JavaInstance.MethodHandle.lookupType(targetTypeLookup);
String lambdaClassName = targetType.getName() + LAMBDA_TYPE_INFIX + LAMBDA_NAME_COUNTER.incrementAndGet();
DynamicType.Builder<?> builder = byteBuddy
.subclass(factoryMethod.getReturnType(), ConstructorStrategy.Default.NO_CONSTRUCTORS)
.modifiers(TypeManifestation.FINAL, Visibility.PUBLIC)
.implement(markerInterfaces)
.name(lambdaClassName)
.defineConstructor(Visibility.PUBLIC)
.withParameters(factoryMethod.getParameterTypes())
.intercept(ConstructorImplementation.INSTANCE)
.method(named(lambdaMethodName)
.and(takesArguments(lambdaMethod.getParameterTypes()))
.and(returns(lambdaMethod.getReturnType())))
.intercept(new LambdaMethodImplementation(targetMethod, specializedLambdaMethod));
int index = 0;
for (TypeDescription capturedType : factoryMethod.getParameterTypes()) {
builder = builder.defineField(FIELD_PREFIX + ++index, capturedType, Visibility.PRIVATE, FieldManifestation.FINAL);
}
if (!factoryMethod.getParameterTypes().isEmpty()) {
builder = builder.defineMethod(LAMBDA_FACTORY, factoryMethod.getReturnType(), Visibility.PRIVATE, Ownership.STATIC)
.withParameters(factoryMethod.getParameterTypes())
.intercept(FactoryImplementation.INSTANCE);
}
if (serializable) {
if (!markerInterfaces.contains(Serializable.class)) {
builder = builder.implement(Serializable.class);
}
builder = builder.defineMethod("writeReplace", Object.class, Visibility.PRIVATE)
.intercept(new SerializationImplementation(new TypeDescription.ForLoadedType(targetType),
factoryMethod.getReturnType(),
lambdaMethodName,
lambdaMethod,
targetMethod,
JavaInstance.MethodType.ofLoaded(specializedLambdaMethodType)));
} else if (factoryMethod.getReturnType().isAssignableTo(Serializable.class)) {
builder = builder.defineMethod("readObject", void.class, Visibility.PRIVATE)
.withParameters(ObjectInputStream.class)
.throwing(NotSerializableException.class)
.intercept(ExceptionMethod.throwing(NotSerializableException.class, "Non-serializable lambda"))
.defineMethod("writeObject", void.class, Visibility.PRIVATE)
.withParameters(ObjectOutputStream.class)
.throwing(NotSerializableException.class)
.intercept(ExceptionMethod.throwing(NotSerializableException.class, "Non-serializable lambda"));
}
for (Object additionalBridgeType : additionalBridges) {
JavaInstance.MethodType additionalBridge = JavaInstance.MethodType.ofLoaded(additionalBridgeType);
builder = builder.defineMethod(lambdaMethodName, additionalBridge.getReturnType(), MethodManifestation.BRIDGE, Visibility.PUBLIC)
.withParameters(additionalBridge.getParameterTypes())
.intercept(new BridgeMethodImplementation(lambdaMethodName, lambdaMethod));
}
byte[] classFile = builder.make().getBytes();
for (ClassFileTransformer classFileTransformer : classFileTransformers) {
try {
byte[] transformedClassFile = classFileTransformer.transform(targetType.getClassLoader(),
lambdaClassName.replace('.', '/'),
NOT_PREVIOUSLY_DEFINED,
targetType.getProtectionDomain(),
classFile);
classFile = transformedClassFile == null
? classFile
: transformedClassFile;
} catch (Throwable ignored) {
/* do nothing */
}
}
return classFile;
}
@Override
public boolean equals(Object other) {
return this == other || !(other == null || getClass() != other.getClass())
&& byteBuddy.equals(((LambdaInstanceFactory) other).byteBuddy);
}
@Override
public int hashCode() {
return byteBuddy.hashCode();
}
@Override
public String toString() {
return "AgentBuilder.LambdaInstrumentationStrategy.LambdaInstanceFactory{" +
"byteBuddy=" + byteBuddy +
'}';
}
/**
* Implements a lambda class's constructor.
*/
protected enum ConstructorImplementation implements Implementation {
/**
* The singleton instance.
*/
INSTANCE;
/**
* A reference to the {@link Object} class's default constructor.
*/
private final MethodDescription.InDefinedShape objectConstructor;
/**
* Creates a new constructor implementation.
*/
ConstructorImplementation() {
objectConstructor = TypeDescription.OBJECT.getDeclaredMethods().filter(isConstructor()).getOnly();
}
@Override
public ByteCodeAppender appender(Target implementationTarget) {
return new Appender(implementationTarget.getInstrumentedType().getDeclaredFields());
}
@Override
public InstrumentedType prepare(InstrumentedType instrumentedType) {
return instrumentedType;
}
@Override
public String toString() {
return "AgentBuilder.LambdaInstrumentationStrategy.LambdaInstanceFactory.ConstructorImplementation." + name();
}
/**
* An appender to implement the constructor.
*/
protected static class Appender implements ByteCodeAppender {
/**
* The fields that are declared by the instrumented type.
*/
private final List<FieldDescription.InDefinedShape> declaredFields;
/**
* Creates a new appender.
*
* @param declaredFields The fields that are declared by the instrumented type.
*/
protected Appender(List<FieldDescription.InDefinedShape> declaredFields) {
this.declaredFields = declaredFields;
}
@Override
public Size apply(MethodVisitor methodVisitor, Context implementationContext, MethodDescription instrumentedMethod) {
List<StackManipulation> fieldAssignments = new ArrayList<StackManipulation>(declaredFields.size() * 3);
for (ParameterDescription parameterDescription : instrumentedMethod.getParameters()) {
fieldAssignments.add(MethodVariableAccess.REFERENCE.loadOffset(0));
fieldAssignments.add(MethodVariableAccess.of(parameterDescription.getType()).loadOffset(parameterDescription.getOffset()));
fieldAssignments.add(FieldAccess.forField(declaredFields.get(parameterDescription.getIndex())).putter());
}
return new Size(new StackManipulation.Compound(
MethodVariableAccess.REFERENCE.loadOffset(0),
MethodInvocation.invoke(INSTANCE.objectConstructor),
new StackManipulation.Compound(fieldAssignments),
MethodReturn.VOID
).apply(methodVisitor, implementationContext).getMaximalSize(), instrumentedMethod.getStackSize());
}
@Override
public boolean equals(Object other) {
return this == other || !(other == null || getClass() != other.getClass())
&& declaredFields.equals(((Appender) other).declaredFields);
}
@Override
public int hashCode() {
return declaredFields.hashCode();
}
@Override
public String toString() {
return "AgentBuilder.LambdaInstrumentationStrategy.LambdaInstanceFactory.ConstructorImplementation.Appender{" +
"declaredFields=" + declaredFields +
'}';
}
}
}
/**
* An implementation of a instance factory for a lambda expression's class.
*/
protected enum FactoryImplementation implements Implementation {
/**
* The singleton instance.
*/
INSTANCE;
@Override
public ByteCodeAppender appender(Target implementationTarget) {
return new Appender(implementationTarget.getInstrumentedType());
}
@Override
public InstrumentedType prepare(InstrumentedType instrumentedType) {
return instrumentedType;
}
@Override
public String toString() {
return "AgentBuilder.LambdaInstrumentationStrategy.LambdaInstanceFactory.FactoryImplementation." + name();
}
/**
* An appender for a lambda expression factory.
*/
protected static class Appender implements ByteCodeAppender {
/**
* The instrumented type.
*/
private final TypeDescription instrumentedType;
/**
* Creates a new appender.
*
* @param instrumentedType The instrumented type.
*/
protected Appender(TypeDescription instrumentedType) {
this.instrumentedType = instrumentedType;
}
@Override
public Size apply(MethodVisitor methodVisitor, Context implementationContext, MethodDescription instrumentedMethod) {
return new Size(new StackManipulation.Compound(
TypeCreation.of(instrumentedType),
Duplication.SINGLE,
MethodVariableAccess.allArgumentsOf(instrumentedMethod),
MethodInvocation.invoke(instrumentedType.getDeclaredMethods().filter(isConstructor()).getOnly()),
MethodReturn.REFERENCE
).apply(methodVisitor, implementationContext).getMaximalSize(), instrumentedMethod.getStackSize());
}
@Override
public boolean equals(Object other) {
return this == other || !(other == null || getClass() != other.getClass())
&& instrumentedType.equals(((Appender) other).instrumentedType);
}
@Override
public int hashCode() {
return instrumentedType.hashCode();
}
@Override
public String toString() {
return "AgentBuilder.LambdaInstrumentationStrategy.LambdaInstanceFactory.FactoryImplementation.Appender{" +
"instrumentedType=" + instrumentedType +
'}';
}
}
}
/**
* Implements a lambda expression's functional method.
*/
protected static class LambdaMethodImplementation implements Implementation {
/**
* The handle of the target method of the lambda expression.
*/
private final JavaInstance.MethodHandle targetMethod;
/**
* The specialized type of the lambda method.
*/
private final JavaInstance.MethodType specializedLambdaMethod;
/**
* Creates a implementation of a lambda expression's functional method.
*
* @param targetMethod The target method of the lambda expression.
* @param specializedLambdaMethod The specialized type of the lambda method.
*/
protected LambdaMethodImplementation(JavaInstance.MethodHandle targetMethod, JavaInstance.MethodType specializedLambdaMethod) {
this.targetMethod = targetMethod;
this.specializedLambdaMethod = specializedLambdaMethod;
}
@Override
public ByteCodeAppender appender(Target implementationTarget) {
return new Appender(targetMethod.getOwnerType()
.getDeclaredMethods()
.filter(named(targetMethod.getName())
.and(returns(targetMethod.getReturnType()))
.and(takesArguments(targetMethod.getParameterTypes())))
.getOnly(),
specializedLambdaMethod,
implementationTarget.getInstrumentedType().getDeclaredFields());
}
@Override
public InstrumentedType prepare(InstrumentedType instrumentedType) {
return instrumentedType;
}
@Override
public boolean equals(Object other) {
if (this == other) return true;
if (other == null || getClass() != other.getClass()) return false;
LambdaMethodImplementation that = (LambdaMethodImplementation) other;
return targetMethod.equals(that.targetMethod)
&& specializedLambdaMethod.equals(that.specializedLambdaMethod);
}
@Override
public int hashCode() {
int result = targetMethod.hashCode();
result = 31 * result + specializedLambdaMethod.hashCode();
return result;
}
@Override
public String toString() {
return "AgentBuilder.LambdaInstrumentationStrategy.LambdaInstanceFactory.LambdaMethodImplementation{" +
"targetMethod=" + targetMethod +
", specializedLambdaMethod=" + specializedLambdaMethod +
'}';
}
/**
* An appender for a lambda expression's functional method.
*/
protected static class Appender implements ByteCodeAppender {
/**
* The target method of the lambda expression.
*/
private final MethodDescription targetMethod;
/**
* The specialized type of the lambda method.
*/
private final JavaInstance.MethodType specializedLambdaMethod;
/**
* The instrumented type's declared fields.
*/
private final List<FieldDescription.InDefinedShape> declaredFields;
/**
* Creates an appender of a lambda expression's functional method.
*
* @param targetMethod The target method of the lambda expression.
* @param specializedLambdaMethod The specialized type of the lambda method.
* @param declaredFields The instrumented type's declared fields.
*/
protected Appender(MethodDescription targetMethod,
JavaInstance.MethodType specializedLambdaMethod,
List<FieldDescription.InDefinedShape> declaredFields) {
this.targetMethod = targetMethod;
this.specializedLambdaMethod = specializedLambdaMethod;
this.declaredFields = declaredFields;
}
@Override
public Size apply(MethodVisitor methodVisitor, Context implementationContext, MethodDescription instrumentedMethod) {
List<StackManipulation> fieldAccess = new ArrayList<StackManipulation>(declaredFields.size() * 2);
for (FieldDescription.InDefinedShape fieldDescription : declaredFields) {
fieldAccess.add(MethodVariableAccess.REFERENCE.loadOffset(0));
fieldAccess.add(FieldAccess.forField(fieldDescription).getter());
}
List<StackManipulation> parameterAccess = new ArrayList<StackManipulation>(instrumentedMethod.getParameters().size() * 2);
for (ParameterDescription parameterDescription : instrumentedMethod.getParameters()) {
parameterAccess.add(MethodVariableAccess.of(parameterDescription.getType()).loadOffset(parameterDescription.getOffset()));
parameterAccess.add(Assigner.DEFAULT.assign(parameterDescription.getType(),
specializedLambdaMethod.getParameterTypes().get(parameterDescription.getIndex()).asGenericType(),
Assigner.Typing.DYNAMIC));
}
return new Size(new StackManipulation.Compound(
new StackManipulation.Compound(fieldAccess),
new StackManipulation.Compound(parameterAccess),
MethodInvocation.invoke(targetMethod),
MethodReturn.returning(targetMethod.getReturnType().asErasure())
).apply(methodVisitor, implementationContext).getMaximalSize(), instrumentedMethod.getStackSize());
}
@Override
public boolean equals(Object other) {
if (this == other) return true;
if (other == null || getClass() != other.getClass()) return false;
Appender appender = (Appender) other;
return targetMethod.equals(appender.targetMethod)
&& declaredFields.equals(appender.declaredFields)
&& specializedLambdaMethod.equals(appender.specializedLambdaMethod);
}
@Override
public int hashCode() {
int result = targetMethod.hashCode();
result = 31 * result + declaredFields.hashCode();
result = 31 * result + specializedLambdaMethod.hashCode();
return result;
}
@Override
public String toString() {
return "AgentBuilder.LambdaInstrumentationStrategy.LambdaInstanceFactory.LambdaMethodImplementation.Appender{" +
"targetMethod=" + targetMethod +
", specializedLambdaMethod=" + specializedLambdaMethod +
", declaredFields=" + declaredFields +
'}';
}
}
}
/**
* Implements the {@code writeReplace} method for serializable lambda expressions.
*/
protected static class SerializationImplementation implements Implementation {
/**
* The lambda expression's declaring type.
*/
private final TypeDescription targetType;
/**
* The lambda expression's functional type.
*/
private final TypeDescription lambdaType;
/**
* The lambda expression's functional method name.
*/
private final String lambdaMethodName;
/**
* The method type of the lambda expression's functional method.
*/
private final JavaInstance.MethodType lambdaMethod;
/**
* A handle that references the lambda expressions invocation target.
*/
private final JavaInstance.MethodHandle targetMethod;
/**
* The specialized method type of the lambda expression's functional method.
*/
private final JavaInstance.MethodType specializedMethod;
/**
* Creates a new implementation for a serializable's lambda expression's {@code writeReplace} method.
*
* @param targetType The lambda expression's declaring type.
* @param lambdaType The lambda expression's functional type.
* @param lambdaMethodName The lambda expression's functional method name.
* @param lambdaMethod The method type of the lambda expression's functional method.
* @param targetMethod A handle that references the lambda expressions invocation target.
* @param specializedMethod The specialized method type of the lambda expression's functional method.
*/
protected SerializationImplementation(TypeDescription targetType,
TypeDescription lambdaType,
String lambdaMethodName,
JavaInstance.MethodType lambdaMethod,
JavaInstance.MethodHandle targetMethod,
JavaInstance.MethodType specializedMethod) {
this.targetType = targetType;
this.lambdaType = lambdaType;
this.lambdaMethodName = lambdaMethodName;
this.lambdaMethod = lambdaMethod;
this.targetMethod = targetMethod;
this.specializedMethod = specializedMethod;
}
@Override
public ByteCodeAppender appender(Target implementationTarget) {
TypeDescription serializedLambda;
try {
serializedLambda = new TypeDescription.ForLoadedType(Class.forName("java.lang.invoke.SerializedLambda"));
} catch (ClassNotFoundException exception) {
throw new IllegalStateException("Cannot find class for lambda serialization", exception);
}
List<StackManipulation> lambdaArguments = new ArrayList<StackManipulation>(implementationTarget.getInstrumentedType().getDeclaredFields().size());
for (FieldDescription.InDefinedShape fieldDescription : implementationTarget.getInstrumentedType().getDeclaredFields()) {
lambdaArguments.add(new StackManipulation.Compound(MethodVariableAccess.REFERENCE.loadOffset(0),
FieldAccess.forField(fieldDescription).getter(),
Assigner.DEFAULT.assign(fieldDescription.getType(), TypeDescription.Generic.OBJECT, Assigner.Typing.STATIC)));
}
return new ByteCodeAppender.Simple(new StackManipulation.Compound(
TypeCreation.of(serializedLambda),
Duplication.SINGLE,
ClassConstant.of(targetType),
new TextConstant(lambdaType.getInternalName()),
new TextConstant(lambdaMethodName),
new TextConstant(lambdaMethod.getDescriptor()),
IntegerConstant.forValue(targetMethod.getHandleType().getIdentifier()),
new TextConstant(targetMethod.getOwnerType().getInternalName()),
new TextConstant(targetMethod.getName()),
new TextConstant(targetMethod.getDescriptor()),
new TextConstant(specializedMethod.getDescriptor()),
ArrayFactory.forType(TypeDescription.Generic.OBJECT).withValues(lambdaArguments),
MethodInvocation.invoke(serializedLambda.getDeclaredMethods().filter(isConstructor()).getOnly()),
MethodReturn.REFERENCE
));
}
@Override
public InstrumentedType prepare(InstrumentedType instrumentedType) {
return instrumentedType;
}
@Override
public boolean equals(Object other) {
if (this == other) return true;
if (other == null || getClass() != other.getClass()) return false;
SerializationImplementation that = (SerializationImplementation) other;
return targetType.equals(that.targetType)
&& lambdaType.equals(that.lambdaType)
&& lambdaMethodName.equals(that.lambdaMethodName)
&& lambdaMethod.equals(that.lambdaMethod)
&& targetMethod.equals(that.targetMethod)
&& specializedMethod.equals(that.specializedMethod);
}
@Override
public int hashCode() {
int result = targetType.hashCode();
result = 31 * result + lambdaType.hashCode();
result = 31 * result + lambdaMethodName.hashCode();
result = 31 * result + lambdaMethod.hashCode();
result = 31 * result + targetMethod.hashCode();
result = 31 * result + specializedMethod.hashCode();
return result;
}
@Override
public String toString() {
return "AgentBuilder.LambdaInstrumentationStrategy.LambdaInstanceFactory.SerializationImplementation{" +
"targetType=" + targetType +
", lambdaType=" + lambdaType +
", lambdaMethodName='" + lambdaMethodName + '\'' +
", lambdaMethod=" + lambdaMethod +
", targetMethod=" + targetMethod +
", specializedMethod=" + specializedMethod +
'}';
}
}
/**
* Implements an explicit bridge method for a lambda expression.
*/
protected static class BridgeMethodImplementation implements Implementation {
/**
* The name of the lambda expression's functional method.
*/
private final String lambdaMethodName;
/**
* The actual type of the lambda expression's functional method.
*/
private final JavaInstance.MethodType lambdaMethod;
/**
* Creates a new bridge method implementation for a lambda expression.
*
* @param lambdaMethodName The name of the lambda expression's functional method.
* @param lambdaMethod The actual type of the lambda expression's functional method.
*/
protected BridgeMethodImplementation(String lambdaMethodName, JavaInstance.MethodType lambdaMethod) {
this.lambdaMethodName = lambdaMethodName;
this.lambdaMethod = lambdaMethod;
}
@Override
public ByteCodeAppender appender(Target implementationTarget) {
return new Appender(implementationTarget.invokeSuper(new MethodDescription.SignatureToken(lambdaMethodName,
lambdaMethod.getReturnType(),
lambdaMethod.getParameterTypes())));
}
@Override
public InstrumentedType prepare(InstrumentedType instrumentedType) {
return instrumentedType;
}
@Override
public boolean equals(Object other) {
if (this == other) return true;
if (other == null || getClass() != other.getClass()) return false;
BridgeMethodImplementation that = (BridgeMethodImplementation) other;
return lambdaMethodName.equals(that.lambdaMethodName) && lambdaMethod.equals(that.lambdaMethod);
}
@Override
public int hashCode() {
int result = lambdaMethodName.hashCode();
result = 31 * result + lambdaMethod.hashCode();
return result;
}
@Override
public String toString() {
return "AgentBuilder.LambdaInstrumentationStrategy.LambdaInstanceFactory.BridgeMethodImplementation{" +
"lambdaMethodName='" + lambdaMethodName + '\'' +
", lambdaMethod=" + lambdaMethod +
'}';
}
/**
* An appender for implementing a bridge method for a lambda expression.
*/
protected static class Appender implements ByteCodeAppender {
/**
* The invocation of the bridge's target method.
*/
private final SpecialMethodInvocation bridgeTargetInvocation;
/**
* Creates a new appender for invoking a lambda expression's bridge method target.
*
* @param bridgeTargetInvocation The invocation of the bridge's target method.
*/
protected Appender(SpecialMethodInvocation bridgeTargetInvocation) {
this.bridgeTargetInvocation = bridgeTargetInvocation;
}
@Override
public Size apply(MethodVisitor methodVisitor, Context implementationContext, MethodDescription instrumentedMethod) {
return new Compound(new Simple(
MethodVariableAccess.allArgumentsOf(instrumentedMethod)
.asBridgeOf(bridgeTargetInvocation.getMethodDescription())
.prependThisReference(),
bridgeTargetInvocation,
bridgeTargetInvocation.getMethodDescription().getReturnType().asErasure().isAssignableTo(instrumentedMethod.getReturnType().asErasure())
? StackManipulation.Trivial.INSTANCE
: TypeCasting.to(instrumentedMethod.getReceiverType().asErasure()),
MethodReturn.returning(instrumentedMethod.getReturnType().asErasure())
)).apply(methodVisitor, implementationContext, instrumentedMethod);
}
@Override
public boolean equals(Object other) {
return this == other || !(other == null || getClass() != other.getClass())
&& bridgeTargetInvocation.equals(((Appender) other).bridgeTargetInvocation);
}
@Override
public int hashCode() {
return bridgeTargetInvocation.hashCode();
}
@Override
public String toString() {
return "AgentBuilder.LambdaInstrumentationStrategy.LambdaInstanceFactory.BridgeMethodImplementation.Appender{" +
"bridgeTargetInvocation=" + bridgeTargetInvocation +
'}';
}
}
}
}
/**
* Implements the regular lambda meta factory. The implementation represents the following code:
* <blockquote><pre>
* public static CallSite metafactory(MethodHandles.Lookup caller,
* String invokedName,
* MethodType invokedType,
* MethodType samMethodType,
* MethodHandle implMethod,
* MethodType instantiatedMethodType) throws Exception {
* Unsafe unsafe = Unsafe.getUnsafe();
* {@code Class<?>} lambdaClass = unsafe.defineAnonymousClass(caller.lookupClass(),
* (byte[]) ClassLoader.getSystemClassLoader().loadClass("net.bytebuddy.agent.builder.LambdaFactory").getDeclaredMethod("make",
* Object.class,
* String.class,
* Object.class,
* Object.class,
* Object.class,
* Object.class,
* boolean.class,
* List.class,
* List.class).invoke(null,
* caller,
* invokedName,
* invokedType,
* samMethodType,
* implMethod,
* instantiatedMethodType,
* false,
* Collections.emptyList(),
* Collections.emptyList()),
* null);
* unsafe.ensureClassInitialized(lambdaClass);
* return invokedType.parameterCount() == 0
* ? new ConstantCallSite(MethodHandles.constant(invokedType.returnType(), lambdaClass.getDeclaredConstructors()[0].newInstance()))
* : new ConstantCallSite(MethodHandles.Lookup.IMPL_LOOKUP.findStatic(lambdaClass, "get$Lambda", invokedType));
* </pre></blockquote>
*/
protected enum MetaFactoryRedirection implements AsmVisitorWrapper.ForDeclaredMethods.MethodVisitorWrapper {
/**
* The singleton instance.
*/
INSTANCE;
@Override
public MethodVisitor wrap(TypeDescription instrumentedType, MethodDescription.InDefinedShape methodDescription, MethodVisitor methodVisitor) {
methodVisitor.visitCode();
methodVisitor.visitMethodInsn(Opcodes.INVOKESTATIC, "sun/misc/Unsafe", "getUnsafe", "()Lsun/misc/Unsafe;", false);
methodVisitor.visitVarInsn(Opcodes.ASTORE, 6);
methodVisitor.visitVarInsn(Opcodes.ALOAD, 6);
methodVisitor.visitVarInsn(Opcodes.ALOAD, 0);
methodVisitor.visitMethodInsn(Opcodes.INVOKEVIRTUAL, "java/lang/invoke/MethodHandles$Lookup", "lookupClass", "()Ljava/lang/Class;", false);
methodVisitor.visitMethodInsn(Opcodes.INVOKESTATIC, "java/lang/ClassLoader", "getSystemClassLoader", "()Ljava/lang/ClassLoader;", false);
methodVisitor.visitLdcInsn("net.bytebuddy.agent.builder.LambdaFactory");
methodVisitor.visitMethodInsn(Opcodes.INVOKEVIRTUAL, "java/lang/ClassLoader", "loadClass", "(Ljava/lang/String;)Ljava/lang/Class;", false);
methodVisitor.visitLdcInsn("make");
methodVisitor.visitIntInsn(Opcodes.BIPUSH, 9);
methodVisitor.visitTypeInsn(Opcodes.ANEWARRAY, "java/lang/Class");
methodVisitor.visitInsn(Opcodes.DUP);
methodVisitor.visitInsn(Opcodes.ICONST_0);
methodVisitor.visitLdcInsn(Type.getType("Ljava/lang/Object;"));
methodVisitor.visitInsn(Opcodes.AASTORE);
methodVisitor.visitInsn(Opcodes.DUP);
methodVisitor.visitInsn(Opcodes.ICONST_1);
methodVisitor.visitLdcInsn(Type.getType("Ljava/lang/String;"));
methodVisitor.visitInsn(Opcodes.AASTORE);
methodVisitor.visitInsn(Opcodes.DUP);
methodVisitor.visitInsn(Opcodes.ICONST_2);
methodVisitor.visitLdcInsn(Type.getType("Ljava/lang/Object;"));
methodVisitor.visitInsn(Opcodes.AASTORE);
methodVisitor.visitInsn(Opcodes.DUP);
methodVisitor.visitInsn(Opcodes.ICONST_3);
methodVisitor.visitLdcInsn(Type.getType("Ljava/lang/Object;"));
methodVisitor.visitInsn(Opcodes.AASTORE);
methodVisitor.visitInsn(Opcodes.DUP);
methodVisitor.visitInsn(Opcodes.ICONST_4);
methodVisitor.visitLdcInsn(Type.getType("Ljava/lang/Object;"));
methodVisitor.visitInsn(Opcodes.AASTORE);
methodVisitor.visitInsn(Opcodes.DUP);
methodVisitor.visitInsn(Opcodes.ICONST_5);
methodVisitor.visitLdcInsn(Type.getType("Ljava/lang/Object;"));
methodVisitor.visitInsn(Opcodes.AASTORE);
methodVisitor.visitInsn(Opcodes.DUP);
methodVisitor.visitIntInsn(Opcodes.BIPUSH, 6);
methodVisitor.visitFieldInsn(Opcodes.GETSTATIC, "java/lang/Boolean", "TYPE", "Ljava/lang/Class;");
methodVisitor.visitInsn(Opcodes.AASTORE);
methodVisitor.visitInsn(Opcodes.DUP);
methodVisitor.visitIntInsn(Opcodes.BIPUSH, 7);
methodVisitor.visitLdcInsn(Type.getType("Ljava/util/List;"));
methodVisitor.visitInsn(Opcodes.AASTORE);
methodVisitor.visitInsn(Opcodes.DUP);
methodVisitor.visitIntInsn(Opcodes.BIPUSH, 8);
methodVisitor.visitLdcInsn(Type.getType("Ljava/util/List;"));
methodVisitor.visitInsn(Opcodes.AASTORE);
methodVisitor.visitMethodInsn(Opcodes.INVOKEVIRTUAL, "java/lang/Class", "getDeclaredMethod", "(Ljava/lang/String;[Ljava/lang/Class;)Ljava/lang/reflect/Method;", false);
methodVisitor.visitInsn(Opcodes.ACONST_NULL);
methodVisitor.visitIntInsn(Opcodes.BIPUSH, 9);
methodVisitor.visitTypeInsn(Opcodes.ANEWARRAY, "java/lang/Object");
methodVisitor.visitInsn(Opcodes.DUP);
methodVisitor.visitInsn(Opcodes.ICONST_0);
methodVisitor.visitVarInsn(Opcodes.ALOAD, 0);
methodVisitor.visitInsn(Opcodes.AASTORE);
methodVisitor.visitInsn(Opcodes.DUP);
methodVisitor.visitInsn(Opcodes.ICONST_1);
methodVisitor.visitVarInsn(Opcodes.ALOAD, 1);
methodVisitor.visitInsn(Opcodes.AASTORE);
methodVisitor.visitInsn(Opcodes.DUP);
methodVisitor.visitInsn(Opcodes.ICONST_2);
methodVisitor.visitVarInsn(Opcodes.ALOAD, 2);
methodVisitor.visitInsn(Opcodes.AASTORE);
methodVisitor.visitInsn(Opcodes.DUP);
methodVisitor.visitInsn(Opcodes.ICONST_3);
methodVisitor.visitVarInsn(Opcodes.ALOAD, 3);
methodVisitor.visitInsn(Opcodes.AASTORE);
methodVisitor.visitInsn(Opcodes.DUP);
methodVisitor.visitInsn(Opcodes.ICONST_4);
methodVisitor.visitVarInsn(Opcodes.ALOAD, 4);
methodVisitor.visitInsn(Opcodes.AASTORE);
methodVisitor.visitInsn(Opcodes.DUP);
methodVisitor.visitInsn(Opcodes.ICONST_5);
methodVisitor.visitVarInsn(Opcodes.ALOAD, 5);
methodVisitor.visitInsn(Opcodes.AASTORE);
methodVisitor.visitInsn(Opcodes.DUP);
methodVisitor.visitIntInsn(Opcodes.BIPUSH, 6);
methodVisitor.visitInsn(Opcodes.ICONST_0);
methodVisitor.visitMethodInsn(Opcodes.INVOKESTATIC, "java/lang/Boolean", "valueOf", "(Z)Ljava/lang/Boolean;", false);
methodVisitor.visitInsn(Opcodes.AASTORE);
methodVisitor.visitInsn(Opcodes.DUP);
methodVisitor.visitIntInsn(Opcodes.BIPUSH, 7);
methodVisitor.visitMethodInsn(Opcodes.INVOKESTATIC, "java/util/Collections", "emptyList", "()Ljava/util/List;", false);
methodVisitor.visitInsn(Opcodes.AASTORE);
methodVisitor.visitInsn(Opcodes.DUP);
methodVisitor.visitIntInsn(Opcodes.BIPUSH, 8);
methodVisitor.visitMethodInsn(Opcodes.INVOKESTATIC, "java/util/Collections", "emptyList", "()Ljava/util/List;", false);
methodVisitor.visitInsn(Opcodes.AASTORE);
methodVisitor.visitMethodInsn(Opcodes.INVOKEVIRTUAL, "java/lang/reflect/Method", "invoke", "(Ljava/lang/Object;[Ljava/lang/Object;)Ljava/lang/Object;", false);
methodVisitor.visitTypeInsn(Opcodes.CHECKCAST, "[B");
methodVisitor.visitInsn(Opcodes.ACONST_NULL);
methodVisitor.visitMethodInsn(Opcodes.INVOKEVIRTUAL, "sun/misc/Unsafe", "defineAnonymousClass", "(Ljava/lang/Class;[B[Ljava/lang/Object;)Ljava/lang/Class;", false);
methodVisitor.visitVarInsn(Opcodes.ASTORE, 7);
methodVisitor.visitVarInsn(Opcodes.ALOAD, 6);
methodVisitor.visitVarInsn(Opcodes.ALOAD, 7);
methodVisitor.visitMethodInsn(Opcodes.INVOKEVIRTUAL, "sun/misc/Unsafe", "ensureClassInitialized", "(Ljava/lang/Class;)V", false);
methodVisitor.visitVarInsn(Opcodes.ALOAD, 2);
methodVisitor.visitMethodInsn(Opcodes.INVOKEVIRTUAL, "java/lang/invoke/MethodType", "parameterCount", "()I", false);
Label conditionalDefault = new Label();
methodVisitor.visitJumpInsn(Opcodes.IFNE, conditionalDefault);
methodVisitor.visitTypeInsn(Opcodes.NEW, "java/lang/invoke/ConstantCallSite");
methodVisitor.visitInsn(Opcodes.DUP);
methodVisitor.visitVarInsn(Opcodes.ALOAD, 2);
methodVisitor.visitMethodInsn(Opcodes.INVOKEVIRTUAL, "java/lang/invoke/MethodType", "returnType", "()Ljava/lang/Class;", false);
methodVisitor.visitVarInsn(Opcodes.ALOAD, 7);
methodVisitor.visitMethodInsn(Opcodes.INVOKEVIRTUAL, "java/lang/Class", "getDeclaredConstructors", "()[Ljava/lang/reflect/Constructor;", false);
methodVisitor.visitInsn(Opcodes.ICONST_0);
methodVisitor.visitInsn(Opcodes.AALOAD);
methodVisitor.visitInsn(Opcodes.ICONST_0);
methodVisitor.visitTypeInsn(Opcodes.ANEWARRAY, "java/lang/Object");
methodVisitor.visitMethodInsn(Opcodes.INVOKEVIRTUAL, "java/lang/reflect/Constructor", "newInstance", "([Ljava/lang/Object;)Ljava/lang/Object;", false);
methodVisitor.visitMethodInsn(Opcodes.INVOKESTATIC, "java/lang/invoke/MethodHandles", "constant", "(Ljava/lang/Class;Ljava/lang/Object;)Ljava/lang/invoke/MethodHandle;", false);
methodVisitor.visitMethodInsn(Opcodes.INVOKESPECIAL, "java/lang/invoke/ConstantCallSite", "<init>", "(Ljava/lang/invoke/MethodHandle;)V", false);
Label conditionalAlternative = new Label();
methodVisitor.visitJumpInsn(Opcodes.GOTO, conditionalAlternative);
methodVisitor.visitLabel(conditionalDefault);
methodVisitor.visitFrame(Opcodes.F_APPEND, 2, new Object[]{"sun/misc/Unsafe", "java/lang/Class"}, 0, null);
methodVisitor.visitTypeInsn(Opcodes.NEW, "java/lang/invoke/ConstantCallSite");
methodVisitor.visitInsn(Opcodes.DUP);
methodVisitor.visitFieldInsn(Opcodes.GETSTATIC, "java/lang/invoke/MethodHandles$Lookup", "IMPL_LOOKUP", "Ljava/lang/invoke/MethodHandles$Lookup;");
methodVisitor.visitVarInsn(Opcodes.ALOAD, 7);
methodVisitor.visitLdcInsn("get$Lambda");
methodVisitor.visitVarInsn(Opcodes.ALOAD, 2);
methodVisitor.visitMethodInsn(Opcodes.INVOKEVIRTUAL, "java/lang/invoke/MethodHandles$Lookup", "findStatic", "(Ljava/lang/Class;Ljava/lang/String;Ljava/lang/invoke/MethodType;)Ljava/lang/invoke/MethodHandle;", false);
methodVisitor.visitMethodInsn(Opcodes.INVOKESPECIAL, "java/lang/invoke/ConstantCallSite", "<init>", "(Ljava/lang/invoke/MethodHandle;)V", false);
methodVisitor.visitLabel(conditionalAlternative);
methodVisitor.visitFrame(Opcodes.F_SAME1, 0, null, 1, new Object[]{"java/lang/invoke/CallSite"});
methodVisitor.visitInsn(Opcodes.ARETURN);
methodVisitor.visitMaxs(8, 8);
methodVisitor.visitEnd();
return IGNORE_ORIGINAL;
}
@Override
public String toString() {
return "AgentBuilder.LambdaInstrumentationStrategy.MetaFactoryRedirection." + name();
}
}
/**
* Implements the alternative lambda meta factory. The implementation represents the following code:
* <blockquote><pre>
* public static CallSite altMetafactory(MethodHandles.Lookup caller,
* String invokedName,
* MethodType invokedType,
* Object... args) throws Exception {
* int flags = (Integer) args[3];
* int argIndex = 4;
* {@code Class<?>[]} markerInterface;
* if ((flags {@code &} FLAG_MARKERS) != 0) {
* int markerCount = (Integer) args[argIndex++];
* markerInterface = new {@code Class<?>}[markerCount];
* System.arraycopy(args, argIndex, markerInterface, 0, markerCount);
* argIndex += markerCount;
* } else {
* markerInterface = new {@code Class<?>}[0];
* }
* MethodType[] additionalBridge;
* if ((flags {@code &} FLAG_BRIDGES) != 0) {
* int bridgeCount = (Integer) args[argIndex++];
* additionalBridge = new MethodType[bridgeCount];
* System.arraycopy(args, argIndex, additionalBridge, 0, bridgeCount);
* // argIndex += bridgeCount;
* } else {
* additionalBridge = new MethodType[0];
* }
* Unsafe unsafe = Unsafe.getUnsafe();
* {@code Class<?>} lambdaClass = unsafe.defineAnonymousClass(caller.lookupClass(),
* (byte[]) ClassLoader.getSystemClassLoader().loadClass("net.bytebuddy.agent.builder.LambdaFactory").getDeclaredMethod("make",
* Object.class,
* String.class,
* Object.class,
* Object.class,
* Object.class,
* Object.class,
* boolean.class,
* List.class,
* List.class).invoke(null,
* caller,
* invokedName,
* invokedType,
* args[0],
* args[1],
* args[2],
* (flags {@code &} FLAG_SERIALIZABLE) != 0,
* Arrays.asList(markerInterface),
* Arrays.asList(additionalBridge)),
* null);
* unsafe.ensureClassInitialized(lambdaClass);
* return invokedType.parameterCount() == 0
* ? new ConstantCallSite(MethodHandles.constant(invokedType.returnType(), lambdaClass.getDeclaredConstructors()[0].newInstance()))
* : new ConstantCallSite(MethodHandles.Lookup.IMPL_LOOKUP.findStatic(lambdaClass, "get$Lambda", invokedType));
* }
* </pre></blockquote>
*/
protected enum AlternativeMetaFactoryRedirection implements AsmVisitorWrapper.ForDeclaredMethods.MethodVisitorWrapper {
/**
* The singleton instance.
*/
INSTANCE;
@Override
public MethodVisitor wrap(TypeDescription instrumentedType, MethodDescription.InDefinedShape methodDescription, MethodVisitor methodVisitor) {
methodVisitor.visitCode();
methodVisitor.visitVarInsn(Opcodes.ALOAD, 3);
methodVisitor.visitInsn(Opcodes.ICONST_3);
methodVisitor.visitInsn(Opcodes.AALOAD);
methodVisitor.visitTypeInsn(Opcodes.CHECKCAST, "java/lang/Integer");
methodVisitor.visitMethodInsn(Opcodes.INVOKEVIRTUAL, "java/lang/Integer", "intValue", "()I", false);
methodVisitor.visitVarInsn(Opcodes.ISTORE, 4);
methodVisitor.visitInsn(Opcodes.ICONST_4);
methodVisitor.visitVarInsn(Opcodes.ISTORE, 5);
methodVisitor.visitVarInsn(Opcodes.ILOAD, 4);
methodVisitor.visitInsn(Opcodes.ICONST_2);
methodVisitor.visitInsn(Opcodes.IAND);
Label markerInterfaceLoop = new Label();
methodVisitor.visitJumpInsn(Opcodes.IFEQ, markerInterfaceLoop);
methodVisitor.visitVarInsn(Opcodes.ALOAD, 3);
methodVisitor.visitVarInsn(Opcodes.ILOAD, 5);
methodVisitor.visitIincInsn(5, 1);
methodVisitor.visitInsn(Opcodes.AALOAD);
methodVisitor.visitTypeInsn(Opcodes.CHECKCAST, "java/lang/Integer");
methodVisitor.visitMethodInsn(Opcodes.INVOKEVIRTUAL, "java/lang/Integer", "intValue", "()I", false);
methodVisitor.visitVarInsn(Opcodes.ISTORE, 7);
methodVisitor.visitVarInsn(Opcodes.ILOAD, 7);
methodVisitor.visitTypeInsn(Opcodes.ANEWARRAY, "java/lang/Class");
methodVisitor.visitVarInsn(Opcodes.ASTORE, 6);
methodVisitor.visitVarInsn(Opcodes.ALOAD, 3);
methodVisitor.visitVarInsn(Opcodes.ILOAD, 5);
methodVisitor.visitVarInsn(Opcodes.ALOAD, 6);
methodVisitor.visitInsn(Opcodes.ICONST_0);
methodVisitor.visitVarInsn(Opcodes.ILOAD, 7);
methodVisitor.visitMethodInsn(Opcodes.INVOKESTATIC, "java/lang/System", "arraycopy", "(Ljava/lang/Object;ILjava/lang/Object;II)V", false);
methodVisitor.visitVarInsn(Opcodes.ILOAD, 5);
methodVisitor.visitVarInsn(Opcodes.ILOAD, 7);
methodVisitor.visitInsn(Opcodes.IADD);
methodVisitor.visitVarInsn(Opcodes.ISTORE, 5);
Label markerInterfaceExit = new Label();
methodVisitor.visitJumpInsn(Opcodes.GOTO, markerInterfaceExit);
methodVisitor.visitLabel(markerInterfaceLoop);
methodVisitor.visitFrame(Opcodes.F_APPEND, 2, new Object[]{Opcodes.INTEGER, Opcodes.INTEGER}, 0, null);
methodVisitor.visitInsn(Opcodes.ICONST_0);
methodVisitor.visitTypeInsn(Opcodes.ANEWARRAY, "java/lang/Class");
methodVisitor.visitVarInsn(Opcodes.ASTORE, 6);
methodVisitor.visitLabel(markerInterfaceExit);
methodVisitor.visitFrame(Opcodes.F_APPEND, 1, new Object[]{"[Ljava/lang/Class;"}, 0, null);
methodVisitor.visitVarInsn(Opcodes.ILOAD, 4);
methodVisitor.visitInsn(Opcodes.ICONST_4);
methodVisitor.visitInsn(Opcodes.IAND);
Label additionalBridgesLoop = new Label();
methodVisitor.visitJumpInsn(Opcodes.IFEQ, additionalBridgesLoop);
methodVisitor.visitVarInsn(Opcodes.ALOAD, 3);
methodVisitor.visitVarInsn(Opcodes.ILOAD, 5);
methodVisitor.visitIincInsn(5, 1);
methodVisitor.visitInsn(Opcodes.AALOAD);
methodVisitor.visitTypeInsn(Opcodes.CHECKCAST, "java/lang/Integer");
methodVisitor.visitMethodInsn(Opcodes.INVOKEVIRTUAL, "java/lang/Integer", "intValue", "()I", false);
methodVisitor.visitVarInsn(Opcodes.ISTORE, 8);
methodVisitor.visitVarInsn(Opcodes.ILOAD, 8);
methodVisitor.visitTypeInsn(Opcodes.ANEWARRAY, "java/lang/invoke/MethodType");
methodVisitor.visitVarInsn(Opcodes.ASTORE, 7);
methodVisitor.visitVarInsn(Opcodes.ALOAD, 3);
methodVisitor.visitVarInsn(Opcodes.ILOAD, 5);
methodVisitor.visitVarInsn(Opcodes.ALOAD, 7);
methodVisitor.visitInsn(Opcodes.ICONST_0);
methodVisitor.visitVarInsn(Opcodes.ILOAD, 8);
methodVisitor.visitMethodInsn(Opcodes.INVOKESTATIC, "java/lang/System", "arraycopy", "(Ljava/lang/Object;ILjava/lang/Object;II)V", false);
Label additionalBridgesExit = new Label();
methodVisitor.visitJumpInsn(Opcodes.GOTO, additionalBridgesExit);
methodVisitor.visitLabel(additionalBridgesLoop);
methodVisitor.visitFrame(Opcodes.F_SAME, 0, null, 0, null);
methodVisitor.visitInsn(Opcodes.ICONST_0);
methodVisitor.visitTypeInsn(Opcodes.ANEWARRAY, "java/lang/invoke/MethodType");
methodVisitor.visitVarInsn(Opcodes.ASTORE, 7);
methodVisitor.visitLabel(additionalBridgesExit);
methodVisitor.visitFrame(Opcodes.F_APPEND, 1, new Object[]{"[Ljava/lang/invoke/MethodType;"}, 0, null);
methodVisitor.visitMethodInsn(Opcodes.INVOKESTATIC, "sun/misc/Unsafe", "getUnsafe", "()Lsun/misc/Unsafe;", false);
methodVisitor.visitVarInsn(Opcodes.ASTORE, 8);
methodVisitor.visitVarInsn(Opcodes.ALOAD, 8);
methodVisitor.visitVarInsn(Opcodes.ALOAD, 0);
methodVisitor.visitMethodInsn(Opcodes.INVOKEVIRTUAL, "java/lang/invoke/MethodHandles$Lookup", "lookupClass", "()Ljava/lang/Class;", false);
methodVisitor.visitMethodInsn(Opcodes.INVOKESTATIC, "java/lang/ClassLoader", "getSystemClassLoader", "()Ljava/lang/ClassLoader;", false);
methodVisitor.visitLdcInsn("net.bytebuddy.agent.builder.LambdaFactory");
methodVisitor.visitMethodInsn(Opcodes.INVOKEVIRTUAL, "java/lang/ClassLoader", "loadClass", "(Ljava/lang/String;)Ljava/lang/Class;", false);
methodVisitor.visitLdcInsn("make");
methodVisitor.visitIntInsn(Opcodes.BIPUSH, 9);
methodVisitor.visitTypeInsn(Opcodes.ANEWARRAY, "java/lang/Class");
methodVisitor.visitInsn(Opcodes.DUP);
methodVisitor.visitInsn(Opcodes.ICONST_0);
methodVisitor.visitLdcInsn(Type.getType("Ljava/lang/Object;"));
methodVisitor.visitInsn(Opcodes.AASTORE);
methodVisitor.visitInsn(Opcodes.DUP);
methodVisitor.visitInsn(Opcodes.ICONST_1);
methodVisitor.visitLdcInsn(Type.getType("Ljava/lang/String;"));
methodVisitor.visitInsn(Opcodes.AASTORE);
methodVisitor.visitInsn(Opcodes.DUP);
methodVisitor.visitInsn(Opcodes.ICONST_2);
methodVisitor.visitLdcInsn(Type.getType("Ljava/lang/Object;"));
methodVisitor.visitInsn(Opcodes.AASTORE);
methodVisitor.visitInsn(Opcodes.DUP);
methodVisitor.visitInsn(Opcodes.ICONST_3);
methodVisitor.visitLdcInsn(Type.getType("Ljava/lang/Object;"));
methodVisitor.visitInsn(Opcodes.AASTORE);
methodVisitor.visitInsn(Opcodes.DUP);
methodVisitor.visitInsn(Opcodes.ICONST_4);
methodVisitor.visitLdcInsn(Type.getType("Ljava/lang/Object;"));
methodVisitor.visitInsn(Opcodes.AASTORE);
methodVisitor.visitInsn(Opcodes.DUP);
methodVisitor.visitInsn(Opcodes.ICONST_5);
methodVisitor.visitLdcInsn(Type.getType("Ljava/lang/Object;"));
methodVisitor.visitInsn(Opcodes.AASTORE);
methodVisitor.visitInsn(Opcodes.DUP);
methodVisitor.visitIntInsn(Opcodes.BIPUSH, 6);
methodVisitor.visitFieldInsn(Opcodes.GETSTATIC, "java/lang/Boolean", "TYPE", "Ljava/lang/Class;");
methodVisitor.visitInsn(Opcodes.AASTORE);
methodVisitor.visitInsn(Opcodes.DUP);
methodVisitor.visitIntInsn(Opcodes.BIPUSH, 7);
methodVisitor.visitLdcInsn(Type.getType("Ljava/util/List;"));
methodVisitor.visitInsn(Opcodes.AASTORE);
methodVisitor.visitInsn(Opcodes.DUP);
methodVisitor.visitIntInsn(Opcodes.BIPUSH, 8);
methodVisitor.visitLdcInsn(Type.getType("Ljava/util/List;"));
methodVisitor.visitInsn(Opcodes.AASTORE);
methodVisitor.visitMethodInsn(Opcodes.INVOKEVIRTUAL, "java/lang/Class", "getDeclaredMethod", "(Ljava/lang/String;[Ljava/lang/Class;)Ljava/lang/reflect/Method;", false);
methodVisitor.visitInsn(Opcodes.ACONST_NULL);
methodVisitor.visitIntInsn(Opcodes.BIPUSH, 9);
methodVisitor.visitTypeInsn(Opcodes.ANEWARRAY, "java/lang/Object");
methodVisitor.visitInsn(Opcodes.DUP);
methodVisitor.visitInsn(Opcodes.ICONST_0);
methodVisitor.visitVarInsn(Opcodes.ALOAD, 0);
methodVisitor.visitInsn(Opcodes.AASTORE);
methodVisitor.visitInsn(Opcodes.DUP);
methodVisitor.visitInsn(Opcodes.ICONST_1);
methodVisitor.visitVarInsn(Opcodes.ALOAD, 1);
methodVisitor.visitInsn(Opcodes.AASTORE);
methodVisitor.visitInsn(Opcodes.DUP);
methodVisitor.visitInsn(Opcodes.ICONST_2);
methodVisitor.visitVarInsn(Opcodes.ALOAD, 2);
methodVisitor.visitInsn(Opcodes.AASTORE);
methodVisitor.visitInsn(Opcodes.DUP);
methodVisitor.visitInsn(Opcodes.ICONST_3);
methodVisitor.visitVarInsn(Opcodes.ALOAD, 3);
methodVisitor.visitInsn(Opcodes.ICONST_0);
methodVisitor.visitInsn(Opcodes.AALOAD);
methodVisitor.visitInsn(Opcodes.AASTORE);
methodVisitor.visitInsn(Opcodes.DUP);
methodVisitor.visitInsn(Opcodes.ICONST_4);
methodVisitor.visitVarInsn(Opcodes.ALOAD, 3);
methodVisitor.visitInsn(Opcodes.ICONST_1);
methodVisitor.visitInsn(Opcodes.AALOAD);
methodVisitor.visitInsn(Opcodes.AASTORE);
methodVisitor.visitInsn(Opcodes.DUP);
methodVisitor.visitInsn(Opcodes.ICONST_5);
methodVisitor.visitVarInsn(Opcodes.ALOAD, 3);
methodVisitor.visitInsn(Opcodes.ICONST_2);
methodVisitor.visitInsn(Opcodes.AALOAD);
methodVisitor.visitInsn(Opcodes.AASTORE);
methodVisitor.visitInsn(Opcodes.DUP);
methodVisitor.visitIntInsn(Opcodes.BIPUSH, 6);
methodVisitor.visitVarInsn(Opcodes.ILOAD, 4);
methodVisitor.visitInsn(Opcodes.ICONST_1);
methodVisitor.visitInsn(Opcodes.IAND);
Label callSiteConditional = new Label();
methodVisitor.visitJumpInsn(Opcodes.IFEQ, callSiteConditional);
methodVisitor.visitInsn(Opcodes.ICONST_1);
Label callSiteAlternative = new Label();
methodVisitor.visitJumpInsn(Opcodes.GOTO, callSiteAlternative);
methodVisitor.visitLabel(callSiteConditional);
methodVisitor.visitFrame(Opcodes.F_FULL, 9, new Object[]{"java/lang/invoke/MethodHandles$Lookup", "java/lang/String", "java/lang/invoke/MethodType", "[Ljava/lang/Object;", Opcodes.INTEGER, Opcodes.INTEGER, "[Ljava/lang/Class;", "[Ljava/lang/invoke/MethodType;", "sun/misc/Unsafe"}, 7, new Object[]{"sun/misc/Unsafe", "java/lang/Class", "java/lang/reflect/Method", Opcodes.NULL, "[Ljava/lang/Object;", "[Ljava/lang/Object;", Opcodes.INTEGER});
methodVisitor.visitInsn(Opcodes.ICONST_0);
methodVisitor.visitLabel(callSiteAlternative);
methodVisitor.visitFrame(Opcodes.F_FULL, 9, new Object[]{"java/lang/invoke/MethodHandles$Lookup", "java/lang/String", "java/lang/invoke/MethodType", "[Ljava/lang/Object;", Opcodes.INTEGER, Opcodes.INTEGER, "[Ljava/lang/Class;", "[Ljava/lang/invoke/MethodType;", "sun/misc/Unsafe"}, 8, new Object[]{"sun/misc/Unsafe", "java/lang/Class", "java/lang/reflect/Method", Opcodes.NULL, "[Ljava/lang/Object;", "[Ljava/lang/Object;", Opcodes.INTEGER, Opcodes.INTEGER});
methodVisitor.visitMethodInsn(Opcodes.INVOKESTATIC, "java/lang/Boolean", "valueOf", "(Z)Ljava/lang/Boolean;", false);
methodVisitor.visitInsn(Opcodes.AASTORE);
methodVisitor.visitInsn(Opcodes.DUP);
methodVisitor.visitIntInsn(Opcodes.BIPUSH, 7);
methodVisitor.visitVarInsn(Opcodes.ALOAD, 6);
methodVisitor.visitMethodInsn(Opcodes.INVOKESTATIC, "java/util/Arrays", "asList", "([Ljava/lang/Object;)Ljava/util/List;", false);
methodVisitor.visitInsn(Opcodes.AASTORE);
methodVisitor.visitInsn(Opcodes.DUP);
methodVisitor.visitIntInsn(Opcodes.BIPUSH, 8);
methodVisitor.visitVarInsn(Opcodes.ALOAD, 7);
methodVisitor.visitMethodInsn(Opcodes.INVOKESTATIC, "java/util/Arrays", "asList", "([Ljava/lang/Object;)Ljava/util/List;", false);
methodVisitor.visitInsn(Opcodes.AASTORE);
methodVisitor.visitMethodInsn(Opcodes.INVOKEVIRTUAL, "java/lang/reflect/Method", "invoke", "(Ljava/lang/Object;[Ljava/lang/Object;)Ljava/lang/Object;", false);
methodVisitor.visitTypeInsn(Opcodes.CHECKCAST, "[B");
methodVisitor.visitInsn(Opcodes.ACONST_NULL);
methodVisitor.visitMethodInsn(Opcodes.INVOKEVIRTUAL, "sun/misc/Unsafe", "defineAnonymousClass", "(Ljava/lang/Class;[B[Ljava/lang/Object;)Ljava/lang/Class;", false);
methodVisitor.visitVarInsn(Opcodes.ASTORE, 9);
methodVisitor.visitVarInsn(Opcodes.ALOAD, 8);
methodVisitor.visitVarInsn(Opcodes.ALOAD, 9);
methodVisitor.visitMethodInsn(Opcodes.INVOKEVIRTUAL, "sun/misc/Unsafe", "ensureClassInitialized", "(Ljava/lang/Class;)V", false);
methodVisitor.visitVarInsn(Opcodes.ALOAD, 2);
methodVisitor.visitMethodInsn(Opcodes.INVOKEVIRTUAL, "java/lang/invoke/MethodType", "parameterCount", "()I", false);
Label callSiteJump = new Label();
methodVisitor.visitJumpInsn(Opcodes.IFNE, callSiteJump);
methodVisitor.visitTypeInsn(Opcodes.NEW, "java/lang/invoke/ConstantCallSite");
methodVisitor.visitInsn(Opcodes.DUP);
methodVisitor.visitVarInsn(Opcodes.ALOAD, 2);
methodVisitor.visitMethodInsn(Opcodes.INVOKEVIRTUAL, "java/lang/invoke/MethodType", "returnType", "()Ljava/lang/Class;", false);
methodVisitor.visitVarInsn(Opcodes.ALOAD, 9);
methodVisitor.visitMethodInsn(Opcodes.INVOKEVIRTUAL, "java/lang/Class", "getDeclaredConstructors", "()[Ljava/lang/reflect/Constructor;", false);
methodVisitor.visitInsn(Opcodes.ICONST_0);
methodVisitor.visitInsn(Opcodes.AALOAD);
methodVisitor.visitInsn(Opcodes.ICONST_0);
methodVisitor.visitTypeInsn(Opcodes.ANEWARRAY, "java/lang/Object");
methodVisitor.visitMethodInsn(Opcodes.INVOKEVIRTUAL, "java/lang/reflect/Constructor", "newInstance", "([Ljava/lang/Object;)Ljava/lang/Object;", false);
methodVisitor.visitMethodInsn(Opcodes.INVOKESTATIC, "java/lang/invoke/MethodHandles", "constant", "(Ljava/lang/Class;Ljava/lang/Object;)Ljava/lang/invoke/MethodHandle;", false);
methodVisitor.visitMethodInsn(Opcodes.INVOKESPECIAL, "java/lang/invoke/ConstantCallSite", "<init>", "(Ljava/lang/invoke/MethodHandle;)V", false);
Label callSiteExit = new Label();
methodVisitor.visitJumpInsn(Opcodes.GOTO, callSiteExit);
methodVisitor.visitLabel(callSiteJump);
methodVisitor.visitFrame(Opcodes.F_APPEND, 1, new Object[]{"java/lang/Class"}, 0, null);
methodVisitor.visitTypeInsn(Opcodes.NEW, "java/lang/invoke/ConstantCallSite");
methodVisitor.visitInsn(Opcodes.DUP);
methodVisitor.visitFieldInsn(Opcodes.GETSTATIC, "java/lang/invoke/MethodHandles$Lookup", "IMPL_LOOKUP", "Ljava/lang/invoke/MethodHandles$Lookup;");
methodVisitor.visitVarInsn(Opcodes.ALOAD, 9);
methodVisitor.visitLdcInsn("get$Lambda");
methodVisitor.visitVarInsn(Opcodes.ALOAD, 2);
methodVisitor.visitMethodInsn(Opcodes.INVOKEVIRTUAL, "java/lang/invoke/MethodHandles$Lookup", "findStatic", "(Ljava/lang/Class;Ljava/lang/String;Ljava/lang/invoke/MethodType;)Ljava/lang/invoke/MethodHandle;", false);
methodVisitor.visitMethodInsn(Opcodes.INVOKESPECIAL, "java/lang/invoke/ConstantCallSite", "<init>", "(Ljava/lang/invoke/MethodHandle;)V", false);
methodVisitor.visitLabel(callSiteExit);
methodVisitor.visitFrame(Opcodes.F_SAME1, 0, null, 1, new Object[]{"java/lang/invoke/CallSite"});
methodVisitor.visitInsn(Opcodes.ARETURN);
methodVisitor.visitMaxs(9, 10);
methodVisitor.visitEnd();
return IGNORE_ORIGINAL;
}
@Override
public String toString() {
return "AgentBuilder.LambdaInstrumentationStrategy.AlternativeMetaFactoryRedirection." + name();
}
}
}
/**
* The default implementation of an {@link net.bytebuddy.agent.builder.AgentBuilder}.
*/
class Default implements AgentBuilder {
/**
* The name of the Byte Buddy {@code net.bytebuddy.agent.Installer} class.
*/
private static final String INSTALLER_TYPE = "net.bytebuddy.agent.Installer";
/**
* The name of the {@code net.bytebuddy.agent.Installer} field containing an installed {@link Instrumentation}.
*/
private static final String INSTRUMENTATION_FIELD = "instrumentation";
/**
* Indicator for access to a static member via reflection to make the code more readable.
*/
private static final Object STATIC_FIELD = null;
/**
* The value that is to be returned from a {@link java.lang.instrument.ClassFileTransformer} to indicate
* that no class file transformation is to be applied.
*/
private static final byte[] NO_TRANSFORMATION = null;
/**
* The {@link net.bytebuddy.ByteBuddy} instance to be used.
*/
private final ByteBuddy byteBuddy;
/**
* The binary locator to use.
*/
private final BinaryLocator binaryLocator;
/**
* The definition handler to use.
*/
private final TypeStrategy typeStrategy;
/**
* The listener to notify on transformations.
*/
private final Listener listener;
/**
* The native method strategy to use.
*/
private final NativeMethodStrategy nativeMethodStrategy;
/**
* The access control context to use for loading classes.
*/
private final AccessControlContext accessControlContext;
/**
* The initialization strategy to use for creating classes.
*/
private final InitializationStrategy initializationStrategy;
/**
* The redefinition strategy to apply.
*/
private final RedefinitionStrategy redefinitionStrategy;
/**
* The injection strategy for injecting classes into the bootstrap class loader.
*/
private final BootstrapInjectionStrategy bootstrapInjectionStrategy;
/**
* A strategy to determine of the {@code LambdaMetfactory} should be instrumented to allow for the instrumentation
* of classes that represent lambda expressions.
*/
private final LambdaInstrumentationStrategy lambdaInstrumentationStrategy;
/**
* A matcher that indicates any type that should be excluded from instrumentation.
*/
private final ElementMatcher<? super TypeDescription> ignoredTypes;
/**
* The transformation object for handling type transformations.
*/
private final Transformation transformation;
/**
* Creates a new default agent builder that uses a default {@link net.bytebuddy.ByteBuddy} instance for
* creating classes.
*/
public Default() {
this(new ByteBuddy());
}
/**
* Creates a new agent builder with default settings.
*
* @param byteBuddy The Byte Buddy instance to be used.
*/
public Default(ByteBuddy byteBuddy) {
this(byteBuddy,
BinaryLocator.Default.FAST,
TypeStrategy.Default.REBASE,
Listener.NoOp.INSTANCE,
NativeMethodStrategy.Disabled.INSTANCE,
AccessController.getContext(),
InitializationStrategy.SelfInjection.SPLIT,
RedefinitionStrategy.DISABLED,
BootstrapInjectionStrategy.Disabled.INSTANCE,
LambdaInstrumentationStrategy.DISABLED,
isSynthetic(),
Transformation.Ignored.INSTANCE);
}
/**
* Creates a new default agent builder.
*
* @param byteBuddy The Byte Buddy instance to be used.
* @param binaryLocator The binary locator to use.
* @param typeStrategy The definition handler to use.
* @param listener The listener to notify on transformations.
* @param nativeMethodStrategy The native method strategy to apply.
* @param accessControlContext The access control context to use for loading classes.
* @param initializationStrategy The initialization strategy to use for transformed types.
* @param redefinitionStrategy The redefinition strategy to apply.
* @param bootstrapInjectionStrategy The injection strategy for injecting classes into the bootstrap class loader.
* @param lambdaInstrumentationStrategy A strategy to determine of the {@code LambdaMetfactory} should be instrumented to allow for the
* instrumentation of classes that represent lambda expressions.
* @param ignoredTypes A matcher that indicates any type that should be excluded from instrumentation.
* @param transformation The transformation object for handling type transformations.
*/
protected Default(ByteBuddy byteBuddy,
BinaryLocator binaryLocator,
TypeStrategy typeStrategy,
Listener listener,
NativeMethodStrategy nativeMethodStrategy,
AccessControlContext accessControlContext,
InitializationStrategy initializationStrategy,
RedefinitionStrategy redefinitionStrategy,
BootstrapInjectionStrategy bootstrapInjectionStrategy,
LambdaInstrumentationStrategy lambdaInstrumentationStrategy,
ElementMatcher<? super TypeDescription> ignoredTypes,
Transformation transformation) {
this.byteBuddy = byteBuddy;
this.binaryLocator = binaryLocator;
this.typeStrategy = typeStrategy;
this.listener = listener;
this.nativeMethodStrategy = nativeMethodStrategy;
this.accessControlContext = accessControlContext;
this.initializationStrategy = initializationStrategy;
this.redefinitionStrategy = redefinitionStrategy;
this.bootstrapInjectionStrategy = bootstrapInjectionStrategy;
this.lambdaInstrumentationStrategy = lambdaInstrumentationStrategy;
this.ignoredTypes = ignoredTypes;
this.transformation = transformation;
}
@Override
public Identified type(RawMatcher matcher) {
return new Matched(matcher, Transformer.NoOp.INSTANCE);
}
@Override
public Identified type(ElementMatcher<? super TypeDescription> typeMatcher) {
return type(typeMatcher, any());
}
@Override
public Identified type(ElementMatcher<? super TypeDescription> typeMatcher, ElementMatcher<? super ClassLoader> classLoaderMatcher) {
return type(new RawMatcher.ForElementMatcherPair(typeMatcher, classLoaderMatcher));
}
@Override
public AgentBuilder with(ByteBuddy byteBuddy) {
return new Default(byteBuddy,
binaryLocator,
typeStrategy,
listener,
nativeMethodStrategy,
accessControlContext,
initializationStrategy,
redefinitionStrategy,
bootstrapInjectionStrategy,
lambdaInstrumentationStrategy,
ignoredTypes,
transformation);
}
@Override
public AgentBuilder with(Listener listener) {
return new Default(byteBuddy,
binaryLocator,
typeStrategy,
new Listener.Compound(this.listener, listener),
nativeMethodStrategy,
accessControlContext,
initializationStrategy,
redefinitionStrategy,
bootstrapInjectionStrategy,
lambdaInstrumentationStrategy,
ignoredTypes,
transformation);
}
@Override
public AgentBuilder with(TypeStrategy typeStrategy) {
return new Default(byteBuddy,
binaryLocator,
typeStrategy,
listener,
nativeMethodStrategy,
accessControlContext,
initializationStrategy,
redefinitionStrategy,
bootstrapInjectionStrategy,
lambdaInstrumentationStrategy,
ignoredTypes,
transformation);
}
@Override
public AgentBuilder with(BinaryLocator binaryLocator) {
return new Default(byteBuddy,
binaryLocator,
typeStrategy,
listener,
nativeMethodStrategy,
accessControlContext,
initializationStrategy,
redefinitionStrategy,
bootstrapInjectionStrategy,
lambdaInstrumentationStrategy,
ignoredTypes,
transformation);
}
@Override
public AgentBuilder enableNativeMethodPrefix(String prefix) {
return new Default(byteBuddy,
binaryLocator,
typeStrategy,
listener,
NativeMethodStrategy.ForPrefix.of(prefix),
accessControlContext,
initializationStrategy,
redefinitionStrategy,
bootstrapInjectionStrategy,
lambdaInstrumentationStrategy,
ignoredTypes,
transformation);
}
@Override
public AgentBuilder disableNativeMethodPrefix() {
return new Default(byteBuddy,
binaryLocator,
typeStrategy,
listener,
NativeMethodStrategy.Disabled.INSTANCE,
accessControlContext,
initializationStrategy,
redefinitionStrategy,
bootstrapInjectionStrategy,
lambdaInstrumentationStrategy,
ignoredTypes,
transformation);
}
@Override
public AgentBuilder with(AccessControlContext accessControlContext) {
return new Default(byteBuddy,
binaryLocator,
typeStrategy,
listener,
nativeMethodStrategy,
accessControlContext,
initializationStrategy,
redefinitionStrategy,
bootstrapInjectionStrategy,
lambdaInstrumentationStrategy,
ignoredTypes,
transformation);
}
@Override
public AgentBuilder with(RedefinitionStrategy redefinitionStrategy) {
return new Default(byteBuddy,
binaryLocator,
typeStrategy,
listener,
nativeMethodStrategy,
accessControlContext,
initializationStrategy,
redefinitionStrategy,
bootstrapInjectionStrategy,
lambdaInstrumentationStrategy,
ignoredTypes,
transformation);
}
@Override
public AgentBuilder with(InitializationStrategy initializationStrategy) {
return new Default(byteBuddy,
binaryLocator,
typeStrategy,
listener,
nativeMethodStrategy,
accessControlContext,
initializationStrategy,
redefinitionStrategy,
bootstrapInjectionStrategy,
lambdaInstrumentationStrategy,
ignoredTypes,
transformation);
}
@Override
public AgentBuilder enableBootstrapInjection(File folder, Instrumentation instrumentation) {
return new Default(byteBuddy,
binaryLocator,
typeStrategy,
listener,
nativeMethodStrategy,
accessControlContext,
initializationStrategy,
redefinitionStrategy,
new BootstrapInjectionStrategy.Enabled(folder, instrumentation),
lambdaInstrumentationStrategy,
ignoredTypes,
transformation);
}
@Override
public AgentBuilder disableBootstrapInjection() {
return new Default(byteBuddy,
binaryLocator,
typeStrategy,
listener,
nativeMethodStrategy,
accessControlContext,
initializationStrategy,
redefinitionStrategy,
BootstrapInjectionStrategy.Disabled.INSTANCE,
lambdaInstrumentationStrategy,
ignoredTypes,
transformation);
}
@Override
public AgentBuilder ignore(ElementMatcher<? super TypeDescription> ignoredTypes) {
return new Default(byteBuddy,
binaryLocator,
typeStrategy,
listener,
nativeMethodStrategy,
accessControlContext,
initializationStrategy,
redefinitionStrategy,
bootstrapInjectionStrategy,
lambdaInstrumentationStrategy,
ignoredTypes,
transformation);
}
@Override
public AgentBuilder with(LambdaInstrumentationStrategy lambdaInstrumentationStrategy) {
return new Default(byteBuddy,
binaryLocator,
typeStrategy,
listener,
nativeMethodStrategy,
accessControlContext,
initializationStrategy,
redefinitionStrategy,
bootstrapInjectionStrategy,
lambdaInstrumentationStrategy,
ignoredTypes,
transformation);
}
@Override
public ClassFileTransformer makeRaw() {
return new ExecutingTransformer(byteBuddy,
binaryLocator,
typeStrategy,
listener,
nativeMethodStrategy,
accessControlContext,
initializationStrategy,
bootstrapInjectionStrategy,
ignoredTypes,
transformation);
}
@Override
public ClassFileTransformer installOn(Instrumentation instrumentation) {
ClassFileTransformer classFileTransformer = makeRaw();
instrumentation.addTransformer(classFileTransformer, redefinitionStrategy.isRetransforming(instrumentation));
if (nativeMethodStrategy.isEnabled(instrumentation)) {
instrumentation.setNativeMethodPrefix(classFileTransformer, nativeMethodStrategy.getPrefix());
}
lambdaInstrumentationStrategy.apply(byteBuddy, instrumentation, classFileTransformer);
if (redefinitionStrategy.isEnabled()) {
RedefinitionStrategy.Collector collector = redefinitionStrategy.makeCollector(transformation);
for (Class<?> type : instrumentation.getAllLoadedClasses()) {
TypeDescription typeDescription = new TypeDescription.ForLoadedType(type);
try {
if (!instrumentation.isModifiableClass(type) || !collector.consider(type, ignoredTypes)) {
try {
try {
listener.onIgnored(typeDescription);
} finally {
listener.onComplete(typeDescription.getName());
}
} catch (Throwable ignored) {
// Ignore exceptions that are thrown by listeners to mimic the behavior of a transformation.
}
}
} catch (Throwable throwable) {
try {
try {
listener.onError(typeDescription.getName(), throwable);
} finally {
listener.onComplete(typeDescription.getName());
}
} catch (Throwable ignored) {
// Ignore exceptions that are thrown by listeners to mimic the behavior of a transformation.
}
}
}
try {
collector.apply(instrumentation,
byteBuddy,
binaryLocator,
typeStrategy,
listener,
nativeMethodStrategy,
accessControlContext,
initializationStrategy,
bootstrapInjectionStrategy);
} catch (UnmodifiableClassException exception) {
throw new IllegalStateException("Cannot modify at least one class: " + collector, exception);
} catch (ClassNotFoundException exception) {
throw new IllegalStateException("Cannot find at least one class class: " + collector, exception);
}
}
return classFileTransformer;
}
@Override
public ClassFileTransformer installOnByteBuddyAgent() {
try {
Instrumentation instrumentation = (Instrumentation) ClassLoader.getSystemClassLoader()
.loadClass(INSTALLER_TYPE)
.getDeclaredField(INSTRUMENTATION_FIELD)
.get(STATIC_FIELD);
if (instrumentation == null) {
throw new IllegalStateException("The Byte Buddy agent is not installed");
}
return installOn(instrumentation);
} catch (RuntimeException exception) {
throw exception;
} catch (Exception exception) {
throw new IllegalStateException("The Byte Buddy agent is not installed or not accessible", exception);
}
}
@Override
public boolean equals(Object other) {
if (this == other) return true;
if (other == null || getClass() != other.getClass()) return false;
Default aDefault = (Default) other;
return binaryLocator.equals(aDefault.binaryLocator)
&& byteBuddy.equals(aDefault.byteBuddy)
&& listener.equals(aDefault.listener)
&& nativeMethodStrategy.equals(aDefault.nativeMethodStrategy)
&& typeStrategy.equals(aDefault.typeStrategy)
&& accessControlContext.equals(aDefault.accessControlContext)
&& initializationStrategy == aDefault.initializationStrategy
&& redefinitionStrategy == aDefault.redefinitionStrategy
&& bootstrapInjectionStrategy.equals(aDefault.bootstrapInjectionStrategy)
&& lambdaInstrumentationStrategy.equals(aDefault.lambdaInstrumentationStrategy)
&& ignoredTypes.equals(aDefault.ignoredTypes)
&& transformation.equals(aDefault.transformation);
}
@Override
public int hashCode() {
int result = byteBuddy.hashCode();
result = 31 * result + binaryLocator.hashCode();
result = 31 * result + listener.hashCode();
result = 31 * result + typeStrategy.hashCode();
result = 31 * result + nativeMethodStrategy.hashCode();
result = 31 * result + accessControlContext.hashCode();
result = 31 * result + initializationStrategy.hashCode();
result = 31 * result + redefinitionStrategy.hashCode();
result = 31 * result + bootstrapInjectionStrategy.hashCode();
result = 31 * result + lambdaInstrumentationStrategy.hashCode();
result = 31 * result + ignoredTypes.hashCode();
result = 31 * result + transformation.hashCode();
return result;
}
@Override
public String toString() {
return "AgentBuilder.Default{" +
"byteBuddy=" + byteBuddy +
", binaryLocator=" + binaryLocator +
", typeStrategy=" + typeStrategy +
", listener=" + listener +
", nativeMethodStrategy=" + nativeMethodStrategy +
", accessControlContext=" + accessControlContext +
", initializationStrategy=" + initializationStrategy +
", redefinitionStrategy=" + redefinitionStrategy +
", bootstrapInjectionStrategy=" + bootstrapInjectionStrategy +
", lambdaInstrumentationStrategy=" + lambdaInstrumentationStrategy +
", ignoredTypes=" + ignoredTypes +
", transformation=" + transformation +
'}';
}
/**
* An injection strategy for injecting classes into the bootstrap class loader.
*/
protected interface BootstrapInjectionStrategy {
/**
* Creates an injector for the bootstrap class loader.
*
* @param protectionDomain The protection domain to be used.
* @return A class injector for the bootstrap class loader.
*/
ClassInjector make(ProtectionDomain protectionDomain);
/**
* A disabled bootstrap injection strategy.
*/
enum Disabled implements BootstrapInjectionStrategy {
/**
* The singleton instance.
*/
INSTANCE;
@Override
public ClassInjector make(ProtectionDomain protectionDomain) {
throw new IllegalStateException("Injecting classes into the bootstrap class loader was not enabled");
}
@Override
public String toString() {
return "AgentBuilder.Default.BootstrapInjectionStrategy.Disabled." + name();
}
}
/**
* An enabled bootstrap injection strategy.
*/
class Enabled implements BootstrapInjectionStrategy {
/**
* The folder in which jar files are to be saved.
*/
private final File folder;
/**
* The instrumentation to use for appending jar files.
*/
private final Instrumentation instrumentation;
/**
* Creates a new enabled bootstrap class loader injection strategy.
*
* @param folder The folder in which jar files are to be saved.
* @param instrumentation The instrumentation to use for appending jar files.
*/
public Enabled(File folder, Instrumentation instrumentation) {
this.folder = folder;
this.instrumentation = instrumentation;
}
@Override
public ClassInjector make(ProtectionDomain protectionDomain) {
return ClassInjector.UsingInstrumentation.of(folder, ClassInjector.UsingInstrumentation.Target.BOOTSTRAP, instrumentation);
}
@Override
public boolean equals(Object other) {
if (this == other) return true;
if (other == null || getClass() != other.getClass()) return false;
Enabled enabled = (Enabled) other;
return folder.equals(enabled.folder) && instrumentation.equals(enabled.instrumentation);
}
@Override
public int hashCode() {
int result = folder.hashCode();
result = 31 * result + instrumentation.hashCode();
return result;
}
@Override
public String toString() {
return "AgentBuilder.Default.BootstrapInjectionStrategy.Enabled{" +
"folder=" + folder +
", instrumentation=" + instrumentation +
'}';
}
}
}
/**
* A strategy for determining if a native method name prefix should be used when rebasing methods.
*/
protected interface NativeMethodStrategy {
/**
* Determines if this strategy enables name prefixing for native methods.
*
* @param instrumentation The instrumentation used.
* @return {@code true} if this strategy indicates that a native method prefix should be used.
*/
boolean isEnabled(Instrumentation instrumentation);
/**
* Resolves the method name transformer for this strategy.
*
* @return A method name transformer for this strategy.
*/
MethodNameTransformer resolve();
/**
* Returns the method prefix if the strategy is enabled. This method must only be called if this strategy enables prefixing.
*
* @return The method prefix.
*/
String getPrefix();
/**
* A native method strategy that suffixes method names with a random suffix and disables native method rebasement.
*/
enum Disabled implements NativeMethodStrategy {
/**
* The singleton instance.
*/
INSTANCE;
@Override
public MethodNameTransformer resolve() {
return MethodNameTransformer.Suffixing.withRandomSuffix();
}
@Override
public boolean isEnabled(Instrumentation instrumentation) {
return false;
}
@Override
public String getPrefix() {
throw new IllegalStateException("A disabled native method strategy does not define a method name prefix");
}
@Override
public String toString() {
return "AgentBuilder.Default.NativeMethodStrategy.Disabled." + name();
}
}
/**
* A native method strategy that prefixes method names with a fixed value for supporting rebasing of native methods.
*/
class ForPrefix implements NativeMethodStrategy {
/**
* The method name prefix.
*/
private final String prefix;
/**
* Creates a new name prefixing native method strategy.
*
* @param prefix The method name prefix.
*/
protected ForPrefix(String prefix) {
this.prefix = prefix;
}
/**
* Creates a new native method strategy for prefixing method names.
*
* @param prefix The method name prefix.
* @return An appropriate native method strategy.
*/
protected static NativeMethodStrategy of(String prefix) {
if (prefix.length() == 0) {
throw new IllegalArgumentException("A method name prefix must not be the empty string");
}
return new ForPrefix(prefix);
}
@Override
public MethodNameTransformer resolve() {
return new MethodNameTransformer.Prefixing(prefix);
}
@Override
public boolean isEnabled(Instrumentation instrumentation) {
if (!instrumentation.isNativeMethodPrefixSupported()) {
throw new IllegalArgumentException("A prefix for native methods is not supported: " + instrumentation);
}
return true;
}
@Override
public String getPrefix() {
return prefix;
}
@Override
public boolean equals(Object other) {
return this == other || !(other == null || getClass() != other.getClass()) && prefix.equals(((ForPrefix) other).prefix);
}
@Override
public int hashCode() {
return prefix.hashCode();
}
@Override
public String toString() {
return "AgentBuilder.Default.NativeMethodStrategy.ForPrefix{" +
"prefix='" + prefix + '\'' +
'}';
}
}
}
/**
* A transformation serves as a handler for modifying a class.
*/
protected interface Transformation {
/**
* Resolves an attempted transformation to a specific transformation.
*
* @param typeDescription A description of the type that is to be transformed.
* @param classLoader The class loader of the type being transformed.
* @param classBeingRedefined In case of a type redefinition, the loaded type being transformed or {@code null} if that is not the case.
* @param protectionDomain The protection domain of the type being transformed.
* @param ignoredTypes A matcher for types that are explicitly ignored.
* @return A resolution for the given type.
*/
Resolution resolve(TypeDescription typeDescription,
ClassLoader classLoader,
Class<?> classBeingRedefined,
ProtectionDomain protectionDomain,
ElementMatcher<? super TypeDescription> ignoredTypes);
/**
* A resolution to a transformation.
*/
interface Resolution {
/**
* Returns {@code true} if this resolution represents an actual type transformation. If this value is {@code false},
* this resolution will not attempt to transform a class.
*
* @return {@code true} if this resolution attempts to transform a type, {@code false} otherwise.
*/
boolean isResolved();
/**
* Transforms a type or returns {@code null} if a type is not to be transformed.
*
* @param initializationStrategy The initialization strategy to use.
* @param classFileLocator The class file locator to use.
* @param typeStrategy The definition handler to use.
* @param byteBuddy The Byte Buddy instance to use.
* @param methodNameTransformer The method name transformer to be used.
* @param bootstrapInjectionStrategy The bootstrap injection strategy to be used.
* @param accessControlContext The access control context to be used.
* @param listener The listener to be invoked to inform about an applied or non-applied transformation.
* @return The class file of the transformed class or {@code null} if no transformation is attempted.
*/
byte[] apply(InitializationStrategy initializationStrategy,
ClassFileLocator classFileLocator,
TypeStrategy typeStrategy,
ByteBuddy byteBuddy,
NativeMethodStrategy methodNameTransformer,
BootstrapInjectionStrategy bootstrapInjectionStrategy,
AccessControlContext accessControlContext,
Listener listener);
/**
* A canonical implementation of a non-resolved resolution.
*/
class Unresolved implements Resolution {
/**
* The type that is not transformed.
*/
private final TypeDescription typeDescription;
/**
* Creates a new unresolved resolution.
*
* @param typeDescription The type that is not transformed.
*/
protected Unresolved(TypeDescription typeDescription) {
this.typeDescription = typeDescription;
}
@Override
public boolean isResolved() {
return false;
}
@Override
public byte[] apply(InitializationStrategy initializationStrategy,
ClassFileLocator classFileLocator,
TypeStrategy typeStrategy,
ByteBuddy byteBuddy,
NativeMethodStrategy methodNameTransformer,
BootstrapInjectionStrategy bootstrapInjectionStrategy,
AccessControlContext accessControlContext,
Listener listener) {
listener.onIgnored(typeDescription);
return NO_TRANSFORMATION;
}
@Override
public boolean equals(Object other) {
return this == other || !(other == null || getClass() != other.getClass())
&& typeDescription.equals(((Unresolved) other).typeDescription);
}
@Override
public int hashCode() {
return typeDescription.hashCode();
}
@Override
public String toString() {
return "AgentBuilder.Default.Transformation.Resolution.Unresolved{" +
"typeDescription=" + typeDescription +
'}';
}
}
}
/**
* A transformation that does not attempt to transform any type.
*/
enum Ignored implements Transformation {
/**
* The singleton instance.
*/
INSTANCE;
@Override
public Resolution resolve(TypeDescription typeDescription,
ClassLoader classLoader,
Class<?> classBeingRedefined,
ProtectionDomain protectionDomain, ElementMatcher<? super TypeDescription> ignoredTypes) {
return new Resolution.Unresolved(typeDescription);
}
@Override
public String toString() {
return "AgentBuilder.Default.Transformation.Ignored." + name();
}
}
/**
* A simple, active transformation.
*/
class Simple implements Transformation {
/**
* The raw matcher that is represented by this transformation.
*/
private final RawMatcher rawMatcher;
/**
* The transformer that is represented by this transformation.
*/
private final Transformer transformer;
/**
* Creates a new transformation.
*
* @param rawMatcher The raw matcher that is represented by this transformation.
* @param transformer The transformer that is represented by this transformation.
*/
protected Simple(RawMatcher rawMatcher, Transformer transformer) {
this.rawMatcher = rawMatcher;
this.transformer = transformer;
}
@Override
public Transformation.Resolution resolve(TypeDescription typeDescription,
ClassLoader classLoader,
Class<?> classBeingRedefined,
ProtectionDomain protectionDomain,
ElementMatcher<? super TypeDescription> ignoredTypes) {
return !ignoredTypes.matches(typeDescription) && rawMatcher.matches(typeDescription, classLoader, classBeingRedefined, protectionDomain)
? new Resolution(typeDescription, classLoader, protectionDomain, transformer)
: new Transformation.Resolution.Unresolved(typeDescription);
}
@Override
public boolean equals(Object other) {
return this == other || !(other == null || getClass() != other.getClass())
&& rawMatcher.equals(((Simple) other).rawMatcher)
&& transformer.equals(((Simple) other).transformer);
}
@Override
public int hashCode() {
int result = rawMatcher.hashCode();
result = 31 * result + transformer.hashCode();
return result;
}
@Override
public String toString() {
return "AgentBuilder.Default.Transformation.Simple{" +
"rawMatcher=" + rawMatcher +
", transformer=" + transformer +
'}';
}
/**
* A resolution that performs a type transformation.
*/
protected static class Resolution implements Transformation.Resolution {
/**
* A description of the transformed type.
*/
private final TypeDescription typeDescription;
/**
* The class loader of the transformed type.
*/
private final ClassLoader classLoader;
/**
* The protection domain of the transformed type.
*/
private final ProtectionDomain protectionDomain;
/**
* The transformer to be applied.
*/
private final Transformer transformer;
/**
* Creates a new active transformation.
*
* @param typeDescription A description of the transformed type.
* @param classLoader The class loader of the transformed type.
* @param protectionDomain The protection domain of the transformed type.
* @param transformer The transformer to be applied.
*/
protected Resolution(TypeDescription typeDescription,
ClassLoader classLoader,
ProtectionDomain protectionDomain,
Transformer transformer) {
this.typeDescription = typeDescription;
this.classLoader = classLoader;
this.protectionDomain = protectionDomain;
this.transformer = transformer;
}
@Override
public boolean isResolved() {
return true;
}
@Override
public byte[] apply(InitializationStrategy initializationStrategy,
ClassFileLocator classFileLocator,
TypeStrategy typeStrategy,
ByteBuddy byteBuddy,
NativeMethodStrategy methodNameTransformer,
BootstrapInjectionStrategy bootstrapInjectionStrategy,
AccessControlContext accessControlContext,
Listener listener) {
InitializationStrategy.Dispatcher dispatcher = initializationStrategy.dispatcher();
DynamicType.Unloaded<?> dynamicType = dispatcher.apply(transformer.transform(typeStrategy.builder(typeDescription,
byteBuddy,
classFileLocator,
methodNameTransformer.resolve()), typeDescription)).make();
dispatcher.register(dynamicType, classLoader, new BootstrapClassLoaderCapableInjectorFactory(bootstrapInjectionStrategy,
classLoader,
protectionDomain,
accessControlContext));
listener.onTransformation(typeDescription, dynamicType);
return dynamicType.getBytes();
}
@Override
public boolean equals(Object other) {
if (this == other) return true;
if (other == null || getClass() != other.getClass()) return false;
Resolution that = (Resolution) other;
return typeDescription.equals(that.typeDescription)
&& !(classLoader != null ? !classLoader.equals(that.classLoader) : that.classLoader != null)
&& !(protectionDomain != null ? !protectionDomain.equals(that.protectionDomain) : that.protectionDomain != null)
&& transformer.equals(that.transformer);
}
@Override
public int hashCode() {
int result = typeDescription.hashCode();
result = 31 * result + (classLoader != null ? classLoader.hashCode() : 0);
result = 31 * result + (protectionDomain != null ? protectionDomain.hashCode() : 0);
result = 31 * result + transformer.hashCode();
return result;
}
@Override
public String toString() {
return "AgentBuilder.Default.Transformation.Simple.Resolution{" +
"typeDescription=" + typeDescription +
", classLoader=" + classLoader +
", protectionDomain=" + protectionDomain +
", transformer=" + transformer +
'}';
}
/**
* An injector factory that resolves to a bootstrap class loader injection if this is necessary and enabled.
*/
protected static class BootstrapClassLoaderCapableInjectorFactory implements InitializationStrategy.Dispatcher.InjectorFactory {
/**
* The bootstrap injection strategy being used.
*/
private final BootstrapInjectionStrategy bootstrapInjectionStrategy;
/**
* The class loader for which to create an injection factory.
*/
private final ClassLoader classLoader;
/**
* The protection domain of the created classes.
*/
private final ProtectionDomain protectionDomain;
/**
* The access control context to be used.
*/
private final AccessControlContext accessControlContext;
/**
* Creates a new bootstrap class loader capable injector factory.
*
* @param bootstrapInjectionStrategy The bootstrap injection strategy being used.
* @param classLoader The class loader for which to create an injection factory.
* @param protectionDomain The protection domain of the created classes.
* @param accessControlContext The access control context to be used.
*/
protected BootstrapClassLoaderCapableInjectorFactory(BootstrapInjectionStrategy bootstrapInjectionStrategy,
ClassLoader classLoader,
ProtectionDomain protectionDomain,
AccessControlContext accessControlContext) {
this.bootstrapInjectionStrategy = bootstrapInjectionStrategy;
this.classLoader = classLoader;
this.protectionDomain = protectionDomain;
this.accessControlContext = accessControlContext;
}
@Override
public ClassInjector resolve() {
return classLoader == null
? bootstrapInjectionStrategy.make(protectionDomain)
: new ClassInjector.UsingReflection(classLoader, protectionDomain, accessControlContext);
}
@Override
public boolean equals(Object other) {
if (this == other) return true;
if (other == null || getClass() != other.getClass()) return false;
BootstrapClassLoaderCapableInjectorFactory that = (BootstrapClassLoaderCapableInjectorFactory) other;
return bootstrapInjectionStrategy.equals(that.bootstrapInjectionStrategy)
&& !(classLoader != null ? !classLoader.equals(that.classLoader) : that.classLoader != null)
&& !(protectionDomain != null ? !protectionDomain.equals(that.protectionDomain) : that.protectionDomain != null)
&& accessControlContext.equals(that.accessControlContext);
}
@Override
public int hashCode() {
int result = bootstrapInjectionStrategy.hashCode();
result = 31 * result + (protectionDomain != null ? protectionDomain.hashCode() : 0);
result = 31 * result + (classLoader != null ? classLoader.hashCode() : 0);
result = 31 * result + accessControlContext.hashCode();
return result;
}
@Override
public String toString() {
return "AgentBuilder.Default.Transformation.Simple.Resolution.BootstrapClassLoaderCapableInjectorFactory{" +
"bootstrapInjectionStrategy=" + bootstrapInjectionStrategy +
", classLoader=" + classLoader +
", protectionDomain=" + protectionDomain +
", accessControlContext=" + accessControlContext +
'}';
}
}
}
}
/**
* A compound transformation that applied several transformation in the given order and applies the first active transformation.
*/
class Compound implements Transformation {
/**
* The list of transformations to apply in their application order.
*/
private final List<? extends Transformation> transformations;
/**
* Creates a new compound transformation.
*
* @param transformation An array of transformations to apply in their application order.
*/
protected Compound(Transformation... transformation) {
this(Arrays.asList(transformation));
}
/**
* Creates a new compound transformation.
*
* @param transformations A list of transformations to apply in their application order.
*/
protected Compound(List<? extends Transformation> transformations) {
this.transformations = transformations;
}
@Override
public Resolution resolve(TypeDescription typeDescription,
ClassLoader classLoader,
Class<?> classBeingRedefined,
ProtectionDomain protectionDomain,
ElementMatcher<? super TypeDescription> ignoredTypes) {
for (Transformation transformation : transformations) {
Resolution resolution = transformation.resolve(typeDescription, classLoader, classBeingRedefined, protectionDomain, ignoredTypes);
if (resolution.isResolved()) {
return resolution;
}
}
return new Resolution.Unresolved(typeDescription);
}
@Override
public boolean equals(Object other) {
return this == other || !(other == null || getClass() != other.getClass())
&& transformations.equals(((Compound) other).transformations);
}
@Override
public int hashCode() {
return transformations.hashCode();
}
@Override
public String toString() {
return "AgentBuilder.Default.Transformation.Compound{" +
"transformations=" + transformations +
'}';
}
}
}
/**
* A {@link java.lang.instrument.ClassFileTransformer} that implements the enclosing agent builder's
* configuration.
*/
protected static class ExecutingTransformer implements ClassFileTransformer {
/**
* The Byte Buddy instance to be used.
*/
private final ByteBuddy byteBuddy;
/**
* The binary locator to use.
*/
private final BinaryLocator binaryLocator;
/**
* The definition handler to use.
*/
private final TypeStrategy typeStrategy;
/**
* The listener to notify on transformations.
*/
private final Listener listener;
/**
* The native method strategy to apply.
*/
private final NativeMethodStrategy nativeMethodStrategy;
/**
* The access control context to use for loading classes.
*/
private final AccessControlContext accessControlContext;
/**
* The initialization strategy to use for transformed types.
*/
private final InitializationStrategy initializationStrategy;
/**
* The injection strategy for injecting classes into the bootstrap class loader.
*/
private final BootstrapInjectionStrategy bootstrapInjectionStrategy;
/**
* A matcher that indicates any type that should be excluded from instrumentation.
*/
private final ElementMatcher<? super TypeDescription> ignoredTypes;
/**
* The transformation object for handling type transformations.
*/
private final Transformation transformation;
/**
* Creates a new class file transformer.
*
* @param byteBuddy The Byte Buddy instance to be used.
* @param binaryLocator The binary locator to use.
* @param typeStrategy The definition handler to use.
* @param listener The listener to notify on transformations.
* @param nativeMethodStrategy The native method strategy to apply.
* @param accessControlContext The access control context to use for loading classes.
* @param initializationStrategy The initialization strategy to use for transformed types.
* @param bootstrapInjectionStrategy The injection strategy for injecting classes into the bootstrap class loader.
* @param ignoredTypes A matcher that indicates any type that should be excluded from instrumentation.
* @param transformation The transformation object for handling type transformations.
*/
public ExecutingTransformer(ByteBuddy byteBuddy,
BinaryLocator binaryLocator,
TypeStrategy typeStrategy,
Listener listener,
NativeMethodStrategy nativeMethodStrategy,
AccessControlContext accessControlContext,
InitializationStrategy initializationStrategy,
BootstrapInjectionStrategy bootstrapInjectionStrategy,
ElementMatcher<? super TypeDescription> ignoredTypes,
Transformation transformation) {
this.byteBuddy = byteBuddy;
this.binaryLocator = binaryLocator;
this.typeStrategy = typeStrategy;
this.listener = listener;
this.nativeMethodStrategy = nativeMethodStrategy;
this.accessControlContext = accessControlContext;
this.initializationStrategy = initializationStrategy;
this.bootstrapInjectionStrategy = bootstrapInjectionStrategy;
this.ignoredTypes = ignoredTypes;
this.transformation = transformation;
}
@Override
public byte[] transform(ClassLoader classLoader,
String internalTypeName,
Class<?> classBeingRedefined,
ProtectionDomain protectionDomain,
byte[] binaryRepresentation) {
if (internalTypeName == null) {
return NO_TRANSFORMATION;
}
String binaryTypeName = internalTypeName.replace('/', '.');
try {
ClassFileLocator classFileLocator = ClassFileLocator.Simple.of(binaryTypeName,
binaryRepresentation,
binaryLocator.classFileLocator(classLoader));
return transformation.resolve(classBeingRedefined == null
? binaryLocator.typePool(classFileLocator, classLoader).describe(binaryTypeName).resolve()
: new TypeDescription.ForLoadedType(classBeingRedefined),
classLoader,
classBeingRedefined,
protectionDomain,
ignoredTypes).apply(initializationStrategy,
classFileLocator,
typeStrategy,
byteBuddy,
nativeMethodStrategy,
bootstrapInjectionStrategy,
accessControlContext,
listener);
} catch (Throwable throwable) {
listener.onError(binaryTypeName, throwable);
return NO_TRANSFORMATION;
} finally {
listener.onComplete(binaryTypeName);
}
}
@Override
public boolean equals(Object other) {
if (this == other) return true;
if (other == null || getClass() != other.getClass()) return false;
ExecutingTransformer that = (ExecutingTransformer) other;
return byteBuddy.equals(that.byteBuddy)
&& binaryLocator.equals(that.binaryLocator)
&& typeStrategy.equals(that.typeStrategy)
&& initializationStrategy.equals(that.initializationStrategy)
&& listener.equals(that.listener)
&& nativeMethodStrategy.equals(that.nativeMethodStrategy)
&& bootstrapInjectionStrategy.equals(that.bootstrapInjectionStrategy)
&& accessControlContext.equals(that.accessControlContext)
&& ignoredTypes.equals(that.ignoredTypes)
&& transformation.equals(that.transformation);
}
@Override
public int hashCode() {
int result = byteBuddy.hashCode();
result = 31 * result + binaryLocator.hashCode();
result = 31 * result + typeStrategy.hashCode();
result = 31 * result + initializationStrategy.hashCode();
result = 31 * result + listener.hashCode();
result = 31 * result + nativeMethodStrategy.hashCode();
result = 31 * result + bootstrapInjectionStrategy.hashCode();
result = 31 * result + accessControlContext.hashCode();
result = 31 * result + ignoredTypes.hashCode();
result = 31 * result + transformation.hashCode();
return result;
}
@Override
public String toString() {
return "AgentBuilder.Default.ExecutingTransformer{" +
"byteBuddy=" + byteBuddy +
", binaryLocator=" + binaryLocator +
", typeStrategy=" + typeStrategy +
", initializationStrategy=" + initializationStrategy +
", listener=" + listener +
", nativeMethodStrategy=" + nativeMethodStrategy +
", bootstrapInjectionStrategy=" + bootstrapInjectionStrategy +
", accessControlContext=" + accessControlContext +
", ignoredTypes=" + ignoredTypes +
", transformation=" + transformation +
'}';
}
}
/**
* A helper class that describes a {@link net.bytebuddy.agent.builder.AgentBuilder.Default} after supplying
* a {@link net.bytebuddy.agent.builder.AgentBuilder.RawMatcher} such that one or several
* {@link net.bytebuddy.agent.builder.AgentBuilder.Transformer}s can be supplied.
*/
protected class Matched implements Identified.Extendable {
/**
* The supplied raw matcher.
*/
private final RawMatcher rawMatcher;
/**
* The supplied transformer.
*/
private final Transformer transformer;
/**
* Creates a new matched default agent builder.
*
* @param rawMatcher The supplied raw matcher.
* @param transformer The supplied transformer.
*/
protected Matched(RawMatcher rawMatcher, Transformer transformer) {
this.rawMatcher = rawMatcher;
this.transformer = transformer;
}
@Override
public Identified.Extendable transform(Transformer transformer) {
return new Matched(rawMatcher, new Transformer.Compound(this.transformer, transformer));
}
@Override
public Identified type(RawMatcher matcher) {
return materialize().type(matcher);
}
@Override
public Identified type(ElementMatcher<? super TypeDescription> typeMatcher) {
return materialize().type(typeMatcher);
}
@Override
public Identified type(ElementMatcher<? super TypeDescription> typeMatcher, ElementMatcher<? super ClassLoader> classLoaderMatcher) {
return materialize().type(typeMatcher, classLoaderMatcher);
}
@Override
public AgentBuilder with(ByteBuddy byteBuddy) {
return materialize().with(byteBuddy);
}
@Override
public AgentBuilder with(Listener listener) {
return materialize().with(listener);
}
@Override
public AgentBuilder with(TypeStrategy typeStrategy) {
return materialize().with(typeStrategy);
}
@Override
public AgentBuilder with(BinaryLocator binaryLocator) {
return materialize().with(binaryLocator);
}
@Override
public AgentBuilder with(AccessControlContext accessControlContext) {
return materialize().with(accessControlContext);
}
@Override
public AgentBuilder with(InitializationStrategy initializationStrategy) {
return materialize().with(initializationStrategy);
}
@Override
public AgentBuilder with(RedefinitionStrategy redefinitionStrategy) {
return materialize().with(redefinitionStrategy);
}
@Override
public AgentBuilder with(LambdaInstrumentationStrategy lambdaInstrumentationStrategy) {
return materialize().with(lambdaInstrumentationStrategy);
}
@Override
public AgentBuilder enableBootstrapInjection(File folder, Instrumentation instrumentation) {
return materialize().enableBootstrapInjection(folder, instrumentation);
}
@Override
public AgentBuilder disableBootstrapInjection() {
return materialize().disableBootstrapInjection();
}
@Override
public AgentBuilder enableNativeMethodPrefix(String prefix) {
return materialize().enableNativeMethodPrefix(prefix);
}
@Override
public AgentBuilder disableNativeMethodPrefix() {
return materialize().disableNativeMethodPrefix();
}
@Override
public AgentBuilder ignore(ElementMatcher<? super TypeDescription> ignoredTypes) {
return materialize().ignore(ignoredTypes);
}
@Override
public ClassFileTransformer makeRaw() {
return materialize().makeRaw();
}
@Override
public ClassFileTransformer installOn(Instrumentation instrumentation) {
return materialize().installOn(instrumentation);
}
@Override
public ClassFileTransformer installOnByteBuddyAgent() {
return materialize().installOnByteBuddyAgent();
}
/**
* Materializes the currently described {@link net.bytebuddy.agent.builder.AgentBuilder.Default.Transformation}.
*
* @return An agent builder that represents the currently described entry of this instance.
*/
protected AgentBuilder materialize() {
return new Default(byteBuddy,
binaryLocator,
typeStrategy,
listener,
nativeMethodStrategy,
accessControlContext,
initializationStrategy,
redefinitionStrategy,
bootstrapInjectionStrategy,
lambdaInstrumentationStrategy,
ignoredTypes,
new Transformation.Compound(new Transformation.Simple(rawMatcher, transformer), transformation));
}
/**
* Returns the outer instance.
*
* @return The outer instance.
*/
private Default getOuter() {
return Default.this;
}
@Override
public boolean equals(Object other) {
return this == other || !(other == null || getClass() != other.getClass())
&& rawMatcher.equals(((Matched) other).rawMatcher)
&& transformer.equals(((Matched) other).transformer)
&& Default.this.equals(((Matched) other).getOuter());
}
@Override
public int hashCode() {
int result = rawMatcher.hashCode();
result = 31 * result + transformer.hashCode();
result = 31 * result + Default.this.hashCode();
return result;
}
@Override
public String toString() {
return "AgentBuilder.Default.Matched{" +
"rawMatcher=" + rawMatcher +
", transformer=" + transformer +
", agentBuilder=" + Default.this +
'}';
}
}
}
}
|
package com.wmu.churchlogger;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.InputStream;
import java.io.UnsupportedEncodingException;
import java.security.MessageDigest;
import java.security.NoSuchAlgorithmException;
import java.security.SecureRandom;
import java.sql.Connection;
import java.sql.DriverManager;
import java.sql.ResultSet;
import java.sql.ResultSetMetaData;
import java.sql.SQLException;
import java.sql.Statement;
import java.util.Arrays;
import java.util.Scanner;
import javax.swing.table.DefaultTableModel;
public class DBAccess {
String url = "jdbc:mysql://localhost:3306/";
String dbName = "CLogger";
String driver = "com.mysql.jdbc.Driver";
String userName = "pastor";
String password = "loggingrox";
Connection connection;
public DBAccess(){
try {
System.out.println("Connecting to Database...");
Class.forName(driver).newInstance();
connection = DriverManager.getConnection(url+dbName,userName,password);
System.out.println("Connected...");
} catch (InstantiationException | IllegalAccessException
| ClassNotFoundException e) {
e.printStackTrace();
} catch (SQLException e) {
e.printStackTrace();
}
finally {
//what is this for? -Addison
}
//build the database!!
try {
this.buildDatabaseSchema();
} catch (SQLException e) {
e.printStackTrace();
}
}
/**
* @return status of execution
*/
public boolean initializeDBFromScratch() {
return true;
}
private byte[] getPW(String user_name) {
return null;
}
public boolean compareUPass(String user_name, String password) {
MessageDigest digest;
try {
digest = MessageDigest.getInstance("SHA-256");
digest.reset();
digest.update(generateSalt());
byte[] hashedBytes = digest.digest(password.getBytes("UTF-8"));
if(Arrays.equals(hashedBytes, getPW(user_name))) {
}
} catch (NoSuchAlgorithmException e) {
e.printStackTrace();
} catch (UnsupportedEncodingException e) {
e.printStackTrace();
}
return false;
}
public byte[] generateSalt() {
SecureRandom random = new SecureRandom();
byte bytes[] = new byte[20];
random.nextBytes(bytes);
return bytes;
}
/**
* All rights to: Omry Yadan
* @param conn
* @param in
* @throws SQLException
* @throws FileNotFoundException
*/
public void buildDatabaseSchema() throws SQLException {
InputStream in;
try {
in = new FileInputStream(new File("assets/scripts/createTablesChurchLogger.sql"));
Scanner s = new Scanner(in);
s.useDelimiter("(;(\r)?\n)|(
Statement st = null;
try
{
st = connection.createStatement();
while (s.hasNext())
{
String line = s.next();
if (line.startsWith("/*!") && line.endsWith("*/"))
{
int i = line.indexOf(' ');
line = line.substring(i + 1, line.length() - " */".length());
}
if (line.trim().length() > 0)
{
st.execute(line);
}
}
fillDatabase();
s.close();
}
finally {
if (st != null) st.close();
}
} catch (FileNotFoundException e) {
System.err.println("File missing from assets/scripts");
e.printStackTrace();
}
}
/**
* Fills the database with example data
* @throws SQLException
*/
private void fillDatabase() throws SQLException {
System.out.println("About to add Addison.");
addMember("Addison", "Webb", 0, "(269) 615-5084", "addison.f.webb@gmail.com", "2014-04-08", "1991-11-28", "NA", "8380 Copper Harbor St.", "Kalamazoo", "MI", 49009);
addMember("Kendrick", "AWSguy", 0, "(207) 798-0903", "kendrick.cline@wmich.edu", "2014-04-08", "1992-1-1", "Cool guy", "1234 Road St.", "Kalamazoo", "MI", 49009);
addMember("Dillon", "Toughguy", 0, "(517) 974-3360", "dillon.burton@wmich.com", "2014-04-08", "1991-1-1", "Cool guy", "5678 Another St.", "Kalamazoo", "MI", 49009);
addMember("Josh", "MYSQLguy", 0, "(989) 430-6826", "josh.dkyourlastname@wmich.com", "2014-04-08", "1991-1-1", "Cool guy", "9012 Long Rd.", "Kalamazoo", "MI", 49009);
}
/**
* Creates the table model for the member list UI.
* @return the table model to be used to populate a UI table.
* @throws SQLException
*/
public DefaultTableModel updateMemberTable() throws SQLException{
System.out.println("DBAccess: updateMemberTable running");
DefaultTableModel tableModel = new DefaultTableModel();
//initialize result set object
Statement stmt = connection.createStatement();
ResultSet rs = stmt.executeQuery("SELECT fname, lname, phone, email, join_date, straddress, zip"
+ " FROM members NATURAL JOIN info NATURAL JOIN member_address");
//initialize metadata object
ResultSetMetaData rsmd = rs.getMetaData();
int columnCount = rsmd.getColumnCount();
System.out.println("column count: " + rsmd.getColumnCount());
String[] recordString = new String[13];
int i;
//add column headers
Object[] columnHeadings = new String[] {
"First Name", "Last Name", "Phone", "Email", "Join Date", "Stree Address", "Zip"
};
tableModel.setColumnIdentifiers(columnHeadings);
System.out.println("Right before parsing of result set");
while(rs.next()){
for(i = 0; i < columnCount; i++){
System.out.println(i);
try{
recordString[i] = rs.getString(i + 1);
}
catch(NullPointerException e){
recordString[i] = "Null";
}
System.out.println(recordString[i]);
}
tableModel.addRow(recordString);
}
System.out.println("after parsing");
return tableModel;
}
/**
* Adds member to database. All parameters must be passed.
* @param firstName Full first name.
* @param lastName Full last name.
* @param churchID 3 digit church code.
* @param phone Format: (123) 555-1234
* @param email Full email address.
* @param joinDate YYYY-MM-DD
* @param birthDate YYYY-MM-DD
* @param note Any notes about the member.
* @param strAddress Full street address.
* @param city Full city name.
* @param state 2 character state code.
* @param zip Must be 5 digit number.
*/
public void addMember(String firstName, String lastName, int churchID, String phone, String email, String joinDate, String birthDate, String note, String strAddress, String city, String state, int zip){
Statement st = null;
try{
st = connection.createStatement();
st.execute("BEGIN");
st.execute("INSERT INTO members (fname, lname, cID) VALUES ('" + firstName + "', '" + lastName + "', '" + churchID + "')");
st.execute("SELECT LAST_INSERT_ID() INTO @lastID");
st.execute("INSERT INTO info (mID, phone, email, join_date, birth_date, note) VALUES (@lastID, '" + phone + "', '" + email + "', '" + joinDate + "', '" + birthDate + "', '" + note + "')");
st.execute("INSERT INTO member_address (mID, straddress, city, state, zip) VALUES (@lastID, '" + strAddress + "', '" + city + "', '" + state + "', '" + zip + "')");
st.execute("COMMIT");
}
catch(SQLException e){
System.out.println("SQL Exception: " + e);
}
}
public void closeDBConnection() {
try {
connection.close();
} catch (SQLException e) {
e.printStackTrace();
}
}
}
|
package replicant;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import java.util.Objects;
import java.util.logging.Level;
import java.util.logging.Logger;
import javax.annotation.Nonnull;
import javax.annotation.Nullable;
import replicant.spy.RequestCompletedEvent;
/**
* Connection state used by the connector to manage connection to backend system.
* This includes a list of pending requests, pending messages that needs to be applied
* to the local state etc.
*/
public final class Connection
{
//TODO: Make this package access after all classes migrated to replicant package
private static final Logger LOG = Logger.getLogger( Connection.class.getName() );
private static final Level LOG_LEVEL = Level.INFO;
@Nonnull
private final Connector _connector;
private final String _connectionId;
private final Map<String, RequestEntry> _requests = new HashMap<>();
private int _requestId;
/**
* Pending actions that will change the area of interest.
*/
private final LinkedList<AreaOfInterestRequest> _pendingAreaOfInterestRequests = new LinkedList<>();
/**
* The set of data load actions that still need to have the json parsed.
*/
private final LinkedList<MessageResponse> _unparsedResponses = new LinkedList<>();
/**
* The set of data load actions that have their json parsed. They are inserted into
* this list according to their sequence.
*/
private final LinkedList<MessageResponse> _pendingResponses = new LinkedList<>();
/**
* Sometimes a data load action occurs that is not initiated by the server. These do not
* typically need to be sequenced and are prioritized above other actions.
*/
private final LinkedList<MessageResponse> _outOfBandResponses = new LinkedList<>();
private int _lastRxSequence;
/**
* The current message action being processed.
*/
@Nullable
private MessageResponse _currentMessageResponse;
@Nonnull
private List<AreaOfInterestRequest> _currentAreaOfInterestRequests = new ArrayList<>();
public Connection( @Nonnull final Connector connector, @Nonnull final String connectionId )
{
_connector = Objects.requireNonNull( connector );
_connectionId = Objects.requireNonNull( connectionId );
}
@Nonnull
public String getConnectionId()
{
return _connectionId;
}
public final void requestSubscribe( @Nonnull final ChannelAddress address, @Nullable final Object filterParameter )
{
enqueueAreaOfInterestRequest( address, AreaOfInterestAction.ADD, filterParameter );
}
public void requestSubscriptionUpdate( @Nonnull final ChannelAddress address,
@Nullable final Object filterParameter )
{
enqueueAreaOfInterestRequest( address, AreaOfInterestAction.UPDATE, filterParameter );
}
public void requestUnsubscribe( @Nonnull final ChannelAddress address )
{
enqueueAreaOfInterestRequest( address, AreaOfInterestAction.REMOVE, null );
}
private void enqueueAreaOfInterestRequest( @Nonnull final ChannelAddress descriptor,
@Nonnull final AreaOfInterestAction action,
@Nullable final Object filterParameter )
{
getPendingAreaOfInterestRequests().add( new AreaOfInterestRequest( descriptor, action, filterParameter ) );
}
public void enqueueResponse( @Nonnull final String rawJsonData )
{
getUnparsedResponses().add( new MessageResponse( rawJsonData ) );
}
public void enqueueOutOfBandResponse( @Nonnull final String rawJsonData,
@Nonnull final SafeProcedure oobCompletionAction )
{
getOutOfBandResponses().add( new MessageResponse( rawJsonData, oobCompletionAction ) );
}
public LinkedList<AreaOfInterestRequest> getPendingAreaOfInterestRequests()
{
return _pendingAreaOfInterestRequests;
}
public LinkedList<MessageResponse> getUnparsedResponses()
{
return _unparsedResponses;
}
public LinkedList<MessageResponse> getParsedResponses()
{
return _pendingResponses;
}
public LinkedList<MessageResponse> getOutOfBandResponses()
{
return _outOfBandResponses;
}
public int getLastRxSequence()
{
return _lastRxSequence;
}
public void setLastRxSequence( final int lastRxSequence )
{
_lastRxSequence = lastRxSequence;
}
@Nonnull
public final RequestEntry newRequest( @Nullable final String name, @Nullable final String cacheKey )
{
final RequestEntry entry = new RequestEntry( nextRequestId(), name, cacheKey );
_requests.put( entry.getRequestId(), entry );
if ( LOG.isLoggable( LOG_LEVEL ) )
{
LOG.log( LOG_LEVEL, "Created request " + entry );
}
return entry;
}
public final void completeRequest( @Nonnull final RequestEntry request,
@Nonnull final SafeProcedure completionAction )
{
if ( request.isExpectingResults() && !request.haveResultsArrived() )
{
request.setCompletionAction( completionAction );
}
else
{
completionAction.call();
removeRequest( request.getRequestId() );
}
if ( Replicant.areSpiesEnabled() && _connector.getReplicantContext().getSpy().willPropagateSpyEvents() )
{
_connector
.getReplicantContext()
.getSpy()
.reportSpyEvent( new RequestCompletedEvent( _connector.getSystemType(),
request.getRequestId(),
request.getName(),
request.isNormalCompletion(),
request.isExpectingResults(),
request.haveResultsArrived() ) );
}
}
@Nullable
public RequestEntry getRequest( @Nonnull final String requestID )
{
return _requests.get( requestID );
}
public Map<String, RequestEntry> getRequests()
{
return _requests;
}
public boolean removeRequest( @Nonnull final String requestID )
{
return null != _requests.remove( requestID );
}
private String nextRequestId()
{
return String.valueOf( ++_requestId );
}
@Nullable
public MessageResponse getCurrentMessageResponse()
{
return _currentMessageResponse;
}
public void setCurrentMessageResponse( @Nullable final MessageResponse currentMessageResponse )
{
_currentMessageResponse = currentMessageResponse;
}
@Nonnull
public List<AreaOfInterestRequest> getCurrentAreaOfInterestRequests()
{
return _currentAreaOfInterestRequests;
}
}
|
package org.antlr.v4.parse;
import org.antlr.runtime.Token;
import org.antlr.v4.Tool;
import org.antlr.v4.codegen.CodeGenerator;
import org.antlr.v4.tool.ErrorType;
import org.antlr.v4.tool.Grammar;
import org.antlr.v4.tool.ast.GrammarAST;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.IOException;
import java.io.InputStreamReader;
import java.util.LinkedHashMap;
import java.util.Map;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
public class TokenVocabParser {
protected final Grammar g;
public TokenVocabParser(Grammar g) {
this.g = g;
}
/** Load a vocab file {@code <vocabName>.tokens} and return mapping. */
public Map<String,Integer> load() {
Map<String,Integer> tokens = new LinkedHashMap<String,Integer>();
int maxTokenType = -1;
File fullFile = getImportedVocabFile();
FileInputStream fis = null;
BufferedReader br = null;
Tool tool = g.tool;
String vocabName = g.getOptionString("tokenVocab");
try {
Pattern tokenDefPattern = Pattern.compile("([^\n]+?)[ \\t]*?=[ \\t]*?([0-9]+)");
fis = new FileInputStream(fullFile);
InputStreamReader isr;
if (tool.grammarEncoding != null) {
isr = new InputStreamReader(fis, tool.grammarEncoding);
}
else {
isr = new InputStreamReader(fis);
}
br = new BufferedReader(isr);
String tokenDef = br.readLine();
int lineNum = 1;
while ( tokenDef!=null ) {
Matcher matcher = tokenDefPattern.matcher(tokenDef);
if ( matcher.find() ) {
String tokenID = matcher.group(1);
String tokenTypeS = matcher.group(2);
int tokenType;
try {
tokenType = Integer.valueOf(tokenTypeS);
}
catch (NumberFormatException nfe) {
tool.errMgr.toolError(ErrorType.TOKENS_FILE_SYNTAX_ERROR,
vocabName + CodeGenerator.VOCAB_FILE_EXTENSION,
" bad token type: "+tokenTypeS,
lineNum);
tokenType = Token.INVALID_TOKEN_TYPE;
}
tool.log("grammar", "import "+tokenID+"="+tokenType);
tokens.put(tokenID, tokenType);
maxTokenType = Math.max(maxTokenType,tokenType);
lineNum++;
}
else {
if ( tokenDef.length()>0 ) { // ignore blank lines
tool.errMgr.toolError(ErrorType.TOKENS_FILE_SYNTAX_ERROR,
vocabName + CodeGenerator.VOCAB_FILE_EXTENSION,
" bad token def: " + tokenDef,
lineNum);
}
}
tokenDef = br.readLine();
}
}
catch (FileNotFoundException fnfe) {
GrammarAST inTree = g.ast.getOptionAST("tokenVocab");
String inTreeValue = inTree.getToken().getText();
if ( vocabName.equals(inTreeValue) ) {
tool.errMgr.grammarError(ErrorType.CANNOT_FIND_TOKENS_FILE_REFD_IN_GRAMMAR,
g.fileName,
inTree.getToken(),
fullFile);
}
else { // must be from -D option on cmd-line not token in tree
tool.errMgr.toolError(ErrorType.CANNOT_FIND_TOKENS_FILE_GIVEN_ON_CMDLINE,
fullFile,
g.name);
}
}
catch (Exception e) {
tool.errMgr.toolError(ErrorType.ERROR_READING_TOKENS_FILE,
e,
fullFile,
e.getMessage());
}
finally {
try {
if ( br!=null ) br.close();
}
catch (IOException ioe) {
tool.errMgr.toolError(ErrorType.ERROR_READING_TOKENS_FILE,
ioe,
fullFile,
ioe.getMessage());
}
}
return tokens;
}
/** Return a File descriptor for vocab file. Look in library or
* in -o output path. antlr -o foo T.g4 U.g4 where U needs T.tokens
* won't work unless we look in foo too. If we do not find the
* file in the lib directory then must assume that the .tokens file
* is going to be generated as part of this build and we have defined
* .tokens files so that they ALWAYS are generated in the base output
* directory, which means the current directory for the command line tool if there
* was no output directory specified.
*/
public File getImportedVocabFile() {
String vocabName = g.getOptionString("tokenVocab");
File f = new File(g.tool.libDirectory,
File.separator +
vocabName +
CodeGenerator.VOCAB_FILE_EXTENSION);
if (f.exists()) {
return f;
}
// We did not find the vocab file in the lib directory, so we need
// to look for it in the output directory which is where .tokens
// files are generated (in the base, not relative to the input
// location.)
f = new File(g.tool.outputDirectory, vocabName + CodeGenerator.VOCAB_FILE_EXTENSION);
if ( f.exists() ) {
return f;
}
// Still not found? Use the grammar's subfolder then.
String fileDirectory;
if (g.fileName.lastIndexOf(File.separatorChar) == -1) {
// No path is included in the file name, so make the file
// directory the same as the parent grammar (which might still be just ""
// but when it is not, we will write the file in the correct place.
fileDirectory = ".";
}
else {
fileDirectory = g.fileName.substring(0, g.fileName.lastIndexOf(File.separatorChar));
}
return new File(fileDirectory, vocabName + CodeGenerator.VOCAB_FILE_EXTENSION);
}
}
|
import java.lang.Thread;
import com.sun.star.awt.Rectangle;
import com.sun.star.awt.XWindow;
import com.sun.star.beans.Property;
import com.sun.star.beans.PropertyValue;
import com.sun.star.beans.XPropertySet;
import com.sun.star.beans.XPropertySetInfo;
import com.sun.star.container.XIndexAccess;
import com.sun.star.container.XChild;
import com.sun.star.container.XEnumerationAccess;
import com.sun.star.container.XEnumeration;
import com.sun.star.frame.XComponentLoader;
import com.sun.star.frame.XController;
import com.sun.star.frame.XDesktop;
import com.sun.star.frame.XFrame;
import com.sun.star.frame.XTasksSupplier;
import com.sun.star.frame.XTask;
import com.sun.star.lang.XComponent;
import com.sun.star.lang.XMultiServiceFactory;
import com.sun.star.lang.XServiceInfo;
import com.sun.star.lang.XServiceName;
import com.sun.star.lang.XTypeProvider;
import com.sun.star.uno.UnoRuntime;
import com.sun.star.uno.XInterface;
import com.sun.star.uno.Type;
import com.sun.star.drawing.XDrawView;
import com.sun.star.drawing.XDrawPage;
import com.sun.star.drawing.XShapes;
import com.sun.star.drawing.XShape;
import com.sun.star.drawing.XShapeDescriptor;
import drafts.com.sun.star.accessibility.XAccessible;
import drafts.com.sun.star.accessibility.XAccessibleContext;
import drafts.com.sun.star.accessibility.XAccessibleComponent;
import drafts.com.sun.star.accessibility.XAccessibleRelationSet;
import drafts.com.sun.star.accessibility.XAccessibleStateSet;
public class InformationWriter
implements Print
{
Print maPrinter;
public InformationWriter (Print aPrinter)
{
maPrinter = aPrinter;
}
public void drawPageTest (XInterface xPage)
{
try
{
printProperty (xPage, "BorderBottom ", "BorderBottom");
printProperty (xPage, "BorderLeft ", "BorderLeft");
printProperty (xPage, "BorderRight ", "BorderRight");
printProperty (xPage, "BorderTop ", "BorderTop");
printProperty (xPage, "Height ", "Height");
printProperty (xPage, "Width ", "Width");
printProperty (xPage, "Number ", "Number");
}
catch (Exception e)
{
System.out.println ("caught exception while testing draw page:" + e);
}
}
public void printProperty (XInterface xObject, String prefix, String name)
{
try
{
XPropertySet xPropertySet = (XPropertySet) UnoRuntime.queryInterface(
XPropertySet.class, xObject);
println (prefix +
xPropertySet.getPropertyValue (name));
}
catch (Exception e)
{
println ("caught exception while getting property "
+ name + " : " + e);
}
}
public void showShapes (XDrawPage xPage)
{
try
{
XIndexAccess xShapeList = (XIndexAccess) UnoRuntime.queryInterface(
XIndexAccess.class, xPage);
println ("There are " + xShapeList.getCount()
+ " shapes");
for (int i=0; i<xShapeList.getCount(); i++)
{
XShape xShape = (XShape) UnoRuntime.queryInterface(
XShape.class, xShapeList.getByIndex (i));
XShapeDescriptor xShapeDescriptor =
(XShapeDescriptor) UnoRuntime.queryInterface(
XShapeDescriptor.class, xShape);
String sName = xShapeDescriptor.getShapeType ();
println (" shape " + i + " : " + sName);
XPropertySet xPropertySet =
(XPropertySet) UnoRuntime.queryInterface(
XPropertySet.class, xShape);
Integer nZOrder =
(Integer) xPropertySet.getPropertyValue ("ZOrder");
println (" zorder = " + nZOrder);
}
}
catch (Exception e)
{
println ("caught exception in showShapes: " + e);
}
}
/** @descr Print all available services of the given object to the
standard output.
*/
public void showServices (XInterface xObject)
{
try
{
println ("Services:");
XMultiServiceFactory xMSF = (XMultiServiceFactory) UnoRuntime.queryInterface (
XMultiServiceFactory.class,
xObject
);
if (xMSF == null)
println (" object does not support interface XMultiServiceFactory");
else
{
String[] sServiceNames = xMSF.getAvailableServiceNames ();
println (" object can create "
+ sServiceNames.length + " services");
for (int i=0; i<sServiceNames.length; i++)
println (" service " + i + " : " + sServiceNames[i]);
}
}
catch (Exception e)
{
println ("caught exception in showServices : " + e);
}
}
/** @descr Print the service and implementation name of the given
object.
*/
public void showInfo (XInterface xObject)
{
try
{
System.out.println ("Info:");
// Use interface XServiceName to retrieve name of (main) service.
XServiceName xSN = (XServiceName) UnoRuntime.queryInterface (
XServiceName.class, xObject);
if (xSN == null)
println (" interface XServiceName not supported");
else
{
println (" Service name : " + xSN.getServiceName ());
}
// Use interface XServiceInfo to retrieve information about
// supported services.
XServiceInfo xSI = (XServiceInfo) UnoRuntime.queryInterface (
XServiceInfo.class, xObject);
if (xSI == null)
println (" interface XServiceInfo not supported");
else
{
println (" Implementation name : "
+ xSI.getImplementationName ());
}
}
catch (Exception e)
{
println ("caught exception in showInfo : " + e);
}
}
/** @descr Print information about supported interfaces.
*/
public void showInterfaces (XInterface xObject)
{
try
{
println ("Interfaces:");
// Use interface XTypeProvider to retrieve a list of supported
// interfaces.
XTypeProvider xTP = (XTypeProvider) UnoRuntime.queryInterface (
XTypeProvider.class, xObject);
if (xTP == null)
println (" interface XTypeProvider not supported");
else
{
Type[] aTypeList = xTP.getTypes ();
println (" object supports " + aTypeList.length
+ " interfaces");
for (int i=0; i<aTypeList.length; i++)
println (" " + i + " : "
+ aTypeList[i].getTypeName());
}
}
catch (Exception e)
{
println ("caught exception in showInterfaces : " + e);
}
}
/** @descr Print information concerning the accessibility of the given
object.
*/
public boolean showAccessibility (XInterface xObject, int depth)
{
try
{
// Create indentation string.
String sIndent = "";
while (depth
sIndent += " ";
// Get XAccessibleContext object if given object does not
// already support this interface.
XAccessibleContext xContext
= (XAccessibleContext) UnoRuntime.queryInterface (
XAccessibleContext.class, xObject);
if (xContext == null)
{
XAccessible xAccessible
= (XAccessible) UnoRuntime.queryInterface (
XAccessible.class, xObject);
if (xAccessible == null)
{
println (sIndent + "given object " + xObject
+ " is not accessible");
return false;
}
else
xContext = xAccessible.getAccessibleContext();
}
// Print information about the accessible context.
if (xContext != null)
{
println (sIndent + "Name : "
+ xContext.getAccessibleName());
println (sIndent + "Description : "
+ xContext.getAccessibleDescription());
println (sIndent + "Role : "
+ xContext.getAccessibleRole());
String sHasParent;
if (xContext.getAccessibleParent() != null)
{
println (sIndent + "Has parent : yes");
println (sIndent + "Parent index : "
+ xContext.getAccessibleIndexInParent());
}
else
println (sIndent + "Has parent : no");
println (sIndent + "Child count : "
+ xContext.getAccessibleChildCount());
print (sIndent + "Relation set : ");
XAccessibleRelationSet xRelationSet
= xContext.getAccessibleRelationSet();
if (xRelationSet != null)
{
print (xRelationSet.getRelationCount() + " (");
for (int i=0; i<xRelationSet.getRelationCount(); i++)
{
if (i > 0)
print (", ");
print (xRelationSet.getRelation(i).toString());
}
println (")");
}
else
println ("no relation set");
print (sIndent + "State set : ");
XAccessibleStateSet xStateSet =
xContext.getAccessibleStateSet();
if (xStateSet != null)
{
XIndexAccess xStates =
(XIndexAccess) UnoRuntime.queryInterface (
XIndexAccess.class, xStateSet);
print (xStates.getCount() + " (");
for (int i=0; i<xStates.getCount(); i++)
{
if (i > 0)
print (", ");
print (xStates.getByIndex(i).toString());
}
println (")");
}
else
println ("no state set");
showAccessibleComponent (xContext, sIndent);
}
else
println ("object has no accessible context.");
// showInfo (xContext);
// showServices (xContext);
// showInterfaces (xContext);
}
catch (Exception e)
{
System.out.println ("caught exception in showAccessibility :" + e);
}
return true;
}
/** @descr Print information about the given accessible component.
*/
public void showAccessibleComponent (XInterface xObject, String sIndent)
{
try
{
XAccessibleComponent xComponent =
(XAccessibleComponent) UnoRuntime.queryInterface (
XAccessibleComponent.class, xObject);
// Print information about the accessible context.
if (xComponent != null)
{
println (sIndent + "Position : "
+ xComponent.getLocation().X+", "
+ xComponent.getLocation().Y);
println (sIndent + "Screen position : "
+ xComponent.getLocationOnScreen().X+", "
+ xComponent.getLocationOnScreen().Y);
println (sIndent + "Size : "
+ xComponent.getSize().Width+", "
+ xComponent.getSize().Height);
}
}
catch (Exception e)
{
System.out.println (
"caught exception in showAccessibleComponent : " + e);
}
}
/** Show a textual representation of the accessibility subtree rooted in
xRoot.
*/
public boolean showAccessibilityTree (XAccessible xRoot, int depth)
{
try
{
if ( ! showAccessibility (xRoot, depth))
return false;
String sIndent = "";
for (int i=0; i<depth; i++)
sIndent += " ";
// Iterate over children and show them.
XAccessibleContext xContext = xRoot.getAccessibleContext();
if (xContext != null)
{
int n = xContext.getAccessibleChildCount();
for (int i=0; i<n; i++)
{
println (sIndent + "child " + i + " :");
showAccessibilityTree (xContext.getAccessibleChild(i),depth+1);
}
}
else
println ("Accessible object has no context");
}
catch (Exception e)
{
System.out.println (
"caught exception in showAccessibleTree : " + e);
return false;
}
return true;
}
public void showProperties (XInterface xObject)
{
XPropertySet xSet = (XPropertySet) UnoRuntime.queryInterface (
XPropertySet.class, xObject);
if (xSet == null)
println ("object does not support XPropertySet");
else
{
XPropertySetInfo xInfo = xSet.getPropertySetInfo ();
Property[] aProperties = xInfo.getProperties ();
int n = aProperties.length;
for (int i=0; i<n; i++)
println (i + " : " + aProperties[i].Name +", " + aProperties[i].Type);
}
}
public void print (String text)
{
maPrinter.print (text);
}
public void println (String text)
{
maPrinter.println (text);
}
}
|
package com.drone.ui;
import java.lang.reflect.Method;
import java.util.ArrayList;
import java.util.List;
import com.drone.Drone;
import com.drone.GaugeConfiguration;
import com.drone.navdata.DroneNavData;
import com.vaadin.addon.touchkit.ui.HorizontalButtonGroup;
import com.vaadin.addon.touchkit.ui.Popover;
import com.vaadin.server.FontAwesome;
import com.vaadin.ui.Alignment;
import com.vaadin.ui.Button;
import com.vaadin.ui.ComboBox;
import com.vaadin.ui.VerticalLayout;
public class AddGaugeDialog extends Popover {
private static final long serialVersionUID = -2633336549420617084L;
private GaugePanel panel;
private Drone drone;
private ComboBox gaugeSelector;
public AddGaugeDialog(GaugePanel panel, Drone drone) {
this.panel = panel;
setWidth(200, Unit.PIXELS);
setResizable(false);
setClosable(true);
center();
this.drone = drone;
VerticalLayout layout = new VerticalLayout();
layout.setMargin(true);
layout.setSpacing(true);
List<GaugeConfiguration> availableGauges = determineAvailableGauges();
gaugeSelector = new ComboBox("Gauges");
gaugeSelector.setWidth(100, Unit.PERCENTAGE);
gaugeSelector.setNullSelectionAllowed(false);
layout.addComponent(gaugeSelector);
for (GaugeConfiguration configuration : availableGauges) {
gaugeSelector.addItem(configuration);
gaugeSelector.setItemCaption(configuration, configuration
.property().getName());
}
HorizontalButtonGroup buttonLayout = new HorizontalButtonGroup();
Button add = new Button(FontAwesome.PLUS);
Button close = new Button(FontAwesome.MINUS);
add.addClickListener(e -> onAddClicked());
close.addClickListener(e -> close());
buttonLayout.addComponents(add, close);
layout.addComponent(buttonLayout);
layout.setComponentAlignment(buttonLayout, Alignment.BOTTOM_RIGHT);
setContent(layout);
}
private void onAddClicked() {
panel.addGauge((GaugeConfiguration) gaugeSelector.getValue());
close();
}
private List<GaugeConfiguration> determineAvailableGauges() {
List<GaugeConfiguration> droneProperties = new ArrayList<>();
Class<?> navDataInterface = null;
for (Class<?> droneInterface : drone.getNavData().getClass()
.getInterfaces()) {
if (droneInterface.equals(DroneNavData.class)) {
navDataInterface = droneInterface;
}
}
if (navDataInterface == null) {
throw new RuntimeException(
"Drone's nav data does not implement DroneNavData interface");
}
for (Method method : navDataInterface.getMethods()) {
if (method.isAnnotationPresent(GaugeConfiguration.class)) {
droneProperties.add(method
.getAnnotation(GaugeConfiguration.class));
}
}
return droneProperties;
}
}
|
package com.twu.biblioteca;
import org.junit.After;
import org.junit.Before;
import org.junit.Test;
import java.io.ByteArrayOutputStream;
import java.io.PrintStream;
import java.util.LinkedList;
import static com.twu.biblioteca.PredefinedBooksDetails.*;
import static com.twu.biblioteca.PredefinedMovieDetails.*;
import static com.twu.biblioteca.PredefinedUserDetails.*;
import static org.junit.Assert.*;
public class LibraryTest {
private Library library;
private Book bookA, bookB, bookC, bookD, bookE;
private Movie movieA, movieB, movieC, movieD;
private final ByteArrayOutputStream outStream = new ByteArrayOutputStream();
private Customer customer;
@Before
public void setup(){
System.setOut(new PrintStream(outStream));
bookA = new Book(BOOK_ONE_NAME, BOOK_ONE_AUTHOR, BOOK_ONE_PUBLISHING_YEAR);
bookB = new Book(BOOK_TWO_NAME, BOOK_TWO_AUTHOR, BOOK_TWO_PUBLISHING_YEAR);
bookC = new Book(BOOK_THREE_NAME, BOOK_THREE_AUTHOR, BOOK_THREE_PUBLISHING_YEAR);
bookD = new Book(BOOK_FOUR_NAME, BOOK_FOUR_AUTHOR, BOOK_FOUR_PUBLISHING_YEAR);
bookE = new Book(BOOK_FIVE_NAME, BOOK_FIVE_AUTHOR, BOOK_FIVE_PUBLISHING_YEAR);
movieA = new Movie(MOVIE_ONE_NAME, MOVIE_ONE_YEAR, MOVIE_ONE_DIRECTOR, MOVIE_ONE_RATING);
movieB = new Movie(MOVIE_TWO_NAME, MOVIE_TWO_YEAR, MOVIE_TWO_DIRECTOR, MOVIE_TWO_RATING);
movieC = new Movie(MOVIE_THREE_NAME, MOVIE_THREE_YEAR, MOVIE_THREE_DIRECTOR, MOVIE_THREE_RATING);
movieD = new Movie(MOVIE_FOUR_NAME, MOVIE_FOUR_YEAR, MOVIE_FOUR_DIRECTOR, MOVIE_FOUR_RATING);
LinkedList<LibraryItem> itemsList = new LinkedList<LibraryItem>();
itemsList.add(bookA);
itemsList.add(bookB);
itemsList.add(bookC);
itemsList.add(bookD);
itemsList.add(bookE);
itemsList.add(movieA);
itemsList.add(movieB);
itemsList.add(movieC);
itemsList.add(movieD);
library = new Library(itemsList);
customer = new Customer(DEFAULT_USERNAME);
}
@After
public void cleanUp(){
System.setOut(null);
}
@Test
public void testGetAllItemsList(){
assertEquals(9, library.getItemsList().size());
}
@Test
public void testGetAllBooksList(){
assertEquals(5, library.getAllBooksList().size());
}
@Test
public void testGetAllMoviesList(){
assertEquals(4, library.getAllMoviesList().size());
}
@Test
public void testGetAvailableItemListAfterBookAHasBeenCheckedOut(){
assertEquals(9, library.getAvailableItemsList().size());
bookA.checkOut();
assertEquals(8, library.getAvailableItemsList().size());
}
@Test
public void testGetAvailableBooksListAfterBookAHasBeenCheckedOut(){
assertEquals(5, library.getAvailableBooksList().size());
bookA.checkOut();
assertEquals(4, library.getAvailableBooksList().size());
}
@Test
public void testGetAvailableMoviesListAfterBookAHasBeenCheckedOut(){
assertEquals(4, library.getAvailableMoviesList().size());
bookA.checkOut();
assertEquals(4, library.getAvailableMoviesList().size());
}
@Test
public void testGetAvailableItemListAfterMovieAHasBeenCheckedOut(){
assertEquals(9, library.getAvailableItemsList().size());
bookA.checkOut();
assertEquals(8, library.getAvailableItemsList().size());
}
@Test
public void testGetAvailableBooksListAfterMovieAHasBeenCheckedOut(){
assertEquals(5, library.getAvailableBooksList().size());
movieA.checkOut();
assertEquals(5, library.getAvailableBooksList().size());
}
@Test
public void testGetAvailableMoviesListAfterMovieAHasBeenCheckedOut(){
assertEquals(4, library.getAvailableMoviesList().size());
movieA.checkOut();
assertEquals(3, library.getAvailableMoviesList().size());
}
@Test
public void testGetAvailableItemListAfterBookAHasBeenCheckedIn(){
bookA.checkOut();
assertEquals(8, library.getAvailableItemsList().size());
bookA.checkIn();
assertEquals(9, library.getAvailableItemsList().size());
}
@Test
public void testGetAvailableBooksListAfterBookAHasBeenCheckedIn(){
bookA.checkOut();
assertEquals(4, library.getAvailableBooksList().size());
bookA.checkIn();
assertEquals(5, library.getAvailableBooksList().size());
}
@Test
public void testGetAvailableMoviesListAfterMovieAHasBeenCheckedIn(){
bookA.checkOut();
assertEquals(4, library.getAvailableMoviesList().size());
bookA.checkIn();
assertEquals(4, library.getAvailableMoviesList().size());
}
@Test
public void testGetAvailableItemListAfterMovieAHasBeenCheckedIn(){
movieA.checkOut();
assertEquals(8, library.getAvailableItemsList().size());
movieA.checkIn();
assertEquals(9, library.getAvailableItemsList().size());
}
@Test
public void testGetAvailableBooksListAfterMovieAHasBeenCheckedIn(){
movieA.checkOut();
assertEquals(5, library.getAvailableBooksList().size());
movieA.checkIn();
assertEquals(5, library.getAvailableBooksList().size());
}
@Test
public void testGetAvailableMoviesListAfterBookAHasBeenCheckedIn(){
movieA.checkOut();
assertEquals(3, library.getAvailableMoviesList().size());
movieA.checkIn();
assertEquals(4, library.getAvailableMoviesList().size());
}
@Test
public void testShowAvailableBooksList(){
bookA.checkOut();
library.showAvailableBooksList();
assertEquals("The Old Man and the Sea Ernest Hemingway 1990\n" +
"Programming Pearl Jon Bentley 2003\n" +
"Hamlet Shakespeare 1972\n" +
"Gone with the wind Margaret Mitchell 1980\n", outStream.toString());
outStream.reset();
bookD.checkOut();
library.showAvailableBooksList();
assertEquals("The Old Man and the Sea Ernest Hemingway 1990\n" +
"Programming Pearl Jon Bentley 2003\n" +
"Gone with the wind Margaret Mitchell 1980\n", outStream.toString());
}
@Test
public void testShowAvailableMoviesList(){
movieA.checkOut();
library.showAvailableMoviesList();
assertEquals("Jurassic Park 1990 Spielberg 7\n" +
"007 2001 Louis 7\n" +
"Lord of the Ring 2002 Tom 8\n", outStream.toString());
outStream.reset();
movieA.checkIn();
library.showAvailableMoviesList();
assertEquals("Star War 1996 Jim 9\n" +
"Jurassic Park 1990 Spielberg 7\n" +
"007 2001 Louis 7\n" +
"Lord of the Ring 2002 Tom 8\n", outStream.toString());
}
@Test
public void testFindItem(){
assertNotNull(library.findItem(BOOK_ONE_NAME));
assertNotNull(library.findItem(MOVIE_TWO_NAME));
assertNull(library.findItem("Galaxy War"));
}
@Test
public void testBookAIsAvailable(){
assertNotNull(library.findItemIfAvailable(BOOK_ONE_NAME));
assertTrue(library.findItemIfAvailable(BOOK_ONE_NAME) instanceof Book);
}
@Test
public void testBookAIsNotAvailableAfterBeingCheckedOut(){
bookA.checkOut();
assertNull(library.findItemIfAvailable(BOOK_ONE_NAME));
}
@Test
public void testMovieAIsAvailable(){
assertNotNull(library.findItemIfAvailable(MOVIE_ONE_NAME));
assertTrue(library.findItemIfAvailable(MOVIE_ONE_NAME) instanceof Movie);
}
@Test
public void testMovieAIsNotAvailableAfterBeingCheckedOut(){
movieA.checkOut();
assertNull(library.findItemIfAvailable(MOVIE_ONE_NAME));
}
@Test
public void testBuyBookA(){
assertEquals(SystemMessageType.INVALID_BOOK_OPTION, library.processBooksOperations("buy One Hundred Years of Solitude", customer));
assertFalse(bookA.getCheckOutStatus());
}
@Test
public void testSellBookA(){
assertEquals(SystemMessageType.INVALID_BOOK_OPTION, library.processBooksOperations("sell One Hundred Years of Solitude",customer));
assertFalse(bookA.getCheckOutStatus());
}
@Test
public void testBorrowBookA(){
assertEquals(SystemMessageType.SUCCESSFUL_CHECKOUT, library.processBooksOperations("borrow One Hundred Years of Solitude", customer));
assertTrue(bookA.getCheckOutStatus());
}
@Test
public void testBorrowUnknownBook(){
bookA.checkOut();
assertEquals(SystemMessageType.UNSUCCESSFUL_CHECKOUT, library.processBooksOperations("borrow One", customer));
}
@Test
public void testSellBookBAfterBorrowing(){
bookB.checkOut();
assertEquals(SystemMessageType.INVALID_BOOK_OPTION, library.processBooksOperations("sell The Old Man and the Sea", customer));
assertTrue(bookB.getCheckOutStatus());
}
@Test
public void testBuyBookBAfterBorrowing(){
bookB.checkOut();
assertEquals(SystemMessageType.INVALID_BOOK_OPTION, library.processBooksOperations("buy The Old Man and the Sea", customer));
assertTrue(bookB.getCheckOutStatus());
}
@Test
public void testReturnBookBAfterBorrowing(){
customer.borrowBook(bookB);
assertEquals(SystemMessageType.SUCCESSFUL_RETURN, library.processBooksOperations("return The Old Man and the Sea", customer));
assertFalse(bookB.getCheckOutStatus());
}
@Test
public void testReturnUnknownBookAfterBorrowingBookB(){
customer.borrowBook(bookB);
assertEquals(SystemMessageType.UNSUCCESSFUL_RETURN, library.processBooksOperations("return Galaxy War",customer));
}
}
|
package sed.sky;
import ssim.util.MathExt;
import com.jme3.math.Vector3f;
import chlib.noise.NoiseUtil;
public class CloudHeightField {
private int size;
private int numOctaves;
private float zoom;
private Vector3f shift;
private float cloudCover;
public CloudHeightField(int size, int numOctaves) {
this.size = size;
this.numOctaves = numOctaves;
}
public float getZoom() {
return zoom;
}
public void setZoom(float zoom) {
this.zoom = zoom;
}
public Vector3f getShift() {
return shift;
}
public void setShift(Vector3f shift) {
this.shift = shift;
}
public float getCloudCover() {
return cloudCover;
}
public void setCloudCover(float cloudCover) {
this.cloudCover = cloudCover;
}
/**
* @return a rows-first array with height data in [0,255]
*/
public float[][] generate() {
return generate(null);
}
/**
* @param store a float[][] to store the result
* @return a rows-first array with height data in [0,255]
*/
public float[][] generate(float[][] store) {
if(store == null) {
store = new float[size][size];
}
for(int column = 0; column < size; column++) {
for(int row = 0; row < size; row++) {
// alternative: NoiseUtil.turbulance2
float turbulance = NoiseUtil.fBm(
(shift.x * size + column)/zoom,
(shift.y * size + row)/zoom,
shift.z,
numOctaves, 2f, .5f);
// float turbulance = NoiseUtil.turbulance2(
// (shift.x * size + column)/zoom,
// (shift.y * size + row)/zoom,
// shift.z,
// numOctaves);
float height = (turbulance*255f) - cloudCover;
height = MathExt.clamp(height, 0, 255);
store[column][row] = height;
}
}
return store;
}
}
|
package server;
import java.io.FileInputStream;
import java.security.Key;
import java.security.KeyFactory;
import java.security.KeyStore;
import java.security.KeyStoreException;
import java.security.PrivateKey;
import java.security.PublicKey;
import java.security.Signature;
import java.security.cert.Certificate;
import java.security.spec.X509EncodedKeySpec;
import java.util.logging.Level;
import java.util.logging.Logger;
import javax.crypto.Cipher;
import database.DatabaseConnector;
import dto.Validator;
public class SecurityValidator {
private static String securityKeyBasePath;
private static String securityKeystoreAlias;
private static String securityKeystorePassword;
private static String securityKeystoreFile;
private static String securityKeystorePrivatekey;
public SecurityValidator()
{
securityKeyBasePath = ConfigurationProperties.securityKeyBasePath();
securityKeystoreAlias = ConfigurationProperties.securityKeystoreTallierAllias();
securityKeystorePassword = ConfigurationProperties.securityKeystoreTallierPassword();
securityKeystoreFile = securityKeyBasePath + ConfigurationProperties.securityKeystoreTallierFile();
securityKeystorePrivatekey = securityKeyBasePath + ConfigurationProperties.securityKeystoreTallierPrivatekey();
}
public Validator checkSignature(String sig, int user_id) {
DatabaseConnector dbc = new DatabaseConnector();
String pk = (String) dbc.getPubKeyByUserID(user_id).getObject();
Validator val = new Validator();
val.setVerified(false);
if (pk == null) {
val.setStatus("No public key available");
return val;
}
byte[] pubKey = hexStringtoByteArray(pk);
byte[] signature = hexStringtoByteArray(sig);
try {
PublicKey PK = KeyFactory.getInstance("RSA").generatePublic(
new X509EncodedKeySpec(pubKey));
Signature ver = Signature.getInstance("SHA256WITHRSA");
ver.initVerify(PK);
ver.update(signature);
val.setVerified(ver.verify(signature));
if (val.isVerified())
val.setStatus("Signature verified");
else
val.setStatus("Signature did not verify");
return val;
} catch (Exception ex) {
Logger lgr = Logger.getLogger(SecurityValidator.class.getName());
lgr.log(Level.WARNING, ex.getMessage(), ex);
}
return val;
}
public byte[] hexStringtoByteArray(String hex) {
int len = hex.length();
byte[] data = new byte[len / 2];
for (int i = 0; i < len; i += 2) {
data[i / 2] = (byte) ((Character.digit(hex.charAt(i), 16) << 4) + Character
.digit(hex.charAt(i + 1), 16));
}
return data;
}
public static String byteArraytoHex(byte[] arr) {
StringBuffer sb = new StringBuffer();
for (int i = 0; i < arr.length; i++) {
sb.append(Integer.toString((arr[i] & 0xff) + 0x100, 16)
.substring(1));
}
return sb.toString();
}
public String decrypt(String ciph) {
byte[] ct = hexStringtoByteArray(ciph);
try {
PrivateKey priv = getPrivateKey();
Cipher dec = Cipher.getInstance("RSA");
dec.init(Cipher.DECRYPT_MODE, priv);
byte[] plain = dec.doFinal(ct);
String plaintext = byteArraytoHex(plain);
return plaintext;
} catch (Exception ex) {
Logger lgr = Logger.getLogger(SecurityValidator.class.getName());
lgr.log(Level.WARNING, ex.getMessage(), ex);
}
return null;
}
public PrivateKey getPrivateKey() {
KeyStore ks;
try {
ks = KeyStore.getInstance("PKCS12");
// get user password and file input stream
char[] password = "t@l1i3r".toCharArray();
java.io.FileInputStream fis = null;
try {
fis = new java.io.FileInputStream(
"/Users/Steven/School Work/Grad School/"
+ "Research/Du-Vote/CERTUS-Server/resources/keys/pkcs12.p12");
ks.load(fis, password);
} finally {
if (fis != null) {
fis.close();
}
}
KeyStore.ProtectionParameter protParam = new KeyStore.PasswordProtection(
password);
// get my private key
KeyStore.PrivateKeyEntry pkEntry = (KeyStore.PrivateKeyEntry) ks
.getEntry("tallier", protParam);
PrivateKey myPrivateKey = pkEntry.getPrivateKey();
return myPrivateKey;
} catch (Exception ex) {
Logger lgr = Logger.getLogger(SecurityValidator.class.getName());
lgr.log(Level.WARNING, ex.getMessage(), ex);
return null;
}
}
public Validator getTallierPublicKey(){
Validator val=new Validator();
try{
FileInputStream is = new FileInputStream("/Users/Steven/School Work/Grad School/"
+ "Research/Du-Vote/CERTUS-Server/resources/keys/Tallier-Keys");
KeyStore keystore = KeyStore.getInstance(KeyStore.getDefaultType());
keystore.load(is, "t@l1i3r".toCharArray());
String alias = "tallier";
Key key = keystore.getKey(alias, "t@l1i3r".toCharArray());
if (key instanceof PrivateKey) {
// Get certificate of public key
Certificate cert = keystore.getCertificate(alias);
// Get public key
PublicKey publicKey = cert.getPublicKey();
val.setVerified(true);
val.setStatus("Retrieved public key");
val.setObject(publicKey);
return val;
}
else{
val.setVerified(false);
val.setStatus("Failed to retrieve public key");
return val;
}
}
catch(Exception ex){
Logger lgr = Logger.getLogger(DatabaseConnector.class.getName());
lgr.log(Level.WARNING, ex.getMessage(), ex);
val.setStatus("Error occured");
val.setVerified(false);
return val;
}
}
}
|
package servlets;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Map;
import javax.servlet.RequestDispatcher;
import javax.servlet.ServletException;
import javax.servlet.annotation.WebServlet;
import javax.servlet.http.HttpServlet;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import rmi.Initializer;
import service.HtmlService;
import service.ElectionService;
import service.HeaderService;
import service.LoginService;
import service.TallyingService;
import service.VotingService;
import com.sun.xml.internal.messaging.saaj.packaging.mime.Header;
import dto.CandidateDto;
import dto.ElectionDto;
import dto.ElectionProgressDto;
import dto.Validator;
import enumeration.ElectionStatus;
import enumeration.ElectionType;
import enumeration.Status;
/**
* Dmitriy Karmazin | dkarmazi
* Servlet implementation class ElectionServlet
*/
@WebServlet(name = "election", urlPatterns = { "/election" })
public class ElectionServlet extends HttpServlet {
private static final long serialVersionUID = 1L;
private String mode = "1";
private String messageAlert = "";
private String messageLabel = "";
private String outModal = "";
private String outElections = "";
private String placeHoldElecName = "Enter election name here";
private String placeHoldElecDesc = "Enter election description here";
private String placeHoldElecEndTime = "Enter election end time here";
private String placeHoldElecCand = "Enter candidates names, one per line, candidates will appear in the same order as you specify.";
private String placeHoldElecUsers = "Enter users emails, one per line.";
private String tooltipElectionPassword = "Please specify a unique password which will be used to protect votes of this election.<br/> You will need this password in order to start tallying and publish the results of the election.<br/>WARNING: without this password, tallying of this election is impossible.";
/**
* @see HttpServlet#HttpServlet()
*/
public ElectionServlet() {
super();
}
/**
* Dmitriy Karmazin
* @see HttpServlet#doGet(HttpServletRequest request, HttpServletResponse response)
*/
protected void doGet(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException {
// check authentication
if (HeaderService.isTempUser(request)){
RequestDispatcher rd = getServletContext().getRequestDispatcher("/inviteduser");
rd.forward(request, response);
} else if(HeaderService.isAuthenticated(request)) {
resetGlobals();
routineExistingElections(request);
request.setAttribute("mode", mode);
request.setAttribute("message_alert", messageAlert);
request.setAttribute("message_label", messageLabel);
request.setAttribute("out_elections", outElections);
request.setAttribute("out_modal", outModal);
RequestDispatcher rd = getServletContext().getRequestDispatcher("/election.jsp");
rd.forward(request, response);
} else {
RequestDispatcher rd = getServletContext().getRequestDispatcher("/login");
rd.forward(request, response);
}
}
/**
* Dmitriy Karmazin
* @see HttpServlet#doPost(HttpServletRequest request, HttpServletResponse response)
*/
protected void doPost(HttpServletRequest request, HttpServletResponse response) throws ServletException, IOException {
if(HeaderService.isAuthenticated(request)) {
resetGlobals();
if (request.getParameter("button_add_election") != null) {
// SHOW NEW ELECTION SCREEN
routineAddNewElectionModal();
} else if (request.getParameter("save_new_election") != null) {
// ADDING A NEW ELECTION
routineAddNewElection(request);
} else if (request.getParameter("election") != null) {
// SHOW EDIT ELECTION SCREEN
routineEditElectionModal(request);
} else if (request.getParameter("save_edit_election") != null) {
// SAVE EDITED ELECTION
routineEditElectionSave(request);
} else if (request.getParameter("btn_elec_add_users") != null) {
// SHOW USERS SCREEN
routineElectionUsersModal(request);
} else if (request.getParameter("save_edit_election_users") != null) {
routineElectionUsers(request);
} else if (request.getParameter("btn_elec_open") != null ||
request.getParameter("btn_elec_close") != null) {
// PERFORM ACTION ON ELECTION
routineActionOnElection(request);
} else if(request.getParameter("btn_elec_publish") != null) {
// PUBLISH BUTTON PRESSED
routinePublishElectionModal(request);
} else if(request.getParameter("btn_elec_publish_with_password") != null) {
// PUBLISH BUTTON PRESSED
routinePublishElection(request);
}
// refresh existing elections
routineExistingElections(request);
request.setAttribute("mode", mode);
request.setAttribute("message_alert", messageAlert);
request.setAttribute("message_label", messageLabel);
request.setAttribute("out_elections", outElections);
request.setAttribute("out_modal", outModal);
RequestDispatcher rd = getServletContext().getRequestDispatcher(
"/election.jsp");
rd.forward(request, response);
} else {
RequestDispatcher rd = getServletContext().getRequestDispatcher("/login");
rd.forward(request, response);
}
}
/**
* Dmitriy Karmazin
* This function returns HTML output for all existing elections
* @param elections
* @return
*/
public String drawExistingElections(HttpServletRequest request, ArrayList<ElectionDto> elections) {
String out = "";
if(elections != null && elections.size() != 0) {
out += "<h5>Existing elections</h5>";
out += "<form action=\"election\" method=\"post\">";
out += "<table><thead><tr>";
out += "<th>Election Name</th>";
out += "<th>Election Status</th>";
out += "<th>Votes Collected</th>";
out += "<th>Eligible to Vote</th>";
out += "<th>Action</th>";
out += "</tr></thead><tbody>";
for (ElectionDto e : elections) {
int voted = 0, votersTotal = 0;
Validator v2 = TallyingService.voteProgressStatusForElection(request, e.getElectionId());
if(v2.isVerified()) {
ElectionProgressDto epd = (ElectionProgressDto) v2.getObject();
voted = epd.getTotalVotes();
votersTotal = epd.getTotalEligible();
}
String trClass = getElectionTableRowClass(e.getStatus());
out += "<tr class =\"" + trClass + "\">";
out += "<td class =\"" + trClass + "\">" + e.getElectionName() + "</td>";
out += "<td class =\"" + trClass + "\">" + drawElectionStatus(e.getStatus(), e.getStatusDescription()) + "</td>";
out += "<td class =\"" + trClass + "\">" + voted + " votes</td>";
out += "<td class =\"" + trClass + "\">" + votersTotal + "</td>";
out += "<td class =\"" + trClass + "\">" + drawElectionAction(e.getElectionId(), e.getStatus(), e.getElectionType()) + "</td>";
out += "</tr>";
}
out += "</tbody></table></form>";
} else {
out += "<div class=\"label secondary\">No elections exist yet</div>";
}
return out;
}
/**
* Dmitriy Karmazin
* This method draws HTML modal output for a new election
* @param e - election object to draw
* @return HTML output
*/
public String drawNewElection(ElectionDto e) {
String out = "", valElecName = "", valElecDesc = "", valElecCand = "",
valElecEndTime = "", valRegEmails = "", valUnRegEmails = "",
valPasswordErrorMessage = "", valElecCandErrorMessage = "", usersFieldStyle = "";
boolean valEmailListError = false, valPasswordError = false, valRequired = true, valElecCandError = false;
int valElecId = 0, valElecAvailability = ElectionType.PRIVATE.getCode();
// checking null case
if(e != null) {
valElecId = e.getElectionId();
valElecName = e.getElectionName();
valElecDesc = e.getElectionDescription();
valElecCand = e.getCandidatesListString();
valElecCandError = e.isCandidateListError();
valElecCandErrorMessage = e.getCandidateListErrorMessage();
valElecEndTime = e.getCloseDatetime();
valElecAvailability = e.getElectionType();
valRegEmails = e.getRegisteredEmailList();
valEmailListError = e.isEmailListError();
valUnRegEmails = (valEmailListError) ? e.getUnregisteredEmailList() : "";
valPasswordError = e.isPasswordError();
valPasswordErrorMessage = e.getPasswordErrorMessage();
}
if(valElecAvailability != ElectionType.PRIVATE.getCode()) {
usersFieldStyle = "style=\"display: none;\"";
valRequired = false;
}
out += "<form id=\"form_elec_new\" action=\"election\" method=\"post\" data-abide>";
out += "<div class=\"row\">";
out += "<h5>Add new election</h5>";
// draw election info
out += "<div class=\"large-6 medium-6 columns\">";
out += "<fieldset><legend>Election Information</legend>";
out += HtmlService.drawInputTextAlphanumeric("new_election_name", "Election Name", placeHoldElecName, valElecName);
out += HtmlService.drawInputTextareaAlphanumeric("new_election_description", "Election Description", placeHoldElecDesc, valElecDesc, false, "", true, "");
out += HtmlService.drawInputTextAlphanumericOptional("new_election_end_time", "Election Closing Time", placeHoldElecEndTime, valElecEndTime);
out += "</fieldset>";
// password
out += "<fieldset><legend>Protect election by password " + HtmlService.getToolTip(tooltipElectionPassword) + "</legend>";
out += HtmlService.drawInputTextPasswordAndConfirmation("new_election_password", "Election Password", "new_election_password_confirm", "Confirm Election Password", false);
out += "</fieldset>";
out += "</div>";
// column 2
out += "<div class=\"large-6 medium-6 columns\">";
// candidates
out += "<fieldset><legend>Add candidates</legend>";
out += HtmlService.drawInputTextareaAlphanumeric("new_election_candidates", "Candidates names", placeHoldElecCand, valElecCand, valElecCandError, valElecCandErrorMessage, true, "");
out += "</fieldset>";
// public and private
out += "<fieldset><legend>Election availability</legend>";
out += HtmlService.drawSelectBoxElectionPrivateOrPublic("new_election_availability", valElecAvailability);
// draw allowed users info
out += "<div id=\"new_election_users_column\" " + usersFieldStyle + ">";
out += HtmlService.drawInputTextareaAlphanumeric("new_election_users", "Users emails", placeHoldElecUsers, valRegEmails, valEmailListError, "Not all users are registered in the system.", valRequired, "");
out += "</div>";
// draw failed users select
out += "<div id=\"new_election_users_invite\" " + usersFieldStyle + ">";
out += HtmlService.drawCheckBoxesElectionPrivateOrPublic("new_election_users_invited", valEmailListError, valUnRegEmails);
out += "</div>";
out += "</fieldset>";
out += "</div>";
out += "</div>";
// button and password
out += "<div class=\"row\">";
out += "<div class=\"large-3 large-centered medium-3 medium-centered columns\">";
out += "<button class=\"radius button center\" type=\"submit\" name=\"save_new_election\" value=\"" + valElecId + "\">Save Election</button>";
out += "</div>";
out += "</div>";
out += "</form>";
return out;
}
/**
* Dmitriy Karmazin
* This function returns HTML output for editing election modal
* @param e
* @return
*/
public String drawEditElection(ElectionDto e) {
String out = "", valElecName = "", valElecDesc = "", valElecCand = "",
valElecEndTime = "", valRegEmails = "", valUnRegEmails = "", valElecCandErrorMessage = "", usersStyle = "";
int valElecId = 0, valElecAvailability = 0;
boolean valEmailListError = false, valElecCandError = false, valRequired = true;
// checking null case
if(e != null) {
valElecId = e.getElectionId();
valElecName = e.getElectionName();
valElecDesc = e.getElectionDescription();
valElecCand = e.getCandidatesListString();
valElecCandError = e.isCandidateListError();
valElecCandErrorMessage = e.getCandidateListErrorMessage();
valElecEndTime = e.getCloseDatetime();
valElecAvailability = e.getElectionType();
valRegEmails = e.getRegisteredEmailList();
valEmailListError = e.isEmailListError();
valUnRegEmails = (valEmailListError) ? e.getUnregisteredEmailList() : "";
}
if(valElecAvailability != ElectionType.PRIVATE.getCode()) {
usersStyle = "style=\"display: none;\"";
valRequired = false;
}
out += "<form id=\"form_elec_edit\" action=\"election\" method=\"post\" data-abide>";
out += "<div class=\"row\">";
out += "<h5>Edit election</h5>";
// draw election info
out += "<div class=\"large-6 medium-6 columns\">";
out += "<fieldset><legend>Election Information</legend>";
out += HtmlService.drawInputTextAlphanumeric("edit_election_name", "Election Name", placeHoldElecName, valElecName);
out += HtmlService.drawInputTextareaAlphanumeric("edit_election_description", "Election Description", placeHoldElecDesc, valElecDesc, false, "", true, "");
out += HtmlService.drawInputTextAlphanumericOptional("edit_election_end_time", "Election Closing Time", placeHoldElecEndTime, valElecEndTime);
out += "</fieldset>";
out += "<fieldset><legend>Add candidates</legend>";
out += HtmlService.drawInputTextareaAlphanumeric("edit_election_candidates", "Candidates names", placeHoldElecCand, valElecCand, valElecCandError, valElecCandErrorMessage, true, "");
out += "</fieldset>";
out += "</div>";
// draw allowed users info
out += "<div class=\"large-6 medium-6 columns\">";
out += "<fieldset><legend>Election availability</legend>";
out += HtmlService.drawSelectBoxElectionPrivateOrPublic("edit_election_availability", valElecAvailability);
// draw allowed users info
out += "<div id=\"edit_election_users_column\" " + usersStyle + ">";
out += HtmlService.drawInputTextareaAlphanumeric("edit_election_users", "Users emails", placeHoldElecUsers, valRegEmails, valEmailListError, "Not all users are registered in the system.", valRequired, "");
out += "</div>";
out += "<div id=\"edit_election_users_invite\" " + usersStyle + ">";
out += HtmlService.drawCheckBoxesElectionPrivateOrPublic("edit_election_users_invited", valEmailListError, valUnRegEmails);
out += "</div>";
out += "</fieldset>";
out += "</div>";
out += "</div>";
// button
out += "<div class=\"row\">";
out += "<div class=\"large-3 large-centered medium-3 medium-centered columns\">";
out += "<button class=\"radius button right\" type=\"submit\" name=\"save_edit_election\" value=\"" + valElecId + "\">Save Election</button>";
out += "</div>";
out += "</div>";
out += "</form>";
return out;
}
public String drawElectionUsers(ElectionDto e) {
String out = "", valElecName = "", valCurrentEmailList = "", valRegEmails = "",
valUnRegEmails = "", valEmailListErrorMessage = "";
int valElecId = 0;
boolean valEmailListError = false, valRequired = true;
// checking null case
if(e != null) {
valElecId = e.getElectionId();
valElecName = e.getElectionName();
valCurrentEmailList = e.getCurrentEmailList();
valRegEmails = e.getRegisteredEmailList();
valEmailListError = e.isEmailListError();
valEmailListErrorMessage = e.getEmailListMessage();
valUnRegEmails = (valEmailListError) ? e.getUnregisteredEmailList() : "";
}
out += "<h5>Add users to private election: " + valElecName + "</h5>";
out += "<form id=\"form_elec_edit\" action=\"election\" method=\"post\" data-abide>";
out += "<div class=\"row\">";
// draw election info
out += "<div class=\"large-6 medium-6 columns\">";
out += "<fieldset><legend>Existing Users</legend>";
out += HtmlService.drawInputTextareaReadonly("edit_election_users", "Existing users", "No users", valCurrentEmailList, "");
out += "</fieldset>";
out += "</div>";
// draw allowed users info
out += "<div id=\"edit_election_users_column\" class=\"large-6 medium-6 columns\">";
out += "<fieldset><legend>Invite additional users to vote</legend>";
out += HtmlService.drawInputTextareaAlphanumeric("edit_election_new_users", "Users emails", placeHoldElecUsers, valRegEmails, valEmailListError, "Not all users are registered in the system.", true, "");
out += HtmlService.drawCheckBoxesElectionPrivateOrPublic("edit_election_new_users_invited", valEmailListError, valUnRegEmails);
out += "</fieldset>";
out += "</div>";
out += "</div>";
// button
out += "<div class=\"row\">";
out += "<div class=\"large-3 large-centered medium-3 medium-centered columns\">";
out += "<button class=\"radius button right\" type=\"submit\" name=\"save_edit_election_users\" value=\"" + valElecId + "\">Save Election</button>";
out += "</div>";
out += "</div>";
out += "</form>";
return out;
}
/**
* Dmitriy Karmazin
* This function returns HTML output for action for given election and it's status
* @param electionId
* @param statusId
* @return
*/
public String drawElectionAction(int electionId, int statusId, int electionTypeId) {
String out = "";
if(statusId == ElectionStatus.NEW.getCode()) {
out += "<button class=\"label radius\" type=\"submit\" name=\"btn_elec_open\" value=\"" + electionId + "\">Open</button>";
out += " / ";
out += "<button class=\"label radius\" type=\"submit\" name=\"election\" value=\"" + electionId + "\">Edit</button>";
} else if(statusId == ElectionStatus.OPEN.getCode()) {
out += "<button class=\"label radius\" type=\"submit\" name=\"btn_elec_close\" value=\"" + electionId + "\">Close</button>";
if(electionTypeId == ElectionType.PRIVATE.getCode()) {
out += " / ";
out += "<button class=\"label radius\" type=\"submit\" name=\"btn_elec_add_users\" value=\"" + electionId + "\">Add users</button>";
}
} else if(statusId == ElectionStatus.CLOSED.getCode()) {
out += "<button class=\"label radius\" type=\"submit\" name=\"btn_elec_open\" value=\"" + electionId + "\">Reopen</button>";
out += " / ";
out += "<button class=\"label radius\" type=\"submit\" name=\"btn_elec_publish\" value=\"" + electionId + "\">Publish</button>";
} else if(statusId == ElectionStatus.PUBLISHED.getCode()) {
out += "";
}
return out;
}
public String getElectionTableRowClass(int statusId) {
String out = "";
if(statusId == ElectionStatus.NEW.getCode()) {
out += "election_new";
} else if(statusId == ElectionStatus.OPEN.getCode()) {
out += "election_open";
} else if(statusId == ElectionStatus.CLOSED.getCode()) {
out += "election_closed";
} else if(statusId == ElectionStatus.PUBLISHED.getCode()) {
out += "election_published";
}
return out;
}
/**
* Dmitriy Karmazin
* @param status - current status of election
* @param value - string representation of status
* @return
*/
public String drawElectionStatus(int status, String value) {
String out = "", outClass="";
if(status == ElectionStatus.NEW.getCode()) {
outClass = "label clear";
} else if(status == ElectionStatus.OPEN.getCode()) {
outClass = "label clear";
} else if(status == ElectionStatus.CLOSED.getCode()) {
outClass = "label clear";
} else if(status == ElectionStatus.PUBLISHED.getCode()) {
outClass = "label clear";
} else {
return out;
}
out = "<span class=\"" + outClass + "\">" + value + "</span>";
return out;
}
/**
* Dmitriy Karmazin
* This function returns HTML output for edit button for an eletion
*/
public String drawElectionEdit(int electionId, int statusId) {
String out = "";
if(statusId == ElectionStatus.NEW.getCode()) {
out += "<button class=\"label button_link radius\" type=\"submit\" name=\"election\" value=\"" + electionId + "\">Edit</button></td>";
}
return out;
}
/**
* Dmitriy Karmazin
* This functions resets all global variables for this class
*/
private void resetGlobals() {
this.mode = "1";
this.messageAlert = "";
this.messageLabel = "";
this.outModal = "";
this.outElections = "";
}
/**
* Dmitriy Karmazin
* This function sets global variables to display existing elections
*/
public void routineExistingElections(HttpServletRequest request) {
// get the list of elections from DB
ArrayList<ElectionDto> allElections = new ArrayList<ElectionDto>();
Validator v = ElectionService.selectElectionsForOwner(request, HeaderService.getUserId(request));
if(v.isVerified()) {
allElections = (ArrayList<ElectionDto>) v.getObject();
} else {
messageAlert = HtmlService.drawMessageAlert(v.getStatus(), "alert") ;
}
outElections = drawExistingElections(request, allElections);
}
/**
* Dmitriy Karmazin
* This function makes required actions to insert a new election to DB
* @param request
*/
public void routineAddNewElection(HttpServletRequest request) {
resetGlobals();
// prepare new election
ElectionDto newElection = new ElectionDto();
newElection.setElectionName(request.getParameter("new_election_name"));
newElection.setElectionDescription(request.getParameter("new_election_description"));
newElection.setCandidatesListString(request.getParameter("new_election_candidates"));
newElection.setCloseDatetime(request.getParameter("new_election_end_time"));
newElection.setElectionType(Integer.parseInt(request.getParameter("new_election_availability")));
newElection.setEmailList(request.getParameter("new_election_users"));
newElection.setPassword(request.getParameter("new_election_password"));
newElection.setEmailListInvited(getStringFromArray(request.getParameterValues("new_election_users_invited")));
newElection.setOwnerId(HeaderService.getUserId(request));
// insert attempt
Validator vElection = ElectionService.addElection(request, newElection);
if (vElection.isVerified()) {
//insert was successful
mode = "1";
messageAlert = HtmlService.drawMessageAlert(vElection.getStatus(), "success");
} else {
// errors, send back to add election screen
mode = "2";
messageLabel = HtmlService.drawMessageLabel(vElection.getStatus(), "alert");
outModal = drawNewElection((ElectionDto)vElection.getObject());
}
}
/**
* Dmitriy Karmazin
* This function performs required routines to open edit modal
* @param request
*/
public void routineEditElectionModal(HttpServletRequest request) {
resetGlobals();
// get election by provided election id
int electionId = Integer.parseInt(request.getParameter("election"));
Validator vEditElection = ElectionService.selectElectionForOwner(request, electionId);
if (vEditElection.isVerified()) {
ElectionDto editElection = (ElectionDto) vEditElection.getObject();
this.mode = "2";
this.outModal = drawEditElection(editElection);
} else {
messageAlert = HtmlService.drawMessageAlert(vEditElection.getStatus(), "alert");
}
}
/**
* Dmitriy Karmazin
* This performs routines required to update an existing election
* @param request
*/
public void routineEditElectionSave(HttpServletRequest request) {
resetGlobals();
String usersToInvite = getStringFromArray(request.getParameterValues("edit_election_users_invited"));
ElectionDto editElection = new ElectionDto();
editElection.setElectionId(Integer.parseInt(request.getParameter("save_edit_election")));
editElection.setElectionName(request.getParameter("edit_election_name"));
editElection.setElectionDescription(request.getParameter("edit_election_description"));
editElection.setCandidatesListString(request.getParameter("edit_election_candidates"));
editElection.setCloseDatetime(request.getParameter("edit_election_end_time"));
editElection.setElectionType(Integer.parseInt(request.getParameter("edit_election_availability")));
editElection.setEmailList(request.getParameter("edit_election_users"));
editElection.setEmailListInvited(getStringFromArray(request.getParameterValues("edit_election_users_invited")));
editElection.setOwnerId(HeaderService.getUserId(request));
// update existing election
Validator vEditElection = ElectionService.editElection(request, editElection);
if (vEditElection.isVerified()) {
// insert of candidates was successful
this.mode = "1";
this.messageAlert = HtmlService.drawMessageAlert(
vEditElection.getStatus(), "success");
} else {
// error, return to editing screen
this.mode = "2";
this.messageLabel = HtmlService.drawMessageLabel(
vEditElection.getStatus(), "alert");
this.outModal = drawEditElection((ElectionDto) vEditElection.getObject());
}
}
/**
* Dmitriy Karmazin
* This function performs required actions to show add new election modal
*/
public void routineAddNewElectionModal() {
resetGlobals();
mode = "2";
messageLabel = HtmlService.drawMessageLabel("Please fill in required fields", "secondary");
outModal = drawNewElection(null);
}
/**
* Dmitriy Karmazin
* This function performs a particular action on given election
* @param request
*/
public void routineActionOnElection(HttpServletRequest request) {
resetGlobals();
// get election id
int electionId = 0, action = -1;
if(request.getParameter("btn_elec_open") != null) {
electionId = Integer.parseInt(request.getParameter("btn_elec_open"));
action = ElectionStatus.OPEN.getCode();
} else if(request.getParameter("btn_elec_close") != null) {
electionId = Integer.parseInt(request.getParameter("btn_elec_close"));
} else if(request.getParameter("btn_elec_publish") != null) {
electionId = Integer.parseInt(request.getParameter("btn_elec_publish"));
action = ElectionStatus.PUBLISHED.getCode();
}
Validator v1 = ElectionService.selectElectionForOwner(request, electionId);
if (v1.isVerified()) {
ElectionDto e = (ElectionDto) v1.getObject();
if (e.getStatus() == ElectionStatus.NEW.getCode()) {
// open election
Validator v2 = ElectionService.openElection(request, electionId);
messageAlert = HtmlService.drawMessageAlert(
v2.getStatus(), "");
} else if (e.getStatus() == ElectionStatus.OPEN.getCode()) {
// close election
Validator v3 = ElectionService
.closeElection(request, electionId);
messageAlert = HtmlService.drawMessageAlert(
v3.getStatus(), "success");
} else if (e.getStatus() == ElectionStatus.CLOSED.getCode() && action == ElectionStatus.OPEN.getCode()) {
// reopen
Validator v4 = ElectionService.reOpenElection(request, electionId);
messageAlert = HtmlService.drawMessageAlert(
v4.getStatus(), "success");
}
} else {
messageAlert = HtmlService.drawMessageAlert(
v1.getStatus(), "alert");
}
}
/**
* Dmitriy Karmazin
* This function performs all routines required to display users editing modal
* @param request
*/
public void routineElectionUsersModal(HttpServletRequest request) {
resetGlobals();
int electionId = 0;
if(request.getParameter("btn_elec_add_users") != null) {
electionId = Integer.parseInt(request.getParameter("btn_elec_add_users"));
}
Validator vElectionUsers = ElectionService.selectElectionFullDetail(request, electionId);
if (vElectionUsers.isVerified()) {
ElectionDto editElection = (ElectionDto) vElectionUsers.getObject();
this.mode = "2";
this.outModal = drawElectionUsers(editElection);
} else {
messageAlert = HtmlService.drawMessageAlert(vElectionUsers.getStatus(), "alert");
}
}
public void routineElectionUsers(HttpServletRequest request) {
resetGlobals();
int electionId = 0;
if(request.getParameter("save_edit_election_users") != null) {
electionId = Integer.parseInt(request.getParameter("save_edit_election_users"));
}
// prepare new election
ElectionDto newElection = new ElectionDto();
newElection.setElectionId(electionId);
newElection.setEmailList(request.getParameter("edit_election_new_users"));
newElection.setEmailListInvited(getStringFromArray(request.getParameterValues("edit_election_new_users_invited")));
newElection.setOwnerId(HeaderService.getUserId(request));
// insert attempt
Validator vElection = ElectionService.addAdditionalUsersToElection(request, newElection);
if (vElection.isVerified()) {
//insert was successful
mode = "1";
messageAlert = HtmlService.drawMessageAlert(vElection.getStatus(), "success");
} else {
// errors, send back to add election screen
mode = "2";
messageLabel = HtmlService.drawMessageLabel(vElection.getStatus(), "alert");
outModal = drawElectionUsers((ElectionDto) vElection.getObject());
}
}
/**
* Dmitriy Karmazin
* This function performs all activities to display modal before publishing election results
* @param request
*/
public void routinePublishElectionModal(HttpServletRequest request) {
resetGlobals();
int electionId = 0;
if(request.getParameter("btn_elec_publish") != null) {
electionId = Integer.parseInt(request.getParameter("btn_elec_publish"));
}
Validator vEditElection = ElectionService.selectElectionForOwner(request, electionId);
if (vEditElection.isVerified()) {
this.mode = "2";
this.outModal = drawPasswordWithConfirmForElection((ElectionDto) vEditElection.getObject());
} else {
messageAlert = HtmlService.drawMessageAlert(vEditElection.getStatus(), "alert");
}
}
/**
* Dmitriy Karmazin
* This function returns HTML output for password modal
* @param e
* @return
*/
public String drawPasswordWithConfirmForElection(ElectionDto e) {
String out = "", valElecName = "", valPasswordErrorMessage = "";
int valElecId = 0;
boolean valPasswordError = false;
// checking null case
if(e != null) {
valElecId = e.getElectionId();
valElecName = e.getElectionName();
valPasswordError = e.isPasswordError();
valPasswordErrorMessage = (valPasswordError) ? "Invalid password" : "";
}
out += "<form id=\"form_elec_new\" action=\"election\" method=\"post\" data-abide>";
out += "<div class=\"row\">";
out += "<div class=\"large-6 large-centered medium-6 medium-centered columns\">";
out += "<h5>Publish Election Results: " + valElecName + "</h5>";
out += "<fieldset><legend>Please Enter Election Password</legend>";
out += "<p class=\"global_warning\">Warning! Election publishing is irrevocable action.<br>The results of this election will become available to voters and you will not be able to reopen this election anymore.<br> Enter election password and click 'Publish Election' to proceed or click 'Cancel Publishing' otherwise.</p>";
out += HtmlService.drawInputTextPassword("election_publish_password", "Election Password", "", "", valPasswordError, valPasswordErrorMessage);
out += "</fieldset>";
out += "<button class=\"radius button left\" type=\"submit\" name=\"btn_elec_publish_with_password\" value=\"" + valElecId + "\">Publish Election</button>";
out += "<button class=\"button alert right\" type=\"button\" id=\"btn_elec_publish_cancel\" \">Cancel Publishing</button>";
out += "</div>";
out += "</div>";
out += "</form>";
return out;
}
/**
* Dmitriy Karmazin
* This function performes routines required for publishing an election
* @param request
*/
public void routinePublishElection(HttpServletRequest request) {
resetGlobals();
int electionId = 0;
String password = "";
if(request.getParameter("btn_elec_publish_with_password") != null) {
electionId = Integer.parseInt(request.getParameter("btn_elec_publish_with_password"));
}
if(request.getParameter("election_publish_password") != null) {
password = request.getParameter("election_publish_password");
}
Validator v1 = ElectionService.publishResults(request, electionId, password);
if(v1.isVerified()) {
messageAlert = HtmlService.drawMessageAlert("Election published", "success");
} else {
mode = "2";
outModal = drawPasswordWithConfirmForElection((ElectionDto) v1.getObject());
messageLabel = HtmlService.drawMessageLabel(v1.getStatus(), "alert");
}
}
/**
* Dmitriy Karmazin
* This function returns string out of given array
* @param arrayOfStrings
* @return
*/
public String getStringFromArray(String[] arrayOfStrings) {
String out = "";
String deliminter = System.getProperty("line.separator");
if(arrayOfStrings != null) {
for(String str : arrayOfStrings) {
out += str + deliminter;
}
}
return out;
}
}
|
package org.jboss.xnio;
/**
* The version class.
*/
public final class Version {
private Version() {}
/**
* The current XNIO version.
*/
public static final String VERSION = "1.0.0.CR1";
/**
* Print out the current XNIO version on {@code System.out}.
*
* @param args ignored
*/
public static void main(String[] args) {
System.out.print(VERSION);
}
}
|
package com.exedio.cope;
import java.io.File;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.PrintStream;
import java.util.Arrays;
import java.util.Date;
import java.util.Iterator;
import com.exedio.cope.testmodel.AttributeItem;
import com.exedio.cope.testmodel.Main;
/**
* Tests the model itself, without creating/using any persistent data.
* @author Ralf Wiebicke
*/
public class ModelTest extends TestmodelTest
{
public void testSupportsReadCommitted()
{
assertEquals( true, model.hasCurrentTransaction() );
assertEquals(dialect.supportsReadCommitted, model.supportsReadCommitted());
}
public static final void assertEquals(final String expected, final String actual)
{
assertEquals("
}
public void testConnect()
{
final Properties defaultProps = getProperties();
// test duplicate call of connect
final Date connectDate = model.getConnectDate();
assertNotNull(connectDate);
try
{
model.connect(defaultProps);
fail();
}
catch(IllegalStateException e)
{
assertEquals("model already been connected", e.getMessage());
}
assertSame(connectDate, model.getConnectDate());
}
@Deprecated // OK: test deprecated api
public void testAttributeOption() throws IOException
{
final AttributeItem item = null;
assertEquals(false, item.MANDATORY.isFinal);
assertEquals(false, item.MANDATORY.unique);
assertEquals(false, item.MANDATORY.optional);
assertEquals(false, item.OPTIONAL.isFinal);
assertEquals(false, item.OPTIONAL.unique);
assertEquals(true, item.OPTIONAL.optional);
assertEquals(false, item.UNIQUE.isFinal);
assertEquals(true, item.UNIQUE.unique);
assertEquals(false, item.UNIQUE.optional);
assertEquals(false, item.UNIQUE_OPTIONAL.isFinal);
assertEquals(true, item.UNIQUE_OPTIONAL.unique);
assertEquals(true, item.UNIQUE_OPTIONAL.optional);
assertEquals(true, item.FINAL.isFinal);
assertEquals(false, item.FINAL.unique);
assertEquals(false, item.FINAL.optional);
assertEquals(true, item.FINAL_OPTIONAL.isFinal);
assertEquals(false, item.FINAL_OPTIONAL.unique);
assertEquals(true, item.FINAL_OPTIONAL.optional);
assertEquals(true, item.FINAL_UNIQUE.isFinal);
assertEquals(true, item.FINAL_UNIQUE.unique);
assertEquals(false, item.FINAL_UNIQUE.optional);
assertEquals(true, item.FINAL_UNIQUE_OPTIONAL.isFinal);
assertEquals(true, item.FINAL_UNIQUE_OPTIONAL.unique);
assertEquals(true, item.FINAL_UNIQUE_OPTIONAL.optional);
}
public void testType() throws IOException
{
final AttributeItem item = null;
assertEquals(AttributeItem.class, item.TYPE.getJavaClass());
assertEquals(true, item.TYPE.hasUniqueJavaClass());
assertEquals(item.TYPE, Type.findByJavaClass(AttributeItem.class));
try
{
Type.findByJavaClass(Item.class);
fail();
}
catch(IllegalArgumentException e)
{
assertEquals("there is no type for class com.exedio.cope.Item", e.getMessage());
}
assertEquals(item.TYPE, model.findTypeByID(item.TYPE.getID()));
assertSame(item.TYPE, item.TYPE.getThis().getType());
assertEquals("AttributeItem.this", item.TYPE.getThis().getID());
assertEquals("AttributeItem.this", item.TYPE.getThis().toString());
assertEquals("this", item.TYPE.getThis().getName());
final Field[] attributes = {
item.someString,
item.someNotNullString,
item.someInteger,
item.someNotNullInteger,
item.someLong,
item.someNotNullLong,
item.someDouble,
item.someNotNullDouble,
item.someDate,
item.day,
item.someBoolean,
item.someNotNullBoolean,
item.someItem,
item.someNotNullItem,
item.someEnum,
item.someNotNullEnum,
item.someData.getBody(),
item.someData.getContentType(),
item.someData.getLastModified(),
};
assertEqualsUnmodifiable(Arrays.asList(attributes), item.TYPE.getFields());
assertEqualsUnmodifiable(Arrays.asList(attributes), item.TYPE.getDeclaredFields());
assertEqualsUnmodifiable(list(), item.TYPE.getUniqueConstraints());
assertEqualsUnmodifiable(list(), item.TYPE.getDeclaredUniqueConstraints());
final Feature[] features = {
item.TYPE.getThis(),
item.someString,
item.someStringUpperCase,
item.someStringLength,
item.someNotNullString,
item.someInteger,
item.someNotNullInteger,
item.someLong,
item.someNotNullLong,
item.someDouble,
item.someNotNullDouble,
item.someDate,
item.day,
item.someBoolean,
item.someNotNullBoolean,
item.someItem,
item.someNotNullItem,
item.someEnum,
item.someNotNullEnum,
item.someData,
item.someData.getBody(),
item.someData.getContentType(),
item.someData.getLastModified(),
};
assertEqualsUnmodifiable(Arrays.asList(features), item.TYPE.getFeatures());
assertEqualsUnmodifiable(Arrays.asList(features), item.TYPE.getDeclaredFeatures());
assertEquals(item.someString, item.TYPE.getDeclaredFeature("someString"));
assertEquals(item.someStringUpperCase, item.TYPE.getDeclaredFeature("someStringUpperCase"));
try
{
new Type<Item>(null);
fail();
}
catch(NullPointerException e)
{}
try
{
new Type<Item>(Item.class);
fail();
}
catch(IllegalArgumentException e)
{
assertEquals("Cannot make a type for " + Item.class + " itself, but only for subclasses.", e.getMessage());
}
try
{
new Type<Item>(castItemClass(NoItem.class));
fail();
}
catch(IllegalArgumentException e)
{
assertEquals(NoItem.class.toString() + " is not a subclass of Item", e.getMessage());
}
try
{
new Type<NoCreationConstructor>(NoCreationConstructor.class);
fail();
}
catch(IllegalArgumentException e)
{
assertEquals(
NoCreationConstructor.class.getName() +
" does not have a creation constructor", e.getMessage());
assertEquals(NoSuchMethodException.class, e.getCause().getClass());
}
try
{
new Type<NoReactivationConstructor>(NoReactivationConstructor.class);
fail();
}
catch(IllegalArgumentException e)
{
assertEquals(e.getMessage(),
NoReactivationConstructor.class.getName() +
" does not have a reactivation constructor", e.getMessage());
assertEquals(NoSuchMethodException.class, e.getCause().getClass());
}
try
{
new Model((Type[])null);
fail();
}
catch(NullPointerException e)
{
assertEquals("types must not be null", e.getMessage());
}
try
{
new Model(new Type[]{});
fail();
}
catch(IllegalArgumentException e)
{
assertEquals("types must not be empty", e.getMessage());
}
// TODO put this into an extra test called an extra ant target
{
final String prefix = System.getProperty("com.exedio.cope.testprotocol.prefix");
if(prefix!=null)
{
final java.util.Properties databaseInfo = model.getDatabaseInfo();
final java.util.Properties prefixed = new java.util.Properties();
final File file = new File(System.getProperty("com.exedio.cope.testprotocol.file"));
for(Iterator i = databaseInfo.keySet().iterator(); i.hasNext(); )
{
final String name = (String)i.next();
prefixed.setProperty(prefix+'.'+name, databaseInfo.getProperty(name));
}
final Properties p = model.getProperties();
for(final Properties.Field field : p.getFields())
{
if(field.getDefaultValue()!=null
&& field!=p.mediaRooturl
&& !field.hasHiddenValue()
&& field.isSpecified()
&& field.getValue()!=null)
prefixed.setProperty(prefix+".cope."+field.getKey(), field.getValue().toString());
}
final PrintStream out = new PrintStream(new FileOutputStream(file, true));
prefixed.store(out, null);
out.close();
}
}
}
static class NoItem
{
NoItem()
{
// just a dummy constructor
}
}
static class NoCreationConstructor extends Item
{
private static final long serialVersionUID = 1l;
NoCreationConstructor()
{
super(new SetValue[]{});
}
}
static class NoReactivationConstructor extends Item
{
private static final long serialVersionUID = 1l;
NoReactivationConstructor(final SetValue[] initialAttributes)
{
super(initialAttributes);
}
}
@SuppressWarnings("unchecked") // OK: test bad API usage
private static final Class<Item> castItemClass(Class c)
{
return c;
}
public void testDisconnect()
{
assertWithin(Main.beforeModel, Main.afterModel, model.getInitializeDate());
model.commit();
final Properties p = model.getProperties();
assertNotNull(p);
model.disconnect();
try
{
model.getProperties();
fail();
}
catch(IllegalStateException e)
{
assertEquals("model not yet connected, use connect(Properties)", e.getMessage());
}
assertEquals(null, model.getConnectDate());
try
{
model.disconnect();
fail();
}
catch(IllegalStateException e)
{
assertEquals("model not yet connected, use connect(Properties)", e.getMessage());
}
assertEquals(null, model.getConnectDate());
final Date before = new Date();
model.connect(p);
final Date after = new Date();
assertSame(p, model.getProperties());
assertWithin(before, after, model.getConnectDate());
model.startTransaction("ModelTest.testDisconnect");
}
}
|
package io.debezium.connector.postgresql.connection.wal2json;
import java.sql.SQLException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import org.apache.kafka.connect.data.Field;
import org.apache.kafka.connect.errors.ConnectException;
import org.postgresql.core.Oid;
import org.postgresql.geometric.PGpoint;
import org.postgresql.jdbc.PgArray;
import org.postgresql.util.PGInterval;
import org.postgresql.util.PGmoney;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import io.debezium.connector.postgresql.PostgresValueConverter;
import io.debezium.connector.postgresql.RecordsStreamProducer.PgConnectionSupplier;
import io.debezium.connector.postgresql.connection.ReplicationMessage;
import io.debezium.document.Array;
import io.debezium.document.Document;
import io.debezium.document.Value;
import io.debezium.util.Strings;
/**
* Replication message representing message sent by the wal2json logical decoding plug-in.
*
* @author Jiri Pechanec
*/
class Wal2JsonReplicationMessage implements ReplicationMessage {
private static final Logger LOGGER = LoggerFactory.getLogger(Wal2JsonReplicationMessage.class);
private final int txId;
private final long commitTime;
private final Document rawMessage;
public Wal2JsonReplicationMessage(final int txId, final long commitTime, final Document rawMessage) {
this.txId = txId;
this.commitTime = commitTime;
this.rawMessage = rawMessage;
}
@Override
public Operation getOperation() {
final String operation = rawMessage.getString("kind");
switch (operation) {
case "insert":
return Operation.INSERT;
case "update":
return Operation.UPDATE;
case "delete":
return Operation.DELETE;
}
throw new IllegalArgumentException(
"Unknown operation '" + operation + "' in replication stream message");
}
@Override
public long getCommitTime() {
return commitTime;
}
@Override
public int getTransactionId() {
return txId;
}
@Override
public String getTable() {
return "\"" + rawMessage.getString("schema") + "\".\"" + rawMessage.getString("table") + "\"";
}
@Override
public List<ReplicationMessage.Column> getOldTupleList() {
final Document oldkeys = rawMessage.getDocument("oldkeys");
return oldkeys != null ? transform(oldkeys, "keynames", "keytypes", "keyvalues") : null;
}
@Override
public List<ReplicationMessage.Column> getNewTupleList() {
return transform(rawMessage, "columnnames", "columntypes", "columnvalues");
}
private List<ReplicationMessage.Column> transform(final Document data, final String nameField, final String typeField, final String valueField) {
final Array columnNames = data.getArray(nameField);
final Array columnTypes = data.getArray(typeField);
final Array columnValues = data.getArray(valueField);
if (columnNames.size() != columnTypes.size() || columnNames.size() != columnValues.size()) {
throw new ConnectException("Column related arrays do not have the same size");
}
final List<ReplicationMessage.Column> columns = new ArrayList<>(columnNames.size());
for (int i = 0; i < columnNames.size(); i++) {
String columnName = columnNames.get(i).asString();
String columnType = columnTypes.get(i).asString();
Value rawValue = columnValues.get(i);
columns.add(new ReplicationMessage.Column() {
@Override
public Object getValue(PgConnectionSupplier connection) {
return Wal2JsonReplicationMessage.this.getValue(columnName, columnType, rawValue, connection);
}
@Override
public String getType() {
return columnType;
}
@Override
public String getName() {
return columnName;
}
});
}
return columns;
}
/**
* Converts the value (string representation) coming from wal2json plugin to
* a Java value based on the type of the column from the message. This value will be converted later on if necessary by the
* {@link PostgresValueConverter#converter(Column, Field)} instance to match whatever the Connect schema type expects.
*
* Note that the logic here is tightly coupled (i.e. dependent) on the wal2json plugin logic which writes the actual
* JSON messages.
* @param a supplier to get a connection to Postgres instance for array handling
*
* @return the value; may be null
*/
public Object getValue(String columnName, String columnType, Value rawValue, final PgConnectionSupplier connection) {
switch (columnType) {
case "bool":
return rawValue.isNotNull() ? rawValue.asBoolean() : null;
case "int2":
case "int4":
return rawValue.isNotNull() ? rawValue.asInteger() : null;
case "int8":
case "oid":
return rawValue.isNotNull() ? rawValue.asLong() : null;
case "float4":
return rawValue.isNotNull() ? rawValue.asFloat() : null;
case "float8":
return rawValue.isNotNull() ? rawValue.asDouble() : null;
case "numeric":
return rawValue.isNotNull() ? rawValue.asDouble() : null;
case "char":
case "varchar":
case "bpchar":
case "text":
case "json":
case "jsonb":
case "xml":
case "uuid":
case "bit":
case "varbit":
case "tstzrange":
return rawValue.isNotNull() ? rawValue.asString() : null;
case "date":
return rawValue.isNotNull() ? DateTimeFormat.get().date(rawValue.asString()) : null;
case "timestamp":
return rawValue.isNotNull() ? DateTimeFormat.get().timestamp(rawValue.asString()) : null;
case "timestamptz":
return rawValue.isNotNull() ? DateTimeFormat.get().timestampWithTimeZone(rawValue.asString()) : null;
case "time":
return rawValue.isNotNull() ? DateTimeFormat.get().time(rawValue.asString()) : null;
case "timetz":
return rawValue.isNotNull() ? DateTimeFormat.get().timeWithTimeZone(rawValue.asString()) : null;
case "bytea":
return Strings.hexStringToByteArray(rawValue.asString());
case "point":
try {
return rawValue.isNotNull() ? new PGpoint(rawValue.asString()) : null;
} catch (final SQLException e) {
LOGGER.error("Failed to parse point {}, {}", rawValue.asString(), e);
throw new ConnectException(e);
}
case "money":
try {
return rawValue.isNotNull() ? new PGmoney(rawValue.asString()).val : null;
} catch (final SQLException e) {
LOGGER.error("Failed to parse money {}, {}", rawValue.asString(), e);
throw new ConnectException(e);
}
case "interval":
try {
return rawValue.isNotNull() ? new PGInterval(rawValue.asString()) : null;
} catch (final SQLException e) {
LOGGER.error("Failed to parse point {}, {}", rawValue.asString(), e);
throw new ConnectException(e);
}
case "_int2":
case "_int4":
case "_int8":
case "_text":
case "_numeric":
case "_float4":
case "_float8":
case "_bool":
case "_date":
case "_time":
case "_timetz":
case "_timestamp":
case "_timestamptz":
case "_bytea":
case "_varchar":
case "_oid":
case "_bpchar":
case "_money":
case "_name":
case "_interval":
case "_char":
case "_varbit":
case "_uuid":
case "_xml":
case "_point":
case "_jsonb":
case "_json":
case "_ref_cursor":
try {
if (rawValue.isNull()) {
return null;
}
final String dataString = rawValue.asString();
PgArray arrayData = new PgArray(connection.get(), Oid.valueOf(columnType.substring(1) + "_array"), dataString);
Object deserializedArray = arrayData.getArray();
return Arrays.asList((Object[])deserializedArray);
}
catch (SQLException e) {
LOGGER.warn("Unexpected exception trying to process PgArray column '{}'", columnName, e);
}
return null;
}
LOGGER.warn("processing column '{}' with unknown data type '{}' as byte array", columnName,
columnType);
return rawValue.asBytes();
}
}
|
package org.drools.planner.core.localsearch.decider.acceptor.tabu;
import org.drools.planner.core.localsearch.LocalSearchSolverPhaseScope;
import org.drools.planner.core.localsearch.LocalSearchStepScope;
import org.drools.planner.core.localsearch.decider.MoveScope;
import org.drools.planner.core.move.Move;
import org.drools.planner.core.score.buildin.simple.DefaultSimpleScore;
import org.drools.planner.core.solver.DefaultSolverScope;
import org.drools.planner.core.testdata.domain.TestdataValue;
import org.junit.Test;
import java.util.Arrays;
import java.util.Collection;
import static org.junit.Assert.assertEquals;
import static org.mockito.Mockito.mock;
import static org.mockito.Mockito.when;
public class PlanningValueTabuAcceptorTest {
@Test
public void tabuSize() {
PlanningValueTabuAcceptor acceptor = new PlanningValueTabuAcceptor();
acceptor.setTabuSize(2);
acceptor.setAspirationEnabled(true);
TestdataValue v0 = new TestdataValue("v0");
TestdataValue v1 = new TestdataValue("v1");
TestdataValue v2 = new TestdataValue("v2");
TestdataValue v3 = new TestdataValue("v3");
TestdataValue v4 = new TestdataValue("v4");
DefaultSolverScope solverScope = new DefaultSolverScope();
solverScope.setBestScore(new DefaultSimpleScore(0));
LocalSearchSolverPhaseScope solverPhaseScope = new LocalSearchSolverPhaseScope(solverScope);
acceptor.phaseStarted(solverPhaseScope);
//FIRST STEP: no values in tabuList, acceptor should accept everything.
LocalSearchStepScope stepScope0 = new LocalSearchStepScope(solverPhaseScope);
stepScope0.setStepIndex(0);
MoveScope moveScope1 = buildMoveScope(stepScope0, v1);
assertEquals(true, acceptor.isAccepted(buildMoveScope(stepScope0, v0)));
assertEquals(true, acceptor.isAccepted(moveScope1));
assertEquals(true, acceptor.isAccepted(buildMoveScope(stepScope0, v2)));
assertEquals(true, acceptor.isAccepted(buildMoveScope(stepScope0, v3)));
assertEquals(true, acceptor.isAccepted(buildMoveScope(stepScope0, v4)));
//Repeated calls containing values which are not in tabuList should get accepted too.
assertEquals(true, acceptor.isAccepted(buildMoveScope(stepScope0, v2)));
//We accept first move, v1 should be added to tabuList
stepScope0.setStep(moveScope1.getMove());
acceptor.stepEnded(stepScope0);
//SECOND STEP: v1 in tabuList, acceptor should accept every move
//except a move containing v1
LocalSearchStepScope stepScope1 = new LocalSearchStepScope(solverPhaseScope);
stepScope1.setStepIndex(1);
MoveScope moveScope2 = buildMoveScope(stepScope1, v2);
assertEquals(true, acceptor.isAccepted(buildMoveScope(stepScope1, v0)));
//moves containing values which are in tabuList should not get accepted
assertEquals(false, acceptor.isAccepted(buildMoveScope(stepScope1, v1)));
//Any amount of repeated calls containing moves with values which are in tabuList
//should get rejected too
assertEquals(false, acceptor.isAccepted(buildMoveScope(stepScope1, v1)));
assertEquals(false, acceptor.isAccepted(buildMoveScope(stepScope1, v1)));
assertEquals(false, acceptor.isAccepted(buildMoveScope(stepScope1, v1)));
assertEquals(true, acceptor.isAccepted(moveScope2));
assertEquals(true, acceptor.isAccepted(buildMoveScope(stepScope1, v3)));
assertEquals(true, acceptor.isAccepted(buildMoveScope(stepScope1, v4)));
//Repeated calls for same move containing values which are not in tabuList should get accepted too.
assertEquals(true, acceptor.isAccepted(buildMoveScope(stepScope1, v2)));
//We accept move with v2, tabuList should contain v1 and v2
stepScope1.setStep(moveScope2.getMove());
acceptor.stepEnded(stepScope1);
//3rd STEP: v1 & v2 in tabuList, acceptor should accept every move
//except a move containing v1 and v2
LocalSearchStepScope stepScope2 = new LocalSearchStepScope(solverPhaseScope);
stepScope2.setStepIndex(2);
MoveScope moveScope4 = buildMoveScope(stepScope2, v4);
assertEquals(true, acceptor.isAccepted(buildMoveScope(stepScope2, v0)));
//moves containing values which are in tabuList should not get accepted
assertEquals(false, acceptor.isAccepted(buildMoveScope(stepScope2, v1)));
//moves containing values which are in tabuList should not get accepted
assertEquals(false, acceptor.isAccepted(buildMoveScope(stepScope2, v2)));
assertEquals(true, acceptor.isAccepted(buildMoveScope(stepScope2, v3)));
assertEquals(true, acceptor.isAccepted(moveScope4));
//Repeated calls for same move containing values which are in tabuList should not get accepted either
assertEquals(false, acceptor.isAccepted(buildMoveScope(stepScope2, v2)));
//We accept move with v4, tabuList should contain v2 and v4
//v1 should be removed from tabuList
stepScope2.setStep(moveScope4.getMove());
acceptor.stepEnded(stepScope2);
//4th STEP: v2 and v4 in tabuList, acceptor should accept every move
//except a move containing v1 and v2
LocalSearchStepScope stepScope3 = new LocalSearchStepScope(solverPhaseScope);
stepScope3.setStepIndex(3);
MoveScope moveScope3 = buildMoveScope(stepScope3, v3);
assertEquals(true, acceptor.isAccepted(buildMoveScope(stepScope3, v0)));
//v1 not in tabuList anymore, move should get accepted
assertEquals(true, acceptor.isAccepted(buildMoveScope(stepScope3, v1)));
assertEquals(false, acceptor.isAccepted(buildMoveScope(stepScope3, v2)));
assertEquals(true, acceptor.isAccepted(moveScope3));
assertEquals(false, acceptor.isAccepted(buildMoveScope(stepScope3, v4)));
assertEquals(false, acceptor.isAccepted(buildMoveScope(stepScope3, v2)));
//We accept move with v3, tabuList should contain v3 and v4
//v2 should be removed from tabuList
stepScope3.setStep(moveScope3.getMove());
acceptor.stepEnded(stepScope3);
//5th STEP: v4 and v3 in tabuList, acceptor should accept every move
//except a move containing v1 and v2
LocalSearchStepScope stepScope4 = new LocalSearchStepScope(solverPhaseScope);
stepScope4.setStepIndex(4);
MoveScope moveScope1Again = buildMoveScope(stepScope4, v1);
assertEquals(true, acceptor.isAccepted(buildMoveScope(stepScope4, v0)));
assertEquals(true, acceptor.isAccepted(moveScope1Again));
assertEquals(true, acceptor.isAccepted(buildMoveScope(stepScope4, v2)));
assertEquals(false, acceptor.isAccepted(buildMoveScope(stepScope4, v3)));
assertEquals(false, acceptor.isAccepted(buildMoveScope(stepScope4, v4)));
assertEquals(true, acceptor.isAccepted(buildMoveScope(stepScope4, v2)));
//Value one gets accepted again
stepScope4.setStep(moveScope1Again.getMove());
acceptor.stepEnded(stepScope4);
acceptor.phaseEnded(solverPhaseScope);
}
@Test
public void tabuSizeMultipleEntitiesPerStep() {
PlanningValueTabuAcceptor acceptor = new PlanningValueTabuAcceptor();
acceptor.setTabuSize(2);
acceptor.setAspirationEnabled(true);
TestdataValue v0 = new TestdataValue("v0");
TestdataValue v1 = new TestdataValue("v1");
TestdataValue v2 = new TestdataValue("v2");
TestdataValue v3 = new TestdataValue("v3");
TestdataValue v4 = new TestdataValue("v4");
DefaultSolverScope solverScope = new DefaultSolverScope();
solverScope.setBestScore(new DefaultSimpleScore(0));
LocalSearchSolverPhaseScope solverPhaseScope = new LocalSearchSolverPhaseScope(solverScope);
acceptor.phaseStarted(solverPhaseScope);
//FIRST STEP: no values in tabuList, acceptor should accept everything.
LocalSearchStepScope stepScope0 = new LocalSearchStepScope(solverPhaseScope);
stepScope0.setStepIndex(0);
assertEquals(true, acceptor.isAccepted(buildMoveScope(stepScope0, v0)));
assertEquals(true, acceptor.isAccepted(buildMoveScope(stepScope0, v1)));
assertEquals(true, acceptor.isAccepted(buildMoveScope(stepScope0, v2)));
assertEquals(true, acceptor.isAccepted(buildMoveScope(stepScope0, v3)));
assertEquals(true, acceptor.isAccepted(buildMoveScope(stepScope0, v4)));
assertEquals(true, acceptor.isAccepted(buildMoveScope(stepScope0, v0, v1)));
assertEquals(true, acceptor.isAccepted(buildMoveScope(stepScope0, v0, v2)));
assertEquals(true, acceptor.isAccepted(buildMoveScope(stepScope0, v0, v3)));
assertEquals(true, acceptor.isAccepted(buildMoveScope(stepScope0, v0, v4)));
assertEquals(true, acceptor.isAccepted(buildMoveScope(stepScope0, v1, v2)));
assertEquals(true, acceptor.isAccepted(buildMoveScope(stepScope0, v1, v3)));
assertEquals(true, acceptor.isAccepted(buildMoveScope(stepScope0, v1, v4)));
assertEquals(true, acceptor.isAccepted(buildMoveScope(stepScope0, v2, v3)));
assertEquals(true, acceptor.isAccepted(buildMoveScope(stepScope0, v2, v4)));
assertEquals(true, acceptor.isAccepted(buildMoveScope(stepScope0, v3, v4)));
stepScope0.setStep(buildMoveScope(stepScope0, v0, v2).getMove());
acceptor.stepEnded(stepScope0);
//SECOND STEP: v0 and v2 in tabuList, acceptor should accept every move
//except a move containing either v0 or v2 or both
LocalSearchStepScope stepScope1 = new LocalSearchStepScope(solverPhaseScope);
stepScope1.setStepIndex(1);
assertEquals(false, acceptor.isAccepted(buildMoveScope(stepScope1, v0)));
assertEquals(true, acceptor.isAccepted(buildMoveScope(stepScope1, v1)));
assertEquals(false, acceptor.isAccepted(buildMoveScope(stepScope1, v2)));
assertEquals(true, acceptor.isAccepted(buildMoveScope(stepScope1, v3)));
assertEquals(true, acceptor.isAccepted(buildMoveScope(stepScope1, v4)));
assertEquals(false, acceptor.isAccepted(buildMoveScope(stepScope1, v0, v1)));
assertEquals(false, acceptor.isAccepted(buildMoveScope(stepScope1, v0, v2)));
assertEquals(false, acceptor.isAccepted(buildMoveScope(stepScope1, v0, v3)));
assertEquals(false, acceptor.isAccepted(buildMoveScope(stepScope1, v0, v4)));
assertEquals(false, acceptor.isAccepted(buildMoveScope(stepScope1, v1, v2)));
assertEquals(true, acceptor.isAccepted(buildMoveScope(stepScope1, v1, v3)));
assertEquals(true, acceptor.isAccepted(buildMoveScope(stepScope1, v1, v4)));
assertEquals(false, acceptor.isAccepted(buildMoveScope(stepScope1, v2, v3)));
assertEquals(false, acceptor.isAccepted(buildMoveScope(stepScope1, v2, v4)));
assertEquals(true, acceptor.isAccepted(buildMoveScope(stepScope1, v3, v4)));
stepScope1.setStep(buildMoveScope(stepScope1, v1).getMove());
acceptor.stepEnded(stepScope1);
//THIRD STEP: v0, v2, v1 in tabuList, acceptor should accept every move
//except a move containing either v0, v2, v1 or a combination of those
LocalSearchStepScope stepScope2 = new LocalSearchStepScope(solverPhaseScope);
stepScope2.setStepIndex(2);
assertEquals(false, acceptor.isAccepted(buildMoveScope(stepScope2, v0)));
assertEquals(false, acceptor.isAccepted(buildMoveScope(stepScope2, v1)));
assertEquals(false, acceptor.isAccepted(buildMoveScope(stepScope2, v2)));
assertEquals(true, acceptor.isAccepted(buildMoveScope(stepScope2, v3)));
assertEquals(true, acceptor.isAccepted(buildMoveScope(stepScope2, v4)));
assertEquals(false, acceptor.isAccepted(buildMoveScope(stepScope2, v0, v1)));
assertEquals(false, acceptor.isAccepted(buildMoveScope(stepScope2, v0, v2)));
assertEquals(false, acceptor.isAccepted(buildMoveScope(stepScope2, v0, v3)));
assertEquals(false, acceptor.isAccepted(buildMoveScope(stepScope2, v0, v4)));
assertEquals(false, acceptor.isAccepted(buildMoveScope(stepScope2, v1, v2)));
assertEquals(false, acceptor.isAccepted(buildMoveScope(stepScope2, v1, v3)));
assertEquals(false, acceptor.isAccepted(buildMoveScope(stepScope2, v1, v4)));
assertEquals(false, acceptor.isAccepted(buildMoveScope(stepScope2, v2, v3)));
assertEquals(false, acceptor.isAccepted(buildMoveScope(stepScope2, v2, v4)));
assertEquals(true, acceptor.isAccepted(buildMoveScope(stepScope2, v3, v4)));
stepScope2.setStep(buildMoveScope(stepScope2, v3, v4).getMove());
acceptor.stepEnded(stepScope2);
//4TH STEP: v3, v4, v1 in tabuList, acceptor should accept every move
//except a move containing either v3, v4, v1 or a combination of those
//v0 and v2 should've been released from the tabuList
LocalSearchStepScope stepScope3 = new LocalSearchStepScope(solverPhaseScope);
stepScope3.setStepIndex(3);
assertEquals(true, acceptor.isAccepted(buildMoveScope(stepScope3, v0)));
assertEquals(false, acceptor.isAccepted(buildMoveScope(stepScope3, v1)));
assertEquals(true, acceptor.isAccepted(buildMoveScope(stepScope3, v2)));
assertEquals(false, acceptor.isAccepted(buildMoveScope(stepScope3, v3)));
assertEquals(false, acceptor.isAccepted(buildMoveScope(stepScope3, v4)));
assertEquals(false, acceptor.isAccepted(buildMoveScope(stepScope3, v0, v1)));
assertEquals(true, acceptor.isAccepted(buildMoveScope(stepScope3, v0, v2)));
assertEquals(false, acceptor.isAccepted(buildMoveScope(stepScope3, v0, v3)));
assertEquals(false, acceptor.isAccepted(buildMoveScope(stepScope3, v0, v4)));
assertEquals(false, acceptor.isAccepted(buildMoveScope(stepScope3, v1, v2)));
assertEquals(false, acceptor.isAccepted(buildMoveScope(stepScope3, v1, v3)));
assertEquals(false, acceptor.isAccepted(buildMoveScope(stepScope3, v1, v4)));
assertEquals(false, acceptor.isAccepted(buildMoveScope(stepScope3, v2, v3)));
assertEquals(false, acceptor.isAccepted(buildMoveScope(stepScope3, v2, v4)));
assertEquals(false, acceptor.isAccepted(buildMoveScope(stepScope3, v3, v4)));
stepScope3.setStep(buildMoveScope(stepScope3, v0).getMove());
acceptor.stepEnded(stepScope3);
acceptor.phaseEnded(solverPhaseScope);
}
@Test
public void aspiration() {
PlanningValueTabuAcceptor acceptor = new PlanningValueTabuAcceptor();
acceptor.setTabuSize(2);
//We want to accepted moves containing values from tabuList
//if moves are better than best solution found (not working solution)
acceptor.setAspirationEnabled(true);
TestdataValue v0 = new TestdataValue("v0");
TestdataValue v1 = new TestdataValue("v1");
DefaultSolverScope solverScope = new DefaultSolverScope();
//We set best score to -100
solverScope.setBestScore(new DefaultSimpleScore(-100));
LocalSearchSolverPhaseScope solverPhaseScope = new LocalSearchSolverPhaseScope(solverScope);
acceptor.phaseStarted(solverPhaseScope);
//First step: we accept a move containing v1, so v1 should be added to
//TabuList
LocalSearchStepScope stepScope0 = new LocalSearchStepScope(solverPhaseScope);
stepScope0.setStepIndex(0);
stepScope0.setStep(buildMoveScope(stepScope0, v1).getMove());
acceptor.stepEnded(stepScope0);
//Second step: tabuList contains v1 so any move containing v1 with a
//resulting score less than the globally best known score (-100) should
//get rejected. Otherwise the move will be accepted even though it
//contains a tabu value
LocalSearchStepScope stepScope2 = new LocalSearchStepScope(solverPhaseScope);
stepScope2.setStepIndex(1);
assertEquals(true, acceptor.isAccepted(buildMoveScope(stepScope2, -120, v0)));
assertEquals(true, acceptor.isAccepted(buildMoveScope(stepScope2, -20, v0)));
assertEquals(false, acceptor.isAccepted(buildMoveScope(stepScope2, -120, v1)));
assertEquals(true, acceptor.isAccepted(buildMoveScope(stepScope2, -20, v1)));
assertEquals(false, acceptor.isAccepted(buildMoveScope(stepScope2, -120, v0, v1)));
assertEquals(true, acceptor.isAccepted(buildMoveScope(stepScope2, -20, v0, v1)));
stepScope2.setStep(buildMoveScope(stepScope2, -20, v1).getMove());
acceptor.stepEnded(stepScope2);
acceptor.phaseEnded(solverPhaseScope);
}
private MoveScope buildMoveScope(LocalSearchStepScope stepScope, TestdataValue... values) {
return buildMoveScope(stepScope, 0, values);
}
private MoveScope buildMoveScope(LocalSearchStepScope stepScope, int score, TestdataValue... values) {
MoveScope moveScope = new MoveScope(stepScope);
Move move = mock(Move.class);
when(move.getPlanningValues()).thenReturn((Collection) Arrays.asList(values));
moveScope.setMove(move);
moveScope.setScore(new DefaultSimpleScore(score));
return moveScope;
}
}
|
package org.vitrivr.cineast.standalone.util;
import com.github.rvesse.airline.model.CommandMetadata;
import com.github.rvesse.airline.parser.errors.ParseRestrictionViolatedException;
import org.jline.builtins.Completers;
import org.jline.reader.Completer;
import org.jline.reader.EndOfFileException;
import org.jline.reader.LineReader;
import org.jline.reader.LineReaderBuilder;
import org.jline.reader.impl.completer.AggregateCompleter;
import org.jline.reader.impl.completer.StringsCompleter;
import org.jline.terminal.Terminal;
import org.jline.terminal.TerminalBuilder;
import org.jline.utils.AttributedStringBuilder;
import org.jline.utils.AttributedStyle;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
import java.util.NoSuchElementException;
import java.util.regex.Matcher;
import java.util.regex.Pattern;
import java.util.stream.Collectors;
/**
* Helper class that can be used to start an interactive CLI.
*
* @author Ralph Gasser
* @version 1.0
*/
public class CLI {
private static final String PROMPT = "cineast> ";
private CLI() {
}
/**
* Starts the interactive CLI. This is method will block.
*/
public static void start(Class<?> cliClass) {
Terminal terminal = null;
try {
terminal = TerminalBuilder.terminal(); //basic terminal
} catch (IOException e) {
System.err.println("Could not initialize Terminal: ");
System.err.println(e.getMessage());
System.err.println("Exiting...");
System.exit(-1);
}
final com.github.rvesse.airline.Cli<Runnable> cli = new com.github.rvesse.airline.Cli<>(cliClass);
final List<String> commandNames = cli.getMetadata().getDefaultGroupCommands().stream()
.map(CommandMetadata::getName).collect(Collectors.toList());
final Completer completer = new AggregateCompleter(
new StringsCompleter("quit", "exit", "stop"),
new StringsCompleter(commandNames),
new Completers.FileNameCompleter()
);
final LineReader lineReader = LineReaderBuilder.builder()
.terminal(terminal)
.completer(completer)
.build();
terminal.writer().println("Welcome to the interactive Cineast CLI.");
try {
while (true) {
final String line;
/* Catch ^D end of file as exit method */
try {
line = lineReader.readLine(PROMPT).trim();
} catch (EndOfFileException e) {
break;
}
if (line.toLowerCase().equals("exit") || line.toLowerCase().equals("quit") || line.toLowerCase().equals("stop")) {
break;
}
/* Try to parse user input. */
try {
final Runnable command = cli.parse(CLI.splitLine(line));
command.run();
} catch (ParseRestrictionViolatedException e) {
terminal.writer().println(
new AttributedStringBuilder().style(AttributedStyle.DEFAULT.foreground(AttributedStyle.RED))
.append("Error: ").append(e.getMessage()).toAnsi()
);
} catch (Exception e) {
terminal.writer().println(
new AttributedStringBuilder().style(AttributedStyle.DEFAULT.foreground(AttributedStyle.RED))
.append("Error: ").append(e.getMessage()).toAnsi()
);
}
}
} catch (IllegalStateException | NoSuchElementException e) {
System.out.println("System.in was closed; exiting");
}
}
final static Pattern lineSplitRegex = Pattern.compile("[^\\s\"']+|\"([^\"]*)\"|'([^']*)'");
private static String[] splitLine(String line){
if (line == null || line.isEmpty()){
return new String[0];
}
List<String> matchList = new ArrayList<String>();
Matcher regexMatcher = lineSplitRegex.matcher(line);
while (regexMatcher.find()) {
if (regexMatcher.group(1) != null) {
// Add double-quoted string without the quotes
matchList.add(regexMatcher.group(1));
} else if (regexMatcher.group(2) != null) {
// Add single-quoted string without the quotes
matchList.add(regexMatcher.group(2));
} else {
// Add unquoted word
matchList.add(regexMatcher.group());
}
}
return matchList.toArray(new String[matchList.size()]);
}
}
|
package ua.com.fielden.platform.swing.review.report.analysis.lifecycle;
import java.awt.Cursor;
import java.awt.Dimension;
import java.awt.Insets;
import java.awt.Point;
import java.awt.event.MouseEvent;
import java.awt.event.MouseListener;
import java.awt.event.MouseMotionListener;
import java.awt.geom.Point2D;
import java.awt.geom.Rectangle2D;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.LinkedHashMap;
import java.util.List;
import org.apache.log4j.xml.DOMConfigurator;
import org.jfree.chart.ChartMouseEvent;
import org.jfree.chart.ChartMouseListener;
import org.jfree.chart.ChartRenderingInfo;
import org.jfree.chart.JFreeChart;
import org.jfree.chart.entity.ChartEntity;
import org.jfree.chart.entity.XYItemEntity;
import org.jfree.chart.plot.XYPlot;
import org.jfree.data.gantt.TaskSeries;
import org.jfree.data.gantt.TaskSeriesCollection;
import org.jfree.ui.RefineryUtilities;
import org.joda.time.DateTime;
import ua.com.fielden.platform.application.AbstractUiApplication;
import ua.com.fielden.platform.branding.SplashController;
import ua.com.fielden.platform.entity.AbstractEntity;
import ua.com.fielden.platform.entity.Entity;
import ua.com.fielden.platform.equery.lifecycle.EntityPropertyLifecycle;
import ua.com.fielden.platform.equery.lifecycle.IGroup;
import ua.com.fielden.platform.equery.lifecycle.IProperty;
import ua.com.fielden.platform.equery.lifecycle.IProperty.ITimeProperty;
import ua.com.fielden.platform.equery.lifecycle.IProperty.IValueProperty;
import ua.com.fielden.platform.equery.lifecycle.LifecycleModel;
import ua.com.fielden.platform.equery.lifecycle.LifecycleModelTest;
import ua.com.fielden.platform.swing.categorychart.ChartPanel;
import ua.com.fielden.platform.swing.utils.SimpleLauncher;
import ua.com.fielden.platform.swing.utils.SwingUtilitiesEx;
import ua.com.fielden.platform.swing.view.BaseFrame;
import ua.com.fielden.platform.swing.view.IEntityMasterCache;
import ua.com.fielden.platform.utils.EntityUtils;
import ua.com.fielden.platform.utils.Pair;
import com.jidesoft.plaf.LookAndFeelFactory;
public class TimelineManagementControlExample extends AbstractUiApplication implements ChartMouseListener, MouseListener, MouseMotionListener {
private LifecycleModel<Entity> chartEntryModel;
private TaskSeriesCollection mainDataSet = new TaskSeriesCollection();
ChartPanel localChartPanel = null;
boolean canMove = false;
double finalMovePointY = 0;
ChartRenderingInfo info = null;;
double initialMovePointY = 0;
JFreeChart jfreechart = null;
// final TaskSeriesCollection mainDataSet = new TaskSeriesCollection();
// if (chartEntryModel != null) {
// for (final EntityPropertyLifecycle<T> epl : chartEntryModel.getLifecycleData()) {
// final TaskSeries taskSeries = new TaskSeries(epl.getInfo(true));
// for (final ValuedInterval vi : epl.getIntervals()) {
// taskSeries.add(new ColoredTask("ColoredTask", new SimpleTimePeriod(vi.getFrom().toDate(), vi.getTo().toDate()), vi.getColor(), vi.getInfo()));
// mainDataSet.add(taskSeries);
XYItemEntity xyItemEntity = null;
@Override
protected void beforeUiExposure(final String[] args, final SplashController splashController) throws Throwable {
SwingUtilitiesEx.installNimbusLnFifPossible();
com.jidesoft.utils.Lm.verifyLicense("Fielden Management Services", "Rollingstock Management System", "xBMpKdqs3vWTvP9gxUR4jfXKGNz9uq52");
LookAndFeelFactory.installJideExtension();
chartEntryModel = createLifecycleModel();
mainDataSet = LifecycleChartFactory.createMainDataSet(chartEntryModel);
super.beforeUiExposure(args, splashController);
}
private TaskSeries localTaskSeries() {
return mainDataSet.getSeries(0); // TODO take an appropriate series
}
/**
* Creates testing lifecycle model.
*
* @return
*/
private static LifecycleModel<Entity> createLifecycleModel() {
final LifecycleModelTest lmt = new LifecycleModelTest();
final List<EntityPropertyLifecycle<Entity>> ld = new ArrayList<EntityPropertyLifecycle<Entity>>();
ld.add(lmt.createEPL("A0001", 0));
ld.add(lmt.createEPL("A0002", 5)); // the same lifecycle just shifted to the right on 5 millis.
ld.add(lmt.createEPL("A0003", -2));
ld.add(lmt.createEPL("A0004", 2));
ld.add(lmt.createEPL("A0005", 1));
ld.add(lmt.createEPL("A0006", -1));
ld.add(lmt.createUnavailableEPL("A0007"));
final LifecycleModel<Entity> lm = new LifecycleModel<Entity>(lmt.date(15), lmt.date(55), ld, new LinkedHashMap<IProperty, Object>(), true){
@Override
protected IGroup<Entity> createGroupByValue(final IValueProperty property, final Object value, final LifecycleModel<Entity> parent, final List<Integer> indexes) {
return null;
}
@Override
protected IGroup<Entity> createGroupByModelAndPeriod(final ITimeProperty timeProperty, final LifecycleModel<Entity> narrowedModel, final LifecycleModel<Entity> parent) {
return null;
}
@Override
public Pair<? extends LifecycleModel<Entity>, ? extends LifecycleModel<Entity>> split(final DateTime moment, final boolean copy, final boolean full) {
return null;
}
@Override
protected LifecycleModel<Entity> copy(final LinkedHashMap<IProperty, Object> extractedGroupingValues) {
return null;
}
};
return lm;
}
@Override
protected void exposeUi(final String[] args, final SplashController splashController) throws Throwable {
final BaseFrame mainApplicationFrame = new BaseFrame("Timeline management control example", new HashMap<Class<? extends AbstractEntity<?>>, IEntityMasterCache>());
final JFreeChart chart = LifecycleChartFactory.createAvailabilityChart(chartEntryModel, mainDataSet);
// final ChartPanel localChartPanel = new ChartPanel(chart);
// localChartPanel.addChartMouseListener(this);
// localChartPanel.addMouseMotionListener(this);
// localChartPanel.addMouseListener(this);
jfreechart = chart; // ChartFactory.createTimeSeriesChart("Series & Point Dragging Demo", "Date", "Price Per Unit", createDataset(), true, true, false);
localChartPanel = new ChartPanel(jfreechart);
localChartPanel.addChartMouseListener(this);
localChartPanel.addMouseMotionListener(this);
localChartPanel.addMouseListener(this);
localChartPanel.setPreferredSize(new Dimension(750, 500));
localChartPanel.setAutoscrolls(false);
// localChartPanel.setMouseZoomable(false);
localChartPanel.setMouseWheelEnabled(true);
this.info = localChartPanel.getChartRenderingInfo();
/* final XYPlot localXYPlot = (XYPlot) jfreechart.getPlot();
final XYItemRenderer localXYItemRenderer = localXYPlot.getRenderer();
localXYItemRenderer.setSeriesStroke(0, new BasicStroke(2.0F));
final XYLineAndShapeRenderer localXYLineAndShapeRenderer = (XYLineAndShapeRenderer) localXYPlot.getRenderer();
localXYLineAndShapeRenderer.setBaseShapesVisible(true);
localXYLineAndShapeRenderer.setSeriesFillPaint(0, Color.white);
localXYLineAndShapeRenderer.setUseFillPaint(true);
localXYLineAndShapeRenderer.setLegendItemToolTipGenerator(new StandardXYSeriesLabelGenerator("Tooltip {0}"));
final ValueAxis range = localXYPlot.getRangeAxis();
range.setLowerBound(0); // set lower limit so that can't move in -ve
// range
range.setUpperBound(10000); // set upper limit as per app. needs
*/
// final ChartPanel chartPanel = new ChartPanel(chart) {
// private static final long serialVersionUID = -4977378293075789317L;
// @Override
// public void mouseDragged(final MouseEvent mouseEvent) {
// super.mouseDragged(mouseEvent);
// /*Insets insets = getInsets();
// int x = (int) ((event.getX() - insets.left) / this.scaleX);
// int y = (int) ((event.getY() - insets.top) / this.scaleY);
//
// this.anchor = new Point2D.Double(x, y);
// ChartEntity entity = null;
// if (this.info != null) {
// EntityCollection entities = this.info.getEntityCollection();
// if (entities != null) {
// entity = entities.getEntity(x, y);
// }
// }*/
// chartPanel.addChartMouseListener(new ChartMouseListener() {
// @Override
// public void chartMouseClicked(final ChartMouseEvent event) {
// if (event.getTrigger().isControlDown() && /*event.getTrigger().getClickCount() == 2 && */ !event.getTrigger().isConsumed()) {
// performCustomAction(new AnalysisDataEvent<>(mainApplicationFrame, event /*chartMouseEvent*/));
// //if (event.getTrigger().getClickCount() == 2 && !event.getTrigger().isConsumed()) {
// // event.getTrigger().consume();
// // mouseDoubleClicked(event);
// //} else if (event.getTrigger().getClickCount() == 1) {
// // event.getTrigger().consume();
// // if (getChart().getPlot() instanceof CategoryPlot) {
// // final CategoryPlot plot = getChart().getCategoryPlot();
// // final CategoryItemRenderer renderer = plot.getRenderer();
// // labelVisible = !labelVisible;
// // renderer.setBaseItemLabelsVisible(labelVisible);
// @Override
// public void chartMouseMoved(final ChartMouseEvent event) {
// // ignored for now
mainApplicationFrame.setPreferredSize(new Dimension(1280, 800));
mainApplicationFrame.add(localChartPanel);
mainApplicationFrame.pack();
RefineryUtilities.centerFrameOnScreen(mainApplicationFrame);
SimpleLauncher.show("Timeline management control example", mainApplicationFrame, null);
}
// protected void performCustomAction(final AnalysisDataEvent<ChartMouseEvent> clickedData) {
// final ChartEntity entity = clickedData.getData().getEntity();
// System.err.println("CTRL + " + entity);
// if (entity instanceof CategoryItemEntity) {
// createDoubleClickAction(createChoosenItem(((CategoryItemEntity) entity).getColumnKey())).actionPerformed(null);
// } else if (entity instanceof CategoryLabelEntity) {
// createDoubleClickAction(createChoosenItem(((CategoryLabelEntity) entity).getKey())).actionPerformed(null);
// private Pair<String, Object> createChoosenItem(final Comparable<?> columnKey) {
// final EntityWrapper entityWrapper = (EntityWrapper) columnKey;
// final List<String> categories = getModel().getChartAnalysisDataProvider().categoryProperties();
// if(categories.size() == 1){
// return new Pair<String, Object>(categories.get(0), entityWrapper.getEntity());
// return null;
public static void main(final String[] args) {
DOMConfigurator.configure("src/main/resources/log4j.xml");
new TimelineManagementControlExample().launch(args);
}
public void chartMouseClicked(final ChartMouseEvent paramChartMouseEvent) {
}
public void chartMouseMoved(final ChartMouseEvent paramChartMouseEvent) {
}
/* public XYDataset createDataset() {
localTimeSeries.add(new Month(1, 2002), 500.19999999999999D);
localTimeSeries.add(new Month(2, 2002), 694.10000000000002D);
localTimeSeries.add(new Month(3, 2002), 734.39999999999998D);
localTimeSeries.add(new Month(4, 2002), 453.19999999999999D);
localTimeSeries.add(new Month(5, 2002), 200.19999999999999D);
localTimeSeries.add(new Month(6, 2002), 345.60000000000002D);
localTimeSeries.add(new Month(7, 2002), 500.19999999999999D);
localTimeSeries.add(new Month(8, 2002), 694.10000000000002D);
localTimeSeries.add(new Month(9, 2002), 734.39999999999998D);
localTimeSeries.add(new Month(10, 2002), 453.19999999999999D);
localTimeSeries.add(new Month(11, 2002), 500.19999999999999D);
localTimeSeries.add(new Month(12, 2002), 345.60000000000002D);
timeseriescollection.addSeries(localTimeSeries);
return timeseriescollection;
}*/
public void mouseClicked(final MouseEvent e) {
}
public void mouseDragged(final MouseEvent e) {
// at a time use one of them.
// moveTimeSeries(e); // comment or uncomment to enable or disable series
// movement
movePoint(e); // comment or uncomment to enable or disable selected
// point movement
}
public void mouseEntered(final MouseEvent e) {
}
public void mouseExited(final MouseEvent e) {
canMove = false; // stop movement if cursor is moved out from the chart
// area
initialMovePointY = 0;
localChartPanel.setCursor(new Cursor(Cursor.DEFAULT_CURSOR));
}
private XYItemEntity determineAnItemUnderACursor(final ChartPanel chartPanel, final int x0, final int y0) {
final Insets insets = chartPanel.getInsets();
final int x = (int) ((x0 - insets.left) / chartPanel.getScaleX());
final int y = (int) ((y0 - insets.top) / chartPanel.getScaleY());
final ChartEntity entity = this.info.getEntityCollection().getEntity(x, y);
if ((entity != null) && (entity instanceof XYItemEntity)) {
return (XYItemEntity) entity;
} else {
return null;
}
}
public void mouseMoved(final MouseEvent e) {
final XYItemEntity newItemEntity = determineAnItemUnderACursor((ChartPanel) e.getSource(), e.getX(), e.getY());
if (!EntityUtils.equalsEx(newItemEntity, xyItemEntity)) {
xyItemEntity = newItemEntity;
System.err.println(" xyItemEntity has been changed to == " + xyItemEntity);
}
provideCursor(e, false);
}
public void provideCursor(final MouseEvent e, final boolean pressed) {
final int gap = 3;
if (xyItemEntity == null) {
localChartPanel.setCursor(new Cursor(Cursor.DEFAULT_CURSOR));
} else if (!EntityUtils.equalsEx(xyItemEntity, determineAnItemUnderACursor((ChartPanel) e.getSource(), e.getX() - gap, e.getY()))) {
// the left boundary of xyItemEntity has been found
localChartPanel.setCursor(new Cursor(Cursor.W_RESIZE_CURSOR));
} else if (!EntityUtils.equalsEx(xyItemEntity, determineAnItemUnderACursor((ChartPanel) e.getSource(), e.getX() + gap, e.getY()))) {
// the right boundary of xyItemEntity has been found
localChartPanel.setCursor(new Cursor(Cursor.E_RESIZE_CURSOR));
} else {
localChartPanel.setCursor(pressed ? new Cursor(Cursor.MOVE_CURSOR) : new Cursor(Cursor.HAND_CURSOR));
}
}
public void mousePressed(final MouseEvent e) {
// final int x = e.getX(); // initialized point whenenver mouse is pressed
// final int y = e.getY();
final ChartPanel chartPanel = (ChartPanel) e.getSource();
final Insets insets = chartPanel.getInsets();
final int x = (int) ((e.getX() - insets.left) / chartPanel.getScaleX());
final int y = (int) ((e.getY() - insets.top) / chartPanel.getScaleY());
// this.anchor = new Point2D.Double(x, y);
// ChartEntity entity = null;
// if (this.info != null) {
// final EntityCollection entities = this.info.getEntityCollection();
// if (entities != null) {
// entity = entities.getEntity(x, y);
// final EntityCollection entities = this.info.getEntityCollection();
// final ChartMouseEvent cme = new ChartMouseEvent(jfreechart, e, entities
// .getEntity(x, y));
// final ChartEntity entity = cme.getEntity();
// if ((entity != null) && (entity instanceof XYItemEntity)) {
// xyItemEntity = (XYItemEntity) entity;
// } else if (!(entity instanceof XYItemEntity)) {
// xyItemEntity = null;
// return;
// if (xyItemEntity == null) {
// return; // return if not pressed on any series point
// System.err.println(" xyItemEntity == " + xyItemEntity);
final Point pt = e.getPoint();
final XYPlot xy = jfreechart.getXYPlot();
final Rectangle2D dataArea = localChartPanel.getChartRenderingInfo()
.getPlotInfo().getDataArea();
final Point2D p = localChartPanel.translateScreenToJava2D(pt);
initialMovePointY = xy.getRangeAxis().java2DToValue(p.getY(), dataArea,
xy.getRangeAxisEdge());
canMove = true;
provideCursor(e, true);
// localChartPanel.setCursor(new Cursor(Cursor.MOVE_CURSOR));
}
public void mouseReleased(final MouseEvent e) {
// stop dragging on mouse released
canMove = false;
initialMovePointY = 0;
provideCursor(e, false);
}
public void movePoint(final MouseEvent me) {
// try {
// if (canMove) {
// final int itemIndex = xyItemEntity.getItem();
// final Point pt = me.getPoint();
// final XYPlot xy = jfreechart.getXYPlot();
// final Rectangle2D dataArea = localChartPanel.getChartRenderingInfo()
// .getPlotInfo().getDataArea();
// final Point2D p = localChartPanel.translateScreenToJava2D(pt);
// finalMovePointY = xy.getRangeAxis().java2DToValue(p.getY(),
// dataArea, xy.getRangeAxisEdge());
// final double difference = finalMovePointY - initialMovePointY;
// if (localTaskSeries().getValue(itemIndex).doubleValue()
// + difference > xy.getRangeAxis().getRange().getLength()
// || localTaskSeries().getValue(itemIndex).doubleValue()
// + difference < 0.0D) {
// initialMovePointY = finalMovePointY;
// // retrict movement for upper and lower limit (upper limit
// // should be as per application needs)
// final double targetPoint = localTaskSeries().getValue(itemIndex)
// .doubleValue()
// + difference;
// if (targetPoint > 10000 || targetPoint < 0) {
// return;
// } else
// localTaskSeries().update(itemIndex, targetPoint);
// jfreechart.fireChartChanged();
// localChartPanel.updateUI();
// initialMovePointY = finalMovePointY;
// } catch (final Exception e) {
// e.printStackTrace();
// System.out.println(e);
}
// public void moveTimeSeries(final MouseEvent me) {
// try {
// if (canMove) {
// final Point pt = me.getPoint();
// final XYPlot xy = jfreechart.getXYPlot();
// final Rectangle2D dataArea = localChartPanel.getChartRenderingInfo()
// .getPlotInfo().getDataArea();
// final Point2D p = localChartPanel.translateScreenToJava2D(pt);
// finalMovePointY = xy.getRangeAxis().java2DToValue(p.getY(),
// dataArea, xy.getRangeAxisEdge());
// final double difference = finalMovePointY - initialMovePointY;
// for (int i = 0; i < localTaskSeries().getItemCount(); i++) {
// if (localTaskSeries().getValue(i).doubleValue() + difference > xy
// .getRangeAxis().getRange().getLength()
// || localTaskSeries().getValue(i).doubleValue()
// + difference < 0.0D) {
// initialMovePointY = finalMovePointY;
// // retrict movement for upper and lower limit (upper limit
// // should be as per application needs)
// for (int i = 0; i < localTaskSeries().getItemCount(); i++) {
// final double targetPoint = localTaskSeries().getValue(i)
// .doubleValue()
// + difference;
// if (targetPoint > 10000 || targetPoint < 0) {
// return;
// for (int i = 0; i < localTaskSeries().getItemCount(); i++) {
// final double targetPoint = localTaskSeries().getValue(i)
// .doubleValue()
// + difference;
// localTaskSeries().update(i, targetPoint);
// jfreechart.fireChartChanged();
// localChartPanel.updateUI();
// initialMovePointY = finalMovePointY;
// } catch (final Exception e) {
// System.out.println(e);
}
|
package info.evanchik.eclipse.karaf.workbench;
import info.evanchik.eclipse.karaf.core.LogWrapper;
import info.evanchik.eclipse.karaf.ui.KarafUIPluginActivator;
import info.evanchik.eclipse.karaf.workbench.internal.MBeanProviderManager;
import info.evanchik.eclipse.karaf.workbench.internal.RuntimeDataProviderManager;
import info.evanchik.eclipse.karaf.workbench.internal.eclipse.EclipseRuntimeDataProvider;
import info.evanchik.eclipse.karaf.workbench.jmx.IJMXTransportRegistry;
import info.evanchik.eclipse.karaf.workbench.jmx.JMXServiceDescriptor;
import info.evanchik.eclipse.karaf.workbench.jmx.internal.JMXServiceManager;
import info.evanchik.eclipse.karaf.workbench.jmx.internal.JMXTransportRegistry;
import org.eclipse.jface.resource.ImageDescriptor;
import org.eclipse.jface.resource.ImageRegistry;
import org.eclipse.ui.plugin.AbstractUIPlugin;
import org.osgi.framework.BundleContext;
/**
* The activator class controls the plug-in life cycle
*/
public class KarafWorkbenchActivator extends AbstractUIPlugin {
// The plug-in ID
public static final String PLUGIN_ID = "info.evanchik.eclipse.karaf.workbench";
public static final String JMX_CONNECTOR_PROVIDER_EXTENSION_ID = "jmxConnectorProvider";
public static final String BUNDLE_OBJ_IMG = "bundle_obj"; //$NON-NLS-1$
public static final String LOGO_16X16_IMG = "logo16"; //$NON-NLS-1$
public static final String SERVICE_IMG = "service";
private EclipseRuntimeDataProvider eclipseWorkbenchDataProvider;
private JMXServiceManager jmxServiceManager;
private JMXTransportRegistry jmxTransportRegistry;
private MBeanProviderManager mbeanProviderManager;
private RuntimeDataProviderManager runtimeDataProviderManager;
private static KarafWorkbenchActivator plugin;
/**
* Returns the shared instance
*
* @return the shared instance
*/
public static KarafWorkbenchActivator getDefault() {
return plugin;
}
/**
* Getter for the {@link LogWrapper} object that makes logging much easier
* on the caller.
*
* @return the {@link LogWrapper} instance
*/
public static LogWrapper getLogger() {
return new LogWrapper(getDefault().getLog(), PLUGIN_ID);
}
/**
* The constructor
*/
public KarafWorkbenchActivator() {
}
/**
*
* @return
*/
public EclipseRuntimeDataProvider getEclipseWorkbenchDataProvider() {
return eclipseWorkbenchDataProvider;
}
/**
* Getter for the {@link WorkbenchServiceManager<JMXServiceDescriptor>}
* implementation. There is only one per plugin instance.
*
* @return the {@code WorkbenchServiceManager<JMXServiceDescriptor>}
* instance
*/
public WorkbenchServiceManager<JMXServiceDescriptor> getJMXServiceManager() {
return jmxServiceManager;
}
/**
* Getter for the {@link IJMXTransportRegistry} implementation. There is
* only on per plugin instance.
*
* @return the {@link IJMXTransportRegistry} instance
*/
public IJMXTransportRegistry getJMXTransportRegistry() {
return jmxTransportRegistry;
}
/**
*
* @return
*/
public WorkbenchServiceManager<MBeanProvider> getMBeanProviderManager() {
return mbeanProviderManager;
}
public RuntimeDataProviderManager getRuntimeDataProviderManager() {
return runtimeDataProviderManager;
}
@Override
public void start(final BundleContext context) throws Exception {
super.start(context);
plugin = this;
jmxServiceManager = new JMXServiceManager();
jmxTransportRegistry = new JMXTransportRegistry();
mbeanProviderManager = new MBeanProviderManager();
runtimeDataProviderManager = new RuntimeDataProviderManager();
eclipseWorkbenchDataProvider = new EclipseRuntimeDataProvider(getBundle().getBundleContext());
registerEclipseRuntimeDataProvider();
}
@Override
public void stop(final BundleContext context) throws Exception {
plugin = null;
super.stop(context);
runtimeDataProviderManager.remove(eclipseWorkbenchDataProvider);
jmxServiceManager = null;
jmxTransportRegistry = null;
mbeanProviderManager = null;
runtimeDataProviderManager = null;
eclipseWorkbenchDataProvider = null;
}
/**
* Creates the {@link ImageRegistery} for this plugin. Images can be
* retrieved using the static accessor method
* {@link KarafUIPluginActivator#getImageDescriptor(String)}
*
* @see org.eclipse.ui.plugin.AbstractUIPlugin#createImageRegistry()
*/
@Override
protected void initializeImageRegistry(final ImageRegistry imageRegistry) {
registerImage(imageRegistry, BUNDLE_OBJ_IMG, "icons/obj16/bundle_obj.gif");
registerImage(imageRegistry, LOGO_16X16_IMG, "icons/obj16/felixLogo16x16.gif");
registerImage(imageRegistry, "logo32", "icons/obj32/felixLogo32x32.gif");
registerImage(imageRegistry, "logo64", "icons/obj64/felixLogo64x64.gif");
registerImage(imageRegistry, SERVICE_IMG, "icons/obj16/generic_element.gif");
}
private void registerEclipseRuntimeDataProvider() {
eclipseWorkbenchDataProvider.start();
runtimeDataProviderManager.add(eclipseWorkbenchDataProvider);
}
/**
* Registers an {@link ImageDescriptor} with the {@link ImageRegistry}
*
* @param registry
* the instance of {@link ImageRegistry}
* @param key
* the key to register the image under
* @param imageUrl
* the URL of the image to be registered
*/
private void registerImage(final ImageRegistry registry, final String key, final String imageUrl) {
final ImageDescriptor id = imageDescriptorFromPlugin(PLUGIN_ID, imageUrl);
registry.put(key, id);
}
}
|
package org.asynchttpclient.netty.channel;
import static org.asynchttpclient.util.MiscUtils.trimStackTrace;
import io.netty.bootstrap.Bootstrap;
import io.netty.buffer.PooledByteBufAllocator;
import io.netty.channel.Channel;
import io.netty.channel.ChannelInitializer;
import io.netty.channel.ChannelOption;
import io.netty.channel.ChannelPipeline;
import io.netty.channel.EventLoopGroup;
import io.netty.channel.group.ChannelGroup;
import io.netty.channel.nio.NioEventLoopGroup;
import io.netty.channel.oio.OioEventLoopGroup;
import io.netty.channel.socket.nio.NioSocketChannel;
import io.netty.handler.codec.http.HttpClientCodec;
import io.netty.handler.codec.http.HttpContentDecompressor;
import io.netty.handler.codec.http.websocketx.WebSocket08FrameDecoder;
import io.netty.handler.codec.http.websocketx.WebSocket08FrameEncoder;
import io.netty.handler.codec.http.websocketx.WebSocketFrameAggregator;
import io.netty.handler.ssl.SslHandler;
import io.netty.handler.stream.ChunkedWriteHandler;
import io.netty.util.Timer;
import io.netty.util.concurrent.DefaultThreadFactory;
import io.netty.util.concurrent.GenericFutureListener;
import java.io.IOException;
import java.util.Map.Entry;
import java.util.concurrent.ConcurrentHashMap;
import java.util.concurrent.Semaphore;
import java.util.concurrent.ThreadFactory;
import java.util.concurrent.TimeUnit;
import javax.net.ssl.SSLEngine;
import javax.net.ssl.SSLException;
import org.asynchttpclient.AsyncHandler;
import org.asynchttpclient.AsyncHttpClientConfig;
import org.asynchttpclient.SslEngineFactory;
import org.asynchttpclient.channel.pool.ConnectionPoolPartitioning;
import org.asynchttpclient.handler.AsyncHandlerExtensions;
import org.asynchttpclient.netty.Callback;
import org.asynchttpclient.netty.NettyResponseFuture;
import org.asynchttpclient.netty.channel.exception.PoolAlreadyClosedException;
import org.asynchttpclient.netty.channel.exception.TooManyConnectionsException;
import org.asynchttpclient.netty.channel.exception.TooManyConnectionsPerHostException;
import org.asynchttpclient.netty.channel.pool.ChannelPool;
import org.asynchttpclient.netty.channel.pool.DefaultChannelPool;
import org.asynchttpclient.netty.channel.pool.NoopChannelPool;
import org.asynchttpclient.netty.handler.AsyncHttpClientHandler;
import org.asynchttpclient.netty.handler.HttpProtocol;
import org.asynchttpclient.netty.handler.WebSocketProtocol;
import org.asynchttpclient.netty.request.NettyRequestSender;
import org.asynchttpclient.netty.ssl.DefaultSslEngineFactory;
import org.asynchttpclient.proxy.ProxyServer;
import org.asynchttpclient.uri.Uri;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
public class ChannelManager {
private static final Logger LOGGER = LoggerFactory.getLogger(ChannelManager.class);
public static final String PINNED_ENTRY = "entry";
public static final String HTTP_CLIENT_CODEC = "http";
public static final String SSL_HANDLER = "ssl";
public static final String DEFLATER_HANDLER = "deflater";
public static final String INFLATER_HANDLER = "inflater";
public static final String CHUNKED_WRITER_HANDLER = "chunked-writer";
public static final String WS_DECODER_HANDLER = "ws-decoder";
public static final String WS_FRAME_AGGREGATOR = "ws-aggregator";
public static final String WS_ENCODER_HANDLER = "ws-encoder";
public static final String AHC_HTTP_HANDLER = "ahc-http";
public static final String AHC_WS_HANDLER = "ahc-ws";
private final AsyncHttpClientConfig config;
private final SslEngineFactory sslEngineFactory;
private final EventLoopGroup eventLoopGroup;
private final boolean allowReleaseEventLoopGroup;
private final Class<? extends Channel> socketChannelClass;
private final Bootstrap httpBootstrap;
private final Bootstrap wsBootstrap;
private final long handshakeTimeout;
private final IOException tooManyConnections;
private final IOException tooManyConnectionsPerHost;
private final ChannelPool channelPool;
private final boolean maxTotalConnectionsEnabled;
private final Semaphore freeChannels;
private final ChannelGroup openChannels;
private final boolean maxConnectionsPerHostEnabled;
private final ConcurrentHashMap<Object, Semaphore> freeChannelsPerHost = new ConcurrentHashMap<>();
private final ConcurrentHashMap<Channel, Object> channelId2PartitionKey = new ConcurrentHashMap<>();
private AsyncHttpClientHandler wsHandler;
public ChannelManager(final AsyncHttpClientConfig config, Timer nettyTimer) {
this.config = config;
try {
this.sslEngineFactory = config.getSslEngineFactory() != null ? config.getSslEngineFactory() : new DefaultSslEngineFactory(config);
} catch (SSLException e) {
throw new ExceptionInInitializerError(e);
}
ChannelPool channelPool = config.getChannelPool();
if (channelPool == null) {
if (config.isKeepAlive()) {
channelPool = new DefaultChannelPool(config, nettyTimer);
} else {
channelPool = NoopChannelPool.INSTANCE;
}
}
this.channelPool = channelPool;
tooManyConnections = trimStackTrace(new TooManyConnectionsException(config.getMaxConnections()));
tooManyConnectionsPerHost = trimStackTrace(new TooManyConnectionsPerHostException(config.getMaxConnectionsPerHost()));
maxTotalConnectionsEnabled = config.getMaxConnections() > 0;
maxConnectionsPerHostEnabled = config.getMaxConnectionsPerHost() > 0;
if (maxTotalConnectionsEnabled || maxConnectionsPerHostEnabled) {
openChannels = new CleanupChannelGroup("asyncHttpClient") {
@Override
public boolean remove(Object o) {
boolean removed = super.remove(o);
if (removed) {
if (maxTotalConnectionsEnabled)
freeChannels.release();
if (maxConnectionsPerHostEnabled) {
Object partitionKey = channelId2PartitionKey.remove(Channel.class.cast(o));
if (partitionKey != null) {
Semaphore hostFreeChannels = freeChannelsPerHost.get(partitionKey);
if (hostFreeChannels != null)
hostFreeChannels.release();
}
}
}
return removed;
}
};
freeChannels = new Semaphore(config.getMaxConnections());
} else {
openChannels = new CleanupChannelGroup("asyncHttpClient");
freeChannels = null;
}
handshakeTimeout = config.getHandshakeTimeout();
// check if external EventLoopGroup is defined
ThreadFactory threadFactory = config.getThreadFactory() != null ? config.getThreadFactory() : new DefaultThreadFactory(config.getThreadPoolName());
allowReleaseEventLoopGroup = config.getEventLoopGroup() == null;
if (allowReleaseEventLoopGroup) {
if (config.isUseNativeTransport()) {
eventLoopGroup = newEpollEventLoopGroup(threadFactory);
socketChannelClass = getEpollSocketChannelClass();
} else {
eventLoopGroup = new NioEventLoopGroup(0, threadFactory);
socketChannelClass = NioSocketChannel.class;
}
} else {
eventLoopGroup = config.getEventLoopGroup();
if (eventLoopGroup instanceof OioEventLoopGroup)
throw new IllegalArgumentException("Oio is not supported");
if (eventLoopGroup instanceof NioEventLoopGroup) {
socketChannelClass = NioSocketChannel.class;
} else {
socketChannelClass = getEpollSocketChannelClass();
}
}
httpBootstrap = new Bootstrap().channel(socketChannelClass).group(eventLoopGroup);
wsBootstrap = new Bootstrap().channel(socketChannelClass).group(eventLoopGroup);
// default to PooledByteBufAllocator
httpBootstrap.option(ChannelOption.ALLOCATOR, PooledByteBufAllocator.DEFAULT);
wsBootstrap.option(ChannelOption.ALLOCATOR, PooledByteBufAllocator.DEFAULT);
if (config.getConnectTimeout() > 0) {
httpBootstrap.option(ChannelOption.CONNECT_TIMEOUT_MILLIS, config.getConnectTimeout());
wsBootstrap.option(ChannelOption.CONNECT_TIMEOUT_MILLIS, config.getConnectTimeout());
}
for (Entry<ChannelOption<Object>, Object> entry : config.getChannelOptions().entrySet()) {
ChannelOption<Object> key = entry.getKey();
Object value = entry.getValue();
httpBootstrap.option(key, value);
wsBootstrap.option(key, value);
}
}
private EventLoopGroup newEpollEventLoopGroup(ThreadFactory threadFactory) {
try {
Class<?> epollEventLoopGroupClass = Class.forName("io.netty.channel.epoll.EpollEventLoopGroup");
return (EventLoopGroup) epollEventLoopGroupClass.getConstructor(int.class, ThreadFactory.class).newInstance(0, threadFactory);
} catch (Exception e) {
throw new IllegalArgumentException(e);
}
}
@SuppressWarnings("unchecked")
private Class<? extends Channel> getEpollSocketChannelClass() {
try {
return (Class<? extends Channel>) Class.forName("io.netty.channel.epoll.EpollSocketChannel");
} catch (ClassNotFoundException e) {
throw new IllegalArgumentException(e);
}
}
public void configureBootstraps(NettyRequestSender requestSender) {
HttpProtocol httpProtocol = new HttpProtocol(this, config, requestSender);
final AsyncHttpClientHandler httpHandler = new AsyncHttpClientHandler(config, this, requestSender, httpProtocol);
WebSocketProtocol wsProtocol = new WebSocketProtocol(this, config, requestSender);
wsHandler = new AsyncHttpClientHandler(config, this, requestSender, wsProtocol);
final NoopHandler pinnedEntry = new NoopHandler();
httpBootstrap.handler(new ChannelInitializer<Channel>() {
@Override
protected void initChannel(Channel ch) throws Exception {
ch.pipeline()
.addLast(PINNED_ENTRY, pinnedEntry)
.addLast(HTTP_CLIENT_CODEC, newHttpClientCodec())
.addLast(INFLATER_HANDLER, newHttpContentDecompressor())
.addLast(CHUNKED_WRITER_HANDLER, new ChunkedWriteHandler())
.addLast(AHC_HTTP_HANDLER, httpHandler);
ch.config().setOption(ChannelOption.AUTO_READ, false);
if (config.getHttpAdditionalChannelInitializer() != null)
config.getHttpAdditionalChannelInitializer().initChannel(ch);
}
});
wsBootstrap.handler(new ChannelInitializer<Channel>() {
@Override
protected void initChannel(Channel ch) throws Exception {
ch.pipeline()
.addLast(PINNED_ENTRY, pinnedEntry)
.addLast(HTTP_CLIENT_CODEC, newHttpClientCodec())
.addLast(AHC_WS_HANDLER, wsHandler);
if (config.getWsAdditionalChannelInitializer() != null)
config.getWsAdditionalChannelInitializer().initChannel(ch);
}
});
}
private HttpContentDecompressor newHttpContentDecompressor() {
if (config.isKeepEncodingHeader())
return new HttpContentDecompressor() {
@Override
protected String getTargetContentEncoding(String contentEncoding) throws Exception {
return contentEncoding;
}
};
else
return new HttpContentDecompressor();
}
public final void tryToOfferChannelToPool(Channel channel, AsyncHandler<?> asyncHandler, boolean keepAlive, Object partitionKey) {
if (channel.isActive() && keepAlive) {
LOGGER.debug("Adding key: {} for channel {}", partitionKey, channel);
Channels.setDiscard(channel);
if (asyncHandler instanceof AsyncHandlerExtensions)
AsyncHandlerExtensions.class.cast(asyncHandler).onConnectionOffer(channel);
channelPool.offer(channel, partitionKey);
if (maxConnectionsPerHostEnabled)
channelId2PartitionKey.putIfAbsent(channel, partitionKey);
} else {
// not offered
closeChannel(channel);
}
}
public Channel poll(Uri uri, String virtualHost, ProxyServer proxy, ConnectionPoolPartitioning connectionPoolPartitioning) {
Object partitionKey = connectionPoolPartitioning.getPartitionKey(uri, virtualHost, proxy);
return channelPool.poll(partitionKey);
}
public boolean removeAll(Channel connection) {
return channelPool.removeAll(connection);
}
private boolean tryAcquireGlobal() {
return !maxTotalConnectionsEnabled || freeChannels.tryAcquire();
}
private Semaphore getFreeConnectionsForHost(Object partitionKey) {
return freeChannelsPerHost.computeIfAbsent(partitionKey, pk -> new Semaphore(config.getMaxConnectionsPerHost()));
}
private boolean tryAcquirePerHost(Object partitionKey) {
return !maxConnectionsPerHostEnabled || getFreeConnectionsForHost(partitionKey).tryAcquire();
}
public void preemptChannel(Object partitionKey) throws IOException {
if (!channelPool.isOpen())
throw PoolAlreadyClosedException.INSTANCE;
if (!tryAcquireGlobal())
throw tooManyConnections;
if (!tryAcquirePerHost(partitionKey)) {
if (maxTotalConnectionsEnabled)
freeChannels.release();
throw tooManyConnectionsPerHost;
}
}
private void doClose() {
channelPool.destroy();
openChannels.close();
for (Channel channel : openChannels) {
Object attribute = Channels.getAttribute(channel);
if (attribute instanceof NettyResponseFuture<?>) {
NettyResponseFuture<?> nettyFuture = (NettyResponseFuture<?>) attribute;
nettyFuture.cancelTimeouts();
}
}
}
@SuppressWarnings({ "unchecked", "rawtypes" })
public void close() {
if (allowReleaseEventLoopGroup) {
io.netty.util.concurrent.Future whenEventLoopGroupClosed = eventLoopGroup.shutdownGracefully(config.getShutdownQuietPeriod(), config.getShutdownTimeout(),
TimeUnit.MILLISECONDS);
whenEventLoopGroupClosed.addListener((GenericFutureListener<?>) new GenericFutureListener<io.netty.util.concurrent.Future<?>>() {
public void operationComplete(io.netty.util.concurrent.Future<?> future) throws Exception {
doClose();
};
});
} else
doClose();
}
public void closeChannel(Channel channel) {
LOGGER.debug("Closing Channel {} ", channel);
Channels.setDiscard(channel);
removeAll(channel);
Channels.silentlyCloseChannel(channel);
openChannels.remove(channel);
}
public void abortChannelPreemption(Object partitionKey) {
if (maxTotalConnectionsEnabled)
freeChannels.release();
if (maxConnectionsPerHostEnabled)
getFreeConnectionsForHost(partitionKey).release();
}
public void registerOpenChannel(Channel channel, Object partitionKey) {
openChannels.add(channel);
if (maxConnectionsPerHostEnabled) {
channelId2PartitionKey.put(channel, partitionKey);
}
}
private HttpClientCodec newHttpClientCodec() {
return new HttpClientCodec(
config.getHttpClientCodecMaxInitialLineLength(),
config.getHttpClientCodecMaxHeaderSize(),
config.getHttpClientCodecMaxChunkSize(),
false);
}
private SslHandler createSslHandler(String peerHost, int peerPort) {
SSLEngine sslEngine = sslEngineFactory.newSslEngine(config, peerHost, peerPort);
SslHandler sslHandler = new SslHandler(sslEngine);
if (handshakeTimeout > 0)
sslHandler.setHandshakeTimeoutMillis(handshakeTimeout);
return sslHandler;
}
public static boolean isSslHandlerConfigured(ChannelPipeline pipeline) {
return pipeline.get(SSL_HANDLER) != null;
}
public void upgradeProtocol(ChannelPipeline pipeline, Uri requestUri) throws SSLException {
if (pipeline.get(HTTP_CLIENT_CODEC) != null)
pipeline.remove(HTTP_CLIENT_CODEC);
if (requestUri.isSecured())
if (isSslHandlerConfigured(pipeline)) {
pipeline.addAfter(SSL_HANDLER, HTTP_CLIENT_CODEC, newHttpClientCodec());
} else {
pipeline.addAfter(PINNED_ENTRY, HTTP_CLIENT_CODEC, newHttpClientCodec());
pipeline.addAfter(PINNED_ENTRY, SSL_HANDLER, createSslHandler(requestUri.getHost(), requestUri.getExplicitPort()));
}
else
pipeline.addAfter(PINNED_ENTRY, HTTP_CLIENT_CODEC, newHttpClientCodec());
if (requestUri.isWebSocket()) {
pipeline.addAfter(AHC_HTTP_HANDLER, AHC_WS_HANDLER, wsHandler);
pipeline.remove(AHC_HTTP_HANDLER);
}
}
public SslHandler addSslHandler(ChannelPipeline pipeline, Uri uri, String virtualHost) {
String peerHost;
int peerPort;
if (virtualHost != null) {
int i = virtualHost.indexOf(':');
if (i == -1) {
peerHost = virtualHost;
peerPort = uri.getSchemeDefaultPort();
} else {
peerHost = virtualHost.substring(0, i);
peerPort = Integer.valueOf(virtualHost.substring(i + 1));
}
} else {
peerHost = uri.getHost();
peerPort = uri.getExplicitPort();
}
SslHandler sslHandler = createSslHandler(peerHost, peerPort);
pipeline.addFirst(ChannelManager.SSL_HANDLER, sslHandler);
return sslHandler;
}
public Bootstrap getBootstrap(Uri uri, ProxyServer proxy) {
return uri.isWebSocket() && proxy == null ? wsBootstrap : httpBootstrap;
}
public void upgradePipelineForWebSockets(ChannelPipeline pipeline) {
pipeline.addAfter(HTTP_CLIENT_CODEC, WS_ENCODER_HANDLER, new WebSocket08FrameEncoder(true));
pipeline.remove(HTTP_CLIENT_CODEC);
pipeline.addBefore(AHC_WS_HANDLER, WS_DECODER_HANDLER, new WebSocket08FrameDecoder(false, false, config.getWebSocketMaxFrameSize()));
pipeline.addAfter(WS_DECODER_HANDLER, WS_FRAME_AGGREGATOR, new WebSocketFrameAggregator(config.getWebSocketMaxBufferSize()));
}
public final Callback newDrainCallback(final NettyResponseFuture<?> future, final Channel channel, final boolean keepAlive, final Object partitionKey) {
return new Callback(future) {
public void call() {
tryToOfferChannelToPool(channel, future.getAsyncHandler(), keepAlive, partitionKey);
}
};
}
public void drainChannelAndOffer(final Channel channel, final NettyResponseFuture<?> future) {
drainChannelAndOffer(channel, future, future.isKeepAlive(), future.getPartitionKey());
}
public void drainChannelAndOffer(final Channel channel, final NettyResponseFuture<?> future, boolean keepAlive, Object partitionKey) {
Channels.setAttribute(channel, newDrainCallback(future, channel, keepAlive, partitionKey));
}
public ChannelPool getChannelPool() {
return channelPool;
}
}
|
package com.newsblur.fragment;
import java.util.ArrayList;
import java.util.List;
import android.app.Activity;
import android.content.ContentResolver;
import android.content.ContentValues;
import android.content.Intent;
import android.content.SharedPreferences;
import android.database.Cursor;
import android.os.AsyncTask;
import android.os.Bundle;
import android.support.v4.app.DialogFragment;
import android.support.v4.app.Fragment;
import android.util.Log;
import android.view.ContextMenu;
import android.view.ContextMenu.ContextMenuInfo;
import android.view.Display;
import android.view.LayoutInflater;
import android.view.MenuInflater;
import android.view.MenuItem;
import android.view.View;
import android.view.View.OnCreateContextMenuListener;
import android.view.ViewGroup;
import android.widget.ExpandableListView;
import android.widget.ExpandableListView.OnChildClickListener;
import android.widget.ExpandableListView.OnGroupClickListener;
import android.widget.Toast;
import com.newsblur.R;
import com.newsblur.activity.AllStoriesItemsList;
import com.newsblur.activity.FeedItemsList;
import com.newsblur.activity.ItemsList;
import com.newsblur.activity.NewsBlurApplication;
import com.newsblur.activity.SavedStoriesItemsList;
import com.newsblur.activity.SocialFeedItemsList;
import com.newsblur.database.DatabaseConstants;
import com.newsblur.database.FeedProvider;
import com.newsblur.database.MixedExpandableListAdapter;
import com.newsblur.network.APIManager;
import com.newsblur.network.MarkFeedAsReadTask;
import com.newsblur.network.MarkFolderAsReadTask;
import com.newsblur.util.AppConstants;
import com.newsblur.util.ImageLoader;
import com.newsblur.util.PrefConstants;
import com.newsblur.util.UIUtils;
import com.newsblur.view.FolderTreeViewBinder;
import com.newsblur.view.SocialFeedViewBinder;
public class FolderListFragment extends Fragment implements OnGroupClickListener, OnChildClickListener, OnCreateContextMenuListener {
private ContentResolver resolver;
private MixedExpandableListAdapter folderAdapter;
private FolderTreeViewBinder groupViewBinder;
private APIManager apiManager;
private int currentState = AppConstants.STATE_SOME;
private SocialFeedViewBinder blogViewBinder;
private SharedPreferences sharedPreferences;
@Override
public void onCreate(Bundle savedInstanceState) {
super.onCreate(savedInstanceState);
// all cursors are initially queried in the "some" unread state to match the default view mode
Cursor folderCursor = resolver.query(FeedProvider.FOLDERS_URI, null, null, new String[] { DatabaseConstants.getFolderSelectionFromState(AppConstants.STATE_SOME) }, null);
Cursor socialFeedCursor = resolver.query(FeedProvider.SOCIAL_FEEDS_URI, null, DatabaseConstants.getBlogSelectionFromState(AppConstants.STATE_SOME), null, null);
Cursor countCursor = resolver.query(FeedProvider.FEED_COUNT_URI, null, DatabaseConstants.getBlogSelectionFromState(AppConstants.STATE_SOME), null, null);
Cursor sharedCountCursor = resolver.query(FeedProvider.SOCIALCOUNT_URI, null, DatabaseConstants.getBlogSelectionFromState(AppConstants.STATE_SOME), null, null);
Cursor savedCountCursor = resolver.query(FeedProvider.STARRED_STORIES_COUNT_URI, null, null, null, null);
ImageLoader imageLoader = ((NewsBlurApplication) getActivity().getApplicationContext()).getImageLoader();
groupViewBinder = new FolderTreeViewBinder(imageLoader);
blogViewBinder = new SocialFeedViewBinder(getActivity());
folderAdapter = new MixedExpandableListAdapter(getActivity(), folderCursor, socialFeedCursor, countCursor, sharedCountCursor, savedCountCursor);
folderAdapter.setViewBinders(groupViewBinder, blogViewBinder);
}
@Override
public void onAttach(Activity activity) {
sharedPreferences = activity.getSharedPreferences(PrefConstants.PREFERENCES, 0);
resolver = activity.getContentResolver();
apiManager = new APIManager(activity);
super.onAttach(activity);
}
@Override
public void onStart() {
super.onStart();
hasUpdated();
}
public void hasUpdated() {
folderAdapter.notifyDataSetChanged();
checkOpenFolderPreferences();
}
@Override
public View onCreateView(LayoutInflater inflater, ViewGroup container, Bundle savedInstanceState) {
View v = inflater.inflate(R.layout.fragment_folderfeedlist, container);
ExpandableListView list = (ExpandableListView) v.findViewById(R.id.folderfeed_list);
list.setGroupIndicator(getResources().getDrawable(R.drawable.transparent));
list.setOnCreateContextMenuListener(this);
Display display = getActivity().getWindowManager().getDefaultDisplay();
list.setIndicatorBounds(
display.getWidth() - UIUtils.convertDPsToPixels(getActivity(), 20),
display.getWidth() - UIUtils.convertDPsToPixels(getActivity(), 10));
list.setChildDivider(getActivity().getResources().getDrawable(R.drawable.divider_light));
list.setAdapter(folderAdapter);
list.setOnGroupClickListener(this);
list.setOnChildClickListener(this);
return v;
}
private ExpandableListView getListView() {
return (ExpandableListView) (this.getView().findViewById(R.id.folderfeed_list));
}
public void checkOpenFolderPreferences() {
if (sharedPreferences == null) {
sharedPreferences = getActivity().getSharedPreferences(PrefConstants.PREFERENCES, 0);
}
for (int i = 0; i < folderAdapter.getGroupCount(); i++) {
String groupName = folderAdapter.getGroupName(i);
if (sharedPreferences.getBoolean(AppConstants.FOLDER_PRE + "_" + groupName, true)) {
this.getListView().expandGroup(i);
} else {
this.getListView().collapseGroup(i);
}
}
}
@Override
public void onCreateContextMenu(ContextMenu menu, View v, ContextMenuInfo menuInfo) {
MenuInflater inflater = getActivity().getMenuInflater();
ExpandableListView.ExpandableListContextMenuInfo info = (ExpandableListView.ExpandableListContextMenuInfo) menuInfo;
int type = ExpandableListView.getPackedPositionType(info.packedPosition);
switch(type) {
case ExpandableListView.PACKED_POSITION_TYPE_GROUP:
int groupPosition = ExpandableListView.getPackedPositionGroup(info.packedPosition);
if (! folderAdapter.isRowSavedStories(groupPosition) ) {
inflater.inflate(R.menu.context_folder, menu);
}
break;
case ExpandableListView.PACKED_POSITION_TYPE_CHILD:
inflater.inflate(R.menu.context_feed, menu);
break;
}
}
@Override
public boolean onContextItemSelected(MenuItem item) {
final ExpandableListView.ExpandableListContextMenuInfo info = (ExpandableListView.ExpandableListContextMenuInfo) item.getMenuInfo();
if (item.getItemId() == R.id.menu_mark_feed_as_read) {
new MarkFeedAsReadTask(getActivity(), apiManager) {
@Override
protected void onPostExecute(Boolean result) {
if (result.booleanValue()) {
ContentValues values = new ContentValues();
values.put(DatabaseConstants.FEED_NEGATIVE_COUNT, 0);
values.put(DatabaseConstants.FEED_NEUTRAL_COUNT, 0);
values.put(DatabaseConstants.FEED_POSITIVE_COUNT, 0);
resolver.update(FeedProvider.FEEDS_URI.buildUpon().appendPath(Long.toString(info.id)).build(), values, null, null);
folderAdapter.notifyDataSetChanged();
Toast.makeText(getActivity(), R.string.toast_marked_feed_as_read, Toast.LENGTH_SHORT).show();
} else {
Toast.makeText(getActivity(), R.string.toast_error_marking_feed_as_read, Toast.LENGTH_LONG).show();
}
}
}.execute(Long.toString(info.id));
return true;
} else if (item.getItemId() == R.id.menu_delete_feed) {
int childPosition = ExpandableListView.getPackedPositionChild(info.packedPosition);
int groupPosition = ExpandableListView.getPackedPositionGroup(info.packedPosition);
Cursor childCursor = folderAdapter.getChild(groupPosition, childPosition);
String feedTitle = childCursor.getString(childCursor.getColumnIndex(DatabaseConstants.FEED_TITLE));
// TODO: is there a better way to map group position onto folderName than asking the list adapter?
Cursor folderCursor = ((MixedExpandableListAdapter) this.getListView().getExpandableListAdapter()).getGroup(groupPosition);
String folderName = folderCursor.getString(folderCursor.getColumnIndex(DatabaseConstants.FOLDER_NAME));
DialogFragment deleteFeedFragment = DeleteFeedFragment.newInstance(info.id, feedTitle, folderName);
deleteFeedFragment.show(getFragmentManager(), "dialog");
return true;
} else if (item.getItemId() == R.id.menu_mark_folder_as_read) {
int groupPosition = ExpandableListView.getPackedPositionGroup(info.packedPosition);
// all folder but the root All Stories one use the simple method
if (!folderAdapter.isFolderRoot(groupPosition)) {
// TODO: is there a better way to get the folder ID for a group position that asking the list view?
final Cursor folderCursor = ((MixedExpandableListAdapter) this.getListView().getExpandableListAdapter()).getGroup(groupPosition);
String folderId = folderCursor.getString(folderCursor.getColumnIndex(DatabaseConstants.FOLDER_NAME));
new MarkFolderAsReadTask(apiManager, resolver) {
@Override
protected void onPostExecute(Boolean result) {
if (result) {
folderAdapter.notifyDataSetChanged();
Toast.makeText(getActivity(), R.string.toast_marked_folder_as_read, Toast.LENGTH_SHORT).show();
} else {
Toast.makeText(getActivity(), R.string.toast_error_marking_feed_as_read, Toast.LENGTH_SHORT).show();
}
}
}.execute(folderId);
} else {
// TODO is social feed actually all shared stories ? Should this be used for expandable and position == 0 ?
/*final Cursor socialFeedCursor = ((MixedExpandableListAdapter) list.getExpandableListAdapter()).getGroup(groupPosition);
String socialFeedId = socialFeedCursor.getString(socialFeedCursor.getColumnIndex(DatabaseConstants.SOCIAL_FEED_ID));
new MarkSocialFeedAsReadTask(apiManager, resolver){
@Override
protected void onPostExecute(Boolean result) {
if (result.booleanValue()) {
folderAdapter.notifyDataSetChanged();
Toast.makeText(getActivity(), R.string.toast_marked_socialfeed_as_read, Toast.LENGTH_SHORT).show();
} else {
Toast.makeText(getActivity(), R.string.toast_error_marking_feed_as_read, Toast.LENGTH_LONG).show();
}
}
}.execute(socialFeedId);*/
new AsyncTask<Void, Void, Boolean>() {
private List<String> feedIds = new ArrayList<String>();
@Override
protected Boolean doInBackground(Void... arg) {
return apiManager.markAllAsRead();
}
@Override
protected void onPostExecute(Boolean result) {
if (result) {
ContentValues values = new ContentValues();
values.put(DatabaseConstants.FEED_NEGATIVE_COUNT, 0);
values.put(DatabaseConstants.FEED_NEUTRAL_COUNT, 0);
values.put(DatabaseConstants.FEED_POSITIVE_COUNT, 0);
resolver.update(FeedProvider.FEEDS_URI, values, null, null);
folderAdapter.notifyDataSetChanged();
UIUtils.safeToast(getActivity(), R.string.toast_marked_all_stories_as_read, Toast.LENGTH_SHORT);
} else {
UIUtils.safeToast(getActivity(), R.string.toast_error_marking_feed_as_read, Toast.LENGTH_SHORT);
}
};
}.execute();
}
return true;
}
return super.onContextItemSelected(item);
}
public void changeState(int state) {
groupViewBinder.setState(state);
blogViewBinder.setState(state);
currentState = state;
String groupSelection = DatabaseConstants.getFolderSelectionFromState(state);
String blogSelection = DatabaseConstants.getBlogSelectionFromState(state);
// the countCursor always counts neutral/"some" unreads, no matter what mode we are in
String countSelection = DatabaseConstants.getBlogSelectionFromState(AppConstants.STATE_SOME);
folderAdapter.currentState = state;
Cursor cursor = resolver.query(FeedProvider.FOLDERS_URI, null, null, new String[] { groupSelection }, null);
Cursor blogCursor = resolver.query(FeedProvider.SOCIAL_FEEDS_URI, null, blogSelection, null, null);
Cursor countCursor = resolver.query(FeedProvider.FEED_COUNT_URI, null, countSelection, null, null);
folderAdapter.setBlogCursor(blogCursor);
folderAdapter.setGroupCursor(cursor);
folderAdapter.setCountCursor(countCursor);
folderAdapter.notifyDataSetChanged();
checkOpenFolderPreferences();
}
@Override
public boolean onGroupClick(ExpandableListView list, View group, int groupPosition, long id) {
// The root "All Stories" folder goes to a special activity
if (folderAdapter.isFolderRoot(groupPosition)) {
Intent i = new Intent(getActivity(), AllStoriesItemsList.class);
i.putExtra(AllStoriesItemsList.EXTRA_STATE, currentState);
startActivity(i);
return true;
} else if (folderAdapter.isRowSavedStories(groupPosition)) {
Intent i = new Intent(getActivity(), SavedStoriesItemsList.class);
startActivity(i);
return true;
} else {
if ((group != null) && (group.findViewById(R.id.row_foldersums) != null)) {
String groupName = folderAdapter.getGroupName(groupPosition);
if (list.isGroupExpanded(groupPosition)) {
group.findViewById(R.id.row_foldersums).setVisibility(View.VISIBLE);
sharedPreferences.edit().putBoolean(AppConstants.FOLDER_PRE + "_" + groupName, false).commit();
} else {
group.findViewById(R.id.row_foldersums).setVisibility(View.INVISIBLE);
sharedPreferences.edit().putBoolean(AppConstants.FOLDER_PRE + "_" + groupName, true).commit();
}
}
return false;
}
}
@Override
public boolean onChildClick(ExpandableListView list, View childView, int groupPosition, int childPosition, long id) {
if (groupPosition == 0) {
Cursor blurblogCursor = folderAdapter.getBlogCursor(childPosition);
String username = blurblogCursor.getString(blurblogCursor.getColumnIndex(DatabaseConstants.SOCIAL_FEED_USERNAME));
String userIcon = blurblogCursor.getString(blurblogCursor.getColumnIndex(DatabaseConstants.SOCIAL_FEED_ICON));
String userId = blurblogCursor.getString(blurblogCursor.getColumnIndex(DatabaseConstants.SOCIAL_FEED_ID));
String blurblogTitle = blurblogCursor.getString(blurblogCursor.getColumnIndex(DatabaseConstants.SOCIAL_FEED_TITLE));
final Intent intent = new Intent(getActivity(), SocialFeedItemsList.class);
intent.putExtra(ItemsList.EXTRA_BLURBLOG_USER_ICON, userIcon);
intent.putExtra(ItemsList.EXTRA_BLURBLOG_USERNAME, username);
intent.putExtra(ItemsList.EXTRA_BLURBLOG_TITLE, blurblogTitle);
intent.putExtra(ItemsList.EXTRA_BLURBLOG_USERID, userId);
intent.putExtra(ItemsList.EXTRA_STATE, currentState);
getActivity().startActivity(intent);
} else {
final Intent intent = new Intent(getActivity(), FeedItemsList.class);
Cursor childCursor = folderAdapter.getChild(groupPosition, childPosition);
String feedId = childCursor.getString(childCursor.getColumnIndex(DatabaseConstants.FEED_ID));
String feedTitle = childCursor.getString(childCursor.getColumnIndex(DatabaseConstants.FEED_TITLE));
final Cursor folderCursor = ((MixedExpandableListAdapter) list.getExpandableListAdapter()).getGroup(groupPosition);
String folderName = folderCursor.getString(folderCursor.getColumnIndex(DatabaseConstants.FOLDER_NAME));
intent.putExtra(FeedItemsList.EXTRA_FEED, feedId);
intent.putExtra(FeedItemsList.EXTRA_FEED_TITLE, feedTitle);
intent.putExtra(FeedItemsList.EXTRA_FOLDER_NAME, folderName);
intent.putExtra(ItemsList.EXTRA_STATE, currentState);
getActivity().startActivity(intent);
}
return true;
}
}
|
package simulation;
import akka.japi.pf.ReceiveBuilder;
import akka.japi.pf.UnitPFBuilder;
import drones.messages.*;
import drones.models.*;
import play.libs.Akka;
import scala.concurrent.Promise;
import scala.concurrent.duration.Duration;
import scala.concurrent.duration.FiniteDuration;
import simulation.messages.SetConnectionLostMessage;
import simulation.messages.SetCrashedMessage;
import java.io.Serializable;
import java.util.concurrent.TimeUnit;
public class DroneActorSimulator extends DroneActor {
private class ProgressToDestinationMessage implements Serializable {
private Location destination;
private FiniteDuration timeStep;
public ProgressToDestinationMessage(Location destination, FiniteDuration timestep) {
this.destination = destination;
this.timeStep = timestep;
}
public Location getDestination() { return destination; }
public FiniteDuration getTimeStep() { return timeStep; }
}
private byte batteryLowLevel = 10;
private byte batteryCriticalLevel = 5;
private boolean initialized = false;
private boolean crashed = false;
private boolean connectionLost = false;
private double maxHeight;
private double topSpeed; // assume m/s
private boolean flyingToDestination;
// TODO: settable delay, sleep/suspend
// Control stuff
@Override
protected UnitPFBuilder<Object> createListeners() {
return ReceiveBuilder.
match(BatteryPercentageChangedMessage.class, m -> processBatteryLevel(m.getPercent())).
match(SetCrashedMessage.class, m -> setCrashed(m.isCrashed())).
match(SetConnectionLostMessage.class, m -> setConnectionLost(m.isConnectionLost())).
match(ProgressToDestinationMessage.class, m -> progressToDestination(m.getDestination(), m.getTimeStep()));
}
protected void processBatteryLevel(byte percentage) {
if(percentage < batteryLowLevel) {
if(percentage < batteryCriticalLevel) {
if(!connectionLost) {
tellSelf(new AlertStateChangedMessage(AlertState.BATTERY_CRITICAL));
tellSelf(new LandRequestMessage());
tellSelf(new NavigationStateChangedMessage(
NavigationState.UNAVAILABLE,
NavigationStateReason.BATTERY_LOW));
} else {
alertState.setValue(AlertState.BATTERY_CRITICAL);
state.setValue(FlyingState.LANDED);
navigationState.setValue(NavigationState.UNAVAILABLE);
navigationStateReason.setValue(NavigationStateReason.BATTERY_LOW);
}
}
else {
if(!connectionLost) {
tellSelf(new AlertStateChangedMessage(AlertState.BATTERY_LOW));
}
else {
alertState.setValue(AlertState.BATTERY_LOW);
}
}
}
}
protected void setCrashed(boolean crashed) {
if (crashed) {
tellSelf(new AltitudeChangedMessage(0.0));
tellSelf(new FlyingStateChangedMessage(FlyingState.EMERGENCY));
tellSelf(new AlertStateChangedMessage(AlertState.USER_EMERGENCY));
tellSelf(new SpeedChangedMessage(0, 0, 0));
tellSelf(new NavigationStateChangedMessage(
NavigationState.UNAVAILABLE,
NavigationStateReason.STOPPED
));
}
else {
tellSelf(new FlyingStateChangedMessage(FlyingState.LANDED));
tellSelf(new AlertStateChangedMessage(AlertState.NONE));
tellSelf(new NavigationStateChangedMessage(
NavigationState.AVAILABLE,
NavigationStateReason.ENABLED
));
}
this.crashed = crashed;
}
protected void setConnectionLost(boolean connectionLost) {
if(connectionLost) {
// Don't tell self (we don't want this messages published as we are out of range
alertState.setValue(AlertState.CUT_OUT);
navigationState.setValue(NavigationState.UNAVAILABLE);
navigationStateReason.setValue(NavigationStateReason.CONNECTION_LOST);
}
else {
tellSelf(new AlertStateChangedMessage(AlertState.NONE));
tellSelf(new NavigationStateChangedMessage(
NavigationState.AVAILABLE,
NavigationStateReason.ENABLED
));
}
this.connectionLost = connectionLost;
}
protected void progressToDestination(Location destination, FiniteDuration timeFlown) {
// Check if moveToLocation wasn't cancelled
if(flyingToDestination) {
Location currentLocation = location.getRawValue();
// Calculate distance
double distance = Location.distance(currentLocation, destination); // assume in meters
double timeTillArrival = distance/topSpeed;
double timeStep = timeFlown.toUnit(TimeUnit.SECONDS);
Location newLocation;
if (timeTillArrival > timeStep) {
// Not there yet
double deltaLongtitude = destination.getLongtitude() - currentLocation.getLongtitude();
double deltaLatitude = destination.getLatitude() - currentLocation.getLatitude();
double deltaAltitude = destination.getHeigth() - currentLocation.getHeigth();
double fraction = timeStep/timeTillArrival;
double newLongtitude = currentLocation.getLongtitude() + deltaLongtitude * fraction;
double newLatitude = currentLocation.getLatitude() + deltaLatitude * fraction;
double newHeight = currentLocation.getHeigth() + deltaAltitude * fraction;
newLocation = new Location(newLatitude, newLongtitude, newHeight);
} else {
newLocation = destination;
}
// Update current location
if (!connectionLost) {
tellSelf(new LocationChangedMessage(
newLocation.getLongtitude(),
newLocation.getLatitude(),
newLocation.getHeigth()));
}
else {
location.setValue(newLocation);
}
// Check if we have arrived ore not
if (timeTillArrival < timeStep) {
// We have arrived
if(!connectionLost) {
tellSelf(new FlyingStateChangedMessage(FlyingState.HOVERING));
tellSelf(new NavigationStateChangedMessage(
NavigationState.AVAILABLE,
NavigationStateReason.FINISHED
));
} else {
state.setValue(FlyingState.HOVERING);
navigationState.setValue(NavigationState.AVAILABLE);
navigationStateReason.setValue(NavigationStateReason.FINISHED);
}
}
else {
// Schedule to fly further
Akka.system().scheduler().scheduleOnce(
timeFlown,
self(),
new ProgressToDestinationMessage(destination, timeFlown),
Akka.system().dispatcher(),
self());
}
} else {
// Flying aborted
if(!connectionLost) {
tellSelf(new FlyingStateChangedMessage(FlyingState.HOVERING));
tellSelf(new NavigationStateChangedMessage(
NavigationState.AVAILABLE,
NavigationStateReason.STOPPED
));
} else {
state.setValue(FlyingState.HOVERING);
navigationState.setValue(NavigationState.AVAILABLE);
navigationStateReason.setValue(NavigationStateReason.STOPPED);
}
}
}
// Utility methods
protected void tellSelf(Object msg) {
self().tell(msg, self());
}
public DroneActorSimulator() {
state.setValue(FlyingState.LANDED);
alertState.setValue(AlertState.NONE);
location.setValue(new Location(0.0, 0.0, 0.0));
batteryPercentage.setValue((byte) 100);
rotation.setValue(new Rotation(0, 0, 0));
speed.setValue(new Speed(0.0, 0.0, 0.0));
altitude.setValue(0.0);
version.setValue(new DroneVersion("1.0", "1.0"));
navigationState.setValue(NavigationState.AVAILABLE);
navigationStateReason.setValue(NavigationStateReason.ENABLED);
gpsFix.setValue(false);
maxHeight = 10;
topSpeed = 10;
}
// Implementation of DroneActor
@Override
protected void init(Promise<Void> p) {
if(connectionLost) {
return;
}
initialized = true;
p.success(null);
}
@Override
protected void takeOff(Promise<Void> p) {
if(connectionLost) {
return;
}
if(!initialized) {
p.failure(new DroneException("Failed to send command. Not initialized yet."));
return;
}
if(crashed) {
p.failure(new DroneException("Drone crashed, unable to execute commands"));
return;
}
switch (state.getRawValue()) {
case EMERGENCY:
p.failure(new DroneException("Drone is in emergency status"));
break;
case LANDING:
// Land drone before taking off again
tellSelf(new FlyingStateChangedMessage(FlyingState.LANDED));
// Fall-through
case LANDED:
tellSelf(new FlyingStateChangedMessage(FlyingState.TAKINGOFF));
tellSelf(new AltitudeChangedMessage(1.0));
tellSelf(new FlyingStateChangedMessage(FlyingState.HOVERING));
// Fall-throug
default:
// TODO: set navigation status?
p.success(null);
}
}
@Override
protected void land(Promise<Void> p) {
if(connectionLost) {
return;
}
if(!initialized) {
p.failure(new DroneException("Failed to send command. Not initialized yet."));
return;
}
if(crashed) {
p.failure(new DroneException("Drone crashed, unable to execute commands"));
return;
}
switch (state.getRawValue()) {
case EMERGENCY:
p.failure(new DroneException("Drone is in emergency status"));
break;
case TAKINGOFF:
// Hover drone before landing again
tellSelf(new FlyingStateChangedMessage(FlyingState.HOVERING));
// Fall-through
case HOVERING:
tellSelf(new FlyingStateChangedMessage(FlyingState.LANDING));
// Fall-through
default:
tellSelf(new AltitudeChangedMessage(0.0));
tellSelf(new FlyingStateChangedMessage(FlyingState.LANDED));
p.success(null);
}
}
@Override
protected void move3d(Promise<Void> p, double vx, double vy, double vz, double vr) {
if(connectionLost) {
return;
}
if(!initialized) {
p.failure(new DroneException("Failed to send command. Not initialized yet."));
return;
}
if(crashed) {
p.failure(new DroneException("Drone crashed, unable to execute commands"));
return;
}
// TODO: need specification of this method
p.success(null);
}
@Override
protected void moveToLocation(Promise<Void> p, double latitude, double longitude, double altitude) {
if(connectionLost) {
return;
}
if(!initialized) {
p.failure(new DroneException("Failed to send command. Not initialized yet."));
return;
}
if(crashed) {
p.failure(new DroneException("Drone crashed, unable to execute commands"));
return;
}
FlyingState flyingState = state.getRawValue();
if(flyingState == FlyingState.FLYING || flyingState == FlyingState.HOVERING) {
double height = Math.min(altitude, maxHeight);
Location destination = new Location(latitude, longitude, height);
tellSelf(new FlyingStateChangedMessage(FlyingState.FLYING));
tellSelf(new NavigationStateChangedMessage(
NavigationState.IN_PROGRESS,
NavigationStateReason.REQUESTED
));
tellSelf(new SpeedChangedMessage(10, 10, 10));
// Schedule to fly further
Akka.system().scheduler().scheduleOnce(
new FiniteDuration(1, TimeUnit.SECONDS),
self(),
new ProgressToDestinationMessage(destination, Duration.create(1, TimeUnit.SECONDS)),
Akka.system().dispatcher(),
self());
p.success(null);
} else {
p.failure(new DroneException("Drone is unable to move in current state: "
+ flyingState.name()));
}
}
@Override
protected void cancelMoveToLocation(Promise<Void> p) {
if(connectionLost) {
return;
}
if(!initialized) {
p.failure(new DroneException("Failed to send command. Not initialized yet."));
return;
}
if(crashed) {
p.failure(new DroneException("Drone crashed, unable to execute commands"));
return;
}
if(state.getRawValue() == FlyingState.EMERGENCY) {
p.failure(new DroneException("Unable to send commands to drone in emergency state"));
} else {
flyingToDestination = false;
p.success(null);
}
}
@Override
protected void setMaxHeight(Promise<Void> p, float meters) {
if(connectionLost) {
return;
}
if(!initialized) {
p.failure(new DroneException("Failed to send command. Not initialized yet."));
return;
}
/* TODO: necessary here?
if(crashed) {
p.failure(new DroneException("Drone crashed, unable to execute commands"));
return;
}
*/
maxHeight = meters;
p.success(null);
}
@Override
protected void setMaxTilt(Promise<Void> p, float degrees) {
if(connectionLost) {
return;
}
if(!initialized) {
p.failure(new DroneException("Failed to send command. Not initialized yet."));
return;
}
/* TODO: necessary here?
if(crashed) {
p.failure(new DroneException("Drone crashed, unable to execute commands"));
return;
}
*/
p.success(null);
}
@Override
protected void setOutdoor(Promise<Void> p, boolean outdoor) {
if(connectionLost) {
return;
}
if(!initialized) {
p.failure(new DroneException("Failed to send command. Not initialized yet."));
return;
}
/* TODO: necessary here?
if(crashed) {
p.failure(new DroneException("Drone crashed, unable to execute commands"));
return;
}
*/
// no effect on simulation
p.success(null);
}
@Override
protected void setHull(Promise<Void> p, boolean hull) {
if(connectionLost) {
return;
}
if(!initialized) {
p.failure(new DroneException("Failed to send command. Not initialized yet."));
return;
}
/* TODO: necessary here?
if(crashed) {
p.failure(new DroneException("Drone crashed, unable to execute commands"));
return;
}
*/
// No effect on simulation
p.success(null);
}
@Override
protected void flatTrim(Promise<Void> p) {
if(connectionLost) {
return;
}
if(!initialized) {
p.failure(new DroneException("Failed to send command. Not initialized yet."));
return;
}
/* TODO: necessary here?
if(crashed) {
p.failure(new DroneException("Drone crashed, unable to execute commands"));
return;
}
*/
// TODO: find out what this should do
p.success(null);
}
}
|
/*
* $Id: NullPlugin.java,v 1.21 2003-02-24 18:39:53 tal Exp $
*/
package org.lockss.test;
import java.io.*;
import java.util.*;
import java.net.*;
import java.security.MessageDigest;
import org.lockss.daemon.*;
import org.lockss.plugin.*;
import org.lockss.state.*;
import org.lockss.test.*;
/**
* Base class for test plugins that don't want to implement all the
* required methods.
* Extend only the nested classes to which you need to add bahavior.
*/
public class NullPlugin {
/**
* Base class for test <code>Plugin</code>s. Default methods do nothing
* or return constants.
*/
public static class Plugin implements org.lockss.plugin.Plugin {
protected Plugin() {
}
public void initPlugin() {
}
public void stopPlugin() {
}
public String getPluginId() {
return "NullPlugin";
}
public String getVersion() {
return "NullVersion";
}
public List getSupportedAUNames() {
return null;
}
public List getAUConfigProperties() {
return null;
}
public String getAUIdFromConfig(Configuration config)
throws org.lockss.daemon.ArchivalUnit.ConfigurationException {
return null;
}
public org.lockss.daemon.ArchivalUnit configureAU(Configuration config)
throws org.lockss.daemon.ArchivalUnit.ConfigurationException {
return null;
}
public org.lockss.daemon.ArchivalUnit createAU(Configuration auConfig)
throws org.lockss.daemon.ArchivalUnit.ConfigurationException {
return null;
}
public org.lockss.daemon.ArchivalUnit getAU(String auId) {
return null;
}
public Collection getAllAUs() {
return null;
};
}
/**
* Base class for test <code>CachedUrl</code>s. Default methods do nothing
* or return constants.
*/
public static class CachedUrl implements org.lockss.daemon.CachedUrl {
protected CachedUrl() {
}
public String toString() {
return "[NullPlugin.CachedUrl]";
}
public String getUrl() {
return null;
}
public boolean hasContent() {
return false;
}
public boolean isLeaf() {
return true;
}
public int getType() {
return CachedUrlSetNode.TYPE_CACHED_URL;
}
public InputStream openForReading() {
return new StringInputStream("");
}
public Properties getProperties() {
return new Properties();
}
}
/**
* Base class for test <code>UrlCacher</code>s. Default methods do nothing
* or return constants.
*/
public static class UrlCacher implements org.lockss.daemon.UrlCacher {
private String url;
private String contents = null;
private Properties props = new Properties();
protected UrlCacher() {
}
public String getUrl() {
return null;
}
public org.lockss.daemon.CachedUrlSet getCachedUrlSet() {
return null;
}
public String toString() {
return "[NullPlugin.UrlCacher]";
}
public org.lockss.daemon.CachedUrl getCachedUrl() {
return new CachedUrl();
}
public boolean shouldBeCached() {
return false;
}
public void cache() throws IOException {
}
public void storeContent(InputStream input,
Properties headers) throws IOException {
}
public InputStream getUncachedInputStream() {
return new StringInputStream("");
}
public Properties getUncachedProperties() {
return new Properties();
}
}
/**
* Base class for test <code>CachedUrlSet</code>s. Default methods do
* nothing or return constants or empty enumerations.
*/
public static class CachedUrlSet implements org.lockss.daemon.CachedUrlSet {
public String toString() {
return "[NullPlugin.CachedUrlSet]";
}
public CachedUrlSetSpec getSpec() {
return null;
}
public org.lockss.daemon.ArchivalUnit getArchivalUnit() {
return null;
}
public void storeActualHashDuration(long elapsed, Exception err) {
}
public Iterator flatSetIterator() {
return null;
}
public Iterator treeSetIterator() {
return null;
}
public Iterator treeIterator() {
return null;
}
public boolean isLeaf() {
return false;
}
public int getType() {
return CachedUrlSetNode.TYPE_CACHED_URL_SET;
}
public org.lockss.daemon.CachedUrlSetHasher
getContentHasher(MessageDigest hasher) {
return new CachedUrlSetHasher();
}
public org.lockss.daemon.CachedUrlSetHasher
getNameHasher(MessageDigest hasher) {
return new CachedUrlSetHasher();
}
public long estimatedHashDuration() {
return 1000;
}
public boolean hasContent() {
return false;
}
public org.lockss.daemon.CachedUrl makeCachedUrl(String url) {
return new CachedUrl();
}
public org.lockss.daemon.UrlCacher makeUrlCacher(String url) {
return new UrlCacher();
}
public boolean containsUrl(String url) {
return false;
}
public int hashCode() {
return 0;
}
public String getUrl() {
return "null";
}
}
public static class ArchivalUnit
implements org.lockss.daemon.ArchivalUnit {
public void setConfiguration(Configuration config) {
}
public org.lockss.daemon.CachedUrlSet makeCachedUrlSet(String url,
String lwrBound,
String uprBound) {
return null;
}
public org.lockss.daemon.CachedUrlSet getAUCachedUrlSet() {
return null;
}
public CrawlSpec getCrawlSpec() {
return null;
}
public boolean shouldBeCached(String url) {
return false;
}
public String getPluginId() {
return "null";
}
public String getAUId() {
return "null";
}
public void pause() {
}
public int hashCode() {
return 0;
}
public List getNewContentCrawlUrls() {
return null;
}
public boolean shouldCrawlForNewContent(AuState aus) {
return false;
}
}
/**
* Base class for test <code>CachedUrlSetHasher</code>s. Default methods
* do nothing or return constants.
*/
public static class CachedUrlSetHasher
implements org.lockss.daemon.CachedUrlSetHasher {
public boolean finished() {
return false;
}
public int hashStep(int numBytes) {
return 0;
}
}
}
|
package analysis.dynamicsim;
import gnu.trove.map.hash.TObjectDoubleHashMap;
import java.awt.Point;
import java.io.BufferedWriter;
import java.io.FileOutputStream;
import java.io.FileWriter;
import java.io.IOException;
import java.io.PrintStream;
import java.util.ArrayList;
import java.util.Comparator;
import java.util.HashMap;
import java.util.HashSet;
import java.util.LinkedHashMap;
import java.util.LinkedHashSet;
import java.util.Map;
import java.util.PriorityQueue;
import javax.swing.JFrame;
import javax.swing.JOptionPane;
import javax.swing.JProgressBar;
import javax.xml.stream.XMLStreamException;
import flanagan.math.Fmath;
import flanagan.math.PsRandom;
import main.Gui;
import main.util.dataparser.DTSDParser;
import main.util.dataparser.DataParser;
import main.util.dataparser.TSDParser;
import odk.lang.FastMath;
import org.apache.commons.math.stat.descriptive.DescriptiveStatistics;
import org.sbml.jsbml.ASTNode;
import org.sbml.jsbml.Annotation;
import org.sbml.jsbml.AssignmentRule;
import org.sbml.jsbml.Compartment;
import org.sbml.jsbml.Constraint;
import org.sbml.jsbml.Event;
import org.sbml.jsbml.EventAssignment;
import org.sbml.jsbml.InitialAssignment;
import org.sbml.jsbml.KineticLaw;
import org.sbml.jsbml.ListOf;
import org.sbml.jsbml.LocalParameter;
import org.sbml.jsbml.Model;
import org.sbml.jsbml.ModifierSpeciesReference;
import org.sbml.jsbml.Parameter;
import org.sbml.jsbml.RateRule;
import org.sbml.jsbml.Reaction;
import org.sbml.jsbml.Rule;
import org.sbml.jsbml.SBMLDocument;
import org.sbml.jsbml.SBMLErrorLog;
import org.sbml.jsbml.SBMLException;
import org.sbml.jsbml.SBMLReader;
import org.sbml.jsbml.Species;
import org.sbml.jsbml.SpeciesReference;
import org.sbml.jsbml.SBMLWriter;
import org.sbml.jsbml.text.parser.ParseException;
import biomodel.util.GlobalConstants;
public abstract class Simulator {
//SBML model
protected Model model = null;
//generates random numbers based on the xorshift method
protected XORShiftRandom randomNumberGenerator = null;
//allows for access to a propensity from a reaction ID
protected TObjectDoubleHashMap<String> reactionToPropensityMap = null;
//allows for access to reactant/product speciesID and stoichiometry from a reaction ID
//note that species and stoichiometries need to be thought of as unique for each reaction
protected HashMap<String, HashSet<StringDoublePair> > reactionToSpeciesAndStoichiometrySetMap = null;
protected HashMap<String, HashSet<StringStringPair> > reactionToNonconstantStoichiometriesSetMap = null;
//allows for access to reactant/modifier speciesID and stoichiometry from a reaction ID
protected HashMap<String, HashSet<StringDoublePair> > reactionToReactantStoichiometrySetMap = null;
//allows for access to a kinetic formula tree from a reaction
protected HashMap<String, ASTNode> reactionToFormulaMap = null;
//allows for access to a set of reactions that a species is in (as a reactant or modifier) from a species ID
protected HashMap<String, HashSet<String> > speciesToAffectedReactionSetMap = null;
//allows for access to species booleans from a species ID
protected HashMap<String, Boolean> speciesToIsBoundaryConditionMap = null;
protected HashMap<String, Boolean> speciesToHasOnlySubstanceUnitsMap = null;
protected HashMap<String, String> speciesToSubstanceUnitsMap = null;
protected HashMap<String, String> speciesToConversionFactorMap = null;
protected HashMap<String, String> speciesToCompartmentNameMap = null;
protected TObjectDoubleHashMap<String> speciesToCompartmentSizeMap = null;
//a linked (ordered) set of all species IDs, to allow easy access to their values via the variableToValue map
protected LinkedHashSet<String> speciesIDSet = null;
//allows for access to species and parameter values from a variable ID
protected TObjectDoubleHashMap<String> variableToValueMap = null;
//stores events in order of fire time and priority
protected PriorityQueue<EventToFire> triggeredEventQueue = null;
protected HashSet<String> untriggeredEventSet = null;
//hashmaps that allow for access to event information from the event's id
protected HashMap<String, ASTNode> eventToPriorityMap = null;
protected HashMap<String, ASTNode> eventToDelayMap = null;
protected HashMap<String, Boolean> eventToHasDelayMap = null;
protected HashMap<String, Boolean> eventToTriggerPersistenceMap = null;
protected HashMap<String, Boolean> eventToUseValuesFromTriggerTimeMap = null;
protected HashMap<String, ASTNode> eventToTriggerMap = null;
protected HashMap<String, Boolean> eventToTriggerInitiallyTrueMap = null;
protected HashMap<String, Boolean> eventToPreviousTriggerValueMap = null;
protected HashMap<String, HashSet<Object> > eventToAssignmentSetMap = null;
//allows for access to the reactions whose propensity changes when an event fires
protected HashMap<String, HashSet<String> > eventToAffectedReactionSetMap = null;
//allows for access to the set of events that a variable is in
protected HashMap<String, HashSet<String> > variableToEventSetMap = null;
//allows for access to the set of assignment rules that a variable (rhs) in an assignment rule affects
protected HashMap<String, HashSet<AssignmentRule> > variableToAffectedAssignmentRuleSetMap = null;
//allows to access to whether or not a variable is in an assignment or rate rule rule (RHS)
protected HashMap<String, Boolean> variableToIsInAssignmentRuleMap = null;
protected HashMap<String, Boolean> variableToIsInRateRuleMap = null;
//allows for access to the set of constraints that a variable affects
protected HashMap<String, HashSet<ASTNode> > variableToAffectedConstraintSetMap = null;
protected HashMap<String, Boolean> variableToIsInConstraintMap = null;
protected HashMap<String, Boolean> variableToIsConstantMap = null;
//compares two events based on fire time and priority
protected EventComparator eventComparator = new EventComparator();
//allows access to a component's location on the grid from its ID
protected LinkedHashMap<String, Point> componentToLocationMap = null;
//allows access to a component's set of reactions from its ID
protected HashMap<String, HashSet<String> > componentToReactionSetMap = null;
//allows access to a component's set of variables (species and parameters) from its ID
protected HashMap<String, HashSet<String> > componentToVariableSetMap = null;
protected HashMap<String, HashSet<String> > componentToEventSetMap = null;
protected HashSet<String> componentIDSet = new HashSet<String>();
protected LinkedHashSet<String> compartmentIDSet = new LinkedHashSet<String>();
protected LinkedHashSet<String> nonconstantParameterIDSet = new LinkedHashSet<String>();
//initial model -- used for resetting when doing multiple dynamic runs
protected ListOf<Species> initialSpecies = new ListOf<Species>();
protected ListOf<Reaction> initialReactions = new ListOf<Reaction>();
protected ListOf<Event> initialEvents = new ListOf<Event>();
protected ListOf<Parameter> initialParameters = new ListOf<Parameter>();
protected ListOf<Compartment> initialCompartments = new ListOf<Compartment>();
//locations parameter annotations for placing compartments
protected HashMap<String, String> submodelIDToLocationsMap = new HashMap<String, String>();
protected ArrayList<String> interestingSpecies = new ArrayList<String>();
protected HashSet<String> ibiosimFunctionDefinitions = new HashSet<String>();
//propensity variables
protected double totalPropensity = 0.0;
protected double minPropensity = Double.MAX_VALUE / 10.0;
protected double maxPropensity = Double.MIN_VALUE / 10.0;
//file writing variables
protected FileWriter TSDWriter = null;
protected BufferedWriter bufferedTSDWriter = null;
//boolean flags
protected boolean cancelFlag = false;
protected boolean constraintFailureFlag = false;
protected boolean sbmlHasErrorsFlag = false;
protected double currentTime;
protected String SBMLFileName;
protected double timeLimit;
protected double maxTimeStep;
protected double minTimeStep;
protected JProgressBar progress;
protected double printInterval;
protected int currentRun;
protected String outputDirectory;
protected long numSpecies;
protected long numParameters;
protected long numReactions;
protected long numEvents;
protected long numRules;
protected int numAssignmentRules;
protected long numConstraints;
protected int numInitialAssignments;
protected int numRateRules;
protected int minRow = Integer.MAX_VALUE;
protected int minCol = Integer.MAX_VALUE;
protected int maxRow = Integer.MIN_VALUE;
protected int maxCol = Integer.MIN_VALUE;
protected boolean stoichAmpBoolean = false;
protected double stoichAmpGridValue = 1.0;
//true means the model is dynamic
protected boolean dynamicBoolean = false;
protected boolean printConcentrations = false;
protected int diffCount = 0;
protected int totalCount = 0;
protected int memCount = 0;
protected JFrame running = new JFrame();
PsRandom prng = new PsRandom();
/**
* does lots of initialization
*
* @param SBMLFileName
* @param outputDirectory
* @param timeLimit
* @param maxTimeStep
* @param randomSeed
* @param progress
* @param printInterval
* @param initializationTime
* @throws IOException
* @throws XMLStreamException
*/
public Simulator(String SBMLFileName, String outputDirectory, double timeLimit,
double maxTimeStep, double minTimeStep, long randomSeed, JProgressBar progress, double printInterval,
Long initializationTime, double stoichAmpValue, JFrame running, String[] interestingSpecies,
String quantityType)
throws IOException, XMLStreamException {
long initTime1 = System.nanoTime();
this.SBMLFileName = SBMLFileName;
this.timeLimit = timeLimit;
this.maxTimeStep = maxTimeStep;
this.minTimeStep = minTimeStep;
this.progress = progress;
this.printInterval = printInterval;
this.outputDirectory = outputDirectory;
this.running = running;
this.interestingSpecies.clear();
for (int i = 0; i < interestingSpecies.length; ++i)
this.interestingSpecies.add(interestingSpecies[i]);
if (quantityType != null && quantityType.equals("concentration"))
this.printConcentrations = true;
if (stoichAmpValue <= 1.0)
stoichAmpBoolean = false;
else {
stoichAmpBoolean = true;
stoichAmpGridValue = stoichAmpValue;
}
SBMLReader reader = new SBMLReader();
SBMLDocument document = null;
document = reader.readSBML(SBMLFileName);
SBMLErrorLog errors = document.getListOfErrors();
//if the sbml document has errors, tell the user and don't simulate
if (document.getNumErrors() > 0) {
String errorString = "";
for (int i = 0; i < errors.getNumErrors(); i++) {
errorString += errors.getError(i);
}
JOptionPane.showMessageDialog(Gui.frame,
"The SBML file contains " + document.getNumErrors() + " error(s):\n" + errorString,
"SBML Error", JOptionPane.ERROR_MESSAGE);
sbmlHasErrorsFlag = true;
}
model = document.getModel();
numSpecies = model.getNumSpecies();
numParameters = model.getNumParameters();
numReactions = model.getNumReactions();
numEvents = model.getNumEvents();
numRules = model.getNumRules();
numConstraints = model.getNumConstraints();
numInitialAssignments = model.getNumInitialAssignments();
//set initial capacities for collections (1.5 is used to multiply numReactions due to reversible reactions)
speciesToAffectedReactionSetMap = new HashMap<String, HashSet<String> >((int) numSpecies);
speciesToIsBoundaryConditionMap = new HashMap<String, Boolean>((int) numSpecies);
variableToIsConstantMap = new HashMap<String, Boolean>((int) (numSpecies + numParameters));
speciesToHasOnlySubstanceUnitsMap = new HashMap<String, Boolean>((int) numSpecies);
speciesToSubstanceUnitsMap = new HashMap<String, String>((int) numSpecies);
speciesToConversionFactorMap = new HashMap<String, String>((int) numSpecies);
speciesToCompartmentNameMap = new HashMap<String, String>((int) numSpecies);
speciesToCompartmentSizeMap = new TObjectDoubleHashMap<String>((int) numSpecies);
speciesIDSet = new LinkedHashSet<String>((int) numSpecies);
reactionToNonconstantStoichiometriesSetMap = new HashMap<String, HashSet<StringStringPair> >();
variableToValueMap = new TObjectDoubleHashMap<String>((int) numSpecies + (int) numParameters);
reactionToPropensityMap = new TObjectDoubleHashMap<String>((int) (numReactions * 1.5));
reactionToSpeciesAndStoichiometrySetMap = new HashMap<String, HashSet<StringDoublePair> >((int) (numReactions * 1.5));
reactionToReactantStoichiometrySetMap = new HashMap<String, HashSet<StringDoublePair> >((int) (numReactions * 1.5));
reactionToFormulaMap = new HashMap<String, ASTNode>((int) (numReactions * 1.5));
componentToLocationMap = new LinkedHashMap<String, Point>();
componentToReactionSetMap = new HashMap<String, HashSet<String> >();
componentToVariableSetMap = new HashMap<String, HashSet<String> >();
componentToEventSetMap = new HashMap<String, HashSet<String> >();
if (numEvents > 0) {
triggeredEventQueue = new PriorityQueue<EventToFire>((int) numEvents, eventComparator);
untriggeredEventSet = new HashSet<String>((int) numEvents);
eventToPriorityMap = new HashMap<String, ASTNode>((int) numEvents);
eventToDelayMap = new HashMap<String, ASTNode>((int) numEvents);
eventToHasDelayMap = new HashMap<String, Boolean>((int) numEvents);
eventToTriggerMap = new HashMap<String, ASTNode>((int) numEvents);
eventToTriggerInitiallyTrueMap = new HashMap<String, Boolean>((int) numEvents);
eventToTriggerPersistenceMap = new HashMap<String, Boolean>((int) numEvents);
eventToUseValuesFromTriggerTimeMap = new HashMap<String, Boolean>((int) numEvents);
eventToAssignmentSetMap = new HashMap<String, HashSet<Object> >((int) numEvents);
eventToAffectedReactionSetMap = new HashMap<String, HashSet<String> >((int) numEvents);
eventToPreviousTriggerValueMap = new HashMap<String, Boolean>((int) numEvents);
variableToEventSetMap = new HashMap<String, HashSet<String> >((int) numEvents);
}
if (numRules > 0) {
variableToAffectedAssignmentRuleSetMap = new HashMap<String, HashSet<AssignmentRule> >((int) numRules);
variableToIsInAssignmentRuleMap = new HashMap<String, Boolean>((int) (numSpecies + numParameters));
variableToIsInRateRuleMap = new HashMap<String, Boolean>((int) (numSpecies + numParameters));
}
if (numConstraints > 0) {
variableToAffectedConstraintSetMap = new HashMap<String, HashSet<ASTNode> >((int) numConstraints);
variableToIsInConstraintMap = new HashMap<String, Boolean>((int) (numSpecies + numParameters));
}
ibiosimFunctionDefinitions.add("uniform");
ibiosimFunctionDefinitions.add("exponential");
ibiosimFunctionDefinitions.add("gamma");
ibiosimFunctionDefinitions.add("chisq");
ibiosimFunctionDefinitions.add("lognormal");
ibiosimFunctionDefinitions.add("laplace");
ibiosimFunctionDefinitions.add("cauchy");
ibiosimFunctionDefinitions.add("poisson");
ibiosimFunctionDefinitions.add("binomial");
ibiosimFunctionDefinitions.add("bernoulli");
ibiosimFunctionDefinitions.add("normal");
initializationTime = System.nanoTime() - initTime1;
}
/**
* replaces ROWX_COLY with ROWA_COLB in a kinetic law
* this has to be done without re-parsing the formula string because the row/col
* values can be negative, which gets parsed incorrectly
*
* @param node
* @param oldString
* @param newString
*/
private void alterNode(ASTNode node, String oldString, String newString) {
if (node.isName() && node.getName().contains(oldString)) {
node.setVariable(model.getSpecies(newString + "__" + node.getName().split("__")[1]));
}
else {
for (ASTNode childNode : node.getChildren())
alterNode(childNode, oldString, newString);
}
}
/**
* replaceArgument() doesn't work when you're replacing a localParameter, so this
* does that -- finds the oldString within node and replaces it with the local parameter
* specified by newString
*
* @param node
* @param reactionID
* @param oldString
* @param newString
*/
private void alterLocalParameter(ASTNode node, Reaction reaction, String oldString, String newString) {
String reactionID = reaction.getId();
if (node.isName() && node.getName().equals(oldString)) {
node.setVariable(reaction.getKineticLaw().getLocalParameter(newString));
}
else {
for (ASTNode childNode : node.getChildren())
alterLocalParameter(childNode, reaction, oldString, newString);
}
}
/**
* alters the kinetic laws and stoichiometries of grid diffusion reactions
* in accordance with the stoichiometry amplification parameters specified by the user
*
* @param model
*/
private static void applyStoichiometryAmplification(Model model, double stoichAmpValue) {
if (stoichAmpValue <= 1.0)
return;
for (Reaction reaction : model.getListOfReactions()) {
//stoichiometry amplification -- alter the stoichiometry
if (reaction.getId().contains("_Diffusion_")) {
//these are all forward reactions, so adjust the stoichiometries of the reactant
for (SpeciesReference reactant : reaction.getListOfReactants())
reactant.setStoichiometry(stoichAmpValue);
//alter the kinetic laws by dividing by the stoichiometry amplification value
//this will alter the propensities accordingly
ASTNode divisionNode = new ASTNode();
divisionNode.setValue(1.0 / stoichAmpValue);
reaction.getKineticLaw().getMath().multiplyWith(divisionNode);
}
}
}
/**
* cancels the current run
*/
protected abstract void cancel();
/**
* clears data structures for new run
*/
protected abstract void clear();
/**
* copies parts of the model that may change during a dynamic run
*/
protected void createModelCopy() {
initialSpecies = model.getListOfSpecies().clone();
initialReactions = model.getListOfReactions().clone();
initialEvents = model.getListOfEvents().clone();
initialParameters = model.getListOfParameters().clone();
initialCompartments = model.getListOfCompartments().clone();
}
/**
* uses an existing component to create a new component and update data structures and the simulation state
* this is used for "birth" events in dynamic models
*
* @param parentComponentID
* @param eventID the ID of the division event that just fired
*/
protected void duplicateComponent(String parentComponentID, String eventID, String symmetry) {
//determine new component ID
int componentNumber = componentToReactionSetMap.size() + 1;
String childComponentID = "C" + String.valueOf(componentNumber);
while (componentToReactionSetMap.keySet().contains(childComponentID) == true ||
componentIDSet.contains(childComponentID) == true) {
++componentNumber;
childComponentID = "C" + String.valueOf(componentNumber);
}
//the component ID is just the child name with no ancestry information
//the compartment ID contains the ancestry information
componentIDSet.add(childComponentID);
//only use the immediate parent for the new ID
childComponentID = childComponentID + "_of_" + parentComponentID.split("_of_")[0];
Compartment childCompartment = model.createCompartment();
String compartID = "";
//duplicate compartment
for (Compartment comp : model.getListOfCompartments()) {
if (comp.getId().contains(parentComponentID + "__")) {
compartID = comp.getId();
childCompartment.setSize(comp.getSize());
childCompartment.setConstant(comp.getConstant());
}
}
childCompartment.setId(childComponentID + "__" + compartID.split("__")[1]);
compartmentIDSet.add(childCompartment.getId());
variableToValueMap.put(childCompartment.getId(), childCompartment.getSize());
variableToIsConstantMap.put(childCompartment.getId(), childCompartment.getConstant());
//reactions that change and thus need their propensities re-evaluated
HashSet<String> reactionsToAdjust = new HashSet<String>();
//determine new component location
//choose a random direction and place the component adjacent to the parent
//0 = left, 1 = right, 2 = above, 3 = below
int randomDirection = (int) (randomNumberGenerator.nextDouble() * 8.0);
Point parentLocation = componentToLocationMap.get(parentComponentID);
Point childLocation = (Point) parentLocation.clone();
//MOVE COMPONENTS
//this places the child and shuffles others around as needed
moveComponent(parentComponentID, childComponentID, parentLocation, childLocation, randomDirection, reactionsToAdjust);
//DUPLICATE VARIABLES and alter them to coincide with the new ID
HashSet<String> childComponentVariableSet = new HashSet<String>();
if (componentToVariableSetMap.containsKey(parentComponentID) == false)
componentToVariableSetMap.put(parentComponentID, new HashSet<String>());
for (String parentVariableID : componentToVariableSetMap.get(parentComponentID)) {
String childVariableID = parentVariableID.replace(parentComponentID, childComponentID);
childComponentVariableSet.add(childVariableID);
//this means it's a species
if (speciesIDSet.contains(parentVariableID)) {
//if it's a promoter, double it first, as it's a dna-based species
if (model.getSpecies(parentVariableID).isSetSBOTerm() &&
model.getSpecies(parentVariableID).getSBOTerm() == GlobalConstants.SBO_PROMOTER_SPECIES)
variableToValueMap.put(parentVariableID, variableToValueMap.get(parentVariableID) * 2);
//duplicate species into the model
Species newSpecies = model.getSpecies(parentVariableID).clone();
newSpecies.setId(childVariableID);
newSpecies.setMetaId(childVariableID);
model.addSpecies(newSpecies);
if (speciesToHasOnlySubstanceUnitsMap.get(parentVariableID) == false)
speciesToCompartmentSizeMap.put(childVariableID, speciesToCompartmentSizeMap.get(parentVariableID));
if (speciesToHasOnlySubstanceUnitsMap.get(parentVariableID) == false)
speciesToCompartmentNameMap.put(childVariableID, speciesToCompartmentNameMap.get(parentVariableID));
//the speciesToAffectedReactionSetMap gets filled-in later
speciesToAffectedReactionSetMap.put(childVariableID, new HashSet<String>(20));
speciesToIsBoundaryConditionMap.put(childVariableID, speciesToIsBoundaryConditionMap.get(parentVariableID));
variableToIsConstantMap.put(childVariableID, variableToIsConstantMap.get(parentVariableID));
speciesToHasOnlySubstanceUnitsMap.put(childVariableID, speciesToHasOnlySubstanceUnitsMap.get(parentVariableID));
speciesIDSet.add(childVariableID);
//divide the parent species amount by two by default
//unless there is an event assignment or if the species is constant/bc
if (variableToIsConstantMap.get(parentVariableID) == true ||
speciesToIsBoundaryConditionMap.get(parentVariableID)) {
variableToValueMap.put(childVariableID, variableToValueMap.get(parentVariableID));
}
else {
//go through the event assignments to find ones that affect this particular species
//this is used to determine, via species quantity conservation, how much the daughter cell gets
HashSet<Object> assignmentSetMap = this.eventToAssignmentSetMap.get(eventID);
boolean setInAssignment = false;
for (Object assignment : assignmentSetMap) {
if (((EventAssignment) assignment).getVariable().equals(parentVariableID)) {
double totalAmount = variableToValueMap.get(parentVariableID);
double afterEventAmount = evaluateExpressionRecursive(((EventAssignment) assignment).getMath());
double childAmount = totalAmount - afterEventAmount;
variableToValueMap.put(childVariableID, childAmount);
variableToValueMap.put(parentVariableID, afterEventAmount);
setInAssignment = true;
}
}
if (setInAssignment == false) {
variableToValueMap.put(childVariableID, (int) ((variableToValueMap.get(parentVariableID) / 2) + 1));
variableToValueMap.put(parentVariableID, (int) ((variableToValueMap.get(parentVariableID) / 2) + 1));
}
}
}
//this means it's a parameter
else {
variableToValueMap.put(childVariableID, variableToValueMap.get(parentVariableID));
}
}
componentToVariableSetMap.put(childComponentID, childComponentVariableSet);
//DUPLICATE REACTIONS and alter them to coincide with the new ID
HashSet<String> childReactionSet = new HashSet<String>();
if (componentToReactionSetMap.containsKey(parentComponentID) == false)
componentToReactionSetMap.put(parentComponentID, new HashSet<String>());
for (String parentReactionID : componentToReactionSetMap.get(parentComponentID)) {
String parentReactionFormula = "";
String childReactionID = parentReactionID.replace(parentComponentID, childComponentID);
childReactionSet.add(childReactionID);
parentReactionFormula = reactionToFormulaMap.get(parentReactionID).toFormula();
ASTNode childFormulaNode = reactionToFormulaMap.get(parentReactionID).clone();
String thing = "";
try {
String childReactionFormula = parentReactionFormula.replace(parentComponentID, childComponentID);
if (parentReactionID.contains("MembraneDiffusion")) {
String parentRowCol = "ROW" + (int) parentLocation.getX() + "_" + "COL" + (int) parentLocation.getY();
String childRowCol = "ROW" + (int) childLocation.getX() + "_" + "COL" + (int) childLocation.getY();
//formulas as ASTNodes can't have negative numbers in species IDs
parentRowCol = parentRowCol.replace("ROW-", "ROW_negative_");
parentRowCol = parentRowCol.replace("COL-", "COL_negative_");
childRowCol = childRowCol.replace("ROW-", "ROW_negative_");
childRowCol = childRowCol.replace("COL-", "COL_negative_");
if (childReactionFormula.contains("ROW") && childReactionFormula.contains("COL")) {
alterNode(childFormulaNode, parentRowCol, childRowCol);
}
else {
String childSpeciesID = ((String[])childReactionFormula.split("\\*"))[1];
String underlyingSpeciesID = childSpeciesID.split("__")[childSpeciesID.split("__").length - 1];
//we want the parent's kmdiff parameter, as the child's doesn't exist
childReactionFormula = childReactionFormula.replace(childSpeciesID + "__kmdiff",
parentComponentID + "__" + underlyingSpeciesID + "__kmdiff");
thing = childReactionFormula;
childFormulaNode = ASTNode.parseFormula(childReactionFormula);
}
}
else
childFormulaNode = ASTNode.parseFormula(childReactionFormula);
} catch (ParseException e) {
System.err.println(thing);
e.printStackTrace();
}
reactionToSpeciesAndStoichiometrySetMap.put(childReactionID, new HashSet<StringDoublePair>());
reactionToReactantStoichiometrySetMap.put(childReactionID, new HashSet<StringDoublePair>());
boolean notEnoughMoleculesFlag = false;
if (reactionToSpeciesAndStoichiometrySetMap.containsKey(parentReactionID) == false)
reactionToSpeciesAndStoichiometrySetMap.put(parentReactionID, new HashSet<StringDoublePair>());
//add species/stoichiometry pairs for this new reaction
for (StringDoublePair parentSpeciesAndStoichiometry : reactionToSpeciesAndStoichiometrySetMap.get(parentReactionID)) {
double childStoichiometry = parentSpeciesAndStoichiometry.doub;
String childSpeciesID = "";
if (parentSpeciesAndStoichiometry.string.contains("ROW") &&
parentSpeciesAndStoichiometry.string.contains("COL")) {
String parentRowCol = "ROW" + (int) parentLocation.getX() + "_" + "COL" + (int) parentLocation.getY();
String childRowCol = "ROW" + (int) childLocation.getX() + "_" + "COL" + (int) childLocation.getY();
childSpeciesID = parentSpeciesAndStoichiometry.string.replace(parentRowCol, childRowCol);
}
else
childSpeciesID = parentSpeciesAndStoichiometry.string.replace(parentComponentID, childComponentID);
reactionToSpeciesAndStoichiometrySetMap.get(childReactionID)
.add(new StringDoublePair(childSpeciesID, childStoichiometry));
if (speciesToAffectedReactionSetMap.containsKey(parentSpeciesAndStoichiometry.string))
speciesToAffectedReactionSetMap.get(childSpeciesID).add(childReactionID);
//make sure there are enough molecules for this species
//(if the molecule is a reactant -- if it's a product then it's being added)
if (variableToValueMap.get(childSpeciesID) < childStoichiometry &&
reactionToReactantStoichiometrySetMap.get(parentReactionID).contains(childSpeciesID))
notEnoughMoleculesFlag = true;
}
if (reactionToReactantStoichiometrySetMap.containsKey(parentReactionID) == false)
reactionToReactantStoichiometrySetMap.put(parentReactionID, new HashSet<StringDoublePair>());
//add reactant/stoichiometry pairs for this new reactions
for (StringDoublePair parentReactantAndStoichiometry : reactionToReactantStoichiometrySetMap.get(parentReactionID)) {
double childStoichiometry = parentReactantAndStoichiometry.doub;
String childSpeciesID = "";
if (parentReactantAndStoichiometry.string.contains("ROW") &&
parentReactantAndStoichiometry.string.contains("COL")) {
String parentRowCol = "ROW" + (int) parentLocation.getX() + "_" + "COL" + (int) parentLocation.getY();
String childRowCol = "ROW" + (int) childLocation.getX() + "_" + "COL" + (int) childLocation.getY();
childSpeciesID = parentReactantAndStoichiometry.string.replace(parentRowCol, childRowCol);
}
else
childSpeciesID = parentReactantAndStoichiometry.string.replace(parentComponentID, childComponentID);
reactionToReactantStoichiometrySetMap.get(childReactionID).add(
new StringDoublePair(childSpeciesID, childStoichiometry));
}
reactionToFormulaMap.put(childReactionID, childFormulaNode);
double propensity;
if (notEnoughMoleculesFlag == true)
propensity = 0.0;
else {
//calculate propensity
propensity = evaluateExpressionRecursive(childFormulaNode);
if (propensity < minPropensity && propensity > 0)
minPropensity = propensity;
if (propensity > maxPropensity)
maxPropensity = propensity;
totalPropensity += propensity;
}
reactionToPropensityMap.put(childReactionID, propensity);
}
componentToReactionSetMap.put(childComponentID, childReactionSet);
reactionsToAdjust.addAll(componentToReactionSetMap.get(parentComponentID));
//update propensities for the parent reactions, as their species values may have changed
updatePropensities(reactionsToAdjust);
updateAfterDynamicChanges();
//DUPLICATE EVENTS
HashSet<String> childEventSet = new HashSet<String>();
if (componentToEventSetMap.containsKey(parentComponentID) == false)
componentToEventSetMap.put(parentComponentID, new HashSet<String>());
for (String parentEventID : componentToEventSetMap.get(parentComponentID)) {
String childEventID = parentEventID.replace(parentComponentID, childComponentID);
untriggeredEventSet.add(childEventID);
childEventSet.add(childEventID);
//hashmaps that allow for access to event information from the event's id
eventToPriorityMap.put(childEventID, eventToPriorityMap.get(parentEventID));
eventToDelayMap.put(childEventID, eventToDelayMap.get(parentEventID).clone());
eventToHasDelayMap.put(childEventID, eventToHasDelayMap.get(parentEventID));
eventToTriggerPersistenceMap.put(childEventID, eventToTriggerPersistenceMap.get(parentEventID));
eventToUseValuesFromTriggerTimeMap.put(childEventID, eventToUseValuesFromTriggerTimeMap.get(parentEventID));
eventToTriggerMap.put(childEventID, eventToTriggerMap.get(parentEventID).clone());
eventToTriggerInitiallyTrueMap.put(childEventID, eventToTriggerInitiallyTrueMap.get(parentEventID));
eventToPreviousTriggerValueMap.put(childEventID, eventToTriggerInitiallyTrueMap.get(childEventID));
//symmetric division creates two new things essentially: there are two children, not a parent and child
//untrigger the parent division event
if (symmetry.equals("symmetric")) {
//untrigger the event
untriggeredEventSet.add(parentEventID);
eventToPreviousTriggerValueMap.put(parentEventID, eventToTriggerInitiallyTrueMap.get(parentEventID));
//remove the event from the queue
//copy the triggered event queue -- except the parent event
PriorityQueue<EventToFire> newTriggeredEventQueue = new PriorityQueue<EventToFire>(5, eventComparator);
while (triggeredEventQueue.size() > 0) {
EventToFire event = triggeredEventQueue.poll();
EventToFire eventToAdd =
new EventToFire(event.eventID, (HashSet<Object>) event.eventAssignmentSet.clone(), event.fireTime);
if (parentEventID.equals(event.eventID) == false)
newTriggeredEventQueue.add(eventToAdd);
}
triggeredEventQueue = newTriggeredEventQueue;
}
HashSet<Object> assignmentSetMap = new HashSet<Object>();
//copy event assignments for the new child event
for (Object assignment : eventToAssignmentSetMap.get(parentEventID)) {
String variableID = ((EventAssignment) assignment).getVariable();
if (variableToEventSetMap.containsKey(variableID) == false)
variableToEventSetMap.put(variableID, new HashSet<String>());
variableToEventSetMap.get(variableID).add(childEventID);
EventAssignment ea = ((EventAssignment)assignment).clone();
ea.setVariable(((EventAssignment)assignment).getVariable()
.replace(parentComponentID, childComponentID));
try {
// ea.setMath(ASTNode.parseFormula(((EventAssignment)assignment).getMath().toFormula()
// .replace(parentComponentID, childComponentID)));
ea.setFormula(((EventAssignment)assignment).getMath().toFormula()
.replace(parentComponentID, childComponentID));
} catch (ParseException e) {
e.printStackTrace();
}
assignmentSetMap.add(ea);
if (speciesToAffectedReactionSetMap.containsKey(variableID)) {
eventToAffectedReactionSetMap.put(childEventID, new HashSet<String>());
eventToAffectedReactionSetMap.get(childEventID).addAll(
speciesToAffectedReactionSetMap.get(variableID));
}
}
eventToAssignmentSetMap.put(childEventID, assignmentSetMap);
}
componentToEventSetMap.put(childComponentID, childEventSet);
// System.err.println("REACTIONS");
// for (String reactionID : reactionToPropensityMap.keySet()) {
// if (//reactionID.contains("_of_") ||
// reactionID.contains("Diffusion")
// System.err.println(reactionID);
// System.err.println();
// System.err.println("VARIABLES");
// for (String variableID : this.speciesIDSet) {
//// if (//variableID.contains("_of_") ||
//// variableID.contains("ROW")
// System.err.println(variableID + " " + variableToValueMap.get(variableID));
// for (String event : this.eventToAssignmentSetMap.keySet()) {
// System.err.println(event);
// System.err.println(this.eventToAssignmentSetMap.get(event));
// System.err.println();
// System.err.println("duplicate finished");
}
/**
* simulator-specific component erasure stuff
* @param reactionIDs
*/
protected abstract void eraseComponentFurther(HashSet<String> reactionIDs);
/**
* erases all traces of a component (ie, its reactions and species and parameters, etc) and updates data structures
* and the simulation state
* used for "death" events in dynamic models
*
* @param componentID
*/
protected HashSet<String> eraseComponent(String componentID) {
for (String reactionID : componentToReactionSetMap.get(componentID)) {
reactionToPropensityMap.remove(reactionID);
reactionToSpeciesAndStoichiometrySetMap.remove(reactionID);
reactionToReactantStoichiometrySetMap.remove(reactionID);
reactionToFormulaMap.remove(reactionID);
}
//simulator-specific data structure erasal
eraseComponentFurther(componentToReactionSetMap.get(componentID));
for (String variableID : componentToVariableSetMap.get(componentID)) {
variableToEventSetMap.remove(variableID);
if (variableToAffectedAssignmentRuleSetMap != null)
variableToAffectedAssignmentRuleSetMap.remove(variableID);
if (variableToIsInAssignmentRuleMap != null)
variableToIsInAssignmentRuleMap.remove(variableID);
if (variableToAffectedConstraintSetMap != null)
variableToAffectedConstraintSetMap.remove(variableID);
if (variableToIsInConstraintMap != null)
variableToIsInConstraintMap.remove(variableID);
variableToIsConstantMap.remove(variableID);
variableToValueMap.remove(variableID);
speciesToIsBoundaryConditionMap.remove(variableID);
speciesToHasOnlySubstanceUnitsMap.remove(variableID);
speciesToCompartmentNameMap.remove(variableID);
speciesToCompartmentSizeMap.remove(variableID);
speciesIDSet.remove(variableID);
}
String compartmentIDToRemove = "";
for (String compartmentID : compartmentIDSet)
if (compartmentID.contains(componentID + "__"))
compartmentIDToRemove = compartmentID;
compartmentIDSet.remove(compartmentIDToRemove);
// for (String eventID : componentToEventSetMap.get(componentID)) {
// triggeredEventQueue.remove(eventID);
// untriggeredEventSet.remove(eventID);
// eventToPriorityMap.remove(eventID);
// eventToDelayMap.remove(eventID);
// eventToHasDelayMap.remove(eventID);
// eventToTriggerPersistenceMap.remove(eventID);
// eventToUseValuesFromTriggerTimeMap.remove(eventID);
// eventToTriggerMap.remove(eventID);
// eventToTriggerInitiallyTrueMap.remove(eventID);
// eventToPreviousTriggerValueMap.remove(eventID);
// eventToAssignmentSetMap.remove(eventID);
// eventToAffectedReactionSetMap.remove(eventID);
HashSet<String> deadEvents = new HashSet<String>();
deadEvents.addAll(componentToEventSetMap.get(componentID));
componentToLocationMap.remove(componentID);
componentToReactionSetMap.remove(componentID);
componentToVariableSetMap.remove(componentID);
componentToEventSetMap.remove(componentID);
updateAfterDynamicChanges();
return deadEvents;
}
/**
* calculates an expression using a recursive algorithm
*
* @param node the AST with the formula
* @return the evaluated expression
*/
protected double evaluateExpressionRecursive(ASTNode node) {
//these if/else-ifs before the else are leaf conditions
//logical constant, logical operator, or relational operator
if (node.isBoolean()) {
switch (node.getType()) {
case CONSTANT_TRUE:
return 1.0;
case CONSTANT_FALSE:
return 0.0;
case LOGICAL_NOT:
return getDoubleFromBoolean(!(getBooleanFromDouble(evaluateExpressionRecursive(node.getLeftChild()))));
case LOGICAL_AND: {
boolean andResult = true;
for (int childIter = 0; childIter < node.getChildCount(); ++childIter)
andResult = andResult && getBooleanFromDouble(evaluateExpressionRecursive(node.getChild(childIter)));
return getDoubleFromBoolean(andResult);
}
case LOGICAL_OR: {
boolean orResult = false;
for (int childIter = 0; childIter < node.getChildCount(); ++childIter)
orResult = orResult || getBooleanFromDouble(evaluateExpressionRecursive(node.getChild(childIter)));
return getDoubleFromBoolean(orResult);
}
case LOGICAL_XOR: {
boolean xorResult = getBooleanFromDouble(evaluateExpressionRecursive(node.getChild(0)));
for (int childIter = 1; childIter < node.getChildCount(); ++childIter)
xorResult = xorResult ^ getBooleanFromDouble(evaluateExpressionRecursive(node.getChild(childIter)));
return getDoubleFromBoolean(xorResult);
}
case RELATIONAL_EQ:
return getDoubleFromBoolean(
evaluateExpressionRecursive(node.getLeftChild()) == evaluateExpressionRecursive(node.getRightChild()));
case RELATIONAL_NEQ:
return getDoubleFromBoolean(
evaluateExpressionRecursive(node.getLeftChild()) != evaluateExpressionRecursive(node.getRightChild()));
case RELATIONAL_GEQ:
return getDoubleFromBoolean(
evaluateExpressionRecursive(node.getLeftChild()) >= evaluateExpressionRecursive(node.getRightChild()));
case RELATIONAL_LEQ:
return getDoubleFromBoolean(
evaluateExpressionRecursive(node.getLeftChild()) <= evaluateExpressionRecursive(node.getRightChild()));
case RELATIONAL_GT:
return getDoubleFromBoolean(
evaluateExpressionRecursive(node.getLeftChild()) > evaluateExpressionRecursive(node.getRightChild()));
case RELATIONAL_LT:
return getDoubleFromBoolean(
evaluateExpressionRecursive(node.getLeftChild()) < evaluateExpressionRecursive(node.getRightChild()));
}
}
//if it's a mathematical constant
else if (node.isConstant()) {
switch (node.getType()) {
case CONSTANT_E:
return Math.E;
case CONSTANT_PI:
return Math.PI;
}
}
//if it's a number
else if (node.isNumber())
return node.getReal();
//if it's a user-defined variable
//eg, a species name or global/local parameter
else if (node.isName()) {
String name = node.getName().replace("_negative_","-");
if (node.getType().equals(org.sbml.jsbml.ASTNode.Type.NAME_TIME)) {
return currentTime;
}
//if it's a reaction id return the propensity
else if (reactionToPropensityMap.keySet().contains(node.getName())) {
return reactionToPropensityMap.get(node.getName());
}
else {
double value;
if (this.speciesToHasOnlySubstanceUnitsMap.containsKey(name) &&
this.speciesToHasOnlySubstanceUnitsMap.get(name) == false) {
value = (variableToValueMap.get(name) / variableToValueMap.get(speciesToCompartmentNameMap.get(name)));
}
else
value = variableToValueMap.get(name);
return value;
}
}
//operators/functions with two children
else {
ASTNode leftChild = node.getLeftChild();
ASTNode rightChild = node.getRightChild();
switch (node.getType()) {
case PLUS: {
double sum = 0.0;
for (int childIter = 0; childIter < node.getChildCount(); ++childIter)
sum += evaluateExpressionRecursive(node.getChild(childIter));
return sum;
}
case MINUS: {
double sum = evaluateExpressionRecursive(leftChild);
for (int childIter = 1; childIter < node.getChildCount(); ++childIter)
sum -= evaluateExpressionRecursive(node.getChild(childIter));
return sum;
}
case TIMES: {
double product = 1.0;
for (int childIter = 0; childIter < node.getChildCount(); ++childIter)
product *= evaluateExpressionRecursive(node.getChild(childIter));
return product;
}
case DIVIDE:
return (evaluateExpressionRecursive(leftChild) / evaluateExpressionRecursive(rightChild));
case FUNCTION_POWER:
return (FastMath.pow(evaluateExpressionRecursive(leftChild), evaluateExpressionRecursive(rightChild)));
case FUNCTION: {
//use node name to determine function
//i'm not sure what to do with completely user-defined functions, though
String nodeName = node.getName();
//generates a uniform random number between the upper and lower bound
if (nodeName.equals("uniform")) {
double leftChildValue = evaluateExpressionRecursive(node.getLeftChild());
double rightChildValue = evaluateExpressionRecursive(node.getRightChild());
double lowerBound = FastMath.min(leftChildValue, rightChildValue);
double upperBound = FastMath.max(leftChildValue, rightChildValue);
return prng.nextDouble(lowerBound, upperBound);
}
else if (nodeName.equals("exponential")) {
return prng.nextExponential(evaluateExpressionRecursive(node.getLeftChild()), 1);
}
else if (nodeName.equals("gamma")) {
return prng.nextGamma(1, evaluateExpressionRecursive(node.getLeftChild()),
evaluateExpressionRecursive(node.getRightChild()));
}
else if (nodeName.equals("chisq")) {
return prng.nextChiSquare((int) evaluateExpressionRecursive(node.getLeftChild()));
}
else if (nodeName.equals("lognormal")) {
return prng.nextLogNormal(evaluateExpressionRecursive(node.getLeftChild()),
evaluateExpressionRecursive(node.getRightChild()));
}
else if (nodeName.equals("laplace")) {
//function doesn't exist in current libraries
return 0;
}
else if (nodeName.equals("cauchy")) {
return prng.nextLorentzian(0, evaluateExpressionRecursive(node.getLeftChild()));
}
else if (nodeName.equals("poisson")) {
return prng.nextPoissonian(evaluateExpressionRecursive(node.getLeftChild()));
}
else if (nodeName.equals("binomial")) {
return prng.nextBinomial(evaluateExpressionRecursive(node.getLeftChild()),
(int) evaluateExpressionRecursive(node.getRightChild()));
}
else if (nodeName.equals("bernoulli")) {
return prng.nextBinomial(evaluateExpressionRecursive(node.getLeftChild()), 1);
}
else if (nodeName.equals("normal")) {
return prng.nextGaussian(evaluateExpressionRecursive(node.getLeftChild()),
evaluateExpressionRecursive(node.getRightChild()));
}
else if (nodeName.equals("get2DArrayElement")) {
// int leftIndex = node.getChild(1).getInteger();
// int rightIndex = node.getChild(2).getInteger();
// String speciesName = "ROW" + leftIndex + "_COL" + rightIndex + "__" + node.getChild(0).getName();
// //check bounds
// //if species exists, return its value/amount
// if (variableToValueMap.containsKey(speciesName))
// return variableToValueMap.get(speciesName);
}
else if (nodeName.equals("neighborQuantityLeftFull")) {
int leftIndex = (int) evaluateExpressionRecursive(node.getChild(1));
int rightIndex = (int) evaluateExpressionRecursive(node.getChild(2));
String specName = node.getChild(0).getName().split("__")[node.getChild(0).getName().split("__").length - 1];
String speciesName = "ROW" + leftIndex + "_COL" + (rightIndex - 1) + "__" + specName;
if (variableToValueMap.containsKey(speciesName))
return variableToValueMap.get(speciesName);
else return 1;
}
else if (nodeName.equals("neighborQuantityRightFull")) {
int leftIndex = (int) evaluateExpressionRecursive(node.getChild(1));
int rightIndex = (int) evaluateExpressionRecursive(node.getChild(2));
String specName = node.getChild(0).getName().split("__")[node.getChild(0).getName().split("__").length - 1];
String speciesName = "ROW" + leftIndex + "_COL" + (rightIndex + 1) + "__" + specName;
if (variableToValueMap.containsKey(speciesName)) {
return variableToValueMap.get(speciesName);
}
else return 1;
}
else if (nodeName.equals("neighborQuantityAboveFull")) {
int leftIndex = (int) evaluateExpressionRecursive(node.getChild(1));
int rightIndex = (int) evaluateExpressionRecursive(node.getChild(2));
String specName = node.getChild(0).getName().split("__")[node.getChild(0).getName().split("__").length - 1];
String speciesName = "ROW" + (leftIndex - 1) + "_COL" + rightIndex + "__" + specName;
if (variableToValueMap.containsKey(speciesName))
return variableToValueMap.get(speciesName);
else return 1;
}
else if (nodeName.equals("neighborQuantityBelowFull")) {
int leftIndex = (int) evaluateExpressionRecursive(node.getChild(1));
int rightIndex = (int) evaluateExpressionRecursive(node.getChild(2));
String specName = node.getChild(0).getName().split("__")[node.getChild(0).getName().split("__").length - 1];
String speciesName = "ROW" + (leftIndex + 1) + "_COL" + rightIndex + "__" + specName;
if (variableToValueMap.containsKey(speciesName))
return variableToValueMap.get(speciesName);
else return 1;
}
else if (nodeName.equals("getCompartmentLocationX")) {
return this.componentToLocationMap.get(node.getChild(0).getName().split("__")[0]).getX();
}
else if (nodeName.equals("getCompartmentLocationY")) {
return this.componentToLocationMap.get(node.getChild(0).getName().split("__")[0]).getY();
}
break;
}
case FUNCTION_ABS:
return FastMath.abs(evaluateExpressionRecursive(node.getChild(0)));
case FUNCTION_ARCCOS:
return FastMath.acos(evaluateExpressionRecursive(node.getChild(0)));
case FUNCTION_ARCSIN:
return FastMath.asin(evaluateExpressionRecursive(node.getChild(0)));
case FUNCTION_ARCTAN:
return FastMath.atan(evaluateExpressionRecursive(node.getChild(0)));
case FUNCTION_CEILING:
return FastMath.ceil(evaluateExpressionRecursive(node.getChild(0)));
case FUNCTION_COS:
return FastMath.cos(evaluateExpressionRecursive(node.getChild(0)));
case FUNCTION_COSH:
return FastMath.cosh(evaluateExpressionRecursive(node.getChild(0)));
case FUNCTION_EXP:
return FastMath.exp(evaluateExpressionRecursive(node.getChild(0)));
case FUNCTION_FLOOR:
return FastMath.floor(evaluateExpressionRecursive(node.getChild(0)));
case FUNCTION_LN:
return FastMath.log(evaluateExpressionRecursive(node.getChild(0)));
case FUNCTION_LOG:
return FastMath.log10(evaluateExpressionRecursive(node.getChild(0)));
case FUNCTION_SIN:
return FastMath.sin(evaluateExpressionRecursive(node.getChild(0)));
case FUNCTION_SINH:
return FastMath.sinh(evaluateExpressionRecursive(node.getChild(0)));
case FUNCTION_TAN:
return FastMath.tan(evaluateExpressionRecursive(node.getChild(0)));
case FUNCTION_TANH:
return FastMath.tanh(evaluateExpressionRecursive(node.getChild(0)));
case FUNCTION_PIECEWISE: {
//loop through child triples
//if child 1 is true, return child 0, else return child 2
for (int childIter = 0; childIter < node.getChildCount(); childIter += 3) {
if ((childIter + 1) < node.getChildCount() &&
getBooleanFromDouble(evaluateExpressionRecursive(node.getChild(childIter + 1)))) {
return evaluateExpressionRecursive(node.getChild(childIter));
}
else if ((childIter + 2) < node.getChildCount()) {
return evaluateExpressionRecursive(node.getChild(childIter + 2));
}
}
return 0;
}
case FUNCTION_ROOT:
return FastMath.pow(evaluateExpressionRecursive(node.getRightChild()),
1 / evaluateExpressionRecursive(node.getLeftChild()));
case FUNCTION_SEC:
return Fmath.sec(evaluateExpressionRecursive(node.getChild(0)));
case FUNCTION_SECH:
return Fmath.sech(evaluateExpressionRecursive(node.getChild(0)));
case FUNCTION_FACTORIAL:
return Fmath.factorial(evaluateExpressionRecursive(node.getChild(0)));
case FUNCTION_COT:
return Fmath.cot(evaluateExpressionRecursive(node.getChild(0)));
case FUNCTION_COTH:
return Fmath.coth(evaluateExpressionRecursive(node.getChild(0)));
case FUNCTION_CSC:
return Fmath.csc(evaluateExpressionRecursive(node.getChild(0)));
case FUNCTION_CSCH:
return Fmath.csch(evaluateExpressionRecursive(node.getChild(0)));
case FUNCTION_DELAY:
//NOT PLANNING TO SUPPORT THIS
return 0;
case FUNCTION_ARCTANH:
return Fmath.atanh(evaluateExpressionRecursive(node.getChild(0)));
case FUNCTION_ARCSINH:
return Fmath.asinh(evaluateExpressionRecursive(node.getChild(0)));
case FUNCTION_ARCCOSH:
return Fmath.acosh(evaluateExpressionRecursive(node.getChild(0)));
case FUNCTION_ARCCOT:
return Fmath.acot(evaluateExpressionRecursive(node.getChild(0)));
case FUNCTION_ARCCOTH:
return Fmath.acoth(evaluateExpressionRecursive(node.getChild(0)));
case FUNCTION_ARCCSC:
return Fmath.acsc(evaluateExpressionRecursive(node.getChild(0)));
case FUNCTION_ARCCSCH:
return Fmath.acsch(evaluateExpressionRecursive(node.getChild(0)));
case FUNCTION_ARCSEC:
return Fmath.asec(evaluateExpressionRecursive(node.getChild(0)));
case FUNCTION_ARCSECH:
return Fmath.asech(evaluateExpressionRecursive(node.getChild(0)));
} //end switch
}
return 0.0;
}
/**
* adds species and reactions to the model that are implicit in arrays
* basically, it takes an arrayed model and flattens it
*
* this also applies stoichiometry amplification at the end (if needed)
* i did it this way to avoid another read/write of the model, as i have to
* do it within the simulator in order to use jsbml instead of libsbml
*/
public static void expandArrays(String filename, double stoichAmpValue) {
//open the sbml file for reading/writing
SBMLReader reader = new SBMLReader();
SBMLDocument document = null;
try {
document = reader.readSBML(filename);
} catch (Exception e) {
e.printStackTrace();
return;
}
Model model = document.getModel();
boolean arraysExist = false;
//ARRAYED SPECIES BUSINESS
//create all new species that are implicit in the arrays and put them into the model
ArrayList<Species> speciesToAdd = new ArrayList<Species>();
ArrayList<String> speciesToRemove = new ArrayList<String>();
HashMap<String, Boolean> speciesToIsArrayedMap = new HashMap<String, Boolean>();
HashMap<String, SpeciesDimensions> arrayedSpeciesToDimensionsMap =
new HashMap<String, SpeciesDimensions>();
for (Species species : model.getListOfSpecies()) {
String speciesID = species.getId();
//check to see if the species is arrayed
if (stripAnnotation(species.getAnnotationString()).contains("array:array")) {
arraysExist = true;
speciesToIsArrayedMap.put(speciesID, true);
speciesToRemove.add(speciesID);
int numRowsLower = 0;
int numColsLower = 0;
int numRowsUpper = 0;
int numColsUpper = 0;
String[] annotationString = stripAnnotation(species.getAnnotationString()).split("=");
numColsLower = Integer.valueOf(((String[])(annotationString[1].split(" ")))[0].replace("\"",""));
numColsUpper = Integer.valueOf(((String[])(annotationString[2].split(" ")))[0].replace("\"",""));
numRowsLower = Integer.valueOf(((String[])(annotationString[3].split(" ")))[0].replace("\"",""));
numRowsUpper = Integer.valueOf(((String[])(annotationString[4].split(" ")))[0].replace("\"",""));
SpeciesDimensions speciesDimensions =
new SpeciesDimensions(numRowsLower, numRowsUpper, numColsLower, numColsUpper);
arrayedSpeciesToDimensionsMap.put(speciesID, speciesDimensions);
//loop through all species in the array
//prepend the row/col information to create a new ID
for (int row = numRowsLower; row <= numRowsUpper; ++row) {
for (int col = numColsLower; col <= numColsUpper; ++col) {
speciesID = "ROW" + row + "_COL" + col + "__" + species.getId();
Species newSpecies = new Species();
newSpecies = species.clone();
newSpecies.setMetaId(speciesID);
newSpecies.setId(speciesID);
newSpecies.setAnnotation(new Annotation());
speciesToAdd.add(newSpecies);
}
}
}
else
speciesToIsArrayedMap.put(speciesID, false);
} //end species for loop
//add new row/col species to the model
for (Species species : speciesToAdd) {
model.addSpecies(species);
}
//ARRAYED EVENTS BUSINESS
ArrayList<String> eventsToRemove = new ArrayList<String>();
ArrayList<Event> eventsToAdd = new ArrayList<Event>();
for (Event event : model.getListOfEvents()) {
if (stripAnnotation(event.getAnnotationString()).contains("array")) {
arraysExist = true;
eventsToRemove.add(event.getId());
String annotationString = stripAnnotation(event.getAnnotationString()).replace("<annotation>","").
replace("</annotation>","").replace("\"","");
String[] splitAnnotation = annotationString.split("array:");
ArrayList<String> eventCompartments = new ArrayList<String>();
splitAnnotation[splitAnnotation.length - 2] = ((String[])splitAnnotation[splitAnnotation.length - 2].split("xmlns:"))[0];
for (int i = 2; i < splitAnnotation.length; ++i) {
String compartmentID = ((String[])splitAnnotation[i].split("="))[0];
eventCompartments.add(compartmentID);
}
//loop through all compartments and create an event for each one
for (String compartmentID : eventCompartments) {
Event newEvent = new Event();
newEvent.setVersion(event.getVersion());
newEvent.setLevel(event.getLevel());
newEvent.setId(compartmentID + "__" + event.getId());
newEvent.setMetaId(compartmentID + "__" + event.getId());
event.getTrigger().getMath().updateVariables();
newEvent.setTrigger(event.getTrigger().clone());
// //at this point, the formula has something like neighborQuantity(Species1)
// //this needs to become neighborQuantity(Species1, CompartmentLocationX(Comp1), CompartmentLocationY(Comp1))
// if (newEvent.getTrigger().getMath().toFormula().contains("neighborQuantity")) {
// String triggerMath = newEvent.getTrigger().getMath().toFormula();
// ArrayList<ASTNode> nqNodes = new ArrayList<ASTNode>();
// this.getSatisfyingNodesLax(newEvent.getTrigger().getMath(), "neighborQuantity", nqNodes);
// //loop through all neighbor quantity nodes in the trigger formula
// for (ASTNode nqNode : nqNodes) {
// String direction = "";
// if (triggerMath.contains("QuantityLeft"))
// direction = "Left";
// else if (triggerMath.contains("QuantityRight"))
// direction = "Right";
// else if (triggerMath.contains("QuantityAbove"))
// direction = "Above";
// else
// direction = "Below";
// String speciesID = nqNode.toFormula().split(
// "neighborQuantity" + direction)[1].replace("(","").replace(")","");
// try {
// ASTNode newFormula = ASTNode.parseFormula(
// "neighborQuantity" + direction + "Full(" + compartmentID + "__" + speciesID +
// ", getCompartmentLocationX(" + compartmentID + "__Cell" +
// "), getCompartmentLocationY(" + compartmentID + "__Cell" + "))");
// for (int i = 0; i < ((ASTNode) nqNode.getParent()).getChildCount(); ++i) {
// if (((ASTNode) nqNode.getParent().getChildAt(i)).isFunction() &&
// ((ASTNode) nqNode.getParent().getChildAt(i)).getVariable().toString()
// .contains("neighborQuantity" + direction)) {
// ((ASTNode) nqNode.getParent()).replaceChild(i, newFormula);
// break;
// } catch (ParseException e) {
// e.printStackTrace();
if (event.isSetPriority())
newEvent.setPriority(event.getPriority().clone());
if (event.isSetDelay()) {
newEvent.setDelay(event.getDelay().clone());
}
newEvent.setUseValuesFromTriggerTime(event.getUseValuesFromTriggerTime());
for (EventAssignment eventAssignment : event.getListOfEventAssignments()) {
EventAssignment ea = eventAssignment.clone();
ea.setMath(eventAssignment.getMath().clone());
ea.setVariable(eventAssignment.getVariable());
newEvent.addEventAssignment(ea);
}
for (EventAssignment eventAssignment : newEvent.getListOfEventAssignments()) {
eventAssignment.setVariable(compartmentID + "__" + eventAssignment.getVariable());
//prepends the compartment ID to all variables in the event assignment
prependToVariableNodes(eventAssignment.getMath(), compartmentID + "__", model);
}
eventsToAdd.add(newEvent);
}
}
}
for (Event eventToAdd : eventsToAdd) {
model.addEvent(eventToAdd);
}
//ARRAYED REACTION BUSINESS
//if a reaction has arrayed species
//new reactions that are implicit are created and added to the model
ArrayList<Reaction> reactionsToAdd = new ArrayList<Reaction>();
ArrayList<String> reactionsToRemove = new ArrayList<String>();
for (Reaction reaction : model.getListOfReactions()) {
String reactionID = reaction.getId();
ArrayList<Integer> membraneDiffusionRows = new ArrayList<Integer>();
ArrayList<Integer> membraneDiffusionCols = new ArrayList<Integer>();
ArrayList<String> membraneDiffusionCompartments = new ArrayList<String>();
//MEMBRANE DIFFUSION REACTIONS
//if it's a membrane diffusion reaction it'll have the appropriate locations as an annotation
//so parse them and store them in the above arraylists
if (reactionID.contains("MembraneDiffusion")) {
arraysExist = true;
String annotationString = stripAnnotation(reaction.getAnnotationString()).replace("<annotation>","").
replace("</annotation>","").replace("\"","");
String[] splitAnnotation = annotationString.split("array:");
if (splitAnnotation.length <= 1) {
continue;
}
splitAnnotation[splitAnnotation.length - 2] = ((String[])splitAnnotation[splitAnnotation.length - 2].split("xmlns:"))[0];
for (int i = 2; i < splitAnnotation.length; ++i) {
String compartmentID = ((String[])splitAnnotation[i].split("="))[0];
String row = ((String[])((String[])splitAnnotation[i].split(" ")[0].split("="))[1].split(","))[0].replace("(","");
String col = ((String[])((String[])splitAnnotation[i].split(" ")[0].split("="))[1].split(","))[1].replace(")","");
membraneDiffusionRows.add(Integer.valueOf(row.trim()));
membraneDiffusionCols.add(Integer.valueOf(col.trim()));
membraneDiffusionCompartments.add(compartmentID);
}
int membraneDiffusionIndex = 0;
reactionsToRemove.add(reaction.getId());
reaction.setAnnotation(new Annotation());
//loop through all appropriate row/col pairs and create a membrane diffusion reaction for each one
for (String compartmentID : membraneDiffusionCompartments) {
int row = membraneDiffusionRows.get(membraneDiffusionIndex);
int col = membraneDiffusionCols.get(membraneDiffusionIndex);
//create a new reaction and set the ID
Reaction newReaction = new Reaction();
newReaction = reaction.clone();
newReaction.setListOfReactants(new ListOf<SpeciesReference>());
newReaction.setListOfProducts(new ListOf<SpeciesReference>());
newReaction.setListOfModifiers(new ListOf<ModifierSpeciesReference>());
newReaction.setId(compartmentID + "__" + reactionID);
newReaction.setMetaId(compartmentID + "__" + reactionID);
newReaction.setReversible(true);
newReaction.setFast(false);
newReaction.setCompartment(reaction.getCompartment());
//alter the kinetic law to so that it has the correct indexes as children for the
//get2DArrayElement function
//get the nodes to alter (that are arguments for the get2DArrayElement method)
ArrayList<ASTNode> get2DArrayElementNodes = new ArrayList<ASTNode>();
getSatisfyingNodes(newReaction.getKineticLaw().getMath(),
"get2DArrayElement", get2DArrayElementNodes);
boolean reactantBool = false;
//replace the get2darrayelement stuff with the proper explicit species/parameters
for (ASTNode node : get2DArrayElementNodes) {
if (node.getLeftChild().getName().contains("kmdiff")) {
String parameterName = node.getLeftChild().getName();
//see if the species-specific one exists
//if it doesn't, use the default
//you'll need to parse the species name from the reaction id, probably
String speciesID = reactionID.replace("MembraneDiffusion_","");
if (model.getParameter(compartmentID + "__" + speciesID + "__" + parameterName) == null)
node.setVariable(model.getParameter(parameterName));
else
node.setVariable(model.getParameter(compartmentID + "__" + speciesID + "__" + parameterName));
for (int i = 0; i < node.getChildCount(); ++i)
node.removeChild(i);
for (int i = 0; i < node.getChildCount(); ++i)
node.removeChild(i);
}
//this means it's a species, which we need to prepend with the row/col prefix
else {
if (node.getChildCount() > 0 &&
model.getParameter(node.getLeftChild().getName()) == null) {
//reactant
if (reactantBool == true) {
node.setVariable(model.getSpecies(
"ROW" + row + "_COL" + col + "__" + node.getLeftChild().getName()));
}
//product
else {
node.setVariable(model.getSpecies(
compartmentID + "__" + node.getLeftChild().getName()));
reactantBool = true;
}
}
for (int i = 0; i < node.getChildCount(); ++i)
node.removeChild(i);
for (int i = 0; i < node.getChildCount(); ++i)
node.removeChild(i);
}
}
//loop through reactants
for (SpeciesReference reactant : reaction.getListOfReactants()) {
//create a new reactant and add it to the new reaction
SpeciesReference newReactant = new SpeciesReference();
newReactant = reactant.clone();
newReactant.setSpecies(compartmentID + "__" + newReactant.getSpecies());
newReactant.setAnnotation(new Annotation());
newReaction.addReactant(newReactant);
}
//loop through products
for (SpeciesReference product : reaction.getListOfProducts()) {
//create a new reactant and add it to the new reaction
SpeciesReference newProduct = new SpeciesReference();
newProduct = product.clone();
newProduct.setSpecies("ROW" + row + "_COL" + col + "__" + newProduct.getSpecies());
newProduct.setAnnotation(new Annotation());
newReaction.addProduct(newProduct);
}
boolean i = false, j = false;
for (LocalParameter lp : newReaction.getKineticLaw().getListOfLocalParameters()) {
if (lp.getId().equals("i"))
i = true;
else if (lp.getId().equals("j"))
j = true;
}
if (i)
newReaction.getKineticLaw().getListOfLocalParameters().remove("i");
if (j)
newReaction.getKineticLaw().getListOfLocalParameters().remove("j");
reactionsToAdd.add(newReaction);
++membraneDiffusionIndex;
}
} //end if membrane diffusion
//NON-MEMBRANE DIFFUSION REACTIONS
//check to see if the (non-membrane-diffusion) reaction has arrayed species
//right now i'm only checking the first reactant species, due to a bad assumption
//about the homogeneity of the arrayed reaction (ie, if one species is arrayed, they all are)
else if (reaction.getNumReactants() > 0 &&
speciesToIsArrayedMap.get(reaction.getReactant(0).getSpeciesInstance().getId()) == true) {
arraysExist = true;
reactionsToRemove.add(reaction.getId());
//get the reactant dimensions, which tells us how many new reactions are going to be created
SpeciesDimensions reactantDimensions =
arrayedSpeciesToDimensionsMap.get(reaction.getReactant(0).getSpeciesInstance().getId());
boolean abort = false;
//loop through all of the new formerly-implicit reactants
for (int row = reactantDimensions.numRowsLower; row <= reactantDimensions.numRowsUpper; ++row) {
for (int col = reactantDimensions.numColsLower; col <= reactantDimensions.numColsUpper; ++col) {
//create a new reaction and set the ID
Reaction newReaction = new Reaction();
newReaction = reaction.clone();
newReaction.setListOfReactants(new ListOf<SpeciesReference>());
newReaction.setListOfProducts(new ListOf<SpeciesReference>());
newReaction.setListOfModifiers(new ListOf<ModifierSpeciesReference>());
newReaction.setId("ROW" + row + "_COL" + col + "_" + reactionID);
newReaction.setMetaId("ROW" + row + "_COL" + col + "_" + reactionID);
newReaction.setReversible(false);
newReaction.setFast(false);
newReaction.setCompartment(reaction.getCompartment());
//get the nodes to alter
ArrayList<ASTNode> get2DArrayElementNodes = new ArrayList<ASTNode>();
//return the head node of the get2DArrayElement function
getSatisfyingNodes(newReaction.getKineticLaw().getMath(),
"get2DArrayElement", get2DArrayElementNodes);
//loop through all reactants
for (SpeciesReference reactant : reaction.getListOfReactants()) {
reactant.unsetMetaId();
//find offsets
//the row offset is in the kinetic law via i
//the col offset is in the kinetic law via j
int rowOffset = 0;
int colOffset = 0;
ASTNode reactantHeadNode = null;
//go through the get2DArrayElement nodes and find the one corresponding to the reactant
for (ASTNode headNode : get2DArrayElementNodes) {
//make sure it's a reactant node
if (headNode.getChildCount() > 0 &&
model.getParameter(headNode.getLeftChild().getName()) == null) {
reactantHeadNode = headNode;
break;
}
}
if (reactantHeadNode.getChild(1).getType().name().equals("PLUS"))
rowOffset = reactantHeadNode.getChild(1).getRightChild().getInteger();
else if (reactantHeadNode.getChild(1).getType().name().equals("MINUS"))
rowOffset = -1 * reactantHeadNode.getChild(1).getRightChild().getInteger();
if (reactantHeadNode.getChild(2).getType().name().equals("PLUS"))
colOffset = reactantHeadNode.getChild(2).getRightChild().getInteger();
else if (reactantHeadNode.getChild(2).getType().name().equals("MINUS"))
colOffset = -1 * reactantHeadNode.getChild(2).getRightChild().getInteger();
//create a new reactant and add it to the new reaction
SpeciesReference newReactant = new SpeciesReference();
newReactant = reactant.clone();
newReactant.setSpecies(model.getSpecies("ROW" + (row + rowOffset) + "_COL"
+ (col + colOffset) + "__" + newReactant.getSpecies()));
newReactant.setAnnotation(new Annotation());
newReaction.addReactant(newReactant);
//put this reactant in place of the get2DArrayElement function call
for (int i = 0; i < reactantHeadNode.getChildCount(); ++i)
reactantHeadNode.removeChild(i);
for (int i = 0; i < reactantHeadNode.getChildCount(); ++i)
reactantHeadNode.removeChild(i);
reactantHeadNode.setVariable(model.getSpecies(newReactant.getSpecies()));
}// end looping through reactants
//loop through all modifiers
for (ModifierSpeciesReference modifier : reaction.getListOfModifiers()) {
modifier.unsetMetaId();
}
//loop through all products
for (SpeciesReference product : reaction.getListOfProducts()) {
product.unsetMetaId();
//find offsets
int rowOffset = 0;
int colOffset = 0;
ASTNode productHeadNode = null;
//go through the get2DArrayElement nodes and find the one corresponding to the product
for (ASTNode headNode : get2DArrayElementNodes) {
//make sure it's a product node
//only the product has children, as the reactant's children get deleted
if (headNode.getChildCount() > 0 &&
model.getParameter(headNode.getLeftChild().getName()) == null) {
productHeadNode = headNode;
break;
}
}
if (productHeadNode.getChild(1).getType().name().equals("PLUS"))
rowOffset = productHeadNode.getChild(1).getRightChild().getInteger();
else if (productHeadNode.getChild(1).getType().name().equals("MINUS"))
rowOffset = -1 * productHeadNode.getChild(1).getRightChild().getInteger();
if (productHeadNode.getChild(2).getType().name().equals("PLUS"))
colOffset = productHeadNode.getChild(2).getRightChild().getInteger();
else if (productHeadNode.getChild(2).getType().name().equals("MINUS"))
colOffset = -1 * productHeadNode.getChild(2).getRightChild().getInteger();
//don't create reactions with products that don't exist
if (row + rowOffset < reactantDimensions.numRowsLower ||
col + colOffset < reactantDimensions.numColsLower ||
row + rowOffset > reactantDimensions.numRowsUpper ||
col + colOffset > reactantDimensions.numColsUpper) {
abort = true;
break;
}
//create a new product and add it to the new reaction
SpeciesReference newProduct = new SpeciesReference();
newProduct = product.clone();
newProduct.setSpecies(model.getSpecies("ROW" + (row + rowOffset) + "_COL"
+ (col + colOffset) + "__" + newProduct.getSpecies()));
newProduct.setAnnotation(new Annotation());
newReaction.addProduct(newProduct);
//put this reactant in place of the get2DArrayElement function call
for (int i = 0; i < productHeadNode.getChildCount(); ++i)
productHeadNode.removeChild(i);
//put this reactant in place of the get2DArrayElement function call
for (int i = 0; i < productHeadNode.getChildCount(); ++i)
productHeadNode.removeChild(i);
productHeadNode.setVariable(model.getSpecies(newProduct.getSpecies()));
} //end looping through products
if (abort == false) {
boolean i = false, j = false;
//checking for these local parameters using getLocalParameters() doesn't seem to work
for (LocalParameter lp : newReaction.getKineticLaw().getListOfLocalParameters()) {
lp.unsetMetaId();
if (lp.getId().equals("i"))
i = true;
else if (lp.getId().equals("j"))
j = true;
}
if (i)
newReaction.getKineticLaw().getListOfLocalParameters().remove("i");
if (j)
newReaction.getKineticLaw().getListOfLocalParameters().remove("j");
//this isn't a reversible reaction; only take the left side
if (newReaction.getId().contains("Degradation") == false) {
newReaction.getKineticLaw().setMath(newReaction.getKineticLaw().getMath().getLeftChild());
}
reactionsToAdd.add(newReaction);
}
else
abort = false;
}
}
}
}// end looping through reactions
//add in the new explicit array reactions
for (Reaction reactionToAdd : reactionsToAdd) {
reactionToAdd.setMetaId(reactionToAdd.getId());
if (model.getReaction(reactionToAdd.getId())!=null) {
model.removeReaction(reactionToAdd.getId());
}
model.addReaction(reactionToAdd);
}
ListOf<Reaction> allReactions = model.getListOfReactions();
//remove original array reaction(s)
for (String reactionToRemove : reactionsToRemove)
allReactions.remove(reactionToRemove);
model.setListOfReactions(allReactions);
ListOf<Species> allSpecies = model.getListOfSpecies();
//remove the original array species from the model
for (String speciesID : speciesToRemove)
allSpecies.remove(speciesID);
model.setListOfSpecies(allSpecies);
ListOf<Event> allEvents = model.getListOfEvents();
//remove original array event(s)
for (String eventID : eventsToRemove)
allEvents.remove(eventID);
model.setListOfEvents(allEvents);
ArrayList<String> parametersToRemove = new ArrayList<String>();
//get rid of the locations parameters
for (Parameter parameter : model.getListOfParameters()) {
if (parameter.getId().contains("_locations")) {
// if (parameter.getId().contains("_locations"))
// this.submodelIDToLocationsMap.put(
// parameter.getId().replace("__locations",""), stripAnnotation(parameter.getAnnotationString()));
parametersToRemove.add(parameter.getId());
}
}
for (String parameterID : parametersToRemove)
model.removeParameter(parameterID);
applyStoichiometryAmplification(model, stoichAmpValue);
if (arraysExist) {
SBMLWriter writer = new SBMLWriter();
PrintStream p;
try {
p = new PrintStream(new FileOutputStream(filename), true, "UTF-8");
p.print(writer.writeSBMLToString(model.getSBMLDocument()));
} catch (Exception e) {
e.printStackTrace();
}
}
}
/**
* fires events
*
* @param noAssignmentRulesFlag
* @param noConstraintsFlag
*/
protected HashSet<String> fireEvents(final boolean noAssignmentRulesFlag, final boolean noConstraintsFlag) {
//temporary set of events to remove from the triggeredEventQueue
HashSet<String> untriggeredEvents = new HashSet<String>();
//loop through all triggered events
//if they aren't persistent and the trigger is no longer true
//remove from triggered queue and put into untriggered set
for (EventToFire triggeredEvent : triggeredEventQueue) {
String triggeredEventID = triggeredEvent.eventID;
//if the trigger evaluates to false and the trigger isn't persistent
if (eventToTriggerPersistenceMap.get(triggeredEventID) == false &&
getBooleanFromDouble(evaluateExpressionRecursive(eventToTriggerMap.get(triggeredEventID))) == false) {
untriggeredEvents.add(triggeredEventID);
eventToPreviousTriggerValueMap.put(triggeredEventID, false);
}
if (eventToTriggerPersistenceMap.get(triggeredEventID) == true &&
getBooleanFromDouble(evaluateExpressionRecursive(eventToTriggerMap.get(triggeredEventID))) == false) {
untriggeredEventSet.add(triggeredEventID);
}
}
//copy the triggered event queue -- except the events that are now untriggered
//this is done because the remove function can't work with just a string; it needs to match events
//this also re-evaluates the priorities in case they have changed
PriorityQueue<EventToFire> newTriggeredEventQueue = new PriorityQueue<EventToFire>(5, eventComparator);
while (triggeredEventQueue.size() > 0) {
EventToFire event = triggeredEventQueue.poll();
EventToFire eventToAdd =
new EventToFire(event.eventID, (HashSet<Object>) event.eventAssignmentSet.clone(), event.fireTime);
if (untriggeredEvents.contains(event.eventID) == false)
newTriggeredEventQueue.add(eventToAdd);
else
untriggeredEventSet.add(event.eventID);
}
triggeredEventQueue = newTriggeredEventQueue;
//loop through untriggered events
//if the trigger is no longer true
//set the previous trigger value to false
for (String untriggeredEventID : untriggeredEventSet) {
if (eventToTriggerPersistenceMap.get(untriggeredEventID) == false &&
getBooleanFromDouble(evaluateExpressionRecursive(eventToTriggerMap.get(untriggeredEventID))) == false)
eventToPreviousTriggerValueMap.put(untriggeredEventID, false);
}
//these are sets of things that need to be re-evaluated or tested due to the event firing
HashSet<String> affectedReactionSet = new HashSet<String>();
HashSet<AssignmentRule> affectedAssignmentRuleSet = new HashSet<AssignmentRule>();
HashSet<ASTNode> affectedConstraintSet = new HashSet<ASTNode>();
//set of fired events to add to the untriggered set
HashSet<String> firedEvents = new HashSet<String>();
//set of events to be removed due to component erasure
HashSet<String> deadEvents = new HashSet<String>();
//fire all events whose fire time is less than the current time
while (triggeredEventQueue.size() > 0 && triggeredEventQueue.peek().fireTime <= currentTime) {
EventToFire eventToFire = triggeredEventQueue.poll();
String eventToFireID = eventToFire.eventID;
//System.err.println("firing " + eventToFireID);
if (eventToAffectedReactionSetMap.get(eventToFireID) != null)
affectedReactionSet.addAll(eventToAffectedReactionSetMap.get(eventToFireID));
firedEvents.add(eventToFireID);
eventToPreviousTriggerValueMap.put(eventToFireID, true);
//handle dynamic events
//the duplication method handles all event assignments
//so those only get executed here if it's not a dynamic event
if (eventToFire.eventID.contains("__AsymmetricDivision__")) {
String compartmentID = ((String[])eventToFire.eventID.split("__"))[0];
duplicateComponent(compartmentID, eventToFire.eventID, "asymmetric");
}
else if (eventToFire.eventID.contains("__SymmetricDivision__")) {
String compartmentID = ((String[])eventToFire.eventID.split("__"))[0];
duplicateComponent(compartmentID, eventToFire.eventID, "symmetric");
}
else if (eventToFire.eventID.contains("__Death__")) {
String compartmentID = ((String[])eventToFire.eventID.split("__"))[0];
deadEvents = eraseComponent(compartmentID);
firedEvents.removeAll(deadEvents);
if (deadEvents.size() > 0) {
for (String eventID : deadEvents) {
untriggeredEventSet.remove(eventID);
eventToPriorityMap.remove(eventID);
eventToDelayMap.remove(eventID);
eventToHasDelayMap.remove(eventID);
eventToTriggerPersistenceMap.remove(eventID);
eventToUseValuesFromTriggerTimeMap.remove(eventID);
eventToTriggerMap.remove(eventID);
eventToTriggerInitiallyTrueMap.remove(eventID);
eventToPreviousTriggerValueMap.remove(eventID);
eventToAssignmentSetMap.remove(eventID);
eventToAffectedReactionSetMap.remove(eventID);
}
//copy the triggered event queue -- except the events that are now dead/removed
newTriggeredEventQueue = new PriorityQueue<EventToFire>(5, eventComparator);
while (triggeredEventQueue.size() > 0) {
EventToFire event = triggeredEventQueue.poll();
EventToFire eventToAdd =
new EventToFire(event.eventID, (HashSet<Object>) event.eventAssignmentSet.clone(), event.fireTime);
if (deadEvents.contains(event.eventID) == false)
newTriggeredEventQueue.add(eventToAdd);
}
triggeredEventQueue = newTriggeredEventQueue;
}
}
else if (eventToFire.eventID.contains("__Move")) {
int direction = (int) (randomNumberGenerator.nextDouble() * 4.0);
if (eventToFire.eventID.contains("__MoveLeft__"))
direction = 0;
else if (eventToFire.eventID.contains("__MoveRight__"))
direction = 1;
else if (eventToFire.eventID.contains("__MoveAbove__"))
direction = 2;
else if (eventToFire.eventID.contains("__MoveBelow__"))
direction = 3;
//reactions that change and thus need their propensities re-evaluated
HashSet<String> reactionsToAdjust = new HashSet<String>();
String compartmentID = ((String[])eventToFire.eventID.split("__"))[0];
Point parentLocation = componentToLocationMap.get(compartmentID);
Point childLocation = (Point) parentLocation.clone();
moveComponent(compartmentID, "", new Point(), childLocation, direction, reactionsToAdjust);
updatePropensities(reactionsToAdjust);
updateAfterDynamicChanges();
}
else {
//execute all assignments for this event
for (Object eventAssignment : eventToFire.eventAssignmentSet) {
String variable;
double assignmentValue;
if (eventToUseValuesFromTriggerTimeMap.get(eventToFireID) == true) {
variable = ((StringDoublePair) eventAssignment).string;
assignmentValue = ((StringDoublePair) eventAssignment).doub;
}
//assignment needs to be evaluated
else {
variable = ((EventAssignment) eventAssignment).getVariable();
assignmentValue = evaluateExpressionRecursive(((EventAssignment) eventAssignment).getMath());
}
//update the species, but only if it's not a constant (bound. cond. is fine)
if (variableToIsConstantMap.get(variable) == false) {
if (speciesToHasOnlySubstanceUnitsMap.containsKey(variable) &&
speciesToHasOnlySubstanceUnitsMap.get(variable) == false)
variableToValueMap.put(variable,
assignmentValue * speciesToCompartmentSizeMap.get(variable));
else
variableToValueMap.put(variable, assignmentValue);
}
//if this variable that was just updated is part of an assignment rule (RHS)
//then re-evaluate that assignment rule
if (noAssignmentRulesFlag == false && variableToIsInAssignmentRuleMap.get(variable) == true)
affectedAssignmentRuleSet.addAll(variableToAffectedAssignmentRuleSetMap.get(variable));
if (noConstraintsFlag == false && variableToIsInConstraintMap.get(variable) == true)
affectedConstraintSet.addAll(variableToAffectedConstraintSetMap.get(variable));
} //end loop through assignments
}
//after an event fires, need to make sure the queue is updated
untriggeredEvents.clear();
//loop through all triggered events
//if they aren't persistent and the trigger is no longer true
//remove from triggered queue and put into untriggered set
for (EventToFire triggeredEvent : triggeredEventQueue) {
String triggeredEventID = triggeredEvent.eventID;
//if the trigger evaluates to false and the trigger isn't persistent
if (eventToTriggerPersistenceMap.get(triggeredEventID) == false &&
getBooleanFromDouble(evaluateExpressionRecursive(eventToTriggerMap.get(triggeredEventID))) == false) {
untriggeredEvents.add(triggeredEventID);
eventToPreviousTriggerValueMap.put(triggeredEventID, false);
}
if (eventToTriggerPersistenceMap.get(triggeredEventID) == true &&
getBooleanFromDouble(evaluateExpressionRecursive(eventToTriggerMap.get(triggeredEventID))) == false)
untriggeredEventSet.add(triggeredEventID);
}
//copy the triggered event queue -- except the events that are now untriggered
//this is done because the remove function can't work with just a string; it needs to match events
//this also re-evaluates the priorities in case they have changed
newTriggeredEventQueue = new PriorityQueue<EventToFire>(5, eventComparator);
while (triggeredEventQueue.size() > 0) {
EventToFire event = triggeredEventQueue.poll();
EventToFire eventToAdd =
new EventToFire(event.eventID, (HashSet<Object>) event.eventAssignmentSet.clone(), event.fireTime);
if (untriggeredEvents.contains(event.eventID) == false)
newTriggeredEventQueue.add(eventToAdd);
else
untriggeredEventSet.add(event.eventID);
}
triggeredEventQueue = newTriggeredEventQueue;
//some events might trigger after this
handleEvents(noAssignmentRulesFlag, noConstraintsFlag);
}//end loop through event queue
//add the fired events back into the untriggered set
//this allows them to trigger/fire again later
untriggeredEventSet.addAll(firedEvents);
if (affectedAssignmentRuleSet.size() > 0)
performAssignmentRules(affectedAssignmentRuleSet);
if (affectedConstraintSet.size() > 0) {
if (testConstraints(affectedConstraintSet) == false)
constraintFailureFlag = true;
}
return affectedReactionSet;
}
/**
* recursively puts every astnode child into the arraylist passed in
*
* @param node
* @param nodeChildrenList
*/
protected void getAllASTNodeChildren(ASTNode node, ArrayList<ASTNode> nodeChildrenList) {
for (ASTNode child : node.getChildren()) {
if (child.getChildCount() == 0)
nodeChildrenList.add(child);
else {
nodeChildrenList.add(child);
getAllASTNodeChildren(child, nodeChildrenList);
}
}
}
/**
* returns a set of all the reactions that the recently performed reaction affects
* "affect" means that the species updates will change the affected reaction's propensity
*
* @param selectedReactionID the reaction that was recently performed
* @return the set of all reactions that the performed reaction affects the propensity of
*/
protected HashSet<String> getAffectedReactionSet(String selectedReactionID, final boolean noAssignmentRulesFlag) {
HashSet<String> affectedReactionSet = new HashSet<String>(20);
affectedReactionSet.add(selectedReactionID);
//loop through the reaction's reactants and products
for (StringDoublePair speciesAndStoichiometry : reactionToSpeciesAndStoichiometrySetMap.get(selectedReactionID)) {
String speciesID = speciesAndStoichiometry.string;
affectedReactionSet.addAll(speciesToAffectedReactionSetMap.get(speciesID));
//if the species is involved in an assignment rule then it its changing may affect a reaction's propensity
if (noAssignmentRulesFlag == false && variableToIsInAssignmentRuleMap.get(speciesID)) {
//this assignment rule is going to be evaluated, so the rule's variable's value will change
for (AssignmentRule assignmentRule : variableToAffectedAssignmentRuleSetMap.get(speciesID)) {
if (speciesToAffectedReactionSetMap.get(assignmentRule.getVariable())!=null) {
affectedReactionSet.addAll(speciesToAffectedReactionSetMap
.get(assignmentRule.getVariable()));
}
}
}
}
return affectedReactionSet;
}
/**
* kind of a hack to mingle doubles and booleans for the expression evaluator
*
* @param value the double to be translated to a boolean
* @return the translated boolean value
*/
protected boolean getBooleanFromDouble(double value) {
if (value == 0.0)
return false;
else
return true;
}
/**
* kind of a hack to mingle doubles and booleans for the expression evaluator
*
* @param value the boolean to be translated to a double
* @return the translated double value
*/
protected double getDoubleFromBoolean(boolean value) {
if (value == true)
return 1.0;
else
return 0.0;
}
/**
* recursively puts the nodes that have the same name as the quarry string passed in into the arraylist passed in
* so, the entire tree is searched through, which i don't think is possible with the jsbml methods
*
* @param node node to search through
* @param quarry string to search for
* @param satisfyingNodes list of nodes that satisfy the condition
*/
static void getSatisfyingNodes(ASTNode node, String quarry, ArrayList<ASTNode> satisfyingNodes) {
if (node.isName() && node.getName().equals(quarry))
satisfyingNodes.add(node);
else if (node.isFunction() && node.getName().equals(quarry))
satisfyingNodes.add(node);
else {
for (ASTNode childNode : node.getChildren())
getSatisfyingNodes(childNode, quarry, satisfyingNodes);
}
}
/**
* recursively puts the nodes that have the same name as the quarry string passed in into the arraylist passed in
* so, the entire tree is searched through, which i don't think is possible with the jsbml methods
* the lax version uses contains instead of equals
*
* @param node node to search through
* @param quarry string to search for
* @param satisfyingNodes list of nodes that satisfy the condition
*/
void getSatisfyingNodesLax(ASTNode node, String quarry, ArrayList<ASTNode> satisfyingNodes) {
if (node.isName() && node.getName().contains(quarry))
satisfyingNodes.add(node);
else if (node.isFunction() && node.getName().contains(quarry))
satisfyingNodes.add(node);
else {
for (ASTNode childNode : node.getChildren())
getSatisfyingNodesLax(childNode, quarry, satisfyingNodes);
}
}
/**
* updates the event queue and fires events and so on
* @param currentTime the current time in the simulation
*/
protected void handleEvents(final boolean noAssignmentRulesFlag, final boolean noConstraintsFlag) {
HashSet<String> triggeredEvents = new HashSet<String>();
//loop through all untriggered events
//if any trigger, evaluate the fire time(s) and add them to the queue
for (String untriggeredEventID : untriggeredEventSet) {
// System.err.println(untriggeredEventID);
// System.err.println(eventToTriggerMap.get(untriggeredEventID));
//if the trigger evaluates to true
if (getBooleanFromDouble(evaluateExpressionRecursive(eventToTriggerMap.get(untriggeredEventID))) == true) {
//skip the event if it's initially true and this is time == 0
if (currentTime == 0.0 && eventToTriggerInitiallyTrueMap.get(untriggeredEventID) == true)
continue;
//switch from false to true must happen
if (eventToPreviousTriggerValueMap.get(untriggeredEventID) == true)
continue;
triggeredEvents.add(untriggeredEventID);
//if assignment is to be evaluated at trigger time, evaluate it and replace the ASTNode assignment
if (eventToUseValuesFromTriggerTimeMap.get(untriggeredEventID) == true) {
//temporary hashset of evaluated assignments
HashSet<Object> evaluatedAssignments = new HashSet<Object>();
for (Object evAssignment : eventToAssignmentSetMap.get(untriggeredEventID)) {
EventAssignment eventAssignment = (EventAssignment) evAssignment;
evaluatedAssignments.add(new StringDoublePair(
eventAssignment.getVariable(), evaluateExpressionRecursive(eventAssignment.getMath())));
}
double fireTime = currentTime;
if (eventToHasDelayMap.get(untriggeredEventID) == true)
fireTime += evaluateExpressionRecursive(eventToDelayMap.get(untriggeredEventID));
triggeredEventQueue.add(new EventToFire(
untriggeredEventID, evaluatedAssignments, fireTime));
}
else {
double fireTime = currentTime;
if (eventToHasDelayMap.get(untriggeredEventID) == true)
fireTime += evaluateExpressionRecursive(eventToDelayMap.get(untriggeredEventID));
triggeredEventQueue.add(new EventToFire(
untriggeredEventID, eventToAssignmentSetMap.get(untriggeredEventID), fireTime));
}
}
else {
eventToPreviousTriggerValueMap.put(untriggeredEventID, false);
}
}
//remove recently triggered events from the untriggered set
//when they're fired, they get put back into the untriggered set
untriggeredEventSet.removeAll(triggeredEvents);
}
public void replaceArgument(ASTNode formula,String bvar, ASTNode arg) {
int n = 0;
for (int i = 0; i < formula.getChildCount(); i++) {
ASTNode child = formula.getChild(i);
if (child.isString() && child.getName().equals(bvar)) {
formula.replaceChild(n, arg.clone());
} else if (child.getChildCount() > 0) {
replaceArgument(child, bvar, arg);
}
n++;
}
}
/**
* inlines a formula with function definitions
*
* @param formula
* @return
*/
protected ASTNode inlineFormula(ASTNode formula) {
if (formula.isFunction() == false || formula.isLeaf() == false) {
for (int i = 0; i < formula.getChildCount(); ++i)
formula.replaceChild(i, inlineFormula(formula.getChild(i)));//.clone()));
}
if (formula.isFunction() && model.getFunctionDefinition(formula.getName()) != null) {
if (ibiosimFunctionDefinitions.contains(formula.getName()))
return formula;
ASTNode inlinedFormula = model.getFunctionDefinition(formula.getName()).getBody().clone();
ASTNode oldFormula = formula.clone();
ArrayList<ASTNode> inlinedChildren = new ArrayList<ASTNode>();
this.getAllASTNodeChildren(inlinedFormula, inlinedChildren);
if (inlinedChildren.size() == 0)
inlinedChildren.add(inlinedFormula);
HashMap<String, Integer> inlinedChildToOldIndexMap = new HashMap<String, Integer>();
for (int i = 0; i < model.getFunctionDefinition(formula.getName()).getNumArguments(); ++i) {
inlinedChildToOldIndexMap.put(model.getFunctionDefinition(formula.getName()).getArgument(i).getName(), i);
}
for (int i = 0; i < inlinedChildren.size(); ++i) {
ASTNode child = inlinedChildren.get(i);
if (child.isLeaf() && child.isName()) {
int index = inlinedChildToOldIndexMap.get(child.getName());
replaceArgument(inlinedFormula,child.toFormula(), oldFormula.getChild(index));
if (inlinedFormula.getChildCount() == 0)
inlinedFormula = oldFormula.getChild(index);
}
}
return inlinedFormula;
}
else {
return formula;
}
}
/**
* moves a component in a given direction
* moves components out of the way if needed
* creates grid reactions if the grid expands
*
* @param parentComponentID
* @param direction
*/
protected void moveComponent(String parentComponentID, String childComponentID, Point parentLocation, Point childLocation,
int direction, HashSet<String> reactionsToAdjust) {
HashSet<Integer> newRows = new HashSet<Integer>();
HashSet<Integer> newCols = new HashSet<Integer>();
//find the grid bounds
for (Point location : componentToLocationMap.values()) {
if ((int) location.getX() < minRow) {
minRow = (int) location.getX();
}
else if ((int) location.getX() > maxRow) {
maxRow = (int) location.getX();
}
if ((int) location.getY() < minCol) {
minCol = (int) location.getY();
}
else if ((int) location.getY() > maxCol) {
maxCol = (int) location.getY();
}
}
switch (direction) {
case 0: childLocation.y -= 1; break;
case 1: childLocation.y += 1; break;
case 2: childLocation.x -= 1; break;
case 3: childLocation.x += 1; break;
case 4: {childLocation.x += 1; childLocation.y -= 1; break;}
case 5: {childLocation.x -= 1; childLocation.y += 1; break;}
case 6: {childLocation.x -= 1; childLocation.y -= 1; break;}
case 7: {childLocation.x += 1; childLocation.y += 1; break;}
}
HashSet<Point> locationsToMove = new HashSet<Point>();
//if this place is taken, make room by moving the cells in the way
if (componentToLocationMap.containsValue(childLocation)) {
//empty location is the location that needs to become empty so the child can go there
Point emptyLocation = (Point) childLocation.clone();
//find all of the locations that are in the way and put them in the hashset
//this is done my moving in the direction chosen until an empty space is found
while (componentToLocationMap.containsValue(emptyLocation) == true) {
locationsToMove.add((Point) emptyLocation.clone());
switch (direction) {
case 0: emptyLocation.y -= 1; break;
case 1: emptyLocation.y += 1; break;
case 2: emptyLocation.x -= 1; break;
case 3: emptyLocation.x += 1; break;
case 4: {emptyLocation.x += 1; emptyLocation.y -= 1; break;}
case 5: {emptyLocation.x -= 1; emptyLocation.y += 1; break;}
case 6: {emptyLocation.x -= 1; emptyLocation.y -= 1; break;}
case 7: {emptyLocation.x += 1; emptyLocation.y += 1; break;}
}
}
LinkedHashMap<String, Point> componentToLocationMapCopy =
(LinkedHashMap<String, Point>) componentToLocationMap.clone();
//move the cells that are in the way
for (Map.Entry<String, Point> componentAndLocation : componentToLocationMapCopy.entrySet()) {
String compID = componentAndLocation.getKey();
if (locationsToMove.contains(componentAndLocation.getValue())) {
switch (direction) {
case 0: componentToLocationMap.get(compID).y -= 1; break;
case 1: componentToLocationMap.get(compID).y += 1; break;
case 2: componentToLocationMap.get(compID).x -= 1; break;
case 3: componentToLocationMap.get(compID).x += 1; break;
case 4: {componentToLocationMap.get(compID).x += 1; componentToLocationMap.get(compID).y -= 1; break;}
case 5: {componentToLocationMap.get(compID).x -= 1; componentToLocationMap.get(compID).y += 1; break;}
case 6: {componentToLocationMap.get(compID).x -= 1; componentToLocationMap.get(compID).y -= 1; break;}
case 7: {componentToLocationMap.get(compID).x += 1; componentToLocationMap.get(compID).y += 1; break;}
}
//keep track of min row/col and max row/col so you know the bounds of the grid
if ((int) componentToLocationMap.get(compID).getX() < minRow) {
minRow = (int) componentToLocationMap.get(compID).getX();
newRows.add(minRow);
}
else if ((int) componentToLocationMap.get(compID).getX() > maxRow) {
maxRow = (int) componentToLocationMap.get(compID).getX();
newRows.add(maxRow);
}
if ((int) componentToLocationMap.get(compID).getY() < minCol) {
minCol = (int) componentToLocationMap.get(compID).getY();
newCols.add(minCol);
}
else if ((int) componentToLocationMap.get(compID).getY() > maxCol) {
maxCol = (int) componentToLocationMap.get(compID).getY();
newCols.add(maxCol);
}
}
}
}
//now that an empty space has been created (if necessary), put in the child component
//or move the parent component (if the ID is "" then it's a pure move not a duplication)
if (childComponentID.equals(""))
componentToLocationMap.put(parentComponentID, childLocation);
else
componentToLocationMap.put(childComponentID, childLocation);
//keep track of min row/col and max row/col so you know the bounds of the grid
//this set of ifs is necessary because locationsToMove might be empty (if nothing's in the way)
if ((int) childLocation.getX() < minRow) {
minRow = (int) childLocation.getX();
newRows.add(minRow);
}
else if ((int) childLocation.getX() > maxRow) {
maxRow = (int) childLocation.getX();
newRows.add(maxRow);
}
if ((int) childLocation.getY() < minCol) {
minCol = (int) childLocation.getY();
newCols.add(minCol);
}
else if ((int) childLocation.getY() > maxCol) {
maxCol = (int) childLocation.getY();
newCols.add(maxCol);
}
HashSet<String> underlyingSpeciesIDs = new HashSet<String>();
HashSet<String> newGridSpeciesIDs = new HashSet<String>();
HashMap<String, String> newGridSpeciesIDToOldRowSubstring = new HashMap<String, String>();
HashMap<String, String> newGridSpeciesIDToOldColSubstring = new HashMap<String, String>();
HashMap<String, String> newGridSpeciesIDToNewRowSubstring = new HashMap<String, String>();
HashMap<String, String> newGridSpeciesIDToNewColSubstring = new HashMap<String, String>();
for (String speciesID : speciesIDSet) {
//find the grid species
if (speciesID.contains("ROW") && speciesID.contains("COL") && speciesID.contains("__")) {
underlyingSpeciesIDs.add(speciesID.split("__")[1]);
}
}
//if there are new rows or cols added to the grid
//add new grid species
if (newRows.size() > 0) {
for (int newRow : newRows) {
//create new grid species for this new row
for (int col = minCol; col <= maxCol; ++col) {
for (String underlyingSpeciesID : underlyingSpeciesIDs) {
String nonnegRow = Integer.toString(newRow);
String nonnegCol = Integer.toString(col);
if (newRow < 0)
nonnegRow = nonnegRow.replace("-", "_negative_");
if (col < 0)
nonnegCol = nonnegCol.replace("-", "_negative_");
String newID = "ROW" + nonnegRow + "_COL" + nonnegCol + "__" + underlyingSpeciesID;
String newIDWithNegatives = "ROW" + newRow + "_COL" + col + "__" + underlyingSpeciesID;
if (model.getSpecies(newID) != null)
continue;
newGridSpeciesIDs.add(newIDWithNegatives);
newGridSpeciesIDToOldRowSubstring.put(newIDWithNegatives, "ROW" + newRow);
newGridSpeciesIDToOldColSubstring.put(newIDWithNegatives, "COL" + col);
newGridSpeciesIDToNewRowSubstring.put(newIDWithNegatives, "ROW" + nonnegRow);
newGridSpeciesIDToNewColSubstring.put(newIDWithNegatives, "COL" + nonnegCol);
Species gridSpecies = null;
//find a grid species to take values from
for (Species species : model.getListOfSpecies()) {
if (species.getId().contains("__" + underlyingSpeciesID) && species.getId().contains("ROW")
&& species.getId().contains("COL"))
gridSpecies = species;
}
Species newSpecies = gridSpecies.clone();
newSpecies.setId(newID);
newSpecies.setMetaId(newID);
//add new grid species to the model (so that altering the kinetic law through jsbml can work)
model.addSpecies(newSpecies);
//add a new species to the simulation data structures
setupSingleSpecies(gridSpecies, newIDWithNegatives);
variableToValueMap.put(newID.replace("_negative_","-"), 0);
speciesToAffectedReactionSetMap.put(newID.replace("_negative_","-"), new HashSet<String>());
}
}
}
}
if (newCols.size() > 0) {
for (int newCol : newCols) {
//create new grid species for this new col
for (int row = minRow; row <= maxRow; ++row) {
for (String underlyingSpeciesID : underlyingSpeciesIDs) {
String nonnegRow = Integer.toString(row);
String nonnegCol = Integer.toString(newCol);
if (row < 0)
nonnegRow = nonnegRow.replace("-", "_negative_");
if (newCol < 0)
nonnegCol = nonnegCol.replace("-", "_negative_");
String newID = "ROW" + nonnegRow + "_COL" + nonnegCol + "__" + underlyingSpeciesID;
String newIDWithNegatives = "ROW" + row + "_COL" + newCol + "__" + underlyingSpeciesID;
newGridSpeciesIDs.add(newIDWithNegatives);
newGridSpeciesIDToOldRowSubstring.put(newIDWithNegatives, "ROW" + row);
newGridSpeciesIDToOldColSubstring.put(newIDWithNegatives, "COL" + newCol);
newGridSpeciesIDToNewRowSubstring.put(newIDWithNegatives, "ROW" + nonnegRow);
newGridSpeciesIDToNewColSubstring.put(newIDWithNegatives, "COL" + nonnegCol);
if (model.getSpecies(newID) != null)
continue;
Species gridSpecies = null;
//find a grid species to take values from
for (Species species : model.getListOfSpecies()) {
if (species.getId().contains("__" + underlyingSpeciesID) && species.getId().contains("ROW")
&& species.getId().contains("COL"))
gridSpecies = species;
}
Species newSpecies = gridSpecies.clone();
newSpecies.setId(newID);
newSpecies.setMetaId(newID);
//add new grid species to the model (so that altering the kinetic law through jsbml can work)
model.addSpecies(newSpecies);
//add a new species to the simulation data structures
setupSingleSpecies(gridSpecies, newIDWithNegatives);
variableToValueMap.put(newID.replace("_negative_","-"), 0);
speciesToAffectedReactionSetMap.put(newID.replace("_negative_","-"), new HashSet<String>());
}
}
}
}
//create new grid diffusion and degradation reactions for the new grid species
for (String speciesID : newGridSpeciesIDs) {
String newGridSpeciesID = speciesID.replace(
newGridSpeciesIDToOldRowSubstring.get(speciesID), newGridSpeciesIDToNewRowSubstring.get(speciesID)).replace(
newGridSpeciesIDToOldColSubstring.get(speciesID), newGridSpeciesIDToNewColSubstring.get(speciesID));
String[] splitID = speciesID.split("_");
int row = Integer.valueOf(splitID[0].replace("ROW",""));
int col = Integer.valueOf(splitID[1].replace("COL",""));
ArrayList<Point> neighborLocations = new ArrayList<Point>();
neighborLocations.add(new Point(row+1,col)); //right
neighborLocations.add(new Point(row,col+1)); //below
neighborLocations.add(new Point(row-1,col)); //left
neighborLocations.add(new Point(row,col-1)); //above
String underlyingSpeciesID = speciesID.split("__")[1];
ASTNode newNode = new ASTNode();
//find a grid diffusion reaction with this underlying species to take values from
for (Map.Entry<String, ASTNode> reactionAndFormula : reactionToFormulaMap.entrySet()) {
String reactionID = reactionAndFormula.getKey();
if (reactionID.contains("Diffusion_" + underlyingSpeciesID + "_Below")
|| reactionID.contains("Diffusion_" + underlyingSpeciesID + "_Above")
|| reactionID.contains("Diffusion_" + underlyingSpeciesID + "_Left")
|| reactionID.contains("Diffusion_" + underlyingSpeciesID + "_Right")) {
newNode = reactionAndFormula.getValue().clone();
}
}
int directionIndex = 0;
for (Point neighborLocation : neighborLocations) {
int nRow = (int) neighborLocation.getX();
int nCol = (int) neighborLocation.getY();
String neighborID = "ROW" + nRow + "_COL" + nCol + "__" + underlyingSpeciesID;
String fdString = "", rvString = "";
switch (directionIndex) {
case 0: fdString = "Below"; rvString = "Above"; break;
case 1: fdString = "Right"; rvString = "Left"; break;
case 2: fdString = "Above"; rvString = "Below"; break;
case 3: fdString = "Left"; rvString = "Right"; break;
}
//make sure that the neighbor exists (ie, is a species contained on the current grid size)
if (speciesIDSet.contains(neighborID)) {
if (nRow < 0)
neighborID = neighborID.replace("ROW" + nRow, "ROW" + "_negative_" + (-1 * nRow));
if (nCol < 0)
neighborID = neighborID.replace("COL" + nCol, "COL" + "_negative_" + (-1 * nCol));
//create forward reaction (to the neighbor) if it doesn't exist already
if (reactionToPropensityMap.containsKey("ROW" + row + "_COL" + col
+ "_Diffusion_" + underlyingSpeciesID + "_" + fdString) == false) {
//alter kinetic law for forward reaction
newNode.getRightChild().setVariable(model.getSpecies(newGridSpeciesID));
String newReactionID = "ROW" + row + "_COL" + col + "_Diffusion_"
+ underlyingSpeciesID + "_" + fdString;
if (row < 0)
newReactionID = newReactionID.replace("ROW" + row, "ROW" + "_negative_" + (-1 * row));
if (col < 0)
newReactionID = newReactionID.replace("COL" + col, "COL" + "_negative_" + (-1 * col));
Reaction fdReaction = model.createReaction(newReactionID);
KineticLaw fdKineticLaw = model.createKineticLaw();
fdKineticLaw.setMath(newNode.clone());
fdReaction.setKineticLaw(fdKineticLaw);
if (model.getSpecies(newGridSpeciesID)!=null) {
SpeciesReference reactant = new SpeciesReference(model.getSpecies(newGridSpeciesID));
reactant.setStoichiometry(1);
fdReaction.addReactant(reactant);
}
if (model.getSpecies(neighborID)!=null) {
SpeciesReference product = new SpeciesReference(model.getSpecies(neighborID));
product.setStoichiometry(1);
fdReaction.addProduct(product);
}
setupLocalParameters(fdReaction.getKineticLaw(), fdReaction);
setupSingleReaction(fdReaction.getId(), fdReaction.getKineticLaw().getMath(), false,
fdReaction.getListOfReactants(), fdReaction.getListOfProducts(), fdReaction.getListOfModifiers());
}
//create the reverse reaction (from the neighbor) if it doesn't already exist
if (reactionToPropensityMap.containsKey("ROW" + nRow + "_COL" + nCol
+ "_Diffusion_" + underlyingSpeciesID + "_" + rvString) == false) {
//alter kinetic law for reverse reaction
newNode.getRightChild().setVariable(model.getSpecies(neighborID));
String newReactionID = "ROW" + nRow + "_COL" + nCol + "_Diffusion_"
+ underlyingSpeciesID + "_" + rvString;
if (nRow < 0)
newReactionID = newReactionID.replace("ROW" + nRow, "ROW" + "_negative_" + (-1 * nRow));
if (nCol < 0)
newReactionID = newReactionID.replace("COL" + nCol, "COL" + "_negative_" + (-1 * nCol));
//create reverse reaction
Reaction rvReaction = model.createReaction(newReactionID);
KineticLaw rvKineticLaw = model.createKineticLaw();
rvKineticLaw.setMath(newNode.clone());
rvReaction.setKineticLaw(rvKineticLaw);
if (model.getSpecies(neighborID)!=null) {
SpeciesReference reactant = new SpeciesReference(model.getSpecies(neighborID));
reactant.setStoichiometry(1);
rvReaction.addReactant(reactant);
}
if (model.getSpecies(newGridSpeciesID)!=null) {
SpeciesReference product = new SpeciesReference(model.getSpecies(newGridSpeciesID));
product.setStoichiometry(1);
rvReaction.addProduct(product);
}
setupLocalParameters(rvReaction.getKineticLaw(), rvReaction);
setupSingleReaction(rvReaction.getId(), rvReaction.getKineticLaw().getMath(), false,
rvReaction.getListOfReactants(), rvReaction.getListOfProducts(), rvReaction.getListOfModifiers());
}
}
++directionIndex;
}
ASTNode degradationNode = new ASTNode();
// for (Map.Entry<String, ASTNode> reactionAndFormula : reactionToFormulaMap.entrySet()) {
// String reactionID = reactionAndFormula.getKey();
Boolean isDegradable = false;
//create degradation reaction for each grid species
//find a grid degradation reaction to copy from
for (Map.Entry<String, ASTNode> reactionAndFormula : reactionToFormulaMap.entrySet()) {
String reactionID = reactionAndFormula.getKey();
if (reactionID.contains("Degradation_" + underlyingSpeciesID)) {
degradationNode = reactionAndFormula.getValue().clone();
degradationNode.getRightChild().setVariable(model.getSpecies(newGridSpeciesID));
isDegradable = true;
break;
}
}
if (isDegradable) {
String newDegReactionID = "ROW" + row + "_COL" + col + "_Degradation_" + underlyingSpeciesID;
if (row < 0)
newDegReactionID = newDegReactionID.replace("ROW" + row, "ROW" + "_negative_" + (-1 * row));
if (col < 0)
newDegReactionID = newDegReactionID.replace("COL" + col, "COL" + "_negative_" + (-1 * col));
if (reactionToPropensityMap.containsKey(newDegReactionID) == false) {
Reaction degReaction = model.createReaction(newDegReactionID);
KineticLaw degKineticLaw = model.createKineticLaw();
degKineticLaw.setMath(degradationNode.clone());
degReaction.setKineticLaw(degKineticLaw);
if (model.getSpecies(newGridSpeciesID)!=null) {
SpeciesReference reactant = new SpeciesReference(model.getSpecies(newGridSpeciesID));
reactant.setStoichiometry(1);
degReaction.addReactant(reactant);
}
setupLocalParameters(degReaction.getKineticLaw(), degReaction);
setupSingleReaction(degReaction.getId(), degReaction.getKineticLaw().getMath(), false,
degReaction.getListOfReactants(), degReaction.getListOfProducts(), degReaction.getListOfModifiers());
}
}
}
//MOVE MEMBRANE DIFFUSION REACTIONS FOR COMPONENTS THAT HAVE MOVED
if (locationsToMove.size() > 0) {
for (Point locationToMove : locationsToMove) {
//adjust these locations to their new, moved location
switch (direction) {
case 0: locationToMove.y -= 1; break;
case 1: locationToMove.y += 1; break;
case 2: locationToMove.x -= 1; break;
case 3: locationToMove.x += 1; break;
case 4: {locationToMove.x += 1; locationToMove.y -= 1; break;}
case 5: {locationToMove.x -= 1; locationToMove.y += 1; break;}
case 6: {locationToMove.x -= 1; locationToMove.y -= 1; break;}
case 7: {locationToMove.x += 1; locationToMove.y += 1; break;}
}
}
//find the membrane diffusion reactions for these moved components and alter it
for (String compID : componentToLocationMap.keySet()) {
int compX = (int) componentToLocationMap.get(compID).getX();
int compY = (int) componentToLocationMap.get(compID).getY();
for (Point locationToMove : locationsToMove) {
if (locationToMove.x == compX && locationToMove.y == compY) {
if (componentToReactionSetMap.get(compID)==null) continue;
for (String reactionID : componentToReactionSetMap.get(compID)) {
//only need to change the rv membrane diffusion reaction
if (reactionID.contains("MembraneDiffusion")) {
ASTNode formulaNode = reactionToFormulaMap.get(reactionID);
//the right child is the one to alter
ASTNode speciesNode = formulaNode.getRightChild();
Point oldLocation = (Point) locationToMove.clone();
switch (direction) {
case 0: oldLocation.y = locationToMove.y + 1; break;
case 1: oldLocation.y = locationToMove.y - 1; break;
case 2: oldLocation.x = locationToMove.x + 1; break;
case 3: oldLocation.x = locationToMove.x - 1; break;
case 4: {oldLocation.x = locationToMove.x - 1; oldLocation.y = locationToMove.y + 1; break;}
case 5: {oldLocation.x = locationToMove.x + 1; oldLocation.y = locationToMove.y - 1; break;}
case 6: {oldLocation.x = locationToMove.x + 1; oldLocation.y = locationToMove.y + 1; break;}
case 7: {oldLocation.x = locationToMove.x - 1; oldLocation.y = locationToMove.y - 1; break;}
}
String oldRowCol = "ROW" + (int) oldLocation.x + "_COL" + (int) oldLocation.y;
oldRowCol = oldRowCol.replace("ROW-", "ROW_negative_");
oldRowCol = oldRowCol.replace("COL-", "COL_negative_");
String newRowCol = "ROW" + (int) locationToMove.x + "_COL" + (int) locationToMove.y;
newRowCol = newRowCol.replace("ROW-", "ROW_negative_");
newRowCol = newRowCol.replace("COL-", "COL_negative_");
//adjust kinetic law
speciesNode.setVariable(model.getSpecies(speciesNode.getName().replace(oldRowCol, newRowCol)));
newRowCol = newRowCol.replace("ROW_negative_", "ROW-");
newRowCol = newRowCol.replace("COL_negative_", "COL-");
oldRowCol = oldRowCol.replace("ROW_negative_", "ROW-");
oldRowCol = oldRowCol.replace("COL_negative_", "COL-");
//adjust reactants/products
for (StringDoublePair speciesAndStoichiometry :
reactionToSpeciesAndStoichiometrySetMap.get(reactionID)) {
speciesAndStoichiometry.string =
speciesAndStoichiometry.string.replace(oldRowCol, newRowCol);
}
for (StringDoublePair reactantAndStoichiometry :
reactionToReactantStoichiometrySetMap.get(reactionID)) {
reactantAndStoichiometry.string =
reactantAndStoichiometry.string.replace(oldRowCol, newRowCol);
}
//remove the old, now out-dated species to affected reaction pairs
//put in the new up-to-date pairs
for (String speciesID : speciesToAffectedReactionSetMap.keySet()) {
if (speciesID.contains(oldRowCol + "_")) {
HashSet<String> reactionsToRemove = new HashSet<String>();
for (String reaction : speciesToAffectedReactionSetMap.get(speciesID)) {
if (reaction.contains("MembraneDiffusion"))
reactionsToRemove.add(reaction);
}
for (String reactionToRemove : reactionsToRemove)
speciesToAffectedReactionSetMap.get(speciesID).remove(reactionToRemove);
}
if (speciesID.contains(newRowCol + "_")) {
speciesToAffectedReactionSetMap.get(speciesID).add(reactionID);
}
}
//adjust propensity
reactionsToAdjust.add(reactionID);
}
}
}
}
}
}
}
/**
* performs assignment rules that may have changed due to events or reactions firing
*
* @param affectedAssignmentRuleSet the set of assignment rules that have been affected
*/
protected HashSet<String> performAssignmentRules(HashSet<AssignmentRule> affectedAssignmentRuleSet) {
HashSet<String> affectedVariables = new HashSet<String>();
for (AssignmentRule assignmentRule : affectedAssignmentRuleSet) {
String variable = assignmentRule.getVariable();
//update the species count (but only if the species isn't constant) (bound cond is fine)
if (variableToIsConstantMap.containsKey(variable) && variableToIsConstantMap.get(variable) == false
|| variableToIsConstantMap.containsKey(variable) == false) {
if (speciesToHasOnlySubstanceUnitsMap.containsKey(variable) &&
speciesToHasOnlySubstanceUnitsMap.get(variable) == false) {
variableToValueMap.put(variable,
evaluateExpressionRecursive(assignmentRule.getMath()) *
variableToValueMap.get(speciesToCompartmentNameMap.get(variable)));
}
else {
variableToValueMap.put(variable, evaluateExpressionRecursive(assignmentRule.getMath()));
}
affectedVariables.add(variable);
}
}
return affectedVariables;
}
/**
* performs every rate rule using the current time step
*
* @param delta_t
* @return
*/
protected HashSet<String> performRateRules(double delta_t) {
HashSet<String> affectedVariables = new HashSet<String>();
for (Rule rule : model.getListOfRules()) {
if (rule.isRate()) {
RateRule rateRule = (RateRule) rule;
String variable = rateRule.getVariable();
//update the species count (but only if the species isn't constant) (bound cond is fine)
if (variableToIsConstantMap.containsKey(variable) && variableToIsConstantMap.get(variable) == false) {
if (speciesToHasOnlySubstanceUnitsMap.containsKey(variable) &&
speciesToHasOnlySubstanceUnitsMap.get(variable) == false) {
variableToValueMap.adjustValue(variable, delta_t * (
evaluateExpressionRecursive(rateRule.getMath()) *
variableToValueMap.get(speciesToCompartmentNameMap.get(variable))));
}
else {
variableToValueMap.adjustValue(variable,
delta_t * evaluateExpressionRecursive(rateRule.getMath()));
}
affectedVariables.add(variable);
}
}
}
return affectedVariables;
}
/**
* updates reactant/product species counts based on their stoichiometries
*
* @param selectedReactionID the reaction to perform
*/
protected void performReaction(String selectedReactionID, final boolean noAssignmentRulesFlag, final boolean noConstraintsFlag) {
//these are sets of things that need to be re-evaluated or tested due to the reaction firing
HashSet<AssignmentRule> affectedAssignmentRuleSet = new HashSet<AssignmentRule>();
HashSet<ASTNode> affectedConstraintSet = new HashSet<ASTNode>();
//loop through the reaction's reactants and products and update their amounts
for (StringDoublePair speciesAndStoichiometry : reactionToSpeciesAndStoichiometrySetMap.get(selectedReactionID)) {
double stoichiometry = speciesAndStoichiometry.doub;
String speciesID = speciesAndStoichiometry.string;
//this means the stoichiometry isn't constant, so look to the variableToValue map
if (reactionToNonconstantStoichiometriesSetMap.containsKey(selectedReactionID)) {
for (StringStringPair doubleID : reactionToNonconstantStoichiometriesSetMap.get(selectedReactionID)) {
//string1 is the species ID; string2 is the speciesReference ID
if (doubleID.string1.equals(speciesID)) {
stoichiometry = variableToValueMap.get(doubleID.string2);
//this is to get the plus/minus correct, as the variableToValueMap has
//a stoichiometry without the reactant/product plus/minus data
stoichiometry *= (int)(speciesAndStoichiometry.doub/Math.abs(speciesAndStoichiometry.doub));
break;
}
}
}
//update the species count if the species isn't a boundary condition or constant
//note that the stoichiometries are earlier modified with the correct +/- sign
if (speciesToIsBoundaryConditionMap.get(speciesID) == false &&
variableToIsConstantMap.get(speciesID) == false) {
if (speciesToConversionFactorMap.containsKey(speciesID)) {
variableToValueMap.adjustValue(speciesID, stoichiometry *
variableToValueMap.get(speciesToConversionFactorMap.get(speciesID)));
}
else {
variableToValueMap.adjustValue(speciesID, stoichiometry);
}
}
//if this variable that was just updated is part of an assignment rule (RHS)
//then re-evaluate that assignment rule
if (noAssignmentRulesFlag == false && variableToIsInAssignmentRuleMap.get(speciesID) == true)
affectedAssignmentRuleSet.addAll(variableToAffectedAssignmentRuleSetMap.get(speciesID));
if (noConstraintsFlag == false && variableToIsInConstraintMap.get(speciesID) == true)
affectedConstraintSet.addAll(variableToAffectedConstraintSetMap.get(speciesID));
}
if (affectedAssignmentRuleSet.size() > 0)
performAssignmentRules(affectedAssignmentRuleSet);
if (affectedConstraintSet.size() > 0) {
if (testConstraints(affectedConstraintSet) == false)
constraintFailureFlag = true;
}
}
/**
* recursively finds all variable nodes and prepends a string to the variable
* static version
*
* @param node
* @param toPrepend
*/
private static void prependToVariableNodes(ASTNode node, String toPrepend, Model model) {
if (node.isName()) {
//only prepend to species and parameters
if (model.getSpecies(toPrepend + node.getName()) != null)
node.setVariable(model.getSpecies(toPrepend + node.getName()));
else if (model.getParameter(toPrepend + node.getName()) != null)
node.setVariable(model.getParameter(toPrepend + node.getName()));
}
else {
for (ASTNode childNode : node.getChildren())
prependToVariableNodes(childNode, toPrepend, model);
}
}
/**
* appends the current species states to the TSD file
*
* @throws IOException
*/
protected void printToTSD(double printTime) throws IOException {
String commaSpace = "";
//dynamic printing requires re-printing the species values each time step
if (dynamicBoolean == true) {
bufferedTSDWriter.write("(\"time\"");
commaSpace = ", ";
//if there's an interesting species, only those get printed
if (interestingSpecies.size() > 0) {
for (String speciesID : interestingSpecies)
bufferedTSDWriter.write(commaSpace + "\"" + speciesID + "\"");
//always print compartment location IDs
for (String componentLocationID : componentToLocationMap.keySet()) {
String locationX = componentLocationID + "__locationX";
String locationY = componentLocationID + "__locationY";
bufferedTSDWriter.write(commaSpace + "\"" + locationX + "\", \"" + locationY + "\"");
}
}
else {
//print the species IDs
for (String speciesID : speciesIDSet)
bufferedTSDWriter.write(commaSpace + "\"" + speciesID + "\"");
//print compartment location IDs
for (String componentLocationID : componentToLocationMap.keySet()) {
String locationX = componentLocationID + "__locationX";
String locationY = componentLocationID + "__locationY";
bufferedTSDWriter.write(commaSpace + "\"" + locationX + "\", \"" + locationY + "\"");
}
//print compartment IDs (for sizes)
for (String componentID : compartmentIDSet) {
try {
bufferedTSDWriter.write(", \"" + componentID + "\"");
} catch (IOException e) {
e.printStackTrace();
}
}
//print nonconstant parameter IDs
for (String parameterID : nonconstantParameterIDSet) {
try {
bufferedTSDWriter.write(", \"" + parameterID + "\"");
} catch (IOException e) {
e.printStackTrace();
}
}
}
bufferedTSDWriter.write("),\n");
}
bufferedTSDWriter.write("(");
commaSpace = "";
//print the current time
bufferedTSDWriter.write(printTime + ", ");
//if there's an interesting species, only those get printed
if (interestingSpecies.size() > 0) {
for (String speciesID : interestingSpecies) {
if (printConcentrations == true) {
bufferedTSDWriter.write(commaSpace +
(variableToValueMap.get(speciesID) / variableToValueMap.get(speciesToCompartmentNameMap.get(speciesID))));
}
else
bufferedTSDWriter.write(commaSpace + variableToValueMap.get(speciesID));
commaSpace = ", ";
}
//always print component location values
for (String componentID : componentToLocationMap.keySet()) {
bufferedTSDWriter.write(commaSpace + (int) componentToLocationMap.get(componentID).getX());
bufferedTSDWriter.write(commaSpace + (int) componentToLocationMap.get(componentID).getY());
}
}
else {
//loop through the speciesIDs and print their current value to the file
for (String speciesID : speciesIDSet) {
bufferedTSDWriter.write(commaSpace + variableToValueMap.get(speciesID));
commaSpace = ", ";
}
//print component location values
for (String componentID : componentToLocationMap.keySet()) {
bufferedTSDWriter.write(commaSpace + (int) componentToLocationMap.get(componentID).getX());
commaSpace = ", ";
bufferedTSDWriter.write(commaSpace + (int) componentToLocationMap.get(componentID).getY());
}
//print compartment sizes
for (String componentID : compartmentIDSet) {
bufferedTSDWriter.write(commaSpace + variableToValueMap.get(componentID));
commaSpace = ", ";
}
//print nonconstant parameter values
for (String parameterID : nonconstantParameterIDSet) {
bufferedTSDWriter.write(commaSpace + variableToValueMap.get(parameterID));
commaSpace = ", ";
}
}
bufferedTSDWriter.write(")");
bufferedTSDWriter.flush();
}
/**
* parses TSD files for all runs and prints mean and standard deviation TSDs
*
* @throws IOException
*/
protected void printStatisticsTSD() throws IOException {
//the last run is the number of runs
int numRuns = currentRun;
HashMap<String, ArrayList<DescriptiveStatistics> > speciesStatistics =
new HashMap<String, ArrayList<DescriptiveStatistics> >();
ArrayList<String> allSpecies = new ArrayList<String>();
HashSet<String> speciesSet = new HashSet<String>();
//if it's dynamic, we have to parse every run's file to get the full list of species
if (dynamicBoolean == true) {
for (int run = 1; run <= numRuns; ++run) {
DTSDParser dtsdParser = new DTSDParser(outputDirectory + "run-" + run + ".dtsd");
speciesSet.addAll(dtsdParser.getSpecies());
}
speciesSet.remove("time");
allSpecies.add("time");
allSpecies.addAll(speciesSet);
}
//store the TSD data for analysis
for (int run = 1; run <= numRuns; ++run) {
DTSDParser dtsdParser = null;
TSDParser tsdParser = null;
HashMap<String, ArrayList<Double> > runStatistics = null;
if (dynamicBoolean == true) {
dtsdParser = new DTSDParser(outputDirectory + "run-" + run + ".dtsd");
//allSpecies = dtsdParser.getSpecies();
runStatistics = dtsdParser.getHashMap(allSpecies);
}
else {
tsdParser = new TSDParser(outputDirectory + "run-" + run + ".tsd", false);
allSpecies = tsdParser.getSpecies();
runStatistics = tsdParser.getHashMap();
}
for (int speciesIndex = 0; speciesIndex < allSpecies.size(); ++speciesIndex) {
String species = allSpecies.get(speciesIndex);
for (int index = 0; index < runStatistics.get(species).size(); ++index) {
Double speciesData = runStatistics.get(species).get(index);
if (speciesStatistics.size() <= speciesIndex)
speciesStatistics.put(species, new ArrayList<DescriptiveStatistics>());
if (speciesStatistics.get(species).size() <= index)
speciesStatistics.get(species).add(new DescriptiveStatistics());
speciesStatistics.get(species).get(index).addValue(speciesData.doubleValue());
}
}
}
DataParser statsParser = new DataParser(null, null);
ArrayList<ArrayList<Double> > meanTSDData = new ArrayList<ArrayList<Double> >();
//calculate and print the mean tsd
for (String species : allSpecies) {
ArrayList<Double> speciesData = new ArrayList<Double>();
for (int index = 0; index < speciesStatistics.get(species).size(); ++index)
speciesData.add(speciesStatistics.get(species).get(index).getMean());
meanTSDData.add(speciesData);
}
statsParser.setData(meanTSDData);
statsParser.setSpecies(allSpecies);
statsParser.outputTSD(outputDirectory + "mean.tsd");
//calculate and print the standard deviation tsd
ArrayList<ArrayList<Double> > standardDeviationTSDData = new ArrayList<ArrayList<Double> >();
for (String species : allSpecies) {
ArrayList<Double> speciesData = new ArrayList<Double>();
if (species.equals("time")) {
for (int index = 0; index < speciesStatistics.get(species).size(); ++index)
speciesData.add(speciesStatistics.get(species).get(index).getMean());
}
else {
for (int index = 0; index < speciesStatistics.get(species).size(); ++index)
speciesData.add(speciesStatistics.get(species).get(index).getStandardDeviation());
}
standardDeviationTSDData.add(speciesData);
}
statsParser.setData(standardDeviationTSDData);
statsParser.setSpecies(allSpecies);
statsParser.outputTSD(outputDirectory + "standard_deviation.tsd");
//calculate and print the variance tsd
ArrayList<ArrayList<Double> > varianceTSDData = new ArrayList<ArrayList<Double> >();
for (String species : allSpecies) {
ArrayList<Double> speciesData = new ArrayList<Double>();
if (species.equals("time")) {
for (int index = 0; index < speciesStatistics.get(species).size(); ++index)
speciesData.add(speciesStatistics.get(species).get(index).getMean());
}
else {
for (int index = 0; index < speciesStatistics.get(species).size(); ++index)
speciesData.add(speciesStatistics.get(species).get(index).getVariance());
}
varianceTSDData.add(speciesData);
}
statsParser.setData(varianceTSDData);
statsParser.setSpecies(allSpecies);
statsParser.outputTSD(outputDirectory + "variance.tsd");
}
/**
* reverts the model back to its pre-dynamic state
* (during duplication events, the model is altered because of jsbml restrictions)
*/
protected void resetModel() {
model.setListOfSpecies(initialSpecies.clone());
model.setListOfReactions(initialReactions.clone());
model.setListOfEvents(initialEvents.clone());
model.setListOfParameters(initialParameters.clone());
model.setListOfCompartments(initialCompartments.clone());
}
/**
* non-static version of the method that flattens arrays into the sbml model
* this one doesn't print the model back out, though
*/
protected void setupArrays() {
boolean arraysExist = false;
//ARRAYED SPECIES BUSINESS
//create all new species that are implicit in the arrays and put them into the model
ArrayList<Species> speciesToAdd = new ArrayList<Species>();
ArrayList<String> speciesToRemove = new ArrayList<String>();
HashMap<String, Boolean> speciesToIsArrayedMap = new HashMap<String, Boolean>();
HashMap<String, SpeciesDimensions> arrayedSpeciesToDimensionsMap =
new HashMap<String, SpeciesDimensions>();
for (Species species : model.getListOfSpecies()) {
String speciesID = species.getId();
//check to see if the species is arrayed
if (stripAnnotation(species.getAnnotationString()).contains("array:array")) {
arraysExist = true;
speciesToIsArrayedMap.put(speciesID, true);
speciesToRemove.add(speciesID);
int numRowsLower = 0;
int numColsLower = 0;
int numRowsUpper = 0;
int numColsUpper = 0;
String[] annotationString = stripAnnotation(species.getAnnotationString()).split("=");
numColsLower = Integer.valueOf(((String[])(annotationString[1].split(" ")))[0].replace("\"",""));
numColsUpper = Integer.valueOf(((String[])(annotationString[2].split(" ")))[0].replace("\"",""));
numRowsLower = Integer.valueOf(((String[])(annotationString[3].split(" ")))[0].replace("\"",""));
numRowsUpper = Integer.valueOf(((String[])(annotationString[4].split(" ")))[0].replace("\"",""));
SpeciesDimensions speciesDimensions =
new SpeciesDimensions(numRowsLower, numRowsUpper, numColsLower, numColsUpper);
arrayedSpeciesToDimensionsMap.put(speciesID, speciesDimensions);
//loop through all species in the array
//prepend the row/col information to create a new ID
for (int row = numRowsLower; row <= numRowsUpper; ++row) {
for (int col = numColsLower; col <= numColsUpper; ++col) {
speciesID = "ROW" + row + "_COL" + col + "__" + species.getId();
Species newSpecies = new Species();
newSpecies = species.clone();
newSpecies.setMetaId(speciesID);
newSpecies.setId(speciesID);
newSpecies.setAnnotation(new Annotation());
speciesToAdd.add(newSpecies);
}
}
}
else
speciesToIsArrayedMap.put(speciesID, false);
} //end species for loop
//add new row/col species to the model
for (Species species : speciesToAdd) {
model.addSpecies(species);
}
//ARRAYED EVENTS BUSINESS
ArrayList<String> eventsToRemove = new ArrayList<String>();
ArrayList<Event> eventsToAdd = new ArrayList<Event>();
for (Event event : model.getListOfEvents()) {
if (stripAnnotation(event.getAnnotationString()).contains("array")) {
arraysExist = true;
eventsToRemove.add(event.getId());
String annotationString = stripAnnotation(event.getAnnotationString()).replace("<annotation>","").
replace("</annotation>","").replace("\"","");
String[] splitAnnotation = annotationString.split("array:");
ArrayList<String> eventCompartments = new ArrayList<String>();
splitAnnotation[splitAnnotation.length - 2] = ((String[])splitAnnotation[splitAnnotation.length - 2].split("xmlns:"))[0];
for (int i = 2; i < splitAnnotation.length; ++i) {
String compartmentID = ((String[])splitAnnotation[i].split("="))[0];
eventCompartments.add(compartmentID);
}
//loop through all compartments and create an event for each one
for (String compartmentID : eventCompartments) {
Event newEvent = new Event();
newEvent.setVersion(event.getVersion());
newEvent.setLevel(event.getLevel());
newEvent.setId(compartmentID + "__" + event.getId());
newEvent.setMetaId(compartmentID + "__" + event.getId());
event.getTrigger().getMath().updateVariables();
newEvent.setTrigger(event.getTrigger().clone());
//at this point, the formula has something like neighborQuantity(Species1)
//this needs to become neighborQuantity(Species1, CompartmentLocationX(Comp1), CompartmentLocationY(Comp1))
if (newEvent.getTrigger().getMath().toFormula().contains("neighborQuantity")) {
String triggerMath = newEvent.getTrigger().getMath().toFormula();
ArrayList<ASTNode> nqNodes = new ArrayList<ASTNode>();
this.getSatisfyingNodesLax(newEvent.getTrigger().getMath(), "neighborQuantity", nqNodes);
//loop through all neighbor quantity nodes in the trigger formula
for (ASTNode nqNode : nqNodes) {
String direction = "";
if (triggerMath.contains("QuantityLeft"))
direction = "Left";
else if (triggerMath.contains("QuantityRight"))
direction = "Right";
else if (triggerMath.contains("QuantityAbove"))
direction = "Above";
else
direction = "Below";
String speciesID = nqNode.toFormula().split(
"neighborQuantity" + direction)[1].replace("(","").replace(")","");
try {
ASTNode newFormula = ASTNode.parseFormula(
"neighborQuantity" + direction + "Full(" + compartmentID + "__" + speciesID +
", getCompartmentLocationX(" + compartmentID + "__Cell" +
"), getCompartmentLocationY(" + compartmentID + "__Cell" + "))");
for (int i = 0; i < ((ASTNode) nqNode.getParent()).getChildCount(); ++i) {
if (((ASTNode) nqNode.getParent().getChildAt(i)).isFunction() &&
((ASTNode) nqNode.getParent().getChildAt(i)).getVariable().toString()
.contains("neighborQuantity" + direction)) {
((ASTNode) nqNode.getParent()).replaceChild(i, newFormula);
break;
}
}
} catch (ParseException e) {
e.printStackTrace();
}
}
}
if (event.isSetPriority())
newEvent.setPriority(event.getPriority().clone());
if (event.isSetDelay())
newEvent.setDelay(event.getDelay().clone());
newEvent.setUseValuesFromTriggerTime(event.getUseValuesFromTriggerTime());
for (EventAssignment eventAssignment : event.getListOfEventAssignments()) {
EventAssignment ea = eventAssignment.clone();
ea.setMath(eventAssignment.getMath().clone());
ea.setVariable(eventAssignment.getVariable());
newEvent.addEventAssignment(ea);
}
for (EventAssignment eventAssignment : newEvent.getListOfEventAssignments()) {
eventAssignment.setVariable(compartmentID + "__" + eventAssignment.getVariable());
//prepends the compartment ID to all variables in the event assignment
prependToVariableNodes(eventAssignment.getMath(), compartmentID + "__", model);
}
eventsToAdd.add(newEvent);
}
}
}
for (Event eventToAdd : eventsToAdd) {
model.addEvent(eventToAdd);
}
//ARRAYED REACTION BUSINESS
//if a reaction has arrayed species
//new reactions that are implicit are created and added to the model
ArrayList<Reaction> reactionsToAdd = new ArrayList<Reaction>();
ArrayList<String> reactionsToRemove = new ArrayList<String>();
for (Reaction reaction : model.getListOfReactions()) {
String reactionID = reaction.getId();
ArrayList<Integer> membraneDiffusionRows = new ArrayList<Integer>();
ArrayList<Integer> membraneDiffusionCols = new ArrayList<Integer>();
ArrayList<String> membraneDiffusionCompartments = new ArrayList<String>();
//MEMBRANE DIFFUSION REACTIONS
//if it's a membrane diffusion reaction it'll have the appropriate locations as an annotation
//so parse them and store them in the above arraylists
if (reactionID.contains("MembraneDiffusion")) {
arraysExist = true;
String annotationString = stripAnnotation(reaction.getAnnotationString()).replace("<annotation>","").
replace("</annotation>","").replace("\"","");
String[] splitAnnotation = annotationString.split("array:");
if (splitAnnotation.length <= 1) {
continue;
}
splitAnnotation[splitAnnotation.length - 2] = ((String[])splitAnnotation[splitAnnotation.length - 2].split("xmlns:"))[0];
for (int i = 2; i < splitAnnotation.length; ++i) {
String compartmentID = ((String[])splitAnnotation[i].split("="))[0];
String row = ((String[])((String[])splitAnnotation[i].split(" ")[0].split("="))[1].split(","))[0].replace("(","");
String col = ((String[])((String[])splitAnnotation[i].split(" ")[0].split("="))[1].split(","))[1].replace(")","");
membraneDiffusionRows.add(Integer.valueOf(row.trim()));
membraneDiffusionCols.add(Integer.valueOf(col.trim()));
membraneDiffusionCompartments.add(compartmentID);
}
int membraneDiffusionIndex = 0;
reactionsToRemove.add(reaction.getId());
reaction.setAnnotation(new Annotation());
//loop through all appropriate row/col pairs and create a membrane diffusion reaction for each one
for (String compartmentID : membraneDiffusionCompartments) {
int row = membraneDiffusionRows.get(membraneDiffusionIndex);
int col = membraneDiffusionCols.get(membraneDiffusionIndex);
//create a new reaction and set the ID
Reaction newReaction = new Reaction();
newReaction = reaction.clone();
newReaction.setListOfReactants(new ListOf<SpeciesReference>());
newReaction.setListOfProducts(new ListOf<SpeciesReference>());
newReaction.setListOfModifiers(new ListOf<ModifierSpeciesReference>());
newReaction.setId(compartmentID + "__" + reactionID);
newReaction.setMetaId(compartmentID + "__" + reactionID);
newReaction.setReversible(true);
newReaction.setFast(false);
newReaction.setCompartment(reaction.getCompartment());
//alter the kinetic law to so that it has the correct indexes as children for the
//get2DArrayElement function
//get the nodes to alter (that are arguments for the get2DArrayElement method)
ArrayList<ASTNode> get2DArrayElementNodes = new ArrayList<ASTNode>();
getSatisfyingNodes(newReaction.getKineticLaw().getMath(),
"get2DArrayElement", get2DArrayElementNodes);
boolean reactantBool = false;
//replace the get2darrayelement stuff with the proper explicit species/parameters
for (ASTNode node : get2DArrayElementNodes) {
if (node.getLeftChild().getName().contains("kmdiff")) {
String parameterName = node.getLeftChild().getName();
//see if the species-specific one exists
//if it doesn't, use the default
//you'll need to parse the species name from the reaction id, probably
String speciesID = reactionID.replace("MembraneDiffusion_","");
if (model.getParameter(compartmentID + "__" + speciesID + "__" + parameterName) == null)
node.setVariable(model.getParameter(parameterName));
else
node.setVariable(model.getParameter(compartmentID + "__" + speciesID + "__" + parameterName));
for (int i = 0; i < node.getChildCount(); ++i)
node.removeChild(i);
for (int i = 0; i < node.getChildCount(); ++i)
node.removeChild(i);
}
//this means it's a species, which we need to prepend with the row/col prefix
else {
if (node.getChildCount() > 0 &&
model.getParameter(node.getLeftChild().getName()) == null) {
//reactant
if (reactantBool == true) {
node.setVariable(model.getSpecies(
"ROW" + row + "_COL" + col + "__" + node.getLeftChild().getName()));
}
//product
else {
node.setVariable(model.getSpecies(
compartmentID + "__" + node.getLeftChild().getName()));
reactantBool = true;
}
}
for (int i = 0; i < node.getChildCount(); ++i)
node.removeChild(i);
for (int i = 0; i < node.getChildCount(); ++i)
node.removeChild(i);
}
}
//loop through reactants
for (SpeciesReference reactant : reaction.getListOfReactants()) {
//create a new reactant and add it to the new reaction
SpeciesReference newReactant = new SpeciesReference();
newReactant = reactant.clone();
newReactant.setSpecies(compartmentID + "__" + newReactant.getSpecies());
newReactant.setAnnotation(new Annotation());
newReaction.addReactant(newReactant);
}
//loop through products
for (SpeciesReference product : reaction.getListOfProducts()) {
//create a new reactant and add it to the new reaction
SpeciesReference newProduct = new SpeciesReference();
newProduct = product.clone();
newProduct.setSpecies("ROW" + row + "_COL" + col + "__" + newProduct.getSpecies());
newProduct.setAnnotation(new Annotation());
newReaction.addProduct(newProduct);
}
boolean i = false, j = false;
for (LocalParameter lp : newReaction.getKineticLaw().getListOfLocalParameters()) {
if (lp.getId().equals("i"))
i = true;
else if (lp.getId().equals("j"))
j = true;
}
if (i)
newReaction.getKineticLaw().getListOfLocalParameters().remove("i");
if (j)
newReaction.getKineticLaw().getListOfLocalParameters().remove("j");
reactionsToAdd.add(newReaction);
++membraneDiffusionIndex;
}
} //end if membrane diffusion
//NON-MEMBRANE DIFFUSION REACTIONS
//check to see if the (non-membrane-diffusion) reaction has arrayed species
//right now i'm only checking the first reactant species, due to a bad assumption
//about the homogeneity of the arrayed reaction (ie, if one species is arrayed, they all are)
else if (reaction.getNumReactants() > 0 &&
speciesToIsArrayedMap.get(reaction.getReactant(0).getSpeciesInstance().getId()) == true) {
arraysExist = true;
reactionsToRemove.add(reaction.getId());
//get the reactant dimensions, which tells us how many new reactions are going to be created
SpeciesDimensions reactantDimensions =
arrayedSpeciesToDimensionsMap.get(reaction.getReactant(0).getSpeciesInstance().getId());
boolean abort = false;
//loop through all of the new formerly-implicit reactants
for (int row = reactantDimensions.numRowsLower; row <= reactantDimensions.numRowsUpper; ++row) {
for (int col = reactantDimensions.numColsLower; col <= reactantDimensions.numColsUpper; ++col) {
//create a new reaction and set the ID
Reaction newReaction = new Reaction();
newReaction = reaction.clone();
newReaction.setListOfReactants(new ListOf<SpeciesReference>());
newReaction.setListOfProducts(new ListOf<SpeciesReference>());
newReaction.setListOfModifiers(new ListOf<ModifierSpeciesReference>());
newReaction.setId("ROW" + row + "_COL" + col + "_" + reactionID);
newReaction.setMetaId("ROW" + row + "_COL" + col + "_" + reactionID);
newReaction.setReversible(false);
newReaction.setFast(false);
newReaction.setCompartment(reaction.getCompartment());
//get the nodes to alter
ArrayList<ASTNode> get2DArrayElementNodes = new ArrayList<ASTNode>();
//return the head node of the get2DArrayElement function
getSatisfyingNodes(newReaction.getKineticLaw().getMath(),
"get2DArrayElement", get2DArrayElementNodes);
//loop through all reactants
for (SpeciesReference reactant : reaction.getListOfReactants()) {
//find offsets
//the row offset is in the kinetic law via i
//the col offset is in the kinetic law via j
int rowOffset = 0;
int colOffset = 0;
ASTNode reactantHeadNode = null;
//go through the get2DArrayElement nodes and find the one corresponding to the reactant
for (ASTNode headNode : get2DArrayElementNodes) {
//make sure it's a reactant node
if (headNode.getChildCount() > 0 &&
model.getParameter(headNode.getLeftChild().getName()) == null) {
reactantHeadNode = headNode;
break;
}
}
if (reactantHeadNode.getChild(1).getType().name().equals("PLUS"))
rowOffset = reactantHeadNode.getChild(1).getRightChild().getInteger();
else if (reactantHeadNode.getChild(1).getType().name().equals("MINUS"))
rowOffset = -1 * reactantHeadNode.getChild(1).getRightChild().getInteger();
if (reactantHeadNode.getChild(2).getType().name().equals("PLUS"))
colOffset = reactantHeadNode.getChild(2).getRightChild().getInteger();
else if (reactantHeadNode.getChild(2).getType().name().equals("MINUS"))
colOffset = -1 * reactantHeadNode.getChild(2).getRightChild().getInteger();
//create a new reactant and add it to the new reaction
SpeciesReference newReactant = new SpeciesReference();
newReactant = reactant.clone();
newReactant.setSpecies(model.getSpecies("ROW" + (row + rowOffset) + "_COL"
+ (col + colOffset) + "__" + newReactant.getSpecies()));
newReactant.setAnnotation(new Annotation());
newReaction.addReactant(newReactant);
//put this reactant in place of the get2DArrayElement function call
for (int i = 0; i < reactantHeadNode.getChildCount(); ++i)
reactantHeadNode.removeChild(i);
for (int i = 0; i < reactantHeadNode.getChildCount(); ++i)
reactantHeadNode.removeChild(i);
reactantHeadNode.setVariable(model.getSpecies(newReactant.getSpecies()));
}// end looping through reactants
//loop through all modifiers
//for (ModifierSpeciesReference modifier : reaction.getListOfModifiers()) {
//loop through all products
for (SpeciesReference product : reaction.getListOfProducts()) {
//find offsets
int rowOffset = 0;
int colOffset = 0;
ASTNode productHeadNode = null;
//go through the get2DArrayElement nodes and find the one corresponding to the product
for (ASTNode headNode : get2DArrayElementNodes) {
//make sure it's a product node
//only the product has children, as the reactant's children get deleted
if (headNode.getChildCount() > 0 &&
model.getParameter(headNode.getLeftChild().getName()) == null) {
productHeadNode = headNode;
break;
}
}
if (productHeadNode.getChild(1).getType().name().equals("PLUS"))
rowOffset = productHeadNode.getChild(1).getRightChild().getInteger();
else if (productHeadNode.getChild(1).getType().name().equals("MINUS"))
rowOffset = -1 * productHeadNode.getChild(1).getRightChild().getInteger();
if (productHeadNode.getChild(2).getType().name().equals("PLUS"))
colOffset = productHeadNode.getChild(2).getRightChild().getInteger();
else if (productHeadNode.getChild(2).getType().name().equals("MINUS"))
colOffset = -1 * productHeadNode.getChild(2).getRightChild().getInteger();
//don't create reactions with products that don't exist
if (row + rowOffset < reactantDimensions.numRowsLower ||
col + colOffset < reactantDimensions.numColsLower ||
row + rowOffset > reactantDimensions.numRowsUpper ||
col + colOffset > reactantDimensions.numColsUpper) {
abort = true;
break;
}
//create a new product and add it to the new reaction
SpeciesReference newProduct = new SpeciesReference();
newProduct = product.clone();
newProduct.setSpecies(model.getSpecies("ROW" + (row + rowOffset) + "_COL"
+ (col + colOffset) + "__" + newProduct.getSpecies()));
newProduct.setAnnotation(new Annotation());
newReaction.addProduct(newProduct);
//put this reactant in place of the get2DArrayElement function call
for (int i = 0; i < productHeadNode.getChildCount(); ++i)
productHeadNode.removeChild(i);
//put this reactant in place of the get2DArrayElement function call
for (int i = 0; i < productHeadNode.getChildCount(); ++i)
productHeadNode.removeChild(i);
productHeadNode.setVariable(model.getSpecies(newProduct.getSpecies()));
} //end looping through products
if (abort == false) {
boolean i = false, j = false;
//checking for these local parameters using getLocalParameters() doesn't seem to work
for (LocalParameter lp : newReaction.getKineticLaw().getListOfLocalParameters()) {
if (lp.getId().equals("i"))
i = true;
else if (lp.getId().equals("j"))
j = true;
}
if (i)
newReaction.getKineticLaw().getListOfLocalParameters().remove("i");
if (j)
newReaction.getKineticLaw().getListOfLocalParameters().remove("j");
//this isn't a reversible reaction; only take the left side
if (newReaction.getId().contains("Degradation") == false) {
newReaction.getKineticLaw().setMath(newReaction.getKineticLaw().getMath().getLeftChild());
}
reactionsToAdd.add(newReaction);
}
else
abort = false;
}
}
}
}// end looping through reactions
//add in the new explicit array reactions
for (Reaction reactionToAdd : reactionsToAdd) {
reactionToAdd.setMetaId(reactionToAdd.getId());
if (model.getReaction(reactionToAdd.getId())!=null) {
model.removeReaction(reactionToAdd.getId());
}
model.addReaction(reactionToAdd);
}
ListOf<Reaction> allReactions = model.getListOfReactions();
//remove original array reaction(s)
for (String reactionToRemove : reactionsToRemove)
allReactions.remove(reactionToRemove);
model.setListOfReactions(allReactions);
ListOf<Species> allSpecies = model.getListOfSpecies();
//remove the original array species from the model
for (String speciesID : speciesToRemove)
allSpecies.remove(speciesID);
model.setListOfSpecies(allSpecies);
ListOf<Event> allEvents = model.getListOfEvents();
//remove original array event(s)
for (String eventID : eventsToRemove)
allEvents.remove(eventID);
model.setListOfEvents(allEvents);
ArrayList<String> parametersToRemove = new ArrayList<String>();
//get rid of the locations parameters
for (Parameter parameter : model.getListOfParameters()) {
if (parameter.getId().contains("_locations")) {
if (parameter.getId().contains("_locations"))
this.submodelIDToLocationsMap.put(
parameter.getId().replace("__locations",""), stripAnnotation(parameter.getAnnotationString()));
parametersToRemove.add(parameter.getId());
}
}
for (String parameterID : parametersToRemove)
model.removeParameter(parameterID);
if (arraysExist) {
SBMLWriter writer = new SBMLWriter();
PrintStream p;
try {
p = new PrintStream(new FileOutputStream(SBMLFileName), true, "UTF-8");
p.print(writer.writeSBMLToString(model.getSBMLDocument()));
} catch (Exception e) {
e.printStackTrace();
}
}
}
/**
* creates hashmaps for representing and keeping track of a grid (of cells)
*/
protected void setupGrid() {
//go through all reaction IDs and group them by compartment ID
for (String reactionID : reactionToPropensityMap.keySet()) {
if (reactionID.contains("__") == false)
continue;
//this will leave us with compartmentID or stuff_compartmentID
String componentID = ((String[])reactionID.split("__"))[0];
//if there's an underscore, remove everything before it to leave the compartmentID
String[] splitReactionID = componentID.split("_");
componentID = splitReactionID[splitReactionID.length - 1];
//the location of the component can be parsed from the membrane diffusion reaction product
if (reactionID.contains("MembraneDiffusion")) {
String productID = "";
for (StringDoublePair sdp : reactionToSpeciesAndStoichiometrySetMap.get(reactionID)) {
if (sdp.string.contains("ROW") && sdp.string.contains("COL"))
productID = sdp.string;
}
String[] locationInfo =
((String[])productID.split("__"))[0].split("_");
int row, col;
if (locationInfo[0].length() <= 0) {
row = 0; col = 0;
}
else {
row = Integer.valueOf(locationInfo[0].replace("ROW",""));
col = Integer.valueOf(locationInfo[1].replace("COL",""));
}
componentToLocationMap.put(componentID, new Point(row, col));
}
if (componentToReactionSetMap.containsKey(componentID) == false)
componentToReactionSetMap.put(componentID, new HashSet<String>());
componentToReactionSetMap.get(componentID).add(reactionID);
}
//go through the species and parameters and group them by compartment ID
for (String variableID : variableToValueMap.keySet()) {
if (variableID.contains("__") == false)
continue;
//this will leave us with compartmentID or stuff_compartmentID
String componentID = ((String[])variableID.split("__"))[0];
//if there's an underscore, remove everything before it to leave the compartmentID
String[] splitVariableID = componentID.split("_");
componentID = splitVariableID[splitVariableID.length - 1];
if (componentToVariableSetMap.containsKey(componentID) == false)
componentToVariableSetMap.put(componentID, new HashSet<String>());
componentToVariableSetMap.get(componentID).add(variableID);
}
//go through events and group them by compartment ID
if (eventToDelayMap != null) {
for (String eventID : eventToDelayMap.keySet()) {
if (eventID.contains("__") == false)
continue;
String componentID = ((String[])eventID.split("__"))[0];
//if there's an underscore, remove everything before it to leave the compartmentID
String[] splitEventID = componentID.split("_");
componentID = splitEventID[splitEventID.length - 1];
componentIDSet.add(componentID);
if (componentToEventSetMap.containsKey(componentID) == false)
componentToEventSetMap.put(componentID, new HashSet<String>());
componentToEventSetMap.get(componentID).add(eventID);
}
}
//if the location information couldn't be parsed from membrane diffusion reactions
//(ie, if there aren't any membrane diffusion reactions)
if (componentToLocationMap.size() < componentToVariableSetMap.size()) {
for (String annotationString : this.submodelIDToLocationsMap.values()) {
annotationString = annotationString.replace("<annotation>","").
replace("</annotation>","").replace("\"","");
String[] splitAnnotation = annotationString.split("array:");
splitAnnotation[splitAnnotation.length - 2] = ((String[])splitAnnotation[splitAnnotation.length - 2].split("xmlns:"))[0];
for (int i = 2; i < splitAnnotation.length; ++i) {
String compartmentID = ((String[])splitAnnotation[i].split("="))[0];
String row = ((String[])((String[])splitAnnotation[i].split(" ")[0].split("="))[1].split(","))[0].replace("(","");
String col = ((String[])((String[])splitAnnotation[i].split(" ")[0].split("="))[1].split(","))[1].replace(")","");
componentToLocationMap.put(compartmentID, new Point(Integer.valueOf(row.trim()), Integer.valueOf(col.trim())));
}
}
}
}
/**
* sets up a single species
*
* @param species
* @param speciesID
*/
private void setupSingleSpecies(Species species, String speciesID) {
speciesID = speciesID.replace("_negative_", "-");
if (speciesIDSet.contains(speciesID))
return;
if (species.isSetInitialAmount())
variableToValueMap.put(speciesID, species.getInitialAmount());
else if (species.isSetInitialConcentration()) {
variableToValueMap.put(speciesID, species.getInitialConcentration()
* species.getCompartmentInstance().getSize());
}
if (species.getConversionFactor() != null)
speciesToConversionFactorMap.put(speciesID, species.getConversionFactor());
if (numRules > 0)
variableToIsInAssignmentRuleMap.put(speciesID, false);
if (numConstraints > 0)
variableToIsInConstraintMap.put(speciesID, false);
if (species.hasOnlySubstanceUnits() == false) {
speciesToCompartmentSizeMap.put(speciesID, species.getCompartmentInstance().getSize());
speciesToCompartmentNameMap.put(speciesID, species.getCompartment());
if (Double.isNaN(species.getCompartmentInstance().getSize()))
speciesToCompartmentSizeMap.put(speciesID, 1.0);
}
speciesToAffectedReactionSetMap.put(speciesID, new HashSet<String>(20));
speciesToIsBoundaryConditionMap.put(speciesID, species.isBoundaryCondition());
variableToIsConstantMap.put(speciesID, species.isConstant());
speciesToHasOnlySubstanceUnitsMap.put(speciesID, species.hasOnlySubstanceUnits());
speciesIDSet.add(speciesID);
}
/**
* puts species-related information into data structures
*
* @throws IOException
*/
protected void setupSpecies() throws IOException {
//add values to hashmap for easy access to species amounts
for (Species species : model.getListOfSpecies()) {
setupSingleSpecies(species, species.getId());
}
}
/**
* puts initial assignment-related information into data structures
*/
protected void setupInitialAssignments() {
HashSet<AssignmentRule> allAssignmentRules = new HashSet<AssignmentRule>();
//perform all assignment rules
for (Rule rule : model.getListOfRules()) {
if (rule.isAssignment())
allAssignmentRules.add((AssignmentRule)rule);
}
performAssignmentRules(allAssignmentRules);
HashSet<String> affectedVariables = new HashSet<String>();
//calculate initial assignments a lot of times in case there are dependencies
//running it the number of initial assignments times will avoid problems
//and all of them will be fully calculated and determined
for (int i = 0; i < numInitialAssignments; ++i) {
for (InitialAssignment initialAssignment : model.getListOfInitialAssignments()) {
String variable = initialAssignment.getVariable().replace("_negative_","-");
initialAssignment.setMath(inlineFormula(initialAssignment.getMath()));
if (speciesToHasOnlySubstanceUnitsMap.containsKey(variable) &&
speciesToHasOnlySubstanceUnitsMap.get(variable) == false) {
variableToValueMap.put(variable,
evaluateExpressionRecursive(initialAssignment.getMath()) *
variableToValueMap.get(speciesToCompartmentNameMap.get(variable)));
}
else {
variableToValueMap.put(variable, evaluateExpressionRecursive(initialAssignment.getMath()));
}
affectedVariables.add(variable);
}
}
//perform assignment rules again for variable that may have changed due to the initial assignments
//they aren't set up yet, so just perform them all
performAssignmentRules(allAssignmentRules);
//this is kind of weird, but apparently if an initial assignment changes a compartment size
//i need to go back and update species amounts because they used the non-changed-by-assignment sizes
for (Species species : model.getListOfSpecies()) {
if (species.isSetInitialConcentration()) {
String speciesID = species.getId();
//revert to the initial concentration value
if (Double.isNaN(variableToValueMap.get(speciesID)) == false)
variableToValueMap.put(speciesID,
variableToValueMap.get(speciesID) / species.getCompartmentInstance().getSize());
else
variableToValueMap.put(speciesID, species.getInitialConcentration());
//multiply by the new compartment size to get into amount
variableToValueMap.put(speciesID, variableToValueMap.get(speciesID) *
variableToValueMap.get(speciesToCompartmentNameMap.get(speciesID)));
}
}
}
/**
* sets up the local parameters in a single kinetic law
*
* @param kineticLaw
* @param reactionID
*/
private void setupLocalParameters(KineticLaw kineticLaw, Reaction reaction) {
String reactionID = reaction.getId();
reactionID = reactionID.replace("_negative_","-");
for (int i = 0; i < kineticLaw.getLocalParameterCount(); i++) {
LocalParameter localParameter = kineticLaw.getLocalParameter(i);
String parameterID = "";
//the parameters don't get reset after each run, so don't re-do this prepending
if (localParameter.getId().contains(reactionID + "_") == false)
parameterID = reactionID + "_" + localParameter.getId();
else
parameterID = localParameter.getId();
//System.out.println("Before: " + localParameter.getId() + " after: " + parameterID);
String oldParameterID = localParameter.getId();
variableToValueMap.put(parameterID, localParameter.getValue());
//alter the local parameter ID so that it goes to the local and not global value
if (localParameter.getId() != parameterID) {
localParameter.setId(parameterID);
localParameter.setMetaId(parameterID);
}
//System.out.println("After: " + localParameter.getId());
//for some reason, changing the local parameter sometimes changes the kinetic law instances
//of that parameter id (and sometimes doesn't), so those ones are fine and ignore them
//if (kineticLaw.getMath().toFormula().contains(parameterID) == false) {
alterLocalParameter(kineticLaw.getMath(), reaction, oldParameterID, parameterID);
}
//System.out.println(kineticLaw.getMath().toFormula());
}
/**
* sets up a single (non-local) parameter
*
* @param parameter
*/
private void setupSingleParameter(Parameter parameter) {
String parameterID = parameter.getId();
variableToValueMap.put(parameterID, parameter.getValue());
variableToIsConstantMap.put(parameterID, parameter.getConstant());
if (parameter.getConstant() == false)
nonconstantParameterIDSet.add(parameterID);
if (numRules > 0)
variableToIsInAssignmentRuleMap.put(parameterID, false);
if (numConstraints > 0)
variableToIsInConstraintMap.put(parameterID, false);
}
/**
* puts parameter-related information into data structures
*/
protected void setupParameters() {
//add local parameters
for (Reaction reaction : model.getListOfReactions()) {
KineticLaw kineticLaw = reaction.getKineticLaw();
setupLocalParameters(kineticLaw, reaction);
}
//add values to hashmap for easy access to global parameter values
//NOTE: the IDs for the parameters and species must be unique, so putting them in the
//same hashmap is okay
for (Parameter parameter : model.getListOfParameters()) {
setupSingleParameter(parameter);
}
//add compartment sizes in
for (Compartment compartment : model.getListOfCompartments()) {
String compartmentID = compartment.getId();
compartmentIDSet.add(compartmentID);
variableToValueMap.put(compartmentID, compartment.getSize());
if (Double.isNaN(compartment.getSize()))
variableToValueMap.put(compartmentID, 1.0);
variableToIsConstantMap.put(compartmentID, compartment.getConstant());
if (numRules > 0)
variableToIsInAssignmentRuleMap.put(compartmentID, false);
if (numConstraints > 0)
variableToIsInConstraintMap.put(compartmentID, false);
}
}
/**
* puts rule-related information into data structures
*/
protected void setupRules() {
numAssignmentRules = 0;
numRateRules = 0;
//NOTE: assignmentrules are performed in setupinitialassignments
//loop through all assignment rules
//store which variables (RHS) affect the rule variable (LHS)
//so when those RHS variables change, we know to re-evaluate the rule
//and change the value of the LHS variable
for (Rule rule : model.getListOfRules()) {
if (rule.isAssignment()) {
//Rules don't have a getVariable method, so this needs to be cast to an ExplicitRule
rule.setMath(inlineFormula(rule.getMath()));
AssignmentRule assignmentRule = (AssignmentRule) rule;
//list of all children of the assignmentRule math
ArrayList<ASTNode> formulaChildren = new ArrayList<ASTNode>();
if (assignmentRule.getMath().getChildCount() == 0)
formulaChildren.add(assignmentRule.getMath());
else
getAllASTNodeChildren(assignmentRule.getMath(), formulaChildren);
for (ASTNode ruleNode : formulaChildren) {
if (ruleNode.isName()) {
String nodeName = ruleNode.getName();
variableToAffectedAssignmentRuleSetMap.put(nodeName, new HashSet<AssignmentRule>());
variableToAffectedAssignmentRuleSetMap.get(nodeName).add(assignmentRule);
variableToIsInAssignmentRuleMap.put(nodeName, true);
}
}
++numAssignmentRules;
}
else if (rule.isRate()) {
//Rules don't have a getVariable method, so this needs to be cast to an ExplicitRule
rule.setMath(inlineFormula(rule.getMath()));
RateRule rateRule = (RateRule) rule;
//list of all children of the assignmentRule math
ArrayList<ASTNode> formulaChildren = new ArrayList<ASTNode>();
if (rateRule.getMath().getChildCount() == 0)
formulaChildren.add(rateRule.getMath());
else
getAllASTNodeChildren(rateRule.getMath(), formulaChildren);
for (ASTNode ruleNode : formulaChildren) {
if (ruleNode.isName()) {
String nodeName = ruleNode.getName();
//not sure these are needed, as they only evaluate with each time step
//not when other variables update
// variableToAffectedRateRuleSetMap.put(nodeName, new HashSet<AssignmentRule>());
// variableToAffectedRateRuleSetMap.get(nodeName).add(rateRule);
variableToIsInRateRuleMap.put(nodeName, true);
}
}
++numRateRules;
}
}
//don't think this is necessary
// //loop through the formulas and inline any user-defined functions
// for (Rule rule : model.getListOfRules()) {
// if (rule.isAssignment() || rule.isRate()) {
// rule.setMath(inlineFormula(rule.getMath()));
// System.err.println(rule.getMath());
}
/**
* puts constraint-related information into data structures
*/
protected void setupConstraints() {
//loop through all constraints to find out which variables affect which constraints
//this is stored in a hashmap, as is whether the variable is in a constraint
for (Constraint constraint : model.getListOfConstraints()) {
constraint.setMath(inlineFormula(constraint.getMath()));
for (ASTNode constraintNode : constraint.getMath().getListOfNodes()) {
if (constraintNode.isName()) {
String nodeName = constraintNode.getName();
variableToAffectedConstraintSetMap.put(nodeName, new HashSet<ASTNode>());
variableToAffectedConstraintSetMap.get(nodeName).add(constraint.getMath());
variableToIsInConstraintMap.put(nodeName, true);
}
}
}
}
/**
* sets up a single event
*
* @param event
*/
protected void setupSingleEvent(Event event) {
String eventID = event.getId();
//these events are what determines if a model is dynamic or not
if (eventID.contains("Division__") || eventID.contains("Death__") || eventID.contains("__Move"))
dynamicBoolean = true;
if (event.isSetPriority())
eventToPriorityMap.put(eventID, inlineFormula(event.getPriority().getMath()));
if (event.isSetDelay()) {
eventToDelayMap.put(eventID, inlineFormula(event.getDelay().getMath()));
eventToHasDelayMap.put(eventID, true);
}
else
eventToHasDelayMap.put(eventID, false);
if (event.getTrigger().getMath().toFormula().contains("neighborQuantity") == false)
event.getTrigger().setMath(inlineFormula(event.getTrigger().getMath()));
eventToTriggerMap.put(eventID, event.getTrigger().getMath());
eventToTriggerInitiallyTrueMap.put(eventID, event.getTrigger().isInitialValue());
eventToPreviousTriggerValueMap.put(eventID, event.getTrigger().isInitialValue());
eventToTriggerPersistenceMap.put(eventID, event.getTrigger().getPersistent());
eventToUseValuesFromTriggerTimeMap.put(eventID, event.isUseValuesFromTriggerTime());
eventToAssignmentSetMap.put(eventID, new HashSet<Object>());
eventToAffectedReactionSetMap.put(eventID, new HashSet<String>());
untriggeredEventSet.add(eventID);
for (EventAssignment assignment : event.getListOfEventAssignments()) {
String variableID = assignment.getVariable();
assignment.setMath(inlineFormula(assignment.getMath()));
eventToAssignmentSetMap.get(eventID).add(assignment);
if (variableToEventSetMap.containsKey(variableID) == false)
variableToEventSetMap.put(variableID, new HashSet<String>());
variableToEventSetMap.get(variableID).add(eventID);
//if the variable is a species, add the reactions it's in
//to the event to affected reaction hashmap, which is used
//for updating propensities after an event fires
if (speciesToAffectedReactionSetMap.containsKey(variableID)) {
eventToAffectedReactionSetMap.get(eventID).addAll(
speciesToAffectedReactionSetMap.get(variableID));
}
}
}
/**
* puts event-related information into data structures
*/
protected void setupEvents() {
//add event information to hashmaps for easy/fast access
//this needs to happen after calculating initial propensities
//so that the speciesToAffectedReactionSetMap is populated
for (Event event : model.getListOfEvents()) {
setupSingleEvent(event);
}
}
/**
* does a minimized initialization process to prepare for a new run
*/
protected abstract void setupForNewRun(int newRun);
/**
* opens output file and seeds rng for new run
*
* @param randomSeed
* @param currentRun
* @throws IOException
*/
protected void setupForOutput(long randomSeed, int currentRun) {
this.currentRun = currentRun;
randomNumberGenerator = new XORShiftRandom(randomSeed);
try {
String extension = ".tsd";
if (dynamicBoolean == true)
extension = ".dtsd";
TSDWriter = new FileWriter(outputDirectory + "run-" + currentRun + extension);
bufferedTSDWriter = new BufferedWriter(TSDWriter);
bufferedTSDWriter.write('(');
if (currentRun > 1 && dynamicBoolean == false) {
bufferedTSDWriter.write("(" + "\"" + "time" + "\"");
//if there's an interesting species, only those get printed
if (interestingSpecies.size() > 0) {
for (String speciesID : interestingSpecies)
bufferedTSDWriter.write(", \"" + speciesID + "\"");
if (dynamicBoolean == false)
bufferedTSDWriter.write("),\n");
}
else {
for (String speciesID : speciesIDSet) {
bufferedTSDWriter.write(", \"" + speciesID + "\"");
}
//print compartment IDs (for sizes)
for (String componentID : compartmentIDSet) {
bufferedTSDWriter.write(", \"" + componentID + "\"");
}
//print nonconstant parameter IDs
for (String parameterID : nonconstantParameterIDSet) {
try {
bufferedTSDWriter.write(", \"" + parameterID + "\"");
} catch (IOException e) {
e.printStackTrace();
}
}
bufferedTSDWriter.write("),\n");
}
}
} catch (IOException e) {
e.printStackTrace();
}
}
/**
* calculates the initial propensity of a single reaction
* also does some initialization stuff
*
* @param reactionID
* @param reactionFormula
* @param reversible
* @param reactantsList
* @param productsList
* @param modifiersList
*/
private void setupSingleReaction(String reactionID, ASTNode reactionFormula, boolean reversible,
ListOf<SpeciesReference> reactantsList, ListOf<SpeciesReference> productsList,
ListOf<ModifierSpeciesReference> modifiersList) {
reactionID = reactionID.replace("_negative_","-");
boolean notEnoughMoleculesFlagFd = false;
boolean notEnoughMoleculesFlagRv = false;
boolean notEnoughMoleculesFlag = false;
//if it's a reversible reaction
//split into a forward and reverse reaction (based on the minus sign in the middle)
//and calculate both propensities
if (reversible == true) {
//distributes the left child across the parentheses
if (reactionFormula.getType().equals(ASTNode.Type.TIMES)) {
ASTNode distributedNode = new ASTNode();
reactionFormula = inlineFormula(reactionFormula);
if (reactionFormula.getChildCount() >= 2 &&
reactionFormula.getChild(1).getType().equals(ASTNode.Type.PLUS))
distributedNode = ASTNode.sum(
ASTNode.times(reactionFormula.getLeftChild(), reactionFormula.getRightChild().getLeftChild()),
ASTNode.times(new ASTNode(-1), reactionFormula.getLeftChild(), reactionFormula.getRightChild().getRightChild()));
else if (reactionFormula.getChildCount() >= 2 &&
reactionFormula.getChild(1).getType().equals(ASTNode.Type.MINUS))
distributedNode = ASTNode.diff(
ASTNode.times(reactionFormula.getLeftChild(), reactionFormula.getRightChild().getLeftChild()),
ASTNode.times(reactionFormula.getLeftChild(), reactionFormula.getRightChild().getRightChild()));
reactionFormula = distributedNode;
}
reactionToSpeciesAndStoichiometrySetMap.put(reactionID + "_fd", new HashSet<StringDoublePair>());
reactionToSpeciesAndStoichiometrySetMap.put(reactionID + "_rv", new HashSet<StringDoublePair>());
reactionToReactantStoichiometrySetMap.put(reactionID + "_fd", new HashSet<StringDoublePair>());
reactionToReactantStoichiometrySetMap.put(reactionID + "_rv", new HashSet<StringDoublePair>());
for (SpeciesReference reactant : reactantsList) {
String reactantID = reactant.getSpecies().replace("_negative_","-");
//stoichiometry amplification -- alter the stoichiometry
if (reactionID.contains("_Diffusion_") && stoichAmpBoolean == true)
reactant.setStoichiometry(stoichAmpGridValue);
double reactantStoichiometry;
//if there was an initial assignment for the reactant
//this applies regardless of constancy of the reactant
if (variableToValueMap.containsKey(reactant.getId()))
reactantStoichiometry = variableToValueMap.get(reactant.getId());
else
reactantStoichiometry = reactant.getStoichiometry();
reactionToSpeciesAndStoichiometrySetMap.get(reactionID + "_fd").add(
new StringDoublePair(reactantID, -reactantStoichiometry));
reactionToSpeciesAndStoichiometrySetMap.get(reactionID + "_rv").add(
new StringDoublePair(reactantID, reactantStoichiometry));
//not having a minus sign is intentional as this isn't used for calculations
reactionToReactantStoichiometrySetMap.get(reactionID + "_fd").add(
new StringDoublePair(reactantID, reactantStoichiometry));
//if there was not initial assignment for the reactant
if (reactant.getConstant() == false &&
variableToValueMap.containsKey(reactant.getId()) == false &&
reactant.getId().length() > 0) {
if (reactionToNonconstantStoichiometriesSetMap.containsKey(reactionID + "_fd") == false)
reactionToNonconstantStoichiometriesSetMap.put(reactionID + "_fd", new HashSet<StringStringPair>());
if (reactionToNonconstantStoichiometriesSetMap.containsKey(reactionID + "_rv") == false)
reactionToNonconstantStoichiometriesSetMap.put(reactionID + "_rv", new HashSet<StringStringPair>());
reactionToNonconstantStoichiometriesSetMap.get(reactionID + "_fd")
.add(new StringStringPair(reactantID + "_fd", reactant.getId()));
reactionToNonconstantStoichiometriesSetMap.get(reactionID + "_rv")
.add(new StringStringPair(reactantID + "_rv", reactant.getId()));
variableToValueMap.put(reactant.getId(), reactantStoichiometry);
}
//as a reactant, this species affects the reaction's propensity in the forward direction
speciesToAffectedReactionSetMap.get(reactantID).add(reactionID + "_fd");
//make sure there are enough molecules for this species
//(in the reverse direction, molecules aren't subtracted, but added)
if (variableToValueMap.get(reactantID) < reactantStoichiometry)
notEnoughMoleculesFlagFd = true;
}
for (SpeciesReference product : productsList) {
String productID = product.getSpecies().replace("_negative_","-");
//stoichiometry amplification -- alter the stoichiometry
if (reactionID.contains("_Diffusion_") && stoichAmpBoolean == true)
product.setStoichiometry(stoichAmpGridValue);
double productStoichiometry;
//if there was an initial assignment
if (variableToValueMap.containsKey(product.getId()))
productStoichiometry = variableToValueMap.get(product.getId());
else
productStoichiometry = product.getStoichiometry();
reactionToSpeciesAndStoichiometrySetMap.get(reactionID + "_fd").add(
new StringDoublePair(productID, productStoichiometry));
reactionToSpeciesAndStoichiometrySetMap.get(reactionID + "_rv").add(
new StringDoublePair(productID, -productStoichiometry));
//not having a minus sign is intentional as this isn't used for calculations
reactionToReactantStoichiometrySetMap.get(reactionID + "_rv").add(
new StringDoublePair(productID, productStoichiometry));
//if there wasn't an initial assignment
if (product.getConstant() == false &&
variableToValueMap.containsKey(product.getId()) == false &&
product.getId().length() > 0) {
if (reactionToNonconstantStoichiometriesSetMap.containsKey(reactionID) == false)
reactionToNonconstantStoichiometriesSetMap.put(reactionID, new HashSet<StringStringPair>());
reactionToNonconstantStoichiometriesSetMap.get(reactionID)
.add(new StringStringPair(productID, product.getId()));
variableToValueMap.put(product.getId(), productStoichiometry);
}
//as a product, this species affects the reaction's propensity in the reverse direction
speciesToAffectedReactionSetMap.get(productID).add(reactionID + "_rv");
//make sure there are enough molecules for this species
//(in the forward direction, molecules aren't subtracted, but added)
if (variableToValueMap.get(productID) < productStoichiometry)
notEnoughMoleculesFlagRv = true;
}
for (ModifierSpeciesReference modifier : modifiersList) {
String modifierID = modifier.getSpecies();
modifierID = modifierID.replace("_negative_","-");
String forwardString = "", reverseString = "";
try {
forwardString = ASTNode.formulaToString(reactionFormula.getLeftChild());
reverseString = ASTNode.formulaToString(reactionFormula.getRightChild());
}
catch (SBMLException e) {
e.printStackTrace();
}
//check the kinetic law to see which direction the modifier affects the reaction's propensity
if (forwardString.contains(modifierID))
speciesToAffectedReactionSetMap.get(modifierID).add(reactionID + "_fd");
if (reverseString.contains(modifierID))
speciesToAffectedReactionSetMap.get(modifierID).add(reactionID + "_rv");
}
double propensity;
reactionToFormulaMap.put(reactionID + "_rv", inlineFormula(reactionFormula.getRightChild()));
reactionToFormulaMap.put(reactionID + "_fd", inlineFormula(reactionFormula.getLeftChild()));
//calculate forward reaction propensity
if (notEnoughMoleculesFlagFd == true)
propensity = 0.0;
else {
//the left child is what's left of the minus sign
propensity = evaluateExpressionRecursive(inlineFormula(reactionFormula.getLeftChild()));
//stoichiometry amplification -- alter the propensity
if (reactionID.contains("_Diffusion_") && stoichAmpBoolean == true)
propensity *= (1.0 / stoichAmpGridValue);
if ((propensity < minPropensity) && (propensity > 0))
minPropensity = propensity;
if (propensity > maxPropensity)
maxPropensity = propensity;
totalPropensity += propensity;
}
reactionToPropensityMap.put(reactionID + "_fd", propensity);
//calculate reverse reaction propensity
if (notEnoughMoleculesFlagRv == true)
propensity = 0.0;
else {
//the right child is what's right of the minus sign
propensity = evaluateExpressionRecursive(inlineFormula(reactionFormula.getRightChild()));
//stoichiometry amplification -- alter the propensity
if (reactionID.contains("_Diffusion_") && stoichAmpBoolean == true)
propensity *= (1.0 / stoichAmpGridValue);
if ((propensity < minPropensity) && (propensity > 0))
minPropensity = propensity;
if (propensity > maxPropensity)
maxPropensity = propensity;
totalPropensity += propensity;
}
reactionToPropensityMap.put(reactionID + "_rv", propensity);
}
//if it's not a reversible reaction
else {
reactionToSpeciesAndStoichiometrySetMap.put(reactionID, new HashSet<StringDoublePair>());
reactionToReactantStoichiometrySetMap.put(reactionID, new HashSet<StringDoublePair>());
for (SpeciesReference reactant : reactantsList) {
String reactantID = reactant.getSpecies().replace("_negative_","-");
//stoichiometry amplification -- alter the stoichiometry
if (reactionID.contains("_Diffusion_") && stoichAmpBoolean == true) {
reactant.setStoichiometry(stoichAmpGridValue);
}
double reactantStoichiometry;
//if there was an initial assignment for the speciesref id
if (variableToValueMap.containsKey(reactant.getId()))
reactantStoichiometry = variableToValueMap.get(reactant.getId());
else
reactantStoichiometry = reactant.getStoichiometry();
reactionToSpeciesAndStoichiometrySetMap.get(reactionID).add(
new StringDoublePair(reactantID, -reactantStoichiometry));
reactionToReactantStoichiometrySetMap.get(reactionID).add(
new StringDoublePair(reactantID, reactantStoichiometry));
//if there wasn't an initial assignment
if (reactant.getConstant() == false &&
variableToValueMap.containsKey(reactant.getId()) == false &&
reactant.getId().length() > 0) {
if (reactionToNonconstantStoichiometriesSetMap.containsKey(reactionID) == false)
reactionToNonconstantStoichiometriesSetMap.put(reactionID, new HashSet<StringStringPair>());
reactionToNonconstantStoichiometriesSetMap.get(reactionID)
.add(new StringStringPair(reactantID, reactant.getId()));
variableToValueMap.put(reactant.getId(), reactantStoichiometry);
}
//as a reactant, this species affects the reaction's propensity
speciesToAffectedReactionSetMap.get(reactantID).add(reactionID);
//make sure there are enough molecules for this species
if (variableToValueMap.get(reactantID) < reactantStoichiometry)
notEnoughMoleculesFlag = true;
}
for (SpeciesReference product : productsList) {
//stoichiometry amplification -- alter the stoichiometry
if (reactionID.contains("_Diffusion_") && stoichAmpBoolean == true)
product.setStoichiometry(stoichAmpGridValue);
String productID = product.getSpecies().replace("_negative_","-");
double productStoichiometry;
//if there was an initial assignment for the speciesref id
if (variableToValueMap.containsKey(product.getId()))
productStoichiometry = variableToValueMap.get(product.getId());
else
productStoichiometry = product.getStoichiometry();
reactionToSpeciesAndStoichiometrySetMap.get(reactionID).add(
new StringDoublePair(productID, productStoichiometry));
if (product.getConstant() == false &&
variableToValueMap.containsKey(product.getId()) == false &&
product.getId().length() > 0) {
if (reactionToNonconstantStoichiometriesSetMap.containsKey(reactionID) == false)
reactionToNonconstantStoichiometriesSetMap.put(reactionID, new HashSet<StringStringPair>());
reactionToNonconstantStoichiometriesSetMap.get(reactionID)
.add(new StringStringPair(productID, product.getId()));
variableToValueMap.put(product.getId(), productStoichiometry);
}
//don't need to check if there are enough, because products are added
}
for (ModifierSpeciesReference modifier : modifiersList) {
String modifierID = modifier.getSpecies();
modifierID = modifierID.replace("_negative_","-");
//as a modifier, this species affects the reaction's propensity
speciesToAffectedReactionSetMap.get(modifierID).add(reactionID);
}
reactionToFormulaMap.put(reactionID, inlineFormula(reactionFormula));
double propensity;
if (notEnoughMoleculesFlag == true)
propensity = 0.0;
else {
//calculate propensity
propensity = evaluateExpressionRecursive(inlineFormula(reactionFormula));
//stoichiometry amplification -- alter the propensity
if (reactionID.contains("_Diffusion_") && stoichAmpBoolean == true)
propensity *= (1.0 / stoichAmpGridValue);
if (propensity < minPropensity && propensity > 0)
minPropensity = propensity;
if (propensity > maxPropensity)
maxPropensity = propensity;
totalPropensity += propensity;
}
reactionToPropensityMap.put(reactionID, propensity);
}
}
/**
* calculates the initial propensities for each reaction in the model
*
* @param numReactions the number of reactions in the model
*/
protected void setupReactions() {
//loop through all reactions and calculate their propensities
for (Reaction reaction : model.getListOfReactions()) {
String reactionID = reaction.getId();
ASTNode reactionFormula = reaction.getKineticLaw().getMath();
setupSingleReaction(reactionID, reactionFormula, reaction.getReversible(),
reaction.getListOfReactants(), reaction.getListOfProducts(), reaction.getListOfModifiers());
}
}
/**
* abstract simulate method
* each simulator needs a simulate method
*/
protected abstract void simulate();
/**
* returns an annotation with only array information remaining
*
* @param annotation
* @return
*/
public static String stripAnnotation(String annotation) {
if (annotation.contains("array:array")) {
//only leave the stuff in these two namespaces, which should appear mutually exclusively
annotation = annotation.replace("<annotation>","").replace("</annotation>","");
for (int i = 0; i < annotation.length() - 12; ++i) {
if (annotation.substring(i, i + 12).equals("<array:array"))
annotation = annotation.substring(i);
}
for (int i = 0; i < annotation.length() - 2; ++i) {
if (annotation.substring(i, i + 2).equals("/>")) {
annotation = annotation.substring(0, i + 2);
break;
}
}
return "<annotation>" + annotation + "</annotation>";
}
else if (annotation.contains("ibiosim:ibiosim")) {
//only leave the stuff in these two namespaces, which should appear mutually exclusively
annotation = annotation.replace("<annotation>","").replace("</annotation>","");
for (int i = 0; i < annotation.length() - 16; ++i) {
if (annotation.substring(i, i + 16).equals("<ibiosim:ibiosim"))
annotation = annotation.substring(i);
}
for (int i = 0; i < annotation.length() - 2; ++i) {
if (annotation.substring(i, i + 2).equals("/>")) {
annotation = annotation.substring(0, i + 2);
break;
}
}
return "<annotation>" + annotation + "</annotation>";
}
else return new String("");
}
/**
* this evaluates a set of constraints that have been affected by an event or reaction firing
* and returns the OR'd boolean result
*
* @param affectedConstraintSet the set of constraints affected
* @return the boolean result of the constraints' evaluation
*/
protected boolean testConstraints(HashSet<ASTNode> affectedConstraintSet) {
//check all of the affected constraints
//if one evaluates to true, then the simulation halts
for (ASTNode constraint : affectedConstraintSet) {
if (getBooleanFromDouble(evaluateExpressionRecursive(constraint)) == true)
return true;
}
return false;
}
/**
* is called after duplicateComponent or deleteComponent is called
*/
protected abstract void updateAfterDynamicChanges();
/**
* updates the propensities of the reaction set passed in
*
* @param reactionSet
*/
private void updatePropensities(HashSet<String> reactionSet) {
for (String reactionID : reactionSet) {
boolean notEnoughMoleculesFlag = false;
HashSet<StringDoublePair> reactantStoichiometrySet =
reactionToReactantStoichiometrySetMap.get(reactionID);
//check for enough molecules for the reaction to occur
for (StringDoublePair speciesAndStoichiometry : reactantStoichiometrySet) {
String speciesID = speciesAndStoichiometry.string;
double stoichiometry = speciesAndStoichiometry.doub;
if (reactionToNonconstantStoichiometriesSetMap.containsKey(reactionID)) {
for (StringStringPair doubleID : reactionToNonconstantStoichiometriesSetMap.get(reactionID)) {
//string1 is the species ID; string2 is the speciesReference ID
if (doubleID.string1.equals(speciesID)) {
stoichiometry = variableToValueMap.get(doubleID.string2);
break;
}
}
}
//if there aren't enough molecules to satisfy the stoichiometry
if (variableToValueMap.get(speciesID) < stoichiometry) {
notEnoughMoleculesFlag = true;
break;
}
}
double newPropensity = 0.0;
if (notEnoughMoleculesFlag == false)
newPropensity = evaluateExpressionRecursive(reactionToFormulaMap.get(reactionID));
//stoichiometry amplification -- alter the propensity
if (reactionID.contains("_Diffusion_") && stoichAmpBoolean == true) {
newPropensity *= (1.0 / stoichAmpGridValue);
}
if (newPropensity > 0.0 && newPropensity < minPropensity)
minPropensity = newPropensity;
if (newPropensity > maxPropensity)
maxPropensity = newPropensity;
double oldPropensity = reactionToPropensityMap.get(reactionID);
//add the difference of new v. old propensity to the total propensity
totalPropensity += newPropensity - oldPropensity;
reactionToPropensityMap.put(reactionID, newPropensity);
}
}
//EVENT TO FIRE INNER CLASS
/**
* easy way to store multiple data points for events that are firing
*/
protected class EventToFire {
public String eventID = "";
public HashSet<Object> eventAssignmentSet = null;
public double fireTime = 0.0;
public EventToFire(String eventID, HashSet<Object> eventAssignmentSet, double fireTime) {
this.eventID = eventID;
this.eventAssignmentSet = eventAssignmentSet;
this.fireTime = fireTime;
}
}
//EVENT COMPARATOR INNER CLASS
/**
* compares two events to see which one should be before the other in the priority queue
*/
protected class EventComparator implements Comparator<EventToFire> {
/**
* compares two events based on their fire times and priorities
*/
public int compare(EventToFire event1, EventToFire event2) {
if (event1.fireTime > event2.fireTime)
return 1;
else if (event1.fireTime < event2.fireTime)
return -1;
else {
if (eventToPriorityMap.get(event1.eventID) == null) {
if (eventToPriorityMap.get(event2.eventID) != null)
return -1;
else {
if ((Math.random() * 100) > 50) {
return -1;
}
else {
return 1;
}
}
}
if (evaluateExpressionRecursive(eventToPriorityMap.get(event1.eventID)) >
evaluateExpressionRecursive(eventToPriorityMap.get(event2.eventID)))
return -1;
else if ( evaluateExpressionRecursive(eventToPriorityMap.get(event1.eventID)) <
evaluateExpressionRecursive(eventToPriorityMap.get(event2.eventID)))
return 1;
else {
if ((Math.random() * 100) > 50) {
return -1;
}
else {
return 1;
}
}
}
}
}
//STRING DOUBLE PAIR INNER CLASS
/**
* class to combine a string and a double
*/
protected class StringDoublePair {
public String string;
public double doub;
StringDoublePair(String s, double d) {
string = s;
doub = d;
}
}
//STRING STRING PAIR INNER CLASS
/**
* class to combine a string and a string
*/
protected class StringStringPair {
public String string1;
public String string2;
StringStringPair(String s1, String s2) {
string1 = s1;
string2 = s2;
}
}
}
|
package hex.glrm;
import Jama.CholeskyDecomposition;
import Jama.Matrix;
import Jama.QRDecomposition;
import Jama.SingularValueDecomposition;
import hex.*;
import hex.gram.Gram;
import hex.gram.Gram.*;
import hex.kmeans.KMeans;
import hex.kmeans.KMeansModel;
import hex.pca.PCA;
import hex.pca.PCAModel;
import hex.schemas.GLRMV99;
import hex.glrm.GLRMModel.GLRMParameters;
import hex.schemas.ModelBuilderSchema;
import hex.svd.SVD;
import hex.svd.SVDModel;
import water.*;
import water.fvec.Chunk;
import water.fvec.Frame;
import water.fvec.NewChunk;
import water.fvec.Vec;
import water.util.ArrayUtils;
import water.util.Log;
import water.util.RandomUtils;
import java.util.Arrays;
import java.util.Random;
public class GLRM extends ModelBuilder<GLRMModel,GLRMModel.GLRMParameters,GLRMModel.GLRMOutput> {
// Convergence tolerance
private final double TOLERANCE = 1e-6;
// Maximum number of columns when categoricals expanded
private final int MAX_COLS_EXPANDED = 5000;
// Number of columns in training set (p)
private transient int _ncolA;
private transient int _ncolY; // With categoricals expanded into 0/1 indicator cols
// Number of columns in fitted X matrix (k)
private transient int _ncolX;
@Override public ModelBuilderSchema schema() {
return new GLRMV99();
}
@Override public Job<GLRMModel> trainModelImpl(long work) {
return start(new GLRMDriver(), work);
}
@Override
public long progressUnits() {
return _parms._max_iterations + 1;
}
@Override public ModelCategory[] can_build() {
return new ModelCategory[]{ModelCategory.Clustering};
}
@Override public BuilderVisibility builderVisibility() { return BuilderVisibility.Experimental; };
public enum Initialization {
Random, SVD, PlusPlus, User
}
// Called from an http request
public GLRM(GLRMParameters parms) {
super("GLRM", parms);
init(false);
}
@Override public void init(boolean expensive) {
super.init(expensive);
if (_parms._loading_key == null) _parms._loading_key = Key.make("GLRMLoading_" + Key.rand());
if (_parms._gamma_x < 0) error("_gamma_x", "gamma must be a non-negative number");
if (_parms._gamma_y < 0) error("_gamma_y", "gamma_y must be a non-negative number");
if (_parms._max_iterations < 1 || _parms._max_iterations > 1e6)
error("_max_iterations", "max_iterations must be between 1 and 1e6 inclusive");
if (_parms._init_step_size <= 0)
error ("_init_step_size", "init_step_size must be a positive number");
if (_parms._min_step_size < 0 || _parms._min_step_size > _parms._init_step_size)
error("_min_step_size", "min_step_size must be between 0 and " + _parms._init_step_size);
if (_train == null) return;
if (_train.numCols() < 2) error("_train", "_train must have more than one column");
// TODO: Initialize _parms._k = min(ncol(_train), nrow(_train)) if not set
_ncolY = _train.numColsExp(true, false);
int k_min = (int) Math.min(_ncolY, _train.numRows());
if (_ncolY > MAX_COLS_EXPANDED)
warn("_train", "_train has " + _ncolY + " columns when categoricals are expanded. Algorithm may be slow.");
if (_parms._k < 1 || _parms._k > k_min) error("_k", "_k must be between 1 and " + k_min);
if (null != _parms._user_points) { // Check dimensions of user-specified centers
if (_parms._init != GLRM.Initialization.User)
error("init", "init must be 'User' if providing user-specified points");
if (_parms._user_points.get().numCols() != _train.numCols())
error("_user_points", "The user-specified points must have the same number of columns (" + _train.numCols() + ") as the training observations");
else if (_parms._user_points.get().numRows() != _parms._k)
error("_user_points", "The user-specified points must have k = " + _parms._k + " rows");
else {
int zero_vec = 0;
Vec[] centersVecs = _parms._user_points.get().vecs();
for (int c = 0; c < _train.numCols(); c++) {
if(centersVecs[c].naCnt() > 0) {
error("_user_points", "The user-specified points cannot contain any missing values"); break;
} else if(centersVecs[c].isConst() && centersVecs[c].max() == 0)
zero_vec++;
}
if (zero_vec == _train.numCols())
error("_user_points", "The user-specified points cannot all be zero");
}
}
_ncolX = _parms._k;
_ncolA = _train.numCols();
}
// Squared Frobenius norm of a matrix (sum of squared entries)
public static double frobenius2(double[][] x) {
if(x == null) return 0;
double frob = 0;
for(int i = 0; i < x.length; i++) {
for(int j = 0; j < x[0].length; j++)
frob += x[i][j] * x[i][j];
}
return frob;
}
// Transform each column of a 2-D array, assuming categoricals sorted before numeric cols
public static double[][] transform(double[][] centers, double[] normSub, double[] normMul, int ncats, int nnums) {
int K = centers.length;
int N = centers[0].length;
assert ncats + nnums == N;
double[][] value = new double[K][N];
double[] means = normSub == null ? MemoryManager.malloc8d(nnums) : normSub;
double[] mults = normMul == null ? MemoryManager.malloc8d(nnums) : normMul;
for (int clu = 0; clu < K; clu++) {
System.arraycopy(centers[clu], 0, value[clu], 0, ncats);
for (int col = 0; col < nnums; col++)
value[clu][ncats+col] = (centers[clu][ncats+col] - means[col]) * mults[col];
}
return value;
}
// More efficient implementation assuming sdata cols aligned with adaptedFrame
public static double[][] expandCats(double[][] sdata, DataInfo dinfo) {
if(sdata == null || dinfo._cats == 0) return sdata;
assert sdata[0].length == dinfo._adaptedFrame.numCols();
// Column count for expanded matrix
int catsexp = dinfo._catOffsets[dinfo._catOffsets.length-1];
double[][] cexp = new double[sdata.length][catsexp + dinfo._nums];
// Expand out categorical columns
int cidx;
for(int j = 0; j < dinfo._cats; j++) {
for(int i = 0; i < sdata.length; i++) {
if (Double.isNaN(sdata[i][j])) {
if (dinfo._catMissing[j] == 0) continue; // Skip if entry missing and no NA bucket. All indicators will be zero.
else cidx = dinfo._catOffsets[j+1]-1; // Otherwise, missing value turns into extra (last) factor
} else
cidx = dinfo.getCategoricalId(j, (int)sdata[i][j]);
if(cidx >= 0) cexp[i][cidx] = 1; // Ignore categorical levels outside domain
}
}
// Copy over numeric columns
for(int j = 0; j < dinfo._nums; j++) {
for(int i = 0; i < sdata.length; i++)
cexp[i][catsexp+j] = sdata[i][dinfo._cats+j];
}
return cexp;
}
class GLRMDriver extends H2O.H2OCountedCompleter<GLRMDriver> {
// Initialize Y and X matrices
// tinfo = original training data A, dinfo = [A,X,W] where W is working copy of X (initialized here)
private double[][] initialXY(DataInfo tinfo, DataInfo dinfo) {
double[][] centers, centers_exp = null;
if (null != _parms._user_points) { // User-specified starting points
Vec[] centersVecs = _parms._user_points.get().vecs();
centers = new double[_parms._k][_ncolA];
// Get the centers and put into array
for (int c = 0; c < _ncolA; c++) {
for (int r = 0; r < _parms._k; r++)
centers[r][c] = centersVecs[c].at(r);
}
// Permute cluster columns to align with dinfo and expand out categoricals
centers = ArrayUtils.permuteCols(centers, tinfo._permutation);
centers_exp = expandCats(centers, tinfo);
} else if (_parms._init == Initialization.Random) { // Generate array from standard normal distribution
return ArrayUtils.gaussianArray(_parms._k, _ncolY);
} else if (_parms._init == Initialization.SVD) { // Run SVD on A'A/n (Gram) and set Y to be the right singular vectors
PCAModel.PCAParameters parms = new PCAModel.PCAParameters();
parms._train = _parms._train;
parms._ignored_columns = _parms._ignored_columns;
parms._ignore_const_cols = _parms._ignore_const_cols;
parms._score_each_iteration = _parms._score_each_iteration;
parms._use_all_factor_levels = true; // Since GLRM requires Y matrix to have fully expanded ncols
parms._k = _parms._k;
parms._max_iterations = _parms._max_iterations;
parms._transform = _parms._transform;
parms._seed = _parms._seed;
parms._pca_method = PCAModel.PCAParameters.Method.GramSVD;
PCAModel pca = null;
PCA job = null;
try {
job = new PCA(parms);
pca = job.trainModel().get();
} finally {
if (job != null) job.remove();
if (pca != null) pca.remove();
}
// Ensure SVD centers align with adapted training frame cols
assert pca._output._permutation.length == tinfo._permutation.length;
for(int i = 0; i < tinfo._permutation.length; i++)
assert pca._output._permutation[i] == tinfo._permutation[i];
centers_exp = ArrayUtils.transpose(pca._output._eigenvectors_raw);
// for(int i = 0; i < centers_exp.length; i++)
// ArrayUtils.mult(centers_exp[i], pca._output._std_deviation[i] * Math.sqrt(pca._output._nobs-1));
} else if (_parms._init == Initialization.PlusPlus) { // Run k-means++ and use resulting cluster centers as initial Y
KMeansModel.KMeansParameters parms = new KMeansModel.KMeansParameters();
parms._train = _parms._train;
parms._ignored_columns = _parms._ignored_columns;
parms._ignore_const_cols = _parms._ignore_const_cols;
parms._score_each_iteration = _parms._score_each_iteration;
parms._init = KMeans.Initialization.PlusPlus;
parms._k = _parms._k;
parms._max_iterations = _parms._max_iterations;
parms._standardize = true;
parms._seed = _parms._seed;
parms._pred_indicator = true;
KMeansModel km = null;
KMeans job = null;
try {
job = new KMeans(parms);
km = job.trainModel().get();
// Score only if clusters well-defined and closed-form solution does not exist
double frob = frobenius2(km._output._centers_raw);
if(frob != 0 && !Double.isNaN(frob) && !_parms.hasClosedForm())
initialXKmeans(dinfo, km);
} finally {
if (job != null) job.remove();
if (km != null) km.remove();
}
// Permute cluster columns to align with dinfo, normalize nums, and expand out cats to indicator cols
centers = ArrayUtils.permuteCols(km._output._centers_raw, tinfo.mapNames(km._output._names));
centers = transform(centers, tinfo._normSub, tinfo._normMul, tinfo._cats, tinfo._nums);
centers_exp = expandCats(centers, tinfo);
} else
error("_init", "Initialization method " + _parms._init + " is undefined");
// If all centers are zero or any are NaN, initialize to standard normal random matrix
assert centers_exp != null && centers_exp[0].length == _ncolY;
double frob = frobenius2(centers_exp); // TODO: Don't need to calculate twice if k-means++
if(frob == 0 || Double.isNaN(frob)) {
warn("_init", "Initialization failed. Setting initial Y to standard normal random matrix instead");
centers_exp = ArrayUtils.gaussianArray(_parms._k, _ncolY);
}
return centers_exp;
}
// Set X to matrix of indicator columns, e.g. k = 4, cluster = 3 -> [0, 0, 1, 0]
private void initialXKmeans(DataInfo dinfo, KMeansModel km) {
// Frame pred = km.score(_parms.train());
Log.info("Initializing X to matrix of indicator columns corresponding to cluster assignments");
final KMeansModel model = km;
new MRTask() {
@Override public void map( Chunk chks[] ) {
double tmp [] = new double[_ncolA];
double preds[] = new double[_ncolX];
for(int row = 0; row < chks[0]._len; row++) {
double p[] = model.score_indicator(chks, row, tmp, preds);
for(int c = 0; c < preds.length; c++) {
chks[_ncolA+c].set(row, p[c]);
chks[_ncolA+_ncolX+c].set(row, p[c]);
}
}
}
}.doAll(dinfo._adaptedFrame);
}
// In case of L2 loss and regularization, initialize closed form X = AY'(YY' + \gamma)^(-1)
private void initialXClosedForm(DataInfo dinfo, double[][] yt, double[] normSub, double[] normMul) {
Log.info("Initializing X = AY'(YY' + gamma I)^(-1) where A = training data");
double[][] ygram = ArrayUtils.formGram(yt);
if (_parms._gamma_y > 0) {
for(int i = 0; i < ygram.length; i++)
ygram[i][i] += _parms._gamma_y;
}
CholeskyDecomposition yychol = regularizedCholesky(ygram, 10, false);
if(!yychol.isSPD())
Log.warn("Initialization failed: (YY' + gamma I) is non-SPD. Setting initial X to standard normal random matrix. Results will be numerically unstable");
else {
CholMulTask cmtsk = new CholMulTask(dinfo, _parms, yychol, yt, _ncolA, _ncolX, normSub, normMul);
cmtsk.doAll(dinfo._adaptedFrame);
}
}
// Stopping criteria
private boolean isDone(GLRMModel model, int steps_in_row, double step) {
if (!isRunning()) return true; // Stopped/cancelled
// Stopped for running out of iterations
if (model._output._iterations >= _parms._max_iterations) return true;
// Stopped for falling below minimum step size
if (step <= _parms._min_step_size) return true;
// Stopped when enough steps and average decrease in objective per iteration < TOLERANCE
if (model._output._iterations > 10 && steps_in_row > 3 &&
Math.abs(model._output._avg_change_obj) < TOLERANCE) return true;
return false; // Not stopping
}
// Regularized Cholesky decomposition using H2O implementation
public Cholesky regularizedCholesky(Gram gram, int max_attempts) {
int attempts = 0;
double addedL2 = 0; // TODO: Should I report this to the user?
Cholesky chol = gram.cholesky(null);
while(!chol.isSPD() && attempts < max_attempts) {
if(addedL2 == 0) addedL2 = 1e-5;
else addedL2 *= 10;
++attempts;
gram.addDiag(addedL2); // try to add L2 penalty to make the Gram SPD
Log.info("Added L2 regularization = " + addedL2 + " to diagonal of Gram matrix");
gram.cholesky(chol);
}
if(!chol.isSPD())
throw new Gram.NonSPDMatrixException();
return chol;
}
public Cholesky regularizedCholesky(Gram gram) { return regularizedCholesky(gram, 10); }
// Regularized Cholesky decomposition using JAMA implementation
public CholeskyDecomposition regularizedCholesky(double[][] gram, int max_attempts, boolean throw_exception) {
int attempts = 0;
double addedL2 = 0;
Matrix gmat = new Matrix(gram);
CholeskyDecomposition chol = new CholeskyDecomposition(gmat);
while(!chol.isSPD() && attempts < max_attempts) {
if(addedL2 == 0) addedL2 = 1e-5;
else addedL2 *= 10;
++attempts;
for(int i = 0; i < gram.length; i++) gmat.set(i,i,addedL2); // try to add L2 penalty to make the Gram SPD
Log.info("Added L2 regularization = " + addedL2 + " to diagonal of Gram matrix");
chol = new CholeskyDecomposition(gmat);
}
if(!chol.isSPD() && throw_exception)
throw new Gram.NonSPDMatrixException();
return chol;
}
public CholeskyDecomposition regularizedCholesky(double[][] gram) { return regularizedCholesky(gram, 10, true); }
// Recover singular values and eigenvectors of XY
public void recoverSVD(GLRMModel model, DataInfo xinfo) {
// NOTE: Gram computes X'X/n where n = nrow(A) = number of rows in training set
GramTask xgram = new GramTask(self(), xinfo).doAll(xinfo._adaptedFrame);
Cholesky xxchol = regularizedCholesky(xgram._gram);
// R from QR decomposition of X = QR is upper triangular factor of Cholesky of X'X
// Gram = X'X/n = LL' -> X'X = (L*sqrt(n))(L'*sqrt(n))
Matrix x_r = new Matrix(xxchol.getL()).transpose();
x_r = x_r.times(Math.sqrt(_train.numRows()));
QRDecomposition yt_qr = new QRDecomposition(new Matrix(model._output._archetypes));
Matrix yt_r = yt_qr.getR(); // S from QR decomposition of Y' = ZS
Matrix rrmul = x_r.times(yt_r.transpose());
SingularValueDecomposition rrsvd = new SingularValueDecomposition(rrmul); // RS' = U \Sigma V'
// Eigenvectors are V'Z' = (ZV)'
Matrix eigvec = yt_qr.getQ().times(rrsvd.getV());
model._output._eigenvectors = eigvec.getArray();
// Singular values ordered in weakly descending order by algorithm
model._output._singular_vals = rrsvd.getSingularValues();
}
@Override protected void compute2() {
GLRMModel model = null;
DataInfo dinfo = null, xinfo = null, tinfo = null;
Frame fr = null, x = null;
boolean overwriteX = false;
try {
init(true); // Initialize parameters
_parms.read_lock_frames(GLRM.this); // Fetch & read-lock input frames
if (error_count() > 0) throw new IllegalArgumentException("Found validation errors: " + validationErrors());
// The model to be built
model = new GLRMModel(dest(), _parms, new GLRMModel.GLRMOutput(GLRM.this));
model.delete_and_lock(self());
// Save adapted frame info for scoring later
tinfo = new DataInfo(Key.make(), _train, _valid, 0, true, _parms._transform, DataInfo.TransformType.NONE, false, false, /* weights */ false, /* offset */ false);
DKV.put(tinfo._key, tinfo);
// Save training frame adaptation information for use in scoring later
model._output._normSub = tinfo._normSub == null ? new double[tinfo._nums] : tinfo._normSub;
if(tinfo._normMul == null) {
model._output._normMul = new double[tinfo._nums];
Arrays.fill(model._output._normMul, 1.0);
} else
model._output._normMul = tinfo._normMul;
model._output._permutation = tinfo._permutation;
model._output._nnums = tinfo._nums;
model._output._ncats = tinfo._cats;
model._output._catOffsets = tinfo._catOffsets;
model._output._names_expanded = tinfo.coefNames();
long nobs = _train.numRows() * _train.numCols();
for(int i = 0; i < _train.numCols(); i++) nobs -= _train.vec(i).naCnt(); // TODO: Should we count NAs?
model._output._nobs = nobs;
// 0) Initialize Y and X matrices
// Jam A and X into a single frame for distributed computation
// [A,X,W] A is read-only training data, X is matrix from prior iteration, W is working copy of X this iteration
Vec[] vecs = new Vec[_ncolA + 2*_ncolX];
for (int i = 0; i < _ncolA; i++) vecs[i] = _train.vec(i);
for (int i = _ncolA; i < vecs.length; i++)
vecs[i] = _train.anyVec().makeGaus(_parms._seed); // By default, initialize X to random Gaussian matrix
fr = new Frame(null, vecs);
dinfo = new DataInfo(Key.make(), fr, null, 0, true, _parms._transform, DataInfo.TransformType.NONE, false, false, /* weights */ false, /* offset */ false);
DKV.put(dinfo._key, dinfo);
// Use closed form solution for X if L2 loss and regularization
double[][] yt = initialXY(tinfo, dinfo);
yt = ArrayUtils.transpose(yt);
if (_parms.hasClosedForm()) initialXClosedForm(dinfo, yt, model._output._normSub, model._output._normMul);
// Compute initial objective function
ObjCalc objtsk = new ObjCalc(dinfo, _parms, yt, _ncolA, _ncolX, model._output._normSub, model._output._normMul, _parms._gamma_x != 0).doAll(dinfo._adaptedFrame);
model._output._objective = objtsk._loss + _parms._gamma_x * objtsk._xold_reg + _parms._gamma_y * _parms.regularize_y(yt);
model._output._iterations = 0;
model._output._avg_change_obj = 2 * TOLERANCE; // Run at least 1 iteration
model.update(_key); // Update model in K/V store
update(1); // One unit of work
double step = _parms._init_step_size; // Initial step size
int steps_in_row = 0; // Keep track of number of steps taken that decrease objective
while (!isDone(model, steps_in_row, step)) {
// TODO: Should step be divided by number of original or expanded (with 0/1 categorical) cols?
// 1) Update X matrix given fixed Y
UpdateX xtsk = new UpdateX(dinfo, _parms, yt, step/_ncolA, overwriteX, _ncolA, _ncolX, model._output._normSub, model._output._normMul);
xtsk.doAll(dinfo._adaptedFrame);
// 2) Update Y matrix given fixed X
UpdateY ytsk = new UpdateY(dinfo, _parms, yt, step/_ncolA, _ncolA, _ncolX, model._output._normSub, model._output._normMul);
double[][] ytnew = ytsk.doAll(dinfo._adaptedFrame)._ytnew;
// 3) Compute average change in objective function
objtsk = new ObjCalc(dinfo, _parms, ytnew, _ncolA, _ncolX, model._output._normSub, model._output._normMul).doAll(dinfo._adaptedFrame);
double obj_new = objtsk._loss + _parms._gamma_x * xtsk._xreg + _parms._gamma_y * ytsk._yreg;
model._output._avg_change_obj = (model._output._objective - obj_new) / nobs;
model._output._iterations++;
// step = 1.0 / model._output._iterations; // Step size \alpha_k = 1/iters
if(model._output._avg_change_obj > 0) { // Objective decreased this iteration
model._output._archetypes = yt = ytnew;
model._output._objective = obj_new;
step *= 1.05;
steps_in_row = Math.max(1, steps_in_row+1);
overwriteX = true;
} else { // If objective increased, re-run with smaller step size
step = step / Math.max(1.5, -steps_in_row);
steps_in_row = Math.min(0, steps_in_row-1);
overwriteX = false;
Log.info("Iteration " + model._output._iterations + ": Objective increased to " + obj_new + "; reducing step size to " + step);
}
model._output._step_size = step;
model.update(self()); // Update model in K/V store
update(1); // One unit of work
}
// 4) Save solution to model output
// Save X frame for user reference later
Vec[] xvecs = new Vec[_ncolX];
if(overwriteX) {
for (int i = 0; i < _ncolX; i++) xvecs[i] = fr.vec(idx_xnew(i, _ncolA, _ncolX));
} else {
for (int i = 0; i < _ncolX; i++) xvecs[i] = fr.vec(idx_xold(i, _ncolA));
}
x = new Frame(_parms._loading_key, null, xvecs);
xinfo = new DataInfo(Key.make(), x, null, 0, true, DataInfo.TransformType.NONE, DataInfo.TransformType.NONE, false, false, /* weights */ false, /* offset */ false);
DKV.put(x._key, x);
DKV.put(xinfo._key, xinfo);
model._output._loading_key = _parms._loading_key;
model._output._archetypes = yt;
model._output._step_size = step;
if (_parms._recover_svd) recoverSVD(model, xinfo);
// Optional: This computes XY, but do we need it?
// BMulTask tsk = new BMulTask(self(), xinfo, yt).doAll(dinfo._adaptedFrame.numCols(), xinfo._adaptedFrame);
// tsk.outputFrame(_parms._destination_key, _train._names, null);
model.update(self());
done();
} catch (Throwable t) {
Job thisJob = DKV.getGet(_key);
if (thisJob._state == JobState.CANCELLED) {
Log.info("Job cancelled by user.");
} else {
t.printStackTrace();
failed(t);
throw t;
}
} finally {
_parms.read_unlock_frames(GLRM.this);
if (model != null) model.unlock(_key);
if (tinfo != null) tinfo.remove();
if (dinfo != null) dinfo.remove();
if (xinfo != null) xinfo.remove();
// if (x != null && !_parms._keep_loading) x.delete();
// Clean up unused copy of X matrix
if (fr != null) {
if(overwriteX) {
for (int i = 0; i < _ncolX; i++) fr.vec(idx_xold(i, _ncolA)).remove();
} else {
for (int i = 0; i < _ncolX; i++) fr.vec(idx_xnew(i, _ncolA, _ncolX)).remove();
}
}
}
tryComplete();
}
Key self() {
return _key;
}
}
// In chunk, first _ncolA cols are A, next _ncolX cols are X
protected static int idx_xold(int c, int ncolA) { return ncolA+c; }
protected static int idx_xnew(int c, int ncolA, int ncolX) { return ncolA+ncolX+c; }
protected static int idx_ycat(int c, int level, DataInfo dinfo) { // TODO: Deal with case of missing bucket
// assert !Double.isNaN(level) && level >= 0 && level < dinfo._catLvls[c].length;
assert dinfo._adaptedFrame.domains() != null : "Domain of categorical column cannot be null";
assert !Double.isNaN(level) && level >= 0 && level < dinfo._adaptedFrame.domains()[c].length;
return dinfo._catOffsets[c]+level;
}
protected static int idx_ynum(int c, DataInfo dinfo) {
return dinfo._catOffsets[dinfo._catOffsets.length-1]+c;
}
protected static Chunk chk_xold(Chunk chks[], int c, int ncolA) { return chks[ncolA+c]; }
protected static Chunk chk_xnew(Chunk chks[], int c, int ncolA, int ncolX) { return chks[ncolA+ncolX+c]; }
protected static double[][] yt_block(double[][] yt, int cidx, DataInfo dinfo) {
return yt_block(yt, cidx, dinfo, false);
}
protected static double[][] yt_block(double[][] yt, int cidx, DataInfo dinfo, boolean transpose) {
int catlvls = dinfo._adaptedFrame.domains() == null ? 1 : dinfo._adaptedFrame.domains()[cidx].length;
// double[][] block = new double[dinfo._catLvls[cidx].length][yt[0].length];
double[][] block;
if(transpose) {
block = new double[yt[0].length][catlvls];
for (int col = 0; col < block.length; col++) {
for (int level = 0; level < block[0].length; level++) {
block[col][level] = yt[idx_ycat(cidx, level, dinfo)][col];
}
}
} else {
block = new double[catlvls][yt[0].length];
for (int col = 0; col < block[0].length; col++) {
for (int level = 0; level < block.length; level++) {
block[level][col] = yt[idx_ycat(cidx, level, dinfo)][col];
}
}
}
return block;
}
private static class UpdateX extends MRTask<UpdateX> {
// Input
DataInfo _dinfo;
GLRMParameters _parms;
final double _alpha; // Step size divided by num cols in A
final boolean _update; // Should we update X from working copy?
final double[][] _yt; // _yt = Y' (transpose of Y)
final int _ncolA; // Number of cols in training frame
final int _ncolX; // Number of cols in X (k)
final double[] _normSub; // For standardizing training data
final double[] _normMul;
// Output
double _loss; // Loss evaluated on A - XY using new X (and current Y)
double _xreg; // Regularization evaluated on new X
UpdateX(DataInfo dinfo, GLRMParameters parms, double[][] yt, double alpha, boolean update, int ncolA, int ncolX, double[] normSub, double[] normMul) {
assert yt != null && yt[0].length == ncolX;
_parms = parms;
_yt = yt;
_alpha = alpha;
_update = update;
_ncolA = ncolA;
_ncolX = ncolX;
// dinfo contains [A,X,W], but we only use its info on A (cols 1 to ncolA)
assert dinfo._cats <= ncolA;
_dinfo = dinfo;
_normSub = normSub;
_normMul = normMul;
}
@Override public void map(Chunk[] cs) {
assert (_ncolA + 2*_ncolX) == cs.length;
double[] a = new double[_ncolA];
Random rand = RandomUtils.getRNG(_parms._seed + cs[0].start());
_loss = _xreg = 0;
for(int row = 0; row < cs[0]._len; row++) {
double[] grad = new double[_ncolX];
double[] xnew = new double[_ncolX];
// Copy old working copy of X to current X if requested
if(_update) {
for(int k = 0; k < _ncolX; k++)
chk_xold(cs,k,_ncolA).set(row, chk_xnew(cs,k,_ncolA,_ncolX).atd(row));
}
// Compute gradient of objective at row
// Categorical columns
for(int j = 0; j < _dinfo._cats; j++) {
a[j] = cs[j].atd(row);
if(Double.isNaN(a[j])) continue; // Skip missing observations in row
// Calculate x_i * Y_j where Y_j is sub-matrix corresponding to categorical col j
// double[] xy = new double[_dinfo._catLvls[j].length];
double[] xy = new double[_dinfo._adaptedFrame.domains()[j].length];
for(int level = 0; level < xy.length; level++) {
for(int k = 0; k < _ncolX; k++) {
xy[level] += chk_xold(cs,k,_ncolA).atd(row) * _yt[idx_ycat(j,level,_dinfo)][k];
}
}
// Gradient wrt x_i is matrix product \grad L_{i,j}(x_i * Y_j, A_{i,j}) * Y_j'
double[] weight = _parms.mlgrad(xy, (int)a[j]);
double[][] ytsub = yt_block(_yt,j,_dinfo);
for(int k = 0; k < _ncolX; k++) {
for(int c = 0; c < weight.length; c++)
grad[k] += weight[c] * ytsub[c][k];
}
}
// Numeric columns
for(int j = _dinfo._cats; j < _ncolA; j++) {
int js = j - _dinfo._cats;
int yidx = idx_ynum(js,_dinfo);
a[j] = cs[j].atd(row);
if(Double.isNaN(a[j])) continue; // Skip missing observations in row
// Inner product x_i * y_j
double xy = 0;
for(int k = 0; k < _ncolX; k++)
xy += chk_xold(cs,k,_ncolA).atd(row) * _yt[yidx][k];
// Sum over y_j weighted by gradient of loss \grad L_{i,j}(x_i * y_j, A_{i,j})
double weight = _parms.lgrad(xy, (a[j] - _normSub[js]) * _normMul[js]);
for(int k = 0; k < _ncolX; k++)
grad[k] += weight * _yt[yidx][k];
}
// Update row x_i of working copy with new values
double[] u = new double[_ncolX];
for(int k = 0; k < _ncolX; k++) {
double xold = chk_xold(cs,k,_ncolA).atd(row); // Old value of x_i
u[k] = xold - _alpha * grad[k];
// xnew[k] = _parms.rproxgrad_x(xold - _alpha * grad[k], _alpha); // Proximal gradient
// chk_xnew(cs,k,_ncolA,_ncolX).set(row, xnew[k]);
// _xreg += _parms.regularize_x(xnew[k]);
}
xnew = _parms.rproxgrad_x(u, _alpha, rand);
_xreg += _parms.regularize_x(xnew);
for(int k = 0; k < _ncolX; k++)
chk_xnew(cs,k,_ncolA,_ncolX).set(row,xnew[k]);
// Compute loss function using new x_i
// Categorical columns
for(int j = 0; j < _dinfo._cats; j++) {
if(Double.isNaN(a[j])) continue; // Skip missing observations in row
double[] xy = ArrayUtils.multVecArr(xnew, yt_block(_yt,j,_dinfo,true));
_loss += _parms.mloss(xy, (int) a[j]);
}
// Numeric columns
for(int j = _dinfo._cats; j < _ncolA; j++) {
int js = j - _dinfo._cats;
if(Double.isNaN(a[j])) continue; // Skip missing observations in row
double xy = ArrayUtils.innerProduct(xnew, _yt[idx_ynum(js,_dinfo)]);
_loss += _parms.loss(xy, (a[j] - _normSub[js]) * _normMul[js]);
}
}
}
@Override public void reduce(UpdateX other) {
_loss += other._loss;
_xreg += other._xreg;
}
}
private static class UpdateY extends MRTask<UpdateY> {
// Input
DataInfo _dinfo;
GLRMParameters _parms;
final double _alpha; // Step size divided by num cols in A
final double[][] _ytold; // Old Y' matrix
final int _ncolA; // Number of cols in training frame
final int _ncolX; // Number of cols in X (k)
final double[] _normSub; // For standardizing training data
final double[] _normMul;
// Output
double[][] _ytnew; // New Y matrix
double _yreg; // Regularization evaluated on new Y
UpdateY(DataInfo dinfo, GLRMParameters parms, double[][] yt, double alpha, int ncolA, int ncolX, double[] normSub, double[] normMul) {
assert yt != null && yt[0].length == ncolX;
_parms = parms;
_alpha = alpha;
_ncolA = ncolA;
_ncolX = ncolX;
_ytold = yt;
_yreg = 0;
// _ytnew = new double[_ncolA][_ncolX];
// dinfo contains [A,X,W], but we only use its info on A (cols 1 to ncolA)
assert dinfo._cats <= ncolA;
_dinfo = dinfo;
_normSub = normSub;
_normMul = normMul;
}
@Override public void map(Chunk[] cs) {
assert (_ncolA + 2*_ncolX) == cs.length;
_ytnew = new double[_ytold.length][_ncolX];
// Categorical columns
for(int j = 0; j < _dinfo._cats; j++) {
// Compute gradient of objective at column
for(int row = 0; row < cs[0]._len; row++) {
double a = cs[j].atd(row);
if(Double.isNaN(a)) continue; // Skip missing observations in column
// Calculate x_i * Y_j where Y_j is sub-matrix corresponding to categorical col j
// double[] xy = new double[_dinfo._catLvls[j].length];
double[] xy = new double[_dinfo._adaptedFrame.domains()[j].length];
for(int level = 0; level < xy.length; level++) {
for(int k = 0; k < _ncolX; k++) {
xy[level] += chk_xnew(cs,k,_ncolA,_ncolX).atd(row) * _ytold[idx_ycat(j,level,_dinfo)][k];
}
}
// Gradient for level p is x_i weighted by \grad_p L_{i,j}(x_i * Y_j, A_{i,j})
double[] weight = _parms.mlgrad(xy, (int)a);
for(int level = 0; level < xy.length; level++) {
for(int k = 0; k < _ncolX; k++)
_ytnew[idx_ycat(j,level,_dinfo)][k] += weight[level] * chk_xnew(cs,k,_ncolA,_ncolX).atd(row);
}
}
}
// Numeric columns
for(int j = _dinfo._cats; j < _ncolA; j++) {
int js = j - _dinfo._cats;
int yidx = idx_ynum(js,_dinfo);
// Compute gradient of objective at column
for(int row = 0; row < cs[0]._len; row++) {
double a = cs[j].atd(row);
if(Double.isNaN(a)) continue; // Skip missing observations in column
// Inner product x_i * y_j
double xy = 0;
for(int k = 0; k < _ncolX; k++)
xy += chk_xnew(cs,k,_ncolA,_ncolX).atd(row) * _ytold[yidx][k];
// Sum over x_i weighted by gradient of loss \grad L_{i,j}(x_i * y_j, A_{i,j})
double weight = _parms.lgrad(xy, (a - _normSub[js]) * _normMul[js]);
for(int k = 0; k < _ncolX; k++)
_ytnew[yidx][k] += weight * chk_xnew(cs,k,_ncolA,_ncolX).atd(row);
}
}
}
@Override public void reduce(UpdateY other) {
ArrayUtils.add(_ytnew, other._ytnew);
}
@Override protected void postGlobal() {
assert _ytnew.length == _ytold.length && _ytnew[0].length == _ytold[0].length;
Random rand = RandomUtils.getRNG(_parms._seed);
// Compute new y_j values using proximal gradient
for(int j = 0; j < _ytnew.length; j++) {
double[] u = new double[_ytnew[0].length];
for(int k = 0; k < _ytnew[0].length; k++) {
// double u = _ytold[j][k] - _alpha * _ytnew[j][k];
// _ytnew[j][k] = _parms.rproxgrad_y(u, _alpha);
// _yreg += _parms.regularize_y(_ytnew[j][k]);
u[k] = _ytold[j][k] - _alpha * _ytnew[j][k];
}
_ytnew[j] = _parms.rproxgrad_y(u, _alpha, rand);
_yreg += _parms.regularize_y(_ytnew[j]);
}
}
}
// Calculate the sum loss function in the optimization objective
private static class ObjCalc extends MRTask<ObjCalc> {
// Input
DataInfo _dinfo;
GLRMParameters _parms;
final double[][] _yt; // _yt = Y' (transpose of Y)
final int _ncolA; // Number of cols in training frame
final int _ncolX; // Number of cols in X (k)
final double[] _normSub; // For standardizing training data
final double[] _normMul;
final boolean _regX; // Should I calculate regularization of (old) X matrix?
// Output
double _loss;
double _xold_reg;
ObjCalc(DataInfo dinfo, GLRMParameters parms, double[][] yt, int ncolA, int ncolX, double[] normSub, double[] normMul) {
this(dinfo, parms, yt, ncolA, ncolX, normSub, normMul, false);
}
ObjCalc(DataInfo dinfo, GLRMParameters parms, double[][] yt, int ncolA, int ncolX, double[] normSub, double[] normMul, boolean regX) {
assert yt != null && yt[0].length == ncolX;
_parms = parms;
_yt = yt;
_ncolA = ncolA;
_ncolX = ncolX;
_regX = regX;
_loss = _xold_reg = 0;
assert dinfo._cats <= ncolA;
_dinfo = dinfo;
_normSub = normSub;
_normMul = normMul;
}
@Override public void map(Chunk[] cs) {
assert (_ncolA + 2*_ncolX) == cs.length;
for(int row = 0; row < cs[0]._len; row++) {
// Categorical columns
for(int j = 0; j < _dinfo._cats; j++) {
double a = cs[j].atd(row);
if (Double.isNaN(a)) continue; // Skip missing observations in row
// Calculate x_i * Y_j where Y_j is sub-matrix corresponding to categorical col j
// double[] xy = new double[_dinfo._catLvls[j].length];
double[] xy = new double[_dinfo._adaptedFrame.domains()[j].length];
for(int level = 0; level < xy.length; level++) {
for(int k = 0; k < _ncolX; k++) {
xy[level] += chk_xnew(cs,k,_ncolA,_ncolX).atd(row) * _yt[idx_ycat(j,level,_dinfo)][k];
}
}
_loss += _parms.mloss(xy, (int)a);
}
// Numeric columns
for(int j = _dinfo._cats; j < _ncolA; j++) {
double a = cs[j].atd(row);
if (Double.isNaN(a)) continue; // Skip missing observations in row
// Inner product x_i * y_j
double xy = 0;
int js = j - _dinfo._cats;
for(int k = 0; k < _ncolX; k++)
xy += chk_xnew(cs,k,_ncolA,_ncolX).atd(row) * _yt[idx_ynum(js,_dinfo)][k];
_loss += _parms.loss(xy, (a - _normSub[js]) * _normMul[js]);
}
// Calculate regularization term for old X if requested
if(_regX) {
int idx = 0;
double[] xrow = new double[_ncolX];
for(int j = _ncolA; j < _ncolA+_ncolX; j++) {
// double x = cs[j].atd(row);
// _xold_reg += _parms.regularize_x(x);
xrow[idx] = cs[j].atd(row);
idx++;
}
assert idx == _ncolX;
_xold_reg += _parms.regularize_x(xrow);
}
}
}
}
// Solves XD = AY' for X where A is n by p, Y is k by p, D is k by k, and n >> p > k
// Resulting matrix X = (AY')D^(-1) will have dimensions n by k
private static class CholMulTask extends MRTask<CholMulTask> {
DataInfo _dinfo;
GLRMParameters _parms;
final double[][] _yt; // _yt = Y' (transpose of Y)
final int _ncolA; // Number of cols in training frame
final int _ncolX; // Number of cols in X (k)
final double[] _normSub; // For standardizing training data
final double[] _normMul;
CholeskyDecomposition _chol; // Cholesky decomposition of D = D', since we solve D'X' = DX' = AY'
CholMulTask(DataInfo dinfo, GLRMParameters parms, CholeskyDecomposition chol, double[][] yt, double[] normSub, double[] normMul) {
this(dinfo, parms, chol, yt, yt.length, yt[0].length, normSub, normMul);
}
CholMulTask(DataInfo dinfo, GLRMParameters parms, CholeskyDecomposition chol, double[][] yt, int ncolA, int ncolX, double[] normSub, double[] normMul) {
assert yt != null && yt[0].length == ncolX;
_parms = parms;
_yt = yt;
_ncolA = ncolA;
_ncolX = ncolX;
_chol = chol;
assert dinfo._cats <= ncolA;
_dinfo = dinfo;
_normSub = normSub;
_normMul = normMul;
}
// [A,X,W] A is read-only training data, X is left matrix in A = XY decomposition, W is working copy of X
@Override public void map(Chunk[] cs) {
assert (_ncolA + 2*_ncolX) == cs.length;
double[] xrow = new double[_ncolX];
for(int row = 0; row < cs[0]._len; row++) {
// 1) Compute single row of AY'
for (int k = 0; k < _ncolX; k++) {
// Categorical columns
double x = 0;
for(int d = 0; d < _dinfo._cats; d++) {
double a = cs[d].atd(row);
if (Double.isNaN(a)) continue;
x += _yt[idx_ycat(d, (int)a, _dinfo)][k];
}
// Numeric columns
for (int d = _dinfo._cats; d < _ncolA; d++) {
int ds = d - _dinfo._cats;
double a = cs[d].atd(row);
if (Double.isNaN(a)) continue;
x += (a - _normSub[ds]) * _normMul[ds] * _yt[idx_ynum(ds,_dinfo)][k];
}
xrow[k] = x;
}
// 2) Cholesky solve for single row of X
// _chol.solve(xrow);
Matrix tmp = _chol.solve(new Matrix(new double[][] {xrow}).transpose());
xrow = tmp.getColumnPackedCopy();
// 3) Save row of solved values into X (and copy W = X)
int i = 0;
for(int d = _ncolA; d < _ncolA+_ncolX; d++) {
cs[d].set(row, xrow[i]);
cs[d+_ncolX].set(row, xrow[i++]);
}
assert i == xrow.length;
}
}
}
// Computes XY where X is n by k, Y is k by p, and k <= p
// The resulting matrix Z = XY will have dimensions n by p
private static class BMulTask extends FrameTask<BMulTask> {
double[][] _yt; // _yt = Y' (transpose of Y)
BMulTask(Key jobKey, DataInfo dinfo, final double[][] yt) {
super(jobKey, dinfo);
_yt = yt;
}
@Override protected void processRow(long gid, DataInfo.Row row, NewChunk[] outputs) {
assert row.nBins + _dinfo._nums == _yt[0].length;
for(int p = 0; p < _yt.length; p++) {
double x = row.innerProduct(_yt[p]);
outputs[p].addNum(x);
}
}
}
}
|
import java.io.BufferedReader;
import java.io.FileReader;
import java.io.IOException;
import java.util.Vector;
import org.simgrid.msg.Msg;
import org.simgrid.msg.Host;
import org.simgrid.msg.Process;
public class LFC extends Process {
// A Logical File Catalog service is defined by:
// hostName: the name of the host that runs the service
// catalog: a vector of logical files
protected String hostName;
private Vector<LogicalFile> catalog;
// A simulation can begin with some logical files referenced in the LFC.
// In that case, the LFC process is launched with an argument which is the
// name of a CSV file stored in working directory that contains logical
// file description in the following format:
// name,size,se_1<:se_2:...:se_n>
// The populate function reads and parses that file, create LogicalFile
// objects and add them to the local catalog.
private void populate(String csvFile){
Msg.info("Population of LFC '"+ hostName + "' from '"+ csvFile + "'");
try {
BufferedReader br = new BufferedReader(new FileReader(csvFile));
String line = "";
while ((line = br.readLine()) != null) {
String[] fileInfo = line.split(",");
String[] seNames = fileInfo[2].split(":");
LogicalFile file = new LogicalFile(fileInfo[0],
Long.valueOf(fileInfo[1]).longValue(), seNames);
Msg.info("Importing file '" + file.toString());
catalog.add(file);
}
br.close();
} catch (IOException e) {
e.printStackTrace();
}
}
// A worker might want to register a new logical file, or a replica on an
// existing file in the catalog. This function first checks if a file with
// the same name already exists. If it does, it determines whether it is a
// new replica or not. Otherwise, it creates a new entry in the catalog for
// that file.
private void register(LogicalFile newFile){
if (catalog.contains((Object) newFile)){
LogicalFile file = catalog.get(catalog.indexOf(newFile));
if (!file.getLocations().contains((Object) newFile.getSEName())){
// This has to be a new replica
Msg.info("New replica for '" + newFile.getName () + "' on '" +
newFile.getSEName() + "'");
file.addLocation(newFile.getSEName());
} else {
Msg.debug(file.toString() + "is already registered");
}
} else {
// This file is not registered yet, create and add it
Msg.debug ("'" + newFile.getName() + "' is not registered yet");
catalog.add(newFile);
Msg.debug("LFC '"+ hostName + "' registered " + newFile.toString());
}
}
public LFC(Host host, String name, String[]args) {
super(host,name,args);
this.hostName = getHost().getName();
this.catalog = new Vector<>();
}
public void main(String[] args) {
boolean stop = false;
Msg.debug("Register LFC on "+ hostName);
VIPSimulator.getLFCList().add(hostName);
// If this LFC process is started with an argument, we populate the
// catalog from the CSV file given as args[0]
String csvFile = (args.length > 0 ? args[0] : null);
if (csvFile != null){
populate(csvFile);
Msg.debug(this.toString());
}
while (!stop){
Message message = Message.getFrom(hostName);
// To prevent message mixing, a specific mailbox is used whose name
// is the concatenation of LFC's hostName and sender mailbox
String returnMailbox = hostName+message.getSenderMailbox();
switch(message.getType()){
case REGISTER_FILE:
// Add an entry for the received logical file, if needed
// Then send back an ACK to the the sender
register(message.getFile());
Message.sendTo(returnMailbox, Message.Type.REGISTER_ACK);
Msg.debug("LFC '"+ hostName + "' sent back an ACK to '" +
message.getSenderMailbox() + "'");
break;
case ASK_LOGICAL_FILE:
LogicalFile file =
getLogicalFileByName(message.getLogicalName());
// If this logical file is available on several locations, a
// single one is selected before returning the file to the
// worker asking for it.
file.selectLocation();
Message.sendTo(returnMailbox,
Message.Type.SEND_LOGICAL_FILE, file);
Msg.debug("LFC '"+ hostName + "' returned Logical " +
file.toString() + " back to '" +
message.getSenderMailbox() + "'");
break;
case ASK_LS:
Vector<LogicalFile> directoryContents =
new Vector<LogicalFile>();
for (LogicalFile f : catalog)
if (f.getName().matches(message.getLogicalName()+"(.*)"))
directoryContents.add(f);
Message.sendTo(returnMailbox, Message.Type.SEND_LS,
directoryContents);
break;
case FINALIZE:
Msg.verb("Goodbye!");
stop = true;
break;
default:
break;
}
}
}
public LogicalFile getLogicalFileByName (String logicalFileName) {
LogicalFile file = catalog.get(catalog.indexOf((Object)
new LogicalFile (logicalFileName, 0, "")));
if(file == null){
Msg.error("File '" + logicalFileName +
"' is stored on no SE. Exiting with status 1");
System.exit(1);
}
return file;
}
public Vector<LogicalFile> getResults(){
Vector<LogicalFile> results = new Vector<LogicalFile>();
for (LogicalFile file : catalog)
if (file.getName().matches("results/(.*)partial(.*)")){
results.add(file);
}
return results;
}
public String getSEName (String logicalFileName){
return getLogicalFileByName(logicalFileName).getSEName();
}
public String toString () {
return catalog.toString();
}
}
|
public class Rel extends Node {
public Node left, right;
public int op;
public Rel(int op, Node left, Node right) {
this.op = op;
this.left = left;
this.right = right;
}
@Override
public Value interp(Scope s) {
Value lv = left.interp(s);
Value rv = right.interp(s);
if (lv instanceof StringValue && rv instanceof StringValue) {
String l = ((StringValue) lv).value;
String r = ((StringValue) rv).value;
return new BoolValue(op(l.compareTo(r), 0));
}
if (lv instanceof IntValue && rv instanceof IntValue) {
int l = ((IntValue) lv).value;
int r = ((IntValue) rv).value;
return new BoolValue(op(l, r));
}
if (lv instanceof FloatValue && rv instanceof FloatValue) {
int l = (int) ((FloatValue) lv).value;
int r = (int) ((FloatValue) rv).value;
return new BoolValue(op(l, r));
}
// // eg. Type.Dict == Type.dict
if (lv instanceof Type && rv instanceof Type)
return new BoolValue(lv == rv);
S.error("Type compare unsupport error: %s, %s", lv, rv);
return Value.FALSE; // never touch
}
private boolean op(int l, int r) {
boolean ret = false;
switch (op) {
case '>':
ret = l > r;
break;
case '<':
ret = l < r;
break;
case Tag.EQ:
ret = l == r;
break;
case Tag.NE:
ret = l != r;
break;
case Tag.LE:
ret = l <= r;
break;
case Tag.GE:
ret = l >= r;
break;
default:
S.error(": " + (char) op);
}
return ret;
}
@Override
public String toString() {
return left + " " + Tag.descOf(op) + " " + right;
}
}
|
package ch.ethz.globis.disindex.codec;
import ch.ethz.globis.disindex.codec.api.FieldDecoder;
import ch.ethz.globis.disindex.codec.api.ResponseDecoder;
import java.util.List;
/**
* Decodes response messages sent by the server to the client.
*
* @param <K> The type of the key.
* @param <V> The type of the value.
*/
public class ByteResponseDecoder<K, V> implements ResponseDecoder<K, V> {
FieldDecoder<V> valueDecoder;
public ByteResponseDecoder(FieldDecoder<V> valueDecoder) {
this.valueDecoder = valueDecoder;
}
@Override
public V decodePut(byte[] payload) {
return valueDecoder.decode(payload);
}
@Override
public V decodeGet(byte[] payload) {
return valueDecoder.decode(payload);
}
@Override
public List<V> decodeGetRange(List<byte[]> payload) {
throw new UnsupportedOperationException("Operation not yet implemented");
}
@Override
public List<V> decodeGetKNN(List<byte[]> payload) {
throw new UnsupportedOperationException("Operation not yet implemented");
}
@Override
public boolean decodeCreate(byte[] payload) {
return (payload.length == 1 && payload[0] == MessageCode.SUCCESS);
}
}
|
package com.xpn.xwiki.doc;
import java.io.StringWriter;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.ResourceBundle;
import org.jmock.Mock;
import org.jmock.core.Invocation;
import org.jmock.core.stub.CustomStub;
import org.xwiki.display.internal.DisplayConfiguration;
import org.xwiki.model.reference.DocumentReference;
import org.xwiki.model.reference.EntityReferenceSerializer;
import org.xwiki.rendering.configuration.RenderingConfiguration;
import org.xwiki.rendering.internal.configuration.DefaultRenderingConfiguration;
import org.xwiki.rendering.syntax.Syntax;
import org.xwiki.security.authorization.Right;
import org.xwiki.velocity.VelocityEngine;
import org.xwiki.velocity.VelocityManager;
import org.xwiki.velocity.XWikiVelocityException;
import com.xpn.xwiki.XWiki;
import com.xpn.xwiki.XWikiContext;
import com.xpn.xwiki.objects.BaseObject;
import com.xpn.xwiki.objects.classes.BaseClass;
import com.xpn.xwiki.objects.classes.PropertyClass;
import com.xpn.xwiki.objects.classes.TextAreaClass;
import com.xpn.xwiki.store.XWikiStoreInterface;
import com.xpn.xwiki.store.XWikiVersioningStoreInterface;
import com.xpn.xwiki.test.AbstractBridgedXWikiComponentTestCase;
import com.xpn.xwiki.user.api.XWikiRightService;
import com.xpn.xwiki.web.XWikiMessageTool;
/**
* Unit tests for {@link XWikiDocument}.
*
* @version $Id$
*/
public class XWikiDocumentTest extends AbstractBridgedXWikiComponentTestCase
{
private static final String DOCWIKI = "WikiDescriptor";
private static final String DOCSPACE = "Space";
private static final String DOCNAME = "Page";
private static final String DOCFULLNAME = DOCSPACE + "." + DOCNAME;
private static final DocumentReference DOCUMENT_REFERENCE = new DocumentReference(DOCWIKI, DOCSPACE, DOCNAME);
private static final String CLASSNAME = DOCFULLNAME;
private static final DocumentReference CLASS_REFERENCE = DOCUMENT_REFERENCE;
private XWikiDocument document;
private XWikiDocument translatedDocument;
private Mock mockXWiki;
private Mock mockXWikiVersioningStore;
private Mock mockXWikiStoreInterface;
private Mock mockXWikiMessageTool;
private Mock mockXWikiRightService;
private Mock mockVelocityEngine;
private Mock mockDisplayConfiguration;
private CustomStub velocityEngineEvaluateStub;
private BaseClass baseClass;
private BaseObject baseObject;
private EntityReferenceSerializer<String> defaultEntityReferenceSerializer;
@Override
protected void setUp() throws Exception
{
super.setUp();
this.defaultEntityReferenceSerializer = getComponentManager().getInstance(EntityReferenceSerializer.TYPE_STRING);
this.document = new XWikiDocument(new DocumentReference(DOCWIKI, DOCSPACE, DOCNAME));
this.document.setSyntax(Syntax.XWIKI_1_0);
this.document.setLanguage("en");
this.document.setDefaultLanguage("en");
this.document.setNew(false);
this.translatedDocument = new XWikiDocument();
this.translatedDocument.setSyntax(Syntax.XWIKI_2_0);
this.translatedDocument.setLanguage("fr");
this.translatedDocument.setNew(false);
getContext().put("isInRenderingEngine", true);
this.mockXWiki = mock(XWiki.class);
this.mockXWikiVersioningStore = mock(XWikiVersioningStoreInterface.class);
this.mockXWikiVersioningStore.stubs().method("getXWikiDocumentArchive").will(returnValue(null));
this.mockXWikiStoreInterface = mock(XWikiStoreInterface.class);
this.document.setStore((XWikiStoreInterface) this.mockXWikiStoreInterface.proxy());
this.mockXWikiMessageTool =
mock(XWikiMessageTool.class, new Class[] {ResourceBundle.class, XWikiContext.class}, new Object[] {null,
getContext()});
this.mockXWikiMessageTool.stubs().method("get").will(returnValue("message"));
this.mockXWikiRightService = mock(XWikiRightService.class);
this.mockXWikiRightService.stubs().method("hasProgrammingRights").will(returnValue(true));
this.mockXWiki.stubs().method("getVersioningStore").will(returnValue(this.mockXWikiVersioningStore.proxy()));
this.mockXWiki.stubs().method("getStore").will(returnValue(this.mockXWikiStoreInterface.proxy()));
this.mockXWiki.stubs().method("getDocument").will(returnValue(this.document));
this.mockXWiki.stubs().method("getLanguagePreference").will(returnValue("en"));
this.mockXWiki.stubs().method("getSectionEditingDepth").will(returnValue(2L));
this.mockXWiki.stubs().method("getRightService").will(returnValue(this.mockXWikiRightService.proxy()));
getContext().setWiki((XWiki) this.mockXWiki.proxy());
getContext().put("msg", this.mockXWikiMessageTool.proxy());
this.baseClass = this.document.getxWikiClass();
this.baseClass.addTextField("string", "String", 30);
this.baseClass.addTextAreaField("area", "Area", 10, 10);
this.baseClass.addTextAreaField("puretextarea", "Pure text area", 10, 10);
// set the text areas an non interpreted content
((TextAreaClass) this.baseClass.getField("puretextarea")).setContentType("puretext");
this.baseClass.addPasswordField("passwd", "Password", 30);
this.baseClass.addBooleanField("boolean", "Boolean", "yesno");
this.baseClass.addNumberField("int", "Int", 10, "integer");
this.baseClass.addStaticListField("stringlist", "StringList", "value1, value2");
this.mockXWiki.stubs().method("getClass").will(returnValue(this.baseClass));
this.mockXWiki.stubs().method("getXClass").will(returnValue(this.baseClass));
this.baseObject = this.document.newObject(CLASSNAME, getContext());
this.baseObject.setStringValue("string", "string");
this.baseObject.setLargeStringValue("area", "area");
this.baseObject.setStringValue("passwd", "passwd");
this.baseObject.setIntValue("boolean", 1);
this.baseObject.setIntValue("int", 42);
this.baseObject.setStringListValue("stringlist", Arrays.asList("VALUE1", "VALUE2"));
this.mockXWikiStoreInterface.stubs().method("search").will(returnValue(new ArrayList<XWikiDocument>()));
// Set the default link label generator format to %np for some tests below.
// We need to do this since we don't depend on xwiki-platform-rendering-configuration-default (which contains
// an overridden RenderingConfiguration impl that sets the format to %np by default).
DefaultRenderingConfiguration renderingConfiguration =
getComponentManager().getInstance(RenderingConfiguration.class);
renderingConfiguration.setLinkLabelFormat("%np");
}
@Override
protected void registerComponents() throws Exception
{
super.registerComponents();
getContextualAuthorizationManager().stubs()
.method("hasAccess").with(eq(Right.PROGRAM)).will(returnValue(true));
// Setup display configuration.
this.mockDisplayConfiguration = registerMockComponent(DisplayConfiguration.class);
this.mockDisplayConfiguration.stubs().method("getDocumentDisplayerHint").will(returnValue("default"));
this.mockDisplayConfiguration.stubs().method("getTitleHeadingDepth").will(returnValue(2));
// Setup the mock Velocity engine.
Mock mockVelocityManager = registerMockComponent(VelocityManager.class);
this.mockVelocityEngine = mock(VelocityEngine.class);
mockVelocityManager.stubs().method("getVelocityContext").will(returnValue(null));
mockVelocityManager.stubs().method("getVelocityEngine").will(returnValue(this.mockVelocityEngine.proxy()));
velocityEngineEvaluateStub = new CustomStub("Implements VelocityEngine.evaluate")
{
@Override
public Object invoke(Invocation invocation) throws Throwable
{
// Output the given text without changes.
StringWriter writer = (StringWriter) invocation.parameterValues.get(1);
String text = (String) invocation.parameterValues.get(3);
writer.append(text);
return true;
}
};
this.mockVelocityEngine.stubs().method("evaluate").will(velocityEngineEvaluateStub);
this.mockVelocityEngine.stubs().method("startedUsingMacroNamespace");
this.mockVelocityEngine.stubs().method("stoppedUsingMacroNamespace");
}
public void testGetDisplayTitleWhenNoTitleAndNoContent()
{
this.document.setContent("Some content");
assertEquals("Page", this.document.getDisplayTitle(getContext()));
}
public void testGetDisplayWhenTitleExists()
{
this.document.setContent("Some content");
this.document.setTitle("Title");
this.mockVelocityEngine.expects(once()).method("evaluate").with(null, ANYTHING, ANYTHING, eq("Title"))
.will(velocityEngineEvaluateStub);
assertEquals("Title", this.document.getDisplayTitle(getContext()));
}
public void testGetDisplayWhenNoTitleButSectionExists()
{
getConfigurationSource().setProperty("xwiki.title.compatibility", "1");
this.document.setContent("Some content\n1 Title");
this.mockVelocityEngine.expects(once()).method("evaluate").with(null, ANYTHING, ANYTHING, eq("Title"))
.will(velocityEngineEvaluateStub);
assertEquals("Title", this.document.getDisplayTitle(getContext()));
}
/**
* Verify that if an error happens when evaluation the title, we fallback to the computed title.
*/
public void testGetDisplayTitleWhenVelocityError()
{
this.document.setContent("Some content");
this.document.setTitle("some content that generate a velocity error");
this.mockVelocityEngine.expects(once()).method("evaluate")
.will(throwException(new XWikiVelocityException("message")));
assertEquals("Page", this.document.getDisplayTitle(getContext()));
}
public void testGetxWikiClass()
{
this.document.getxWikiClass();
((PropertyClass)this.baseObject.getxWikiClass(getContext()).get("string")).getxWikiClass(getContext());
}
public void testExtractTitle()
{
this.mockXWiki.stubs().method("exists").will(returnValue(false));
this.document.setSyntax(Syntax.XWIKI_2_0);
this.document.setContent("content not in section\n" + "= header 1=\nheader 1 content\n"
+ "== header 2==\nheader 2 content");
assertEquals("header 1", this.document.extractTitle());
this.document.setContent("content not in section\n" + "= **header 1**=\nheader 1 content\n"
+ "== header 2==\nheader 2 content");
assertEquals("<strong>header 1</strong>", this.document.extractTitle());
this.document.setContent("content not in section\n" + "= [[Space.Page]]=\nheader 1 content\n"
+ "== header 2==\nheader 2 content");
this.mockXWiki.stubs().method("getURL").will(returnValue("/reference"));
assertEquals("<span class=\"wikicreatelink\"><a href=\"/reference\"><span class=\"wikigeneratedlinkcontent\">"
+ "Page" + "</span></a></span>", this.document.extractTitle());
this.document.setContent("content not in section\n" + "= #set($var ~= \"value\")=\nheader 1 content\n"
+ "== header 2==\nheader 2 content");
assertEquals("#set($var = \"value\")", this.document.extractTitle());
this.document.setContent("content not in section\n"
+ "= {{groovy}}print \"value\"{{/groovy}}=\nheader 1 content\n" + "== header 2==\nheader 2 content");
assertEquals("value", this.document.extractTitle());
this.document.setContent("content not in section\n=== header 3===");
assertEquals("", this.document.extractTitle());
}
public void testExtractTitle10()
{
this.document.setContent("content not in section\n" + "1 header 1\nheader 1 content\n"
+ "1.1 header 2\nheader 2 content");
assertEquals("header 1", this.document.extractTitle());
this.document.setContent("content not in section\n");
assertEquals("", this.document.extractTitle());
}
public void testSetAbsoluteParentReference()
{
XWikiDocument doc = new XWikiDocument(new DocumentReference("docwiki", "docspace", "docpage"));
doc.setParentReference(new DocumentReference("docwiki", "docspace", "docpage2"));
assertEquals("docspace.docpage2", doc.getParent());
}
}
|
package gov.hhs.fha.nhinc.admingui.display;
import gov.hhs.fha.nhinc.admingui.services.FhirResourceService;
import gov.hhs.fha.nhinc.connectmgr.ConnectionManagerCache;
import gov.hhs.fha.nhinc.connectmgr.ConnectionManagerException;
import gov.hhs.fha.nhinc.nhinclib.NhincConstants;
import gov.hhs.fha.nhinc.nhinclib.NullChecker;
import org.apache.log4j.Logger;
/**
*
* @author jassmit
*/
public class FhirDisplayController implements DisplayController {
private static final Logger LOG = Logger.getLogger(FhirDisplayController.class);
@Override
public void checkDisplay() {
String[] resourceNames = new String[]{FhirResourceService.BINARY_RESOURCE_NAME, FhirResourceService.DOCREF_RESOURCE_NAME,
FhirResourceService.PATIENT_RESOURCE_NAME };
for(String resourceName : resourceNames) {
boolean hasResource;
try {
hasResource = checkForResource(resourceName);
} catch(ConnectionManagerException e) {
LOG.warn(e, e);
hasResource = false;
}
if(hasResource == true) {
DisplayHolder.getInstance().setFhirEnabled(hasResource);
return;
}
}
DisplayHolder.getInstance().setFhirEnabled(false);
}
private boolean checkForResource(String resourceName) throws ConnectionManagerException {
return NullChecker.isNotNullish(ConnectionManagerCache.getInstance().getAdapterEndpointURL(resourceName, NhincConstants.ADAPTER_API_LEVEL.LEVEL_a0));
}
}
|
package com.hockeyhurd.entity.tileentity.renderer;
import net.minecraft.block.Block;
import net.minecraft.client.model.ModelChest;
import net.minecraft.client.renderer.tileentity.TileEntityChestRenderer;
import net.minecraft.tileentity.TileEntity;
import net.minecraft.util.ResourceLocation;
import org.lwjgl.opengl.GL11;
import org.lwjgl.opengl.GL12;
import com.hockeyhurd.block.machines.BlockGlowChest;
import com.hockeyhurd.entity.tileentity.TileEntityGlowChest;
import cpw.mods.fml.common.FMLLog;
import cpw.mods.fml.relauncher.Side;
import cpw.mods.fml.relauncher.SideOnly;
@SideOnly(Side.CLIENT)
public class TileEntityGlowChestRenderer extends TileEntityChestRenderer {
private static final ResourceLocation texture_ = new ResourceLocation("extratools", "textures/blocks/GlowChest.png");
// private static final ResourceLocation texture_ = new ResourceLocation("textures/entity/chest/normal.png");
private ModelChest field_147510_h = new ModelChest();
private static final String __OBFID = "CL_00000965";
public TileEntityGlowChestRenderer() {
}
public void renderTileEntityAt(TileEntityGlowChest entity, double x, double y, double z, float p_147500_8_) {
int i;
if (!entity.hasWorldObj()) i = 0;
else {
Block block = entity.getBlockType();
i = entity.getBlockMetadata();
if (block instanceof BlockGlowChest && i == 0) {
try {
((BlockGlowChest) block).func_149954_e(entity.getWorldObj(), entity.xCoord, entity.yCoord, entity.zCoord);
}
catch (ClassCastException e) {
FMLLog.severe("Attempted to render a chest at %d, %d, %d that was not a chest", entity.xCoord, entity.yCoord, entity.zCoord);
}
i = entity.getBlockMetadata();
}
}
ModelChest modelchest;
modelchest = this.field_147510_h;
if (entity.func_145980_j() == 0) this.bindTexture(texture_);
GL11.glPushMatrix();
GL11.glEnable(GL12.GL_RESCALE_NORMAL);
GL11.glColor4f(1.0F, 1.0F, 1.0F, 1.0F);
GL11.glTranslatef((float) x, (float) y + 1.0F, (float) z + 1.0F);
GL11.glScalef(1.0F, -1.0F, -1.0F);
GL11.glTranslatef(0.5F, 0.5F, 0.5F);
short short1 = 0;
if (i == 2) short1 = 180;
if (i == 3) short1 = 0;
if (i == 4) short1 = 90;
if (i == 5) short1 = -90;
// if (i == 2) GL11.glTranslatef(1.0F, 0.0F, 0.0F);
// if (i == 5) GL11.glTranslatef(0.0F, 0.0F, -1.0F);
GL11.glRotatef((float) short1, 0.0F, 1.0F, 0.0F);
GL11.glTranslatef(-0.5F, -0.5F, -0.5F);
float f1 = entity.prevLidAngle + (entity.lidAngle - entity.prevLidAngle) * p_147500_8_;
float f2;
f1 = 1.0F - f1;
f1 = 1.0F - f1 * f1 * f1;
modelchest.chestLid.rotateAngleX = -(f1 * (float) Math.PI / 2.0F);
modelchest.renderAll();
GL11.glDisable(GL12.GL_RESCALE_NORMAL);
GL11.glPopMatrix();
GL11.glColor4f(1.0F, 1.0F, 1.0F, 1.0F);
}
public void renderTileEntityAt(TileEntity p_147500_1_, double p_147500_2_, double p_147500_4_, double p_147500_6_, float p_147500_8_) {
this.renderTileEntityAt((TileEntityGlowChest) p_147500_1_, p_147500_2_, p_147500_4_, p_147500_6_, p_147500_8_);
}
}
|
package fr.synchrotron.soleil.ica.msvervice.management;
import fr.synchrotron.soleil.ica.msvervice.management.handlers.POMExportHandler;
import fr.synchrotron.soleil.ica.msvervice.management.handlers.POMImportHandler;
import fr.synchrotron.soleil.ica.msvervice.vertx.verticle.pomexporter.POMExporterWorkerVerticle;
import fr.synchrotron.soleil.ica.msvervice.vertx.verticle.pomimport.POMImporterWorkerVerticle;
import io.netty.handler.codec.http.HttpResponseStatus;
import org.vertx.java.core.AsyncResult;
import org.vertx.java.core.AsyncResultHandler;
import org.vertx.java.core.Handler;
import org.vertx.java.core.eventbus.EventBus;
import org.vertx.java.core.http.HttpServerRequest;
import org.vertx.java.core.http.RouteMatcher;
import org.vertx.java.core.json.JsonObject;
import org.vertx.java.platform.Verticle;
import java.io.IOException;
import java.util.Map;
import java.util.Properties;
/**
* @author Gregory Boissinot
*/
public class HttpEndpointManager extends Verticle {
public static final long SEND_MS_TIMEOUT = 10 * 1000l; // in ms
private static final String MONGODB_PROPERTIES_FILEPATH = "/infra.properties";
@Override
public void start() {
try {
final EventBus eventBus = vertx.eventBus();
//-- Deploy Required Verticle
final AsyncResultHandler<String> asyncResultHandler = new AsyncResultHandler<String>() {
@Override
public void handle(AsyncResult<String> asyncResult) {
onVerticleLoaded(asyncResult);
}
};
final JsonObject jsonObject = createConfig();
container.deployWorkerVerticle(
POMImporterWorkerVerticle.class.getCanonicalName(),
jsonObject, 1, true, asyncResultHandler);
container.deployWorkerVerticle(
POMExporterWorkerVerticle.class.getCanonicalName(),
jsonObject, 1, true, asyncResultHandler);
RouteMatcher routeMatcher = new RouteMatcher();
//-- POM IMPORTER
final POMImportHandler pomImportHandler = new POMImportHandler(eventBus);
routeMatcher.post("/pom/import", pomImportHandler);
routeMatcher.put("/pom/import", pomImportHandler);
//--POM EXPORTER
final POMExportHandler pomExportHandler = new POMExportHandler(eventBus);
routeMatcher.post("/pom/export", pomExportHandler);
routeMatcher.allWithRegEx(".*", new Handler<HttpServerRequest>() {
@Override
public void handle(HttpServerRequest request) {
request.response().setStatusCode(HttpResponseStatus.NOT_FOUND.code());
request.response().end("Path or Http method not supported.\n");
}
});
final int serverPort = getServerPort(container.config());
vertx.createHttpServer().requestHandler(routeMatcher).listen(serverPort);
container.logger().info("Webserver started on " + serverPort);
} catch (Throwable e) {
container.logger().error(e.getMessage());
}
}
private int getServerPort(JsonObject config) {
final Integer port = config.getInteger("port");
if (port == null) {
throw new ConfigurationException("A port number is required");
}
return port;
}
private void onVerticleLoaded(AsyncResult<String> asyncResult) {
if (!asyncResult.succeeded()) {
container.logger().info(asyncResult.cause());
}
}
private JsonObject createConfig() {
final JsonObject config = container.config();
Properties properties = loadInfraFile(MONGODB_PROPERTIES_FILEPATH);
for (Map.Entry<Object, Object> objectObjectEntry : properties.entrySet()) {
String propKey = (String) objectObjectEntry.getKey();
if (!config.containsField(propKey)) {
String propValue = (String) objectObjectEntry.getValue();
config.putString(propKey, propValue);
}
}
return config;
}
private Properties loadInfraFile(String propertiedFilePath) {
Properties properties = new Properties();
try {
properties.load(this.getClass().getResourceAsStream(propertiedFilePath));
return properties;
} catch (IOException ioe) {
throw new RuntimeException(ioe);
}
}
}
|
package org.iidp.ostmap.commons.tokenizer;
import org.junit.Assert;
import org.junit.Test;
import java.util.List;
public class TokenizerTest {
private static final String INPUT_TEXT1 = "this is some text\n and +i love (it) #truelove @test''...../''!+<>!!! " ;
private static final String INPUT_TEXT2 = "Hello Example ...";
private static final String[] TOKENS1 = new String[] { "this" ,"is", "some", "text", "and" , "love", "it", "#truelove", "truelove","@test", "test"};
private static final String[] TOKENS2 = new String[] { "hello" ,"example" };
@Test
public void testGetTokens(){
Tokenizer tokenizer = new Tokenizer();
List<String> tokens1 = tokenizer.tokenizeString(INPUT_TEXT1);
for(String s: tokens1){
System.out.println(s);
Boolean equal1 = false;
for(int i= 0 ; i<TOKENS1.length;i++){
if(s.equals(TOKENS1[i])){
equal1= true;
break;
}
}
Assert.assertTrue(equal1);
}
List<String> tokens2 = tokenizer.tokenizeString(INPUT_TEXT2);
for(String s: tokens2){
Boolean equal2 = false;
for(int i= 0 ; i<TOKENS2.length;i++){
if(s.equals(TOKENS2[i])){
equal2= true;
break;
}
}
Assert.assertTrue(equal2);
}
}
}
|
package simpleserver.nbt;
import java.io.DataInputStream;
import java.io.DataOutputStream;
import java.io.IOException;
import java.util.ArrayList;
import java.util.List;
public class NBTList<T extends NBTag> extends NBTag {
private ArrayList<T> value;
private byte tagId;
NBTList(DataInputStream in, Boolean named) throws Exception {
super(in, named);
}
public NBTList(byte tagId) {
this.tagId = tagId;
value = new ArrayList<T>();
}
public NBTList(NBT tag) {
this(tag.id());
}
public NBTList(String name, byte tagId) {
super(name);
this.tagId = tagId;
value = new ArrayList<T>();
}
public NBTList(String name, NBT tag) {
this(name, tag.id());
}
@Override
protected byte id() {
return 9;
}
@Override
List<T> get() {
return value;
}
public int size() {
return value.size();
}
public void clear() {
value.clear();
}
public NBT type() {
return NBT.values()[tagId];
}
@SuppressWarnings( { "unchecked", "hiding" })
public <T extends NBTag> T cast() {
return (T) this;
}
public void add(T tag) {
if (tagId == tag.id()) {
value.add(tag);
}
}
public boolean contains(T obj) {
return value.contains(obj);
}
public T get(int index) {
return value.get(index);
}
public NBTByte getByte(int index) {
return (NBTByte) value.get(index);
}
public NBTShort getShort(int index) {
return (NBTShort) value.get(index);
}
public NBTInt getInt(int index) {
return (NBTInt) value.get(index);
}
public NBTLong getLong(int name) {
return (NBTLong) value.get(name);
}
public NBTFloat getFloat(int index) {
return (NBTFloat) value.get(index);
}
public NBTDouble getDouble(int index) {
return (NBTDouble) value.get(index);
}
public NBTArray getArray(int index) {
return (NBTArray) value.get(index);
}
public NBTString getString(int index) {
return (NBTString) value.get(index);
}
@SuppressWarnings("unchecked")
public NBTList<NBTag> getList(int index) {
return (NBTList<NBTag>) value.get(index);
}
public NBTCompound getCompound(int index) {
return (NBTCompound) value.get(index);
}
@SuppressWarnings("unchecked")
@Override
protected void loadValue(DataInputStream in) throws Exception {
tagId = in.readByte();
int length = in.readInt();
value = new ArrayList<T>(length);
for (int i = 0; i < length; i++) {
value.add((T) NBT.loadTag(in, false, tagId));
}
}
@Override
protected void saveValue(DataOutputStream out) throws IOException {
out.writeByte(tagId);
out.writeInt(size());
for (NBTag tag : value) {
tag.save(out, false);
}
}
@Override
protected String valueToString(int level) {
StringBuilder string = new StringBuilder();
string.append("[\n");
for (NBTag tag : value) {
string.append(tag.toString(level + 1) + "\n");
}
string.append(indent(level));
string.append("]");
return string.toString();
}
}
|
package ome.xml.meta;
import net.imglib2.meta.Axes;
import org.scijava.plugin.Parameter;
import org.scijava.plugin.Plugin;
import org.scijava.service.AbstractService;
import org.scijava.service.Service;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import ome.scifio.DefaultImageMetadata;
import ome.scifio.FormatException;
import ome.scifio.FormatService;
import ome.scifio.ImageMetadata;
import ome.scifio.Metadata;
import ome.scifio.Reader;
import ome.scifio.common.DateTools;
import ome.scifio.io.Location;
import ome.scifio.services.ServiceException;
import ome.scifio.util.FormatTools;
import ome.scifio.util.SCIFIOMetadataTools;
import ome.xml.model.*;
import ome.xml.model.enums.Correction;
import ome.xml.model.enums.DetectorType;
import ome.xml.model.enums.DimensionOrder;
import ome.xml.model.enums.EnumerationException;
import ome.xml.model.enums.ExperimentType;
import ome.xml.model.enums.Immersion;
import ome.xml.model.enums.LaserMedium;
import ome.xml.model.enums.LaserType;
import ome.xml.model.enums.PixelType;
import ome.xml.model.enums.handlers.CorrectionEnumHandler;
import ome.xml.model.enums.handlers.DetectorTypeEnumHandler;
import ome.xml.model.enums.handlers.ExperimentTypeEnumHandler;
import ome.xml.model.enums.handlers.ImmersionEnumHandler;
import ome.xml.model.enums.handlers.LaserMediumEnumHandler;
import ome.xml.model.enums.handlers.LaserTypeEnumHandler;
import ome.xml.model.primitives.*;
import ome.xml.services.OMEXMLService;
@Plugin(type = Service.class)
public class DefaultOMEXMLMetadataService extends AbstractService
implements OMEXMLMetadataService {
// -- Constants --
private static final Logger LOGGER =
LoggerFactory.getLogger(DefaultOMEXMLMetadataService.class);
// -- Static fields --
private boolean defaultDateEnabled = true;
// -- Parameters --
@Parameter
FormatService formatService;
// -- Utility methods - OME-XML --
/**
* Populates the 'pixels' element of the given metadata store, using core
* metadata from the given reader.
*/
public void populatePixels(MetadataStore store, Metadata meta) {
populatePixels(store, meta, false, true);
}
/**
* Populates the 'pixels' element of the given metadata store, using core
* metadata from the given reader. If the 'doPlane' flag is set,
* then the 'plane' elements will be populated as well.
*/
public void populatePixels(MetadataStore store, Metadata meta,
boolean doPlane)
{
populatePixels(store, meta, doPlane, true);
}
/**
* Populates the 'pixels' element of the given metadata store, using core
* metadata from the given reader. If the 'doPlane' flag is set,
* then the 'plane' elements will be populated as well.
* If the 'doImageName' flag is set, then the image name will be populated
* as well. By default, 'doImageName' is true.
*/
public void populatePixels(MetadataStore store, Metadata meta,
boolean doPlane, boolean doImageName)
{
if (store == null || meta == null) return;
for (int i=0; i<meta.getImageCount(); i++) {
String imageName = null;
if (doImageName) {
Location f = new Location(getContext(), meta.getDatasetName());
imageName = f.getName();
}
String pixelType = FormatTools.getPixelTypeString(meta.getPixelType(i));
String order = FormatTools.findDimensionOrder(meta, i);
int xSize = meta.getAxisLength(i, Axes.X);
int ySize = meta.getAxisLength(i, Axes.Y);
int zSize = meta.getAxisLength(i, Axes.Z);
int cSize = meta.getAxisLength(i, Axes.CHANNEL);
int tSize = meta.getAxisLength(i, Axes.TIME);
populateMetadata(store, meta.getDatasetName(), i, imageName,
meta.isLittleEndian(i), order, pixelType, xSize,
ySize, zSize, cSize, tSize,
meta.getRGBChannelCount(i));
OMEXMLService service = formatService.getInstance(OMEXMLService.class);
if (service.isOMEXMLRoot(store.getRoot())) {
//TODO any way or reason to access a base store?
if(service.isOMEXMLMetadata(store)) {
OMEXMLMetadata omeMeta;
try {
omeMeta = service.getOMEMetadata(service.asRetrieve(store));
omeMeta.resolveReferences();
}
catch (ServiceException e) {
LOGGER.warn("Failed to resolve references", e);
}
}
OME root = (OME) store.getRoot();
BinData bin = root.getImage(i).getPixels().getBinData(0);
bin.setLength(new NonNegativeLong(0L));
store.setRoot(root);
}
if (doPlane) {
for (int q=0; q<meta.getPlaneCount(i); q++) {
int[] coords = FormatTools.getZCTCoords(meta, i, q);
store.setPlaneTheZ(new NonNegativeInteger(coords[0]), i, q);
store.setPlaneTheC(new NonNegativeInteger(coords[1]), i, q);
store.setPlaneTheT(new NonNegativeInteger(coords[2]), i, q);
}
}
}
}
/**
* Populates the given {@link MetadataStore}, for the specified imageIndex, using
* the provided values.
* <p>
* After calling this method, the metadata store will be sufficiently
* populated for use with an {@link IFormatWriter} (assuming it is also a
* {@link MetadataRetrieve}).
* </p>
*/
public void populateMetadata(MetadataStore store, int imageIndex,
String imageName, boolean littleEndian, String dimensionOrder,
String pixelType, int sizeX, int sizeY, int sizeZ, int sizeC, int sizeT,
int samplesPerPixel)
{
populateMetadata(store, null, imageIndex, imageName, littleEndian,
dimensionOrder, pixelType, sizeX, sizeY, sizeZ, sizeC, sizeT,
samplesPerPixel);
}
/**
* Populates the given {@link MetadataStore}, for the specified imageIndex, using
* the values from the provided {@link DatasetMetadata}.
* <p>
* After calling this method, the metadata store will be sufficiently
* populated for use with an {@link IFormatWriter} (assuming it is also a
* {@link MetadataRetrieve}).
* </p>
*/
public void populateMetadata(MetadataStore store, int imageIndex,
String imageName, Metadata datasetMeta)
{
int sizeX = datasetMeta.getAxisLength(imageIndex, Axes.X);
int sizeY = datasetMeta.getAxisLength(imageIndex, Axes.Y);
int sizeZ = datasetMeta.getAxisLength(imageIndex, Axes.Z);
int sizeC = datasetMeta.getAxisLength(imageIndex, Axes.CHANNEL);
int sizeT = datasetMeta.getAxisLength(imageIndex, Axes.TIME);
final String pixelType =
FormatTools.getPixelTypeString(datasetMeta.getPixelType(imageIndex));
final int effSizeC = datasetMeta.getImageCount() / sizeZ / sizeT;
final int samplesPerPixel = sizeC / effSizeC;
populateMetadata(store, null, imageIndex, imageName,
datasetMeta.isLittleEndian(imageIndex),
FormatTools.findDimensionOrder(datasetMeta, imageIndex), pixelType,
sizeX, sizeY, sizeZ, sizeC, sizeT, samplesPerPixel);
}
/**
* Populates the given {@link MetadataStore}, for the specified imageIndex, using
* the provided values.
* <p>
* After calling this method, the metadata store will be sufficiently
* populated for use with an {@link IFormatWriter} (assuming it is also a
* {@link MetadataRetrieve}).
* </p>
*/
public void populateMetadata(MetadataStore store, String file,
int imageIndex, String imageName, boolean littleEndian, String dimensionOrder,
String pixelType, int sizeX, int sizeY, int sizeZ, int sizeC, int sizeT,
int samplesPerPixel)
{
store.setImageID(createLSID("Image", imageIndex), imageIndex);
setDefaultCreationDate(store, file, imageIndex);
if (imageName != null) store.setImageName(imageName, imageIndex);
populatePixelsOnly(store, imageIndex, littleEndian, dimensionOrder, pixelType,
sizeX, sizeY, sizeZ, sizeC, sizeT, samplesPerPixel);
}
public void populatePixelsOnly(MetadataStore store, Reader r) {
Metadata dMeta = r.getMetadata();
for (int imageIndex=0; imageIndex<r.getImageCount(); imageIndex++) {
String pixelType = FormatTools.getPixelTypeString(dMeta.getPixelType(imageIndex));
populatePixelsOnly(store, imageIndex, dMeta.isLittleEndian(imageIndex),
FormatTools.findDimensionOrder(dMeta, imageIndex), pixelType,
dMeta.getAxisLength(imageIndex, Axes.X), dMeta.getAxisLength(imageIndex, Axes.Y),
dMeta.getAxisLength(imageIndex, Axes.Z), dMeta.getAxisLength(imageIndex, Axes.CHANNEL),
dMeta.getAxisLength(imageIndex, Axes.TIME), dMeta.getRGBChannelCount(imageIndex));
}
}
public void populatePixelsOnly(MetadataStore store, int imageIndex,
boolean littleEndian, String dimensionOrder, String pixelType, int sizeX,
int sizeY, int sizeZ, int sizeC, int sizeT, int samplesPerPixel)
{
store.setPixelsID(createLSID("Pixels", imageIndex), imageIndex);
store.setPixelsBinDataBigEndian(!littleEndian, imageIndex, 0);
try {
store.setPixelsDimensionOrder(
DimensionOrder.fromString(dimensionOrder), imageIndex);
}
catch (EnumerationException e) {
LOGGER.warn("Invalid dimension order: " + dimensionOrder, e);
}
try {
store.setPixelsType(PixelType.fromString(pixelType), imageIndex);
}
catch (EnumerationException e) {
LOGGER.warn("Invalid pixel type: " + pixelType, e);
}
store.setPixelsSizeX(new PositiveInteger(sizeX), imageIndex);
store.setPixelsSizeY(new PositiveInteger(sizeY), imageIndex);
store.setPixelsSizeZ(new PositiveInteger(sizeZ), imageIndex);
store.setPixelsSizeC(new PositiveInteger(sizeC), imageIndex);
store.setPixelsSizeT(new PositiveInteger(sizeT), imageIndex);
int effSizeC = sizeC / samplesPerPixel;
for (int i=0; i<effSizeC; i++) {
store.setChannelID(createLSID("Channel", imageIndex, i),
imageIndex, i);
store.setChannelSamplesPerPixel(new PositiveInteger(samplesPerPixel),
imageIndex, i);
}
}
/**
* Disables the setting of a default creation date.
*
* By default, missing creation dates will be replaced with the corresponding
* file's last modification date, or the current time if the modification
* date is not available.
*
* Calling this method with the 'enabled' parameter set to 'false' causes
* missing creation dates to be left as null.
*
* @param enabled See above.
* @see #setDefaultCreationDate(MetadataStore, String, int)
*/
public void setDefaultDateEnabled(boolean enabled) {
defaultDateEnabled = enabled;
}
/**
* Sets a default creation date. If the named file exists, then the creation
* date is set to the file's last modification date. Otherwise, it is set
* to the current date.
*
* @see #setDefaultDateEnabled(boolean)
*/
public void setDefaultCreationDate(MetadataStore store, String id,
int imageIndex)
{
if (!defaultDateEnabled) {
return;
}
Location file = id == null ? null : new Location(getContext(), id).getAbsoluteFile();
long time = System.currentTimeMillis();
if (file != null && file.exists()) time = file.lastModified();
store.setImageAcquisitionDate(new Timestamp(DateTools.convertDate(
time, DateTools.UNIX)), imageIndex);
}
/**
*
* @throws FormatException if there is a missing metadata field,
* or the metadata object is uninitialized
*/
public void verifyMinimumPopulated(MetadataRetrieve src)
throws FormatException
{
verifyMinimumPopulated(src, 0);
}
/**
*
* @throws FormatException if there is a missing metadata field,
* or the metadata object is uninitialized
*/
public void verifyMinimumPopulated(MetadataRetrieve src, int n)
throws FormatException
{
if (src == null) {
throw new FormatException("Metadata object is null; " +
"call IFormatWriter.setMetadataRetrieve() first");
}
if (src instanceof MetadataStore
&& ((MetadataStore) src).getRoot() == null) {
throw new FormatException("Metadata object has null root; " +
"call IMetadata.createRoot() first");
}
if (src.getImageID(n) == null) {
throw new FormatException("Image ID #" + n + " is null");
}
if (src.getPixelsID(n) == null) {
throw new FormatException("Pixels ID #" + n + " is null");
}
for (int i=0; i<src.getChannelCount(n); i++) {
if (src.getChannelID(n, i) == null) {
throw new FormatException("Channel ID #" + i + " in Image #" + n +
" is null");
}
}
if (src.getPixelsBinDataBigEndian(n, 0) == null) {
throw new FormatException("BigEndian #" + n + " is null");
}
if (src.getPixelsDimensionOrder(n) == null) {
throw new FormatException("DimensionOrder #" + n + " is null");
}
if (src.getPixelsType(n) == null) {
throw new FormatException("PixelType #" + n + " is null");
}
if (src.getPixelsSizeC(n) == null) {
throw new FormatException("SizeC #" + n + " is null");
}
if (src.getPixelsSizeT(n) == null) {
throw new FormatException("SizeT #" + n + " is null");
}
if (src.getPixelsSizeX(n) == null) {
throw new FormatException("SizeX #" + n + " is null");
}
if (src.getPixelsSizeY(n) == null) {
throw new FormatException("SizeY #" + n + " is null");
}
if (src.getPixelsSizeZ(n) == null) {
throw new FormatException("SizeZ #" + n + " is null");
}
}
/**
* Adjusts the given dimension order as needed so that it contains exactly
* one of each of the following characters: 'X', 'Y', 'Z', 'C', 'T'.
*/
public String makeSaneDimensionOrder(String dimensionOrder) {
String order = dimensionOrder.toUpperCase();
order = order.replaceAll("[^XYZCT]", "");
String[] axes = new String[] {"X", "Y", "C", "Z", "T"};
for (String axis : axes) {
if (order.indexOf(axis) == -1) order += axis;
while (order.indexOf(axis) != order.lastIndexOf(axis)) {
order = order.replaceFirst(axis, "");
}
}
return order;
}
/**
* Constructs an LSID, given the object type and indices.
* For example, if the arguments are "Detector", 1, and 0, the LSID will
* be "Detector:1:0".
*/
public String createLSID(String type, int... indices) {
StringBuffer lsid = new StringBuffer(type);
for (int index : indices) {
lsid.append(":");
lsid.append(index);
}
return lsid.toString();
}
/**
* Retrieves an {@link ome.xml.model.enums.ExperimentType} enumeration
* value for the given String.
*
* @throws ome.xml.model.enums.EnumerationException if an appropriate
* enumeration value is not found.
*/
public ExperimentType getExperimentType(String value)
throws FormatException
{
ExperimentTypeEnumHandler handler = new ExperimentTypeEnumHandler();
try {
return (ExperimentType) handler.getEnumeration(value);
}
catch (EnumerationException e) {
throw new FormatException("ExperimentType creation failed", e);
}
}
/**
* Retrieves an {@link ome.xml.model.enums.LaserType} enumeration
* value for the given String.
*
* @throws ome.xml.model.enums.EnumerationException if an appropriate
* enumeration value is not found.
*/
public LaserType getLaserType(String value) throws FormatException {
LaserTypeEnumHandler handler = new LaserTypeEnumHandler();
try {
return (LaserType) handler.getEnumeration(value);
}
catch (EnumerationException e) {
throw new FormatException("LaserType creation failed", e);
}
}
/**
* Retrieves an {@link ome.xml.model.enums.LaserMedium} enumeration
* value for the given String.
*
* @throws ome.xml.model.enums.EnumerationException if an appropriate
* enumeration value is not found.
*/
public LaserMedium getLaserMedium(String value) throws FormatException {
LaserMediumEnumHandler handler = new LaserMediumEnumHandler();
try {
return (LaserMedium) handler.getEnumeration(value);
}
catch (EnumerationException e) {
throw new FormatException("LaserMedium creation failed", e);
}
}
/**
* Retrieves an {@link ome.xml.model.enums.Immersion} enumeration
* value for the given String.
*
* @throws ome.xml.model.enums.EnumerationException if an appropriate
* enumeration value is not found.
*/
public Immersion getImmersion(String value) throws FormatException {
ImmersionEnumHandler handler = new ImmersionEnumHandler();
try {
return (Immersion) handler.getEnumeration(value);
}
catch (EnumerationException e) {
throw new FormatException("Immersion creation failed", e);
}
}
/**
* Retrieves an {@link ome.xml.model.enums.Correction} enumeration
* value for the given String.
*
* @throws ome.xml.model.enums.EnumerationException if an appropriate
* enumeration value is not found.
*/
public Correction getCorrection(String value) throws FormatException {
CorrectionEnumHandler handler = new CorrectionEnumHandler();
try {
return (Correction) handler.getEnumeration(value);
}
catch (EnumerationException e) {
throw new FormatException("Correction creation failed", e);
}
}
/**
* Retrieves an {@link ome.xml.model.enums.DetectorType} enumeration
* value for the given String.
*
* @throws ome.xml.model.enums.EnumerationException if an appropriate
* enumeration value is not found.
*/
public DetectorType getDetectorType(String value) throws FormatException {
DetectorTypeEnumHandler handler = new DetectorTypeEnumHandler();
try {
return (DetectorType) handler.getEnumeration(value);
}
catch (EnumerationException e) {
throw new FormatException("DetectorType creation failed", e);
}
}
/**
* Uses the provided MetadataRetrieve to populate the format-agnostic
* image information in the provided Metadata object (that is, the
* ImageMetadata).
*
* @param retrieve
* @param meta
*/
public void populateMetadata(MetadataRetrieve retrieve, Metadata meta) {
meta.setDatasetName(retrieve.getImageName(0));
for (int i=0; i<retrieve.getImageCount(); i++) {
ImageMetadata iMeta;
if (i >= meta.getImageCount()) {
iMeta = new DefaultImageMetadata();
meta.add(iMeta);
}
else iMeta = meta.get(i);
populateImageMetadata(retrieve, i, iMeta);
}
}
/**
* Populates the provided ImageMetadata object using the specified
* image index into the MetadataRetrieve.
*
* @param retrieve
* @param iMeta
*/
public void populateImageMetadata(MetadataRetrieve retrieve,
int imageIndex, ImageMetadata iMeta)
{
int sizeX = retrieve.getPixelsSizeX(imageIndex).getValue();
int sizeY = retrieve.getPixelsSizeY(imageIndex).getValue();
int sizeZ = retrieve.getPixelsSizeZ(imageIndex).getValue();
int sizeC = retrieve.getPixelsSizeC(imageIndex).getValue();
int sizeT = retrieve.getPixelsSizeZ(imageIndex).getValue();
String dimensionOrder = retrieve.getPixelsDimensionOrder(imageIndex).getValue();
boolean little = !retrieve.getPixelsBinDataBigEndian(imageIndex, 0);
String pixelType = retrieve.getPixelsType(imageIndex).getValue();
int rgbCCount = retrieve.getChannelSamplesPerPixel(imageIndex, 0).getValue();
SCIFIOMetadataTools.populateDimensions(iMeta, dimensionOrder,
sizeX, sizeY, sizeZ, sizeC, sizeT);
iMeta.setLittleEndian(little);
iMeta.setPixelType(FormatTools.pixelTypeFromString(pixelType));
iMeta.setBitsPerPixel(FormatTools.getBitsPerPixel(iMeta.getPixelType()));
if (rgbCCount > 1) iMeta.setRGB(true);
iMeta.setPlaneCount(sizeZ * (sizeC / rgbCCount) * sizeT);
}
}
|
package org.deviceconnect.message;
import android.net.Uri;
import android.util.Log;
import org.deviceconnect.message.intent.message.IntentDConnectMessage;
import org.deviceconnect.sdk.BuildConfig;
import org.java_websocket.WebSocket;
import org.java_websocket.client.WebSocketClient;
import org.java_websocket.drafts.Draft_17;
import org.java_websocket.framing.Framedata;
import org.java_websocket.handshake.ServerHandshake;
import org.json.JSONException;
import org.json.JSONObject;
import java.io.IOException;
import java.net.URI;
import java.security.KeyManagementException;
import java.security.NoSuchAlgorithmException;
import java.security.SecureRandom;
import java.security.cert.X509Certificate;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import javax.net.ssl.SSLContext;
import javax.net.ssl.SSLSocketFactory;
import javax.net.ssl.TrustManager;
import javax.net.ssl.X509TrustManager;
/**
* WebSocket.
* @author NTT DOCOMO, INC.
*/
class DConnectWebSocketClient {
private static final boolean DEBUG = BuildConfig.DEBUG;
private static final String TAG = "DConnectSDK";
private static final String JOIN_SERVICE_ID = "_";
/**
* Device Connect Manager.
*/
private final Map<String, List<HttpDConnectSDK.OnEventListener>> mListenerMap = new HashMap<>();
/**
* WebSocket.
*/
private HttpDConnectSDK.OnWebSocketListener mOnWebSocketListener;
/**
* WebSocket.
*/
private WebSocketClient mWebSocketClient;
/**
* WebSocket.
* <p>
* truefalse
* </p>
*/
private boolean isEstablishedWebSocket;
/**
* WebSocket(ms).
*/
private int mTimeout = 30 * 1000;
/**
* WebSocket.
* @param onWebSocketListener
*/
void setOnWebSocketListener(final HttpDConnectSDK.OnWebSocketListener onWebSocketListener) {
mOnWebSocketListener = onWebSocketListener;
}
/**
* WebSocket(ms).
* @param timeout (ms)
*/
void setTimeout(final int timeout) {
mTimeout = timeout;
}
/**
* Device Connect ManagerWebSocket.
* @param uri URI
* @param origin
* @param accessToken
*/
void connect(final String uri, final String origin, final String accessToken) {
if (mWebSocketClient != null) {
if (DEBUG) {
Log.w(TAG, "WebSocketClient is already connected.");
}
return;
}
Map<String, String> headers = new HashMap<>();
if (origin != null) {
headers.put(IntentDConnectMessage.EXTRA_ORIGIN, origin);
}
mWebSocketClient = new WebSocketClient(URI.create(uri), new Draft_17(), headers, mTimeout) {
@Override
public void onMessage(final String message) {
try {
JSONObject json = new JSONObject(message);
if (!isEstablishedWebSocket) {
if (json.getInt(DConnectMessage.EXTRA_RESULT) == DConnectMessage.RESULT_OK) {
isEstablishedWebSocket = true;
if (mOnWebSocketListener != null) {
mOnWebSocketListener.onOpen();
}
} else {
if (mOnWebSocketListener != null) {
RuntimeException ex = new RuntimeException();
mOnWebSocketListener.onError(ex);
}
}
} else {
String key = createPath(json);
synchronized (mListenerMap) {
List<DConnectSDK.OnEventListener> listeners = mListenerMap.get(key);
if (listeners != null) {
for (DConnectSDK.OnEventListener l : listeners) {
l.onMessage(new DConnectEventMessage(message));
}
}
}
}
} catch (JSONException e) {
if (DEBUG) {
Log.w(TAG, "The message from Device Connect Manager is invalid.", e);
}
if (mOnWebSocketListener != null) {
mOnWebSocketListener.onError(e);
}
}
}
@Override
public void onOpen(final ServerHandshake handshake) {
sendAccessToken(accessToken);
}
@Override
public void onClose(final int code, final String reason, final boolean remote) {
isEstablishedWebSocket = false;
DConnectWebSocketClient.this.close();
if (mOnWebSocketListener != null) {
mOnWebSocketListener.onClose();
}
}
@Override
public void onWebsocketPing(final WebSocket conn, final Framedata f) {
super.onWebsocketPing(conn, f);
}
@Override
public void onWebsocketPong(final WebSocket conn, final Framedata f) {
super.onWebsocketPong(conn, f);
}
@Override
public void onError(final Exception ex) {
isEstablishedWebSocket = false;
if (mOnWebSocketListener != null) {
mOnWebSocketListener.onError(ex);
}
}
};
if (uri.startsWith("wss")) {
try {
SSLSocketFactory factory = createSSLSocketFactory();
mWebSocketClient.setSocket(factory.createSocket());
} catch (NoSuchAlgorithmException | KeyManagementException | IOException e) {
if (mOnWebSocketListener != null) {
mOnWebSocketListener.onError(e);
}
return;
}
}
mWebSocketClient.connect();
}
/**
* WebSocket.
* @return truefalse
*/
boolean isConnected() {
return isEstablishedWebSocket;
}
/**
* .
* @param json
* @return
*/
private String createPath(final JSONObject json) {
String uri = "/gotapi";
if (json.has(DConnectMessage.EXTRA_PROFILE)) {
uri += "/";
uri += json.optString(DConnectMessage.EXTRA_PROFILE);
}
if (json.has(DConnectMessage.EXTRA_INTERFACE)) {
uri += "/";
uri += json.optString(DConnectMessage.EXTRA_INTERFACE);
}
if (json.has(DConnectMessage.EXTRA_ATTRIBUTE)) {
uri += "/";
uri += json.optString(DConnectMessage.EXTRA_ATTRIBUTE);
}
uri = uri.toLowerCase();
if (json.has(DConnectMessage.EXTRA_SERVICE_ID)) {
uri += JOIN_SERVICE_ID;
uri += json.optString(DConnectMessage.EXTRA_SERVICE_ID);
}
return uri;
}
/**
* URI.
* @param uri URI
* @return
*/
private String convertUriToPath(final Uri uri) {
return uri.getPath().toLowerCase() + JOIN_SERVICE_ID + uri.getQueryParameter(DConnectMessage.EXTRA_SERVICE_ID);
}
/**
* WebSocket.
*/
void close() {
if (mWebSocketClient != null) {
mWebSocketClient.close();
mWebSocketClient = null;
}
isEstablishedWebSocket = false;
}
/**
* .
*
* @param uri URI
* @return truefalse
*/
boolean hasEventListener(final Uri uri) {
String key = convertUriToPath(uri);
synchronized (mListenerMap) {
List<DConnectSDK.OnEventListener> listeners = mListenerMap.get(key);
return listeners != null && !listeners.isEmpty();
}
}
/**
* .
* @param uri URI
* @param listener
*/
void addEventListener(final Uri uri, final HttpDConnectSDK.OnEventListener listener) {
String key = convertUriToPath(uri);
synchronized (mListenerMap) {
List<DConnectSDK.OnEventListener> listeners = mListenerMap.get(key);
if (listeners == null) {
listeners = new ArrayList<>();
mListenerMap.put(key, listeners);
}
listeners.add(listener);
}
}
/**
* .
* @param uri URI
*/
void removeEventListener(final Uri uri) {
String key = convertUriToPath(uri);
synchronized (mListenerMap) {
mListenerMap.remove(key);
}
}
/**
* .
*
* @param uri URI
* @param listener
*/
void removeEventListener(final Uri uri, final HttpDConnectSDK.OnEventListener listener) {
String key = convertUriToPath(uri);
synchronized (mListenerMap) {
List<DConnectSDK.OnEventListener> listeners = mListenerMap.get(key);
if (listeners != null) {
listeners.remove(listener);
}
}
}
/**
* Device Connect Manager.
* @param accessToken
*/
private void sendAccessToken(final String accessToken) {
mWebSocketClient.send("{\"" + DConnectMessage.EXTRA_ACCESS_TOKEN + "\":\"" + accessToken + "\"}");
}
/**
* SSL.
*
* @return SSLSocketFactory
* @throws NoSuchAlgorithmException SSL
* @throws KeyManagementException
*/
private SSLSocketFactory createSSLSocketFactory() throws NoSuchAlgorithmException, KeyManagementException {
TrustManager[] transManagers = {
new X509TrustManager() {
@Override
public void checkClientTrusted(final X509Certificate[] chain, final String authType) {
}
@Override
public void checkServerTrusted(final X509Certificate[] chain, final String authType) {
}
@Override
public X509Certificate[] getAcceptedIssuers() {
return new X509Certificate[0];
}
}
};
SSLContext sslcontext = SSLContext.getInstance("SSL");
sslcontext.init(null, transManagers, new SecureRandom());
return sslcontext.getSocketFactory();
}
}
|
package edu.cuny.citytech.foreachlooptolambda.ui.visitors;
import org.eclipse.jdt.core.dom.ASTNode;
import org.eclipse.jdt.core.dom.ASTVisitor;
import org.eclipse.jdt.core.dom.BooleanLiteral;
import org.eclipse.jdt.core.dom.BreakStatement;
import org.eclipse.jdt.core.dom.ContinueStatement;
import org.eclipse.jdt.core.dom.IBinding;
import org.eclipse.jdt.core.dom.ITypeBinding;
import org.eclipse.jdt.core.dom.MethodInvocation;
import org.eclipse.jdt.core.dom.ReturnStatement;
import org.eclipse.jdt.core.dom.SimpleName;
public class EnhancedForStatementVisitor extends ASTVisitor {
private boolean encounteredBreakStatement;
private boolean encounteredContinueStatement;
private boolean encounteredInvalidReturnStatement;
private boolean encounteredThrownCheckedException;
private boolean encounteredNonEffectivelyFinalVars;
private int returnCount = 0;
@Override
public boolean visit(BreakStatement node) {
this.encounteredBreakStatement = true;
return super.visit(node);
}
@Override
public boolean visit(ContinueStatement node) {
this.encounteredContinueStatement = true;
return super.visit(node);
}
@Override
public boolean visit(MethodInvocation node) {
SimpleName name = node.getName();
IBinding iBinding = name.resolveBinding();
System.out.println(name);
System.out.println("This is ITypeBinding: "+iBinding);
return super.visit(node);
}
/**
* checking if returnStatement is boolean, not null and has only one return
*
* @see org.eclipse.jdt.core.dom.ASTVisitor#visit(org.eclipse.jdt.core.dom.ReturnStatement)
*/
@Override
public boolean visit(ReturnStatement node) {
// one more return statement encountered.
returnCount++;
// examine what is being returned.
ASTNode expression = node.getExpression();
// if there is a return statement, it must return a boolean literal.
if (expression == null || !(expression instanceof BooleanLiteral)) {
this.encounteredInvalidReturnStatement = true;
}
return super.visit(node);
}
public boolean containsBreak() {
return this.encounteredBreakStatement;
}
public boolean containsContinue() {
return encounteredContinueStatement;
}
public boolean containsInvalidReturn() {
return encounteredInvalidReturnStatement;
}
public boolean containsMultipleReturn() {
return returnCount > 1;
}
public boolean containsException() {
return encounteredThrownCheckedException;
}
public boolean containsNEFS() {
return encounteredNonEffectivelyFinalVars;
}
}
|
package org.javasimon.console;
import java.io.IOException;
import javax.servlet.ServletConfig;
import javax.servlet.ServletException;
import javax.servlet.http.HttpServlet;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
import org.javasimon.Manager;
import org.javasimon.utils.SimonUtils;
/**
* Front controller servlet of Simon Web console.
*
* @author gquintana
*/
@SuppressWarnings("UnusedDeclaration")
public class SimonConsoleServlet extends HttpServlet {
/**
* Serial version UID since class is Serializable.
*/
public static final long serialVersionUID = 1L;
/**
* URL Prefix init parameter name.
*/
public static final String URL_PREFIX_INIT_PARAMETER = "url-prefix";
/**
* Plugin classes init parameter name.
*/
public static final String PLUGIN_CLASSES_INIT_PARAMETER = "plugin-classes";
private SimonConsoleRequestProcessor requestProcessor;
@Override
public void init(ServletConfig config) throws ServletException {
super.init(config);
pickUpSharedManagerIfExists(config);
String urlPrefix = config.getInitParameter(URL_PREFIX_INIT_PARAMETER);
String pluginClasses = config.getInitParameter(PLUGIN_CLASSES_INIT_PARAMETER);
initRequestProcessor(urlPrefix, pluginClasses);
}
public void initRequestProcessor(String urlPrefix, String pluginClasses) {
if (urlPrefix == null) {
urlPrefix = "";
} else {
urlPrefix = urlPrefix.trim();
}
requestProcessor = new SimonConsoleRequestProcessor(urlPrefix);
if (pluginClasses != null) {
requestProcessor.getPluginManager().addPlugins(pluginClasses);
}
requestProcessor.initActionBindings();
}
public SimonConsoleRequestProcessor getRequestProcessor() {
return requestProcessor;
}
private void pickUpSharedManagerIfExists(ServletConfig config) {
Object managerObject = config.getServletContext().getAttribute(SimonUtils.MANAGER_SERVLET_CTX_ATTRIBUTE);
if (managerObject != null && managerObject instanceof Manager) {
requestProcessor.setManager((Manager) managerObject);
}
}
/**
* Handles the HTTP
* <code>GET</code> method.
*
* @param request servlet request
* @param response servlet response
* @throws ServletException if a servlet-specific error occurs
* @throws IOException if an I/O error occurs
*/
@Override
protected void doGet(HttpServletRequest request, HttpServletResponse response)
throws ServletException, IOException
{
requestProcessor.processRequest(request, response);
}
/**
* Handles the HTTP
* <code>POST</code> method.
*
* @param request servlet request
* @param response servlet response
* @throws ServletException if a servlet-specific error occurs
* @throws IOException if an I/O error occurs
*/
@Override
protected void doPost(HttpServletRequest request, HttpServletResponse response)
throws ServletException, IOException
{
requestProcessor.processRequest(request, response);
}
/**
* Returns a short description of the servlet.
*
* @return a String containing servlet description
*/
@Override
public String getServletInfo() {
return "Short description";
}
}
|
package edu.cuny.citytech.foreachlooptolambda.ui.visitors;
import java.util.Arrays;
import java.util.List;
import org.eclipse.jdt.core.dom.ASTNode;
import org.eclipse.jdt.core.dom.ASTVisitor;
import org.eclipse.jdt.core.dom.Block;
import org.eclipse.jdt.core.dom.BooleanLiteral;
import org.eclipse.jdt.core.dom.BreakStatement;
import org.eclipse.jdt.core.dom.CatchClause;
import org.eclipse.jdt.core.dom.ContinueStatement;
import org.eclipse.jdt.core.dom.EnhancedForStatement;
import org.eclipse.jdt.core.dom.IMethodBinding;
import org.eclipse.jdt.core.dom.ITypeBinding;
import org.eclipse.jdt.core.dom.MethodInvocation;
import org.eclipse.jdt.core.dom.ReturnStatement;
import org.eclipse.jdt.core.dom.ThrowStatement;
import org.eclipse.jdt.core.dom.TryStatement;
public class EnhancedForStatementVisitor extends ASTVisitor {
private boolean encounteredBreakStatement;
private boolean encounteredContinueStatement;
private boolean encounteredInvalidReturnStatement;
private boolean encounteredThrownCheckedException;
private boolean encounteredNonEffectivelyFinalVars;
private int returnCount = 0;
/**
* The enhanced for statement that will be visited.
*/
private EnhancedForStatement enhancedForStatement;
/**
* Create a new visitor.
*
* @param enhancedForStatement
* The enhanced for statement that will be visited.
*/
public EnhancedForStatementVisitor(EnhancedForStatement enhancedForStatement) {
this.enhancedForStatement = enhancedForStatement;
}
// finding the TryStatement node
public static ASTNode findTryAncestor(ASTNode node) {
if (node == null || node instanceof TryStatement) {
return node;
}
return findTryAncestor(node);
}
@Override
public boolean visit(BreakStatement node) {
this.encounteredBreakStatement = true;
return super.visit(node);
}
@Override
public boolean visit(ContinueStatement node) {
this.encounteredContinueStatement = true;
return super.visit(node);
}
private void handleException(ASTNode nodeContaingException) {
// gets the top node. If it returns
// null, there is no other top.
ASTNode tryStatementParent = (nodeContaingException.getParent()).getParent();
ASTNode throwStatementParent = tryStatementParent.getParent();
if (throwStatementParent instanceof TryStatement) {
System.out.println("this is throwStatementParent");
this.encounteredThrownCheckedException = false;
}
// findTryStatmaent if there is any catch block
else if (tryStatementParent instanceof TryStatement) {
TryStatement tryStatement = (TryStatement) tryStatementParent;
List catchClauses = tryStatement.catchClauses();
// checking if there is any catchBlock
catchClauses.stream().forEach(s -> System.out.println("this is catchBlock "+s));
if (catchClauses.size() >= 1) {
this.encounteredThrownCheckedException = false; // TODO: Not sufficient condition. See algo.
} else {
//at this point, there are no catch clauses.
this.encounteredThrownCheckedException = true;
}
} else {
this.encounteredThrownCheckedException = true;
}
}
@Override
public boolean visit(MethodInvocation node) {
IMethodBinding iMethodBinding = node.resolveMethodBinding();
ITypeBinding[] exceptionTypes = iMethodBinding.getExceptionTypes();
// if there are exceptions
if (exceptionTypes.length >= 1) {
handleException(node);
}
return super.visit(node);
}
@Override
public boolean visit(ThrowStatement node) {
handleException(node);
return super.visit(node);
}
/**
* checking if returnStatement is boolean, not null and has only one return
*
* @see org.eclipse.jdt.core.dom.ASTVisitor#visit(org.eclipse.jdt.core.dom.ReturnStatement)
*/
@Override
public boolean visit(ReturnStatement node) {
// one more return statement encountered.
returnCount++;
// examine what is being returned.
ASTNode expression = node.getExpression();
// if there is a return statement, it must return a boolean literal.
if (expression == null || !(expression instanceof BooleanLiteral)) {
this.encounteredInvalidReturnStatement = true;
}
return super.visit(node);
}
public boolean containsBreak() {
return this.encounteredBreakStatement;
}
public boolean containsContinue() {
return encounteredContinueStatement;
}
public boolean containsInvalidReturn() {
return encounteredInvalidReturnStatement;
}
public boolean containsMultipleReturn() {
return returnCount > 1;
}
public boolean containsException() {
return encounteredThrownCheckedException;
}
public boolean containsNEFS() {
return encounteredNonEffectivelyFinalVars;
}
}
|
package org.innovateuk.ifs.application.transactional;
import lombok.extern.slf4j.Slf4j;
import org.innovateuk.ifs.activitylog.domain.ActivityLog;
import org.innovateuk.ifs.activitylog.repository.ActivityLogRepository;
import org.innovateuk.ifs.application.domain.*;
import org.innovateuk.ifs.application.repository.*;
import org.innovateuk.ifs.assessment.repository.AssessmentRepository;
import org.innovateuk.ifs.assessment.repository.AverageAssessorScoreRepository;
import org.innovateuk.ifs.commons.service.ServiceResult;
import org.innovateuk.ifs.finance.domain.ApplicationFinance;
import org.innovateuk.ifs.finance.domain.ApplicationFinanceRow;
import org.innovateuk.ifs.finance.repository.ApplicationFinanceRepository;
import org.innovateuk.ifs.finance.repository.ApplicationFinanceRowRepository;
import org.innovateuk.ifs.finance.repository.FinanceRowMetaValueRepository;
import org.innovateuk.ifs.grant.domain.GrantProcess;
import org.innovateuk.ifs.grant.repository.GrantProcessRepository;
import org.innovateuk.ifs.granttransfer.repository.EuGrantTransferRepository;
import org.innovateuk.ifs.horizon.repository.ApplicationHorizonWorkProgrammeRepository;
import org.innovateuk.ifs.interview.repository.InterviewAssignmentRepository;
import org.innovateuk.ifs.interview.repository.InterviewRepository;
import org.innovateuk.ifs.invite.repository.ApplicationInviteRepository;
import org.innovateuk.ifs.invite.repository.ApplicationKtaInviteRepository;
import org.innovateuk.ifs.project.core.repository.ProjectRepository;
import org.innovateuk.ifs.project.core.repository.ProjectToBeCreatedRepository;
import org.innovateuk.ifs.review.repository.ReviewRepository;
import org.innovateuk.ifs.supporter.repository.SupporterAssignmentRepository;
import org.innovateuk.ifs.user.repository.ProcessRoleRepository;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
import org.springframework.transaction.annotation.Transactional;
import java.time.ZonedDateTime;
import java.util.Optional;
import static org.innovateuk.ifs.commons.error.CommonErrors.notFoundError;
import static org.innovateuk.ifs.util.EntityLookupCallbacks.find;
import static org.innovateuk.ifs.commons.service.ServiceResult.serviceSuccess;
@Slf4j
@Service
public class ApplicationMigrationServiceImpl implements ApplicationMigrationService {
@Autowired
private ApplicationMigrationRepository applicationMigrationRepository;
@Autowired
private ApplicationRepository applicationRepository;
@Autowired
private ActivityLogRepository activityLogRepository;
@Autowired
private ApplicationFinanceRepository applicationFinanceRepository;
@Autowired
private ApplicationFinanceRowRepository applicationFinanceRowRepository;
@Autowired
private FinanceRowMetaValueRepository financeRowMetaValueRepository;
@Autowired
private ApplicationHiddenFromDashboardRepository applicationHiddenFromDashboardRepository;
@Autowired
private ApplicationOrganisationAddressRepository applicationOrganisationAddressRepository;
@Autowired
private AverageAssessorScoreRepository averageAssessorScoreRepository;
@Autowired
private EuGrantTransferRepository euGrantTransferRepository;
@Autowired
private FormInputResponseRepository formInputResponseRepository;
@Autowired
private ProcessRoleRepository processRoleRepository;
@Autowired
private ProjectRepository projectRepository;
@Autowired
private ProjectToBeCreatedRepository projectToBeCreatedRepository;
@Autowired
private QuestionStatusRepository questionStatusRepository;
@Autowired
private GrantProcessRepository grantProcessRepository;
@Autowired
private ApplicationProcessRepository applicationProcessRepository;
@Autowired
private AssessmentRepository assessmentRepository;
@Autowired
private InterviewRepository interviewRepository;
@Autowired
private InterviewAssignmentRepository interviewAssignmentRepository;
@Autowired
private ReviewRepository reviewRepository;
@Autowired
private SupporterAssignmentRepository supporterAssignmentRepository;
@Autowired
private ApplicationInviteRepository applicationInviteRepository;
@Autowired
private ApplicationKtaInviteRepository applicationKtaInviteRepository;
@Autowired
private ApplicationHorizonWorkProgrammeRepository applicationHorizonWorkProgrammeRepository;
@Autowired
private ApplicationExpressionOfInterestConfigRepository applicationExpressionOfInterestConfigRepository;
@Autowired
private ApplicationEoiEvidenceResponseRepository applicationEoiEvidenceResponseRepository;
@Override
public ServiceResult<Optional<ApplicationMigration>> findByApplicationIdAndStatus(long applicationId, MigrationStatus status) {
return serviceSuccess(applicationMigrationRepository.findByApplicationIdAndStatus(applicationId, status));
}
@Override
@Transactional
public ServiceResult<Void> migrateApplication(long applicationId) {
return migrateApplication(applicationId, true)
.andOnSuccessReturnVoid();
}
@Override
@Transactional
public ServiceResult<Long> migrateApplication(long applicationId, boolean isDeleteApplication) {
return find(applicationRepository.findById(applicationId), notFoundError(Application.class, applicationId))
.andOnSuccess(application -> {
Application migratedApplication = migrateApplication(application);
migrateApplicationExpressionOfInterestConfig(application, migratedApplication);
migrateApplicationHorizonWorkProgramme(application, migratedApplication);
migrateActivityLog(application, migratedApplication);
migrateApplicationFinance(application, migratedApplication);
migrateApplicationHiddenFromDashboard(application, migratedApplication);
migrateApplicationOrganisationAddress(application, migratedApplication);
migrateAverageAssessorScore(application, migratedApplication);
migrateEuGrantTransfer(application, migratedApplication);
migrateFormInputResponse(application, migratedApplication);
migrateProcessRole(application, migratedApplication);
migrateProject(application, migratedApplication);
migrateProjectToBeCreated(application, migratedApplication);
migrateQuestionStatus(application, migratedApplication);
migrateGrantProcess(application, migratedApplication);
migrateApplicationProcess(application, migratedApplication);
migrateAssessmentProcess(application, migratedApplication);
migrateInterviewProcess(application, migratedApplication);
migrateInterviewAssignmentProcess(application, migratedApplication);
migrateReviewProcess(application, migratedApplication);
migrateSupporterAssignment(application, migratedApplication);
migrateApplicationInvite(application, migratedApplication);
migrateApplicationKtaInvite(application, migratedApplication);
migrateApplicationEoiEvidence(application, migratedApplication);
deleteApplicationDependency(application);
if (isDeleteApplication) {
deleteApplication(application);
}
return serviceSuccess(migratedApplication.getId());
});
}
private void deleteApplication(Application application) {
applicationRepository.delete(application);
log.debug("Deleted application : " + application.getId());
}
private void deleteApplicationDependency(Application application) {
activityLogRepository.deleteByApplicationId(application.getId());
grantProcessRepository.deleteByApplicationId(application.getId());
applicationHiddenFromDashboardRepository.deleteByApplicationId(application.getId());
applicationExpressionOfInterestConfigRepository.deleteByApplicationId(application.getId());
log.debug("Deleted application dependency for application : " + application.getId());
}
private void migrateApplicationEoiEvidence(Application application, Application migratedApplication) {
applicationEoiEvidenceResponseRepository.findOneByApplicationId(application.getId()).ifPresent(
applicationEoiEvidence -> {
applicationEoiEvidence.setApplication(migratedApplication);
applicationEoiEvidenceResponseRepository.save(applicationEoiEvidence);
}
);
log.debug("Migrated application eoi evidence for application : " + application.getId());
}
private void migrateApplicationKtaInvite(Application application, Application migratedApplication) {
applicationKtaInviteRepository.findByApplicationId(application.getId()).ifPresent(
applicationKtaInvite -> {
applicationKtaInvite.setTarget(migratedApplication);
applicationKtaInviteRepository.save(applicationKtaInvite);
}
);
log.debug("Migrated application kta invite for application : " + application.getId());
}
private void migrateApplicationInvite(Application application, Application migratedApplication) {
applicationInviteRepository.findByApplicationId(application.getId()).stream()
.forEach(applicationInvite -> {
applicationInvite.setTarget(migratedApplication);
applicationInviteRepository.save(applicationInvite);
});
log.debug("Migrated application invite for application : " + application.getId());
}
private void migrateSupporterAssignment(Application application, Application migratedApplication) {
supporterAssignmentRepository.findByTargetId(application.getId()).stream()
.forEach(supporterAssignmentProcess -> {
supporterAssignmentProcess.setTarget(migratedApplication);
supporterAssignmentRepository.save(supporterAssignmentProcess);
});
log.debug("Migrated supporter assignment process for application : " + application.getId());
}
private void migrateReviewProcess(Application application, Application migratedApplication) {
reviewRepository.findByTargetId(application.getId()).stream()
.forEach(reviewProcess -> {
reviewProcess.setTarget(migratedApplication);
reviewRepository.save(reviewProcess);
});
log.debug("Migrated review process for application : " + application.getId());
}
private void migrateInterviewAssignmentProcess(Application application, Application migratedApplication) {
interviewAssignmentRepository.findByTargetId(application.getId()).stream()
.forEach(interviewAssignmentProcess -> {
interviewAssignmentProcess.setTarget(migratedApplication);
interviewAssignmentRepository.save(interviewAssignmentProcess);
});
log.debug("Migrated interview assignment process for application : " + application.getId());
}
private void migrateInterviewProcess(Application application, Application migratedApplication) {
interviewRepository.findByTargetId(application.getId()).stream()
.forEach(interviewProcess -> {
interviewProcess.setTarget(migratedApplication);
interviewRepository.save(interviewProcess);
});
log.debug("Migrated interview process for application : " + application.getId());
}
private void migrateAssessmentProcess(Application application, Application migratedApplication) {
assessmentRepository.findByTargetId(application.getId()).stream()
.forEach(assessmentProcess -> {
assessmentProcess.setTarget(migratedApplication);
assessmentRepository.save(assessmentProcess);
});
log.debug("Migrated assessment process for application : " + application.getId());
}
private void migrateApplicationProcess(Application application, Application migratedApplication) {
applicationProcessRepository.findByTargetId(application.getId()).stream()
.forEach(applicationProcess -> {
applicationProcess.setTarget(migratedApplication);
applicationProcessRepository.save(applicationProcess);
});
log.debug("Migrated application process for application : " + application.getId());
}
private void migrateGrantProcess(Application application, Application migratedApplication) {
serviceSuccess(grantProcessRepository.findOneByApplicationId(application.getId()))
.andOnSuccessReturnVoid(grantProcess -> {
if (grantProcess != null) {
GrantProcess migratedGrantProcess = new GrantProcess(migratedApplication.getId(), grantProcess.isPending());
migratedGrantProcess.setMessage(grantProcess.getMessage());
migratedGrantProcess.setLastProcessed(grantProcess.getLastProcessed());
migratedGrantProcess.setSentRequested(grantProcess.getSentRequested());
migratedGrantProcess.setSentSucceeded(grantProcess.getSentSucceeded());
grantProcessRepository.save(migratedGrantProcess);
}
});
log.debug("Migrated grant process for application : " + application.getId());
}
private void migrateQuestionStatus(Application application, Application migratedApplication) {
questionStatusRepository.findByApplicationId(application.getId()).stream()
.forEach(questionStatus -> {
questionStatus.setApplication(migratedApplication);
questionStatusRepository.save(questionStatus);
});
log.debug("Migrated question status for application : " + application.getId());
}
private void migrateProjectToBeCreated(Application application, Application migratedApplication) {
projectToBeCreatedRepository.findByApplicationId(application.getId()).ifPresent(
projectToBeCreated -> {
projectToBeCreated.setApplication(migratedApplication);
projectToBeCreatedRepository.save(projectToBeCreated);
}
);
log.debug("Migrated project to be created for application : " + application.getId());
}
private void migrateProject(Application application, Application migratedApplication) {
projectRepository.findByApplicationId(application.getId()).ifPresent(
project -> {
project.setApplication(migratedApplication);
projectRepository.save(project);
}
);
log.debug("Migrated project for application : " + application.getId());
}
private void migrateProcessRole(Application application, Application migratedApplication) {
processRoleRepository.findByApplicationId(application.getId()).stream()
.forEach(processRole -> {
processRole.setApplicationId(migratedApplication.getId());
processRoleRepository.save(processRole);
});
log.debug("Migrated process role for application : " + application.getId());
}
private void migrateFormInputResponse(Application application, Application migratedApplication) {
formInputResponseRepository.findByApplicationId(application.getId()).stream()
.forEach(formInputResponse -> {
formInputResponse.setApplication(migratedApplication);
formInputResponseRepository.save(formInputResponse);
});
log.debug("Migrated form input response for application : " + application.getId());
}
private void migrateEuGrantTransfer(Application application, Application migratedApplication) {
serviceSuccess(euGrantTransferRepository.findByApplicationId(application.getId()))
.andOnSuccessReturnVoid(euGrantTransfer -> {
if (euGrantTransfer != null) {
euGrantTransfer.setApplication(migratedApplication);
euGrantTransferRepository.save(euGrantTransfer);
}
});
log.debug("Migrated eu grant transfer for application : " + application.getId());
}
private void migrateAverageAssessorScore(Application application, Application migratedApplication) {
averageAssessorScoreRepository.findByApplicationId(application.getId()).ifPresent(
averageAssessorScore -> {
averageAssessorScore.setApplication(migratedApplication);
averageAssessorScoreRepository.save(averageAssessorScore);
});
log.debug("Migrated average assessor score for application : " + application.getId());
}
private void migrateApplicationOrganisationAddress(Application application, Application migratedApplication) {
applicationOrganisationAddressRepository.findByApplicationId(application.getId()).stream()
.forEach(applicationOrganisationAddress -> {
applicationOrganisationAddress.setApplication(migratedApplication);
applicationOrganisationAddressRepository.save(applicationOrganisationAddress);
});
log.debug("Migrated application organisation address for application : " + application.getId());
}
private void migrateApplicationHiddenFromDashboard(Application application, Application migratedApplication) {
applicationHiddenFromDashboardRepository.findByApplicationId(application.getId()).stream()
.forEach(applicationHiddenFromDashboard -> {
ApplicationHiddenFromDashboard migratedApplicationHiddenFromDashboard = new ApplicationHiddenFromDashboard(migratedApplication, applicationHiddenFromDashboard.getUser());
migratedApplicationHiddenFromDashboard.setCreatedOn(applicationHiddenFromDashboard.getCreatedOn());
applicationHiddenFromDashboardRepository.save(migratedApplicationHiddenFromDashboard);
});
log.debug("Migrated application hidden from dashboard for application : " + application.getId());
}
private void migrateApplicationFinance(Application application, Application migratedApplication) {
applicationFinanceRepository.findByApplicationId(application.getId()).stream()
.forEach(applicationFinance -> {
Long applicationFinanceId = applicationFinance.getId();
applicationFinance.setApplication(migratedApplication);
ApplicationFinance migratedApplicationFinance = applicationFinanceRepository.save(applicationFinance);
applicationFinanceRowRepository.findByTargetId(applicationFinanceId).stream()
.forEach(applicationFinanceRow -> {
applicationFinanceRow.setTarget(migratedApplicationFinance);
ApplicationFinanceRow savedClonedApplicationFinanceRow = applicationFinanceRowRepository.save(applicationFinanceRow);
financeRowMetaValueRepository.financeRowId(applicationFinanceRow.getId()).stream()
.forEach(financeRowMetaValue -> {
financeRowMetaValue.setFinanceRowId(savedClonedApplicationFinanceRow.getId());
});
});
});
log.debug("Migrated application finance for application : " + application.getId());
}
private void migrateActivityLog(Application application, Application migratedApplication) {
activityLogRepository.findByApplicationId(application.getId()).stream()
.forEach(activityLog -> {
ActivityLog migratedActivityLog = new ActivityLog(migratedApplication, activityLog.getType(),
activityLog.getOrganisation().orElse(null),
activityLog.getCompetitionDocument().orElse(null),
activityLog.getQuery().orElse(null),
activityLog.getCreatedOn(), activityLog.getCreatedBy(), activityLog.getAuthor());
activityLogRepository.save(migratedActivityLog);
});
log.debug("Migrated activity log for application : " + application.getId());
}
private void migrateApplicationHorizonWorkProgramme(Application application, Application migratedApplication) {
if (migratedApplication.getCompetition().isHorizonEuropeGuarantee()) {
applicationHorizonWorkProgrammeRepository.findByApplicationId(application.getId()).stream()
.forEach(applicationHorizonWorkProgramme -> {
applicationHorizonWorkProgramme.setApplicationId(migratedApplication.getId());
applicationHorizonWorkProgrammeRepository.save(applicationHorizonWorkProgramme);
});
log.debug("Migrated Horizon Work Programme for application : " + application.getId());
}
}
private void migrateApplicationExpressionOfInterestConfig(Application application, Application migratedApplication) {
if (application.getApplicationExpressionOfInterestConfig() != null) {
Long applicationExpressionOfInterestConfigId = application.getApplicationExpressionOfInterestConfig().getId();
applicationExpressionOfInterestConfigRepository.findById(applicationExpressionOfInterestConfigId).ifPresent(
applicationExpressionOfInterestConfig -> {
ApplicationExpressionOfInterestConfig migratedApplicationExpressionOfInterestConfig = ApplicationExpressionOfInterestConfig.builder()
.application(migratedApplication)
.enabledForExpressionOfInterest(applicationExpressionOfInterestConfig.isEnabledForExpressionOfInterest())
.build();
applicationExpressionOfInterestConfigRepository.save(migratedApplicationExpressionOfInterestConfig);
migratedApplication.setApplicationExpressionOfInterestConfig(migratedApplicationExpressionOfInterestConfig);
});
log.debug("Migrated application expression of interest config for application : " + application.getId());
}
}
private Application migrateApplication(Application application) {
Application migratedApplication = applicationRepository.save(new Application(application));
log.debug("Migrated application : " + application.getId());
return migratedApplication;
}
@Override
@Transactional
public ServiceResult<ApplicationMigration> updateApplicationMigrationStatus(ApplicationMigration applicationMigration) {
applicationMigration.setUpdatedOn(ZonedDateTime.now());
return serviceSuccess(applicationMigrationRepository.save(applicationMigration));
}
}
|
package org.tweetwallfx.controls.steps;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import java.util.Comparator;
import java.util.List;
import java.util.stream.Collectors;
import javafx.animation.FadeTransition;
import javafx.animation.ParallelTransition;
import javafx.animation.SequentialTransition;
import javafx.animation.Transition;
import javafx.geometry.BoundingBox;
import javafx.geometry.Bounds;
import javafx.geometry.Rectangle2D;
import javafx.scene.SnapshotParameters;
import javafx.scene.effect.GaussianBlur;
import javafx.scene.image.ImageView;
import javafx.scene.image.WritableImage;
import javafx.scene.text.Text;
import javafx.util.Duration;
import org.tweetwallfx.controls.Word;
import org.tweetwallfx.controls.WordleLayout;
import org.tweetwallfx.controls.WordleSkin;
import org.tweetwallfx.controls.dataprovider.TagCloudDataProvider;
import org.tweetwallfx.stepengine.api.DataProvider;
import org.tweetwallfx.stepengine.api.Step;
import org.tweetwallfx.stepengine.api.StepEngine.MachineContext;
import org.tweetwallfx.stepengine.api.config.AbstractConfig;
import org.tweetwallfx.stepengine.api.config.StepEngineSettings;
public class FadeInCloudStep implements Step {
private final Config config;
private FadeInCloudStep(Config config) {
this.config = config;
}
@Override
public java.time.Duration preferredStepDuration(final MachineContext context) {
return java.time.Duration.ofMillis(config.getStepDuration());
}
@Override
public boolean shouldSkip(MachineContext context) {
List<Word> sortedWords = context.getDataProvider(TagCloudDataProvider.class).getWords();
return sortedWords.isEmpty();
}
@Override
public void doStep(final MachineContext context) {
WordleSkin wordleSkin = (WordleSkin) context.get("WordleSkin");
context.put("cloudConfig", config);
List<Word> sortedWords = context.getDataProvider(TagCloudDataProvider.class).getWords();
List<Word> limitedWords = sortedWords.stream().limit(wordleSkin.getDisplayCloudTags()).toList();
List<Word> cutOfflLimitedWords = limitedWords.stream().
sorted(Comparator.reverseOrder()).
map(w -> new Word(w.getText().substring(0, Math.min(config.tagLength, w.getText().length())), w.getWeight())).toList();
Bounds layoutBounds = new BoundingBox(1,1, config.width, config.height);
WordleLayout.Configuration configuration = new WordleLayout.Configuration(cutOfflLimitedWords, wordleSkin.getFont(), wordleSkin.getFontSizeMax(), layoutBounds);
if (null != wordleSkin.getLogo()) {
configuration.setBlockedAreaBounds(wordleSkin.getLogo().getBoundsInParent());
}
if (null != wordleSkin.getSecondLogo()) {
configuration.setBlockedAreaBounds(wordleSkin.getSecondLogo().getBoundsInParent());
}
WordleLayout cloudWordleLayout = WordleLayout.createWordleLayout(configuration);
Duration defaultDuration = Duration.seconds(1.5);
List<Transition> fadeOutTransitions = new ArrayList<>();
List<Transition> moveTransitions = new ArrayList<>();
List<Transition> fadeInTransitions = new ArrayList<>();
SnapshotParameters snapshotParameters = new SnapshotParameters();
snapshotParameters.setViewport(new Rectangle2D(
config.layoutX,
config.layoutY,
config.width,
config.height));
WritableImage writableImage = new WritableImage((int)config.width, (int) config.height);
wordleSkin.getNode().snapshot(snapshotParameters,
writableImage);
ImageView snapCopy = new ImageView(writableImage);
snapCopy.setLayoutX(config.layoutX);
snapCopy.setLayoutY(config.layoutY);
snapCopy.setEffect(new GaussianBlur());
snapCopy.setId("blurredCopy");
wordleSkin.getPane().getChildren().add(snapCopy);
FadeTransition ftSnapCopy = new FadeTransition(defaultDuration, snapCopy);
ftSnapCopy.setToValue(1);
fadeInTransitions.add(ftSnapCopy);
cloudWordleLayout.getWordLayoutInfo().entrySet().stream().forEach(entry -> {
Word word = entry.getKey();
Bounds bounds = entry.getValue();
Text textNode = cloudWordleLayout.createTextNode(word);
wordleSkin.word2TextMap.put(word, textNode);
textNode.setLayoutX(config.layoutX + bounds.getMinX() + layoutBounds.getWidth() / 2d);
textNode.setLayoutY(config.layoutY + bounds.getMinY() + layoutBounds.getHeight() / 2d + Math.abs(bounds.getHeight()) / 2d);
textNode.setOpacity(0);
wordleSkin.getPane().getChildren().add(textNode);
FadeTransition ftTextNode = new FadeTransition(defaultDuration, textNode);
ftTextNode.setToValue(1);
fadeInTransitions.add(ftTextNode);
});
ParallelTransition fadeOuts = new ParallelTransition();
fadeOuts.getChildren().addAll(fadeOutTransitions);
ParallelTransition moves = new ParallelTransition();
moves.getChildren().addAll(moveTransitions);
ParallelTransition fadeIns = new ParallelTransition();
fadeIns.getChildren().addAll(fadeInTransitions);
SequentialTransition morph = new SequentialTransition(fadeOuts, moves, fadeIns);
morph.setOnFinished(e -> context.proceed());
morph.play();
}
/**
* Implementation of {@link Step.Factory} as Service implementation creating
* {@link FadeInCloudStep}.
*/
public static final class FactoryImpl implements Step.Factory {
@Override
public FadeInCloudStep create(final StepEngineSettings.StepDefinition stepDefinition) {
return new FadeInCloudStep(stepDefinition.getConfig(Config.class));
}
@Override
public Class<FadeInCloudStep> getStepClass() {
return FadeInCloudStep.class;
}
@Override
public Collection<Class<? extends DataProvider>> getRequiredDataProviders(final StepEngineSettings.StepDefinition stepSettings) {
return Arrays.asList(TagCloudDataProvider.class);
}
}
private static class Config extends AbstractConfig {
public double layoutX = 0;
public double layoutY = 0;
public double width = 0;
public double height = 0;
public int tagLength = 15;
}
}
|
package org.eclipse.persistence.internal.jpa.metadata.queries;
import javax.persistence.ParameterMode;
import org.eclipse.persistence.annotations.Direction;
import org.eclipse.persistence.internal.helper.DatabaseField;
import org.eclipse.persistence.internal.jpa.metadata.ORMetadata;
import org.eclipse.persistence.internal.jpa.metadata.accessors.MetadataAccessor;
import org.eclipse.persistence.internal.jpa.metadata.accessors.objects.MetadataAccessibleObject;
import org.eclipse.persistence.internal.jpa.metadata.accessors.objects.MetadataAnnotation;
import org.eclipse.persistence.internal.jpa.metadata.accessors.objects.MetadataClass;
import org.eclipse.persistence.internal.jpa.metadata.xml.XMLEntityMappings;
import org.eclipse.persistence.queries.StoredFunctionCall;
import org.eclipse.persistence.queries.StoredProcedureCall;
/**
* INTERNAL:
* Object to hold onto a stored procedure parameter metadata.
*
* Key notes:
* - any metadata mapped from XML to this class must be compared in the
* equals method.
* - all metadata mapped from XML should be initialized in the initXMLObject
* method.
* - when loading from annotations, the constructor accepts the metadata
* accessor this metadata was loaded from. Used it to look up any
* 'companion' annotation needed for processing.
* - methods should be preserved in alphabetical order.
*
* @author Guy Pelletier
* @since TopLink 11g
*/
public class StoredProcedureParameterMetadata extends ORMetadata {
private Boolean m_optional;
private Integer m_jdbcType;
private MetadataClass m_type;
private String m_direction;
private String m_mode;
private String m_jdbcTypeName;
private String m_name;
private String m_queryParameter;
private String m_typeName;
/**
* INTERNAL:
* Used for XML loading.
*/
public StoredProcedureParameterMetadata() {
super("<stored-procedure-parameter>");
}
/**
* INTERNAL:
* Used for annotation loading.
*/
public StoredProcedureParameterMetadata(MetadataAnnotation storedProcedureParameter, MetadataAccessor accessor) {
super(storedProcedureParameter, accessor);
m_direction = (String) storedProcedureParameter.getAttribute("direction");
m_mode = (String) storedProcedureParameter.getAttribute("mode");
m_name = (String) storedProcedureParameter.getAttribute("name");
m_queryParameter = (String) storedProcedureParameter.getAttribute("queryParameter");
m_type = getMetadataClass((String) storedProcedureParameter.getAttributeClass("type"));
m_jdbcType = (Integer) storedProcedureParameter.getAttribute("jdbcType");
m_jdbcTypeName = (String) storedProcedureParameter.getAttribute("jdbcTypeName");
m_optional = (Boolean) storedProcedureParameter.getAttribute("optional");
}
/**
* INTERNAL:
*/
@Override
public boolean equals(Object objectToCompare) {
if (objectToCompare instanceof StoredProcedureParameterMetadata) {
StoredProcedureParameterMetadata parameter = (StoredProcedureParameterMetadata) objectToCompare;
if (! valuesMatch(m_type, parameter.getType())) {
return false;
}
if (! valuesMatch(m_direction, parameter.getDirection())) {
return false;
}
if (! valuesMatch(m_mode, parameter.getMode())) {
return false;
}
if (! valuesMatch(m_jdbcType, parameter.getJdbcType())) {
return false;
}
if (! valuesMatch(m_jdbcTypeName, parameter.getJdbcTypeName())) {
return false;
}
if (! valuesMatch(m_name, parameter.getName())) {
return false;
}
if (! valuesMatch(m_optional, parameter.getOptional())) {
return false;
}
return valuesMatch(m_queryParameter, parameter.getQueryParameter());
}
return false;
}
/**
* INTERNAL:
* Used for OX mapping.
*/
public String getDirection() {
return m_direction;
}
/**
* INTERNAL:
* Used for OX mapping.
*/
public Integer getJdbcType() {
return m_jdbcType;
}
/**
* INTERNAL:
* Used for OX mapping.
*/
public String getJdbcTypeName() {
return m_jdbcTypeName;
}
/**
* INTERNAL:
* Used for OX mapping.
*/
public String getMode() {
return m_mode;
}
/**
* INTERNAL:
* Used for OX mapping.
*/
public String getName() {
return m_name;
}
/**
* INTERNAL:
* Used for OX mapping.
*/
public Boolean getOptional() {
return m_optional;
}
/**
* INTERNAL:
* Used for OX mapping.
*/
public String getQueryParameter() {
return m_queryParameter;
}
/**
* INTERNAL:
*/
public MetadataClass getType() {
return m_type;
}
/**
* INTERNAL:
* Used for OX mapping.
*/
public String getTypeName() {
return m_typeName;
}
/**
* INTERNAL:
*/
protected boolean hasJdbcType() {
return m_jdbcType != null && m_jdbcType.equals(-1);
}
/**
* INTERNAL:
*/
protected boolean hasJdbcTypeName() {
return m_jdbcTypeName != null && ! m_jdbcTypeName.equals("");
}
/**
* INTERNAL:
*/
protected boolean hasType() {
return !m_type.isVoid();
}
/**
* INTERNAL:
*/
@Override
public void initXMLObject(MetadataAccessibleObject accessibleObject, XMLEntityMappings entityMappings) {
super.initXMLObject(accessibleObject, entityMappings);
m_type = initXMLClassName(m_typeName);
}
/**
* INTERNAL:
*/
public boolean isOutParameter() {
String parameterMode = (m_direction == null) ? m_mode : m_direction;
return parameterMode != null && ( parameterMode.equals(ParameterMode.OUT.name())
|| parameterMode.equals(ParameterMode.INOUT.name())
|| parameterMode.equals(ParameterMode.REF_CURSOR.name())
|| parameterMode.equals(Direction.OUT_CURSOR.name()));
}
/**
* INTERNAL:
*/
private boolean process(StoredProcedureCall call, int index) {
boolean shouldCallByIndex = false;
// Process the procedure parameter name, defaults to the argument field name.
if (m_name == null || m_name.equals("")) {
if (m_queryParameter == null || m_queryParameter.equals("")) {
// JPA 2.1 make the query parameter positional
shouldCallByIndex = true;
m_queryParameter = String.valueOf(index);
} else {
// EclipseLink support, a query parameter is required to be specified.
// TODO: Log a message when defaulting.
m_name = m_queryParameter;
}
}
// There is no such thing as queryParameter in JPA's version.
if (m_queryParameter == null || m_queryParameter.equals("")) {
m_queryParameter = m_name;
}
if ((m_optional != null) && m_optional) {
call.addOptionalArgument(m_queryParameter);
}
if (m_mode == null) {
if (m_direction == null) {
// TODO: Log a defaulting message if parameterMode is null.
m_mode = ParameterMode.IN.name();
} else {
m_mode = m_direction;
}
}
return shouldCallByIndex;
}
/**
* INTERNAL:
*/
public void processArgument(StoredProcedureCall call, boolean callByIndex, int index) {
boolean shouldCallByIndex = process(call, index);
if (! callByIndex) {
callByIndex = shouldCallByIndex;
}
if (m_mode.equals(ParameterMode.IN.name())) {
if (hasType()) {
if (callByIndex) {
call.addUnamedArgument(m_queryParameter, getJavaClass(m_type));
} else {
call.addNamedArgument(m_name, m_queryParameter, getJavaClass(m_type));
}
} else if (hasJdbcType() && hasJdbcTypeName()) {
if (callByIndex) {
call.addUnamedArgument(m_queryParameter, m_jdbcType, m_jdbcTypeName);
} else {
call.addNamedArgument(m_name, m_queryParameter, m_jdbcType, m_jdbcTypeName);
}
} else if (hasJdbcType()) {
if (callByIndex) {
call.addUnamedArgument(m_queryParameter, m_jdbcType);
} else {
call.addNamedArgument(m_name, m_queryParameter, m_jdbcType);
}
} else {
if (callByIndex) {
call.addUnamedArgument(m_queryParameter);
} else {
call.addNamedArgument(m_name, m_queryParameter);
}
}
} else if (m_mode.equals(ParameterMode.OUT.name())) {
if (hasType()) {
if (callByIndex) {
call.addUnamedOutputArgument(m_queryParameter, getJavaClass(m_type));
} else {
call.addNamedOutputArgument(m_name, m_queryParameter, getJavaClass(m_type));
}
} else if (hasJdbcType() && hasJdbcTypeName()) {
if (callByIndex) {
call.addUnamedOutputArgument(m_queryParameter, m_jdbcType, m_jdbcTypeName);
} else {
call.addNamedOutputArgument(m_name, m_queryParameter, m_jdbcType, m_jdbcTypeName);
}
} else if (hasJdbcType()) {
if (callByIndex) {
call.addUnamedOutputArgument(m_queryParameter, m_jdbcType);
} else {
call.addNamedOutputArgument(m_name, m_queryParameter, m_jdbcType);
}
} else {
if (callByIndex) {
call.addUnamedOutputArgument(m_queryParameter);
} else {
call.addNamedOutputArgument(m_name, m_queryParameter);
}
}
//set the project level settings on the argument's database fields
setDatabaseFieldSettings((DatabaseField)call.getParameters().get(call.getParameters().size() - 1));
} else if (m_mode.equals(Direction.IN_OUT.name()) || m_mode.equals(ParameterMode.INOUT.name())) {
if (hasType()) {
if (callByIndex) {
call.addUnamedInOutputArgument(m_queryParameter, m_queryParameter, getJavaClass(m_type));
} else {
call.addNamedInOutputArgument(m_name, m_queryParameter, m_queryParameter, getJavaClass(m_type));
}
} else if (hasJdbcType() && hasJdbcTypeName()) {
if (callByIndex) {
call.addUnamedInOutputArgument(m_queryParameter, m_queryParameter, m_jdbcType, m_jdbcTypeName);
} else {
call.addNamedInOutputArgument(m_name, m_queryParameter, m_queryParameter, m_jdbcType, m_jdbcTypeName);
}
} else if (hasJdbcType()) {
if (callByIndex) {
call.addUnamedInOutputArgument(m_queryParameter, m_queryParameter, m_jdbcType);
} else {
call.addNamedInOutputArgument(m_name, m_queryParameter, m_queryParameter, m_jdbcType);
}
} else {
if (callByIndex) {
call.addUnamedInOutputArgument(m_queryParameter);
} else {
call.addNamedInOutputArgument(m_name, m_queryParameter);
}
}
//set the project level settings on the argument's out database field
Object[] array = (Object[])call.getParameters().get(call.getParameters().size() - 1);
if (array[0] == array[1]){
array[1] = ((DatabaseField)array[1]).clone();
}
setDatabaseFieldSettings((DatabaseField) array[1]);
} else if (m_mode.equals(Direction.OUT_CURSOR.name()) || m_mode.equals(ParameterMode.REF_CURSOR.name())) {
boolean multipleCursors = call.getParameterTypes().contains(call.OUT_CURSOR);
if (callByIndex) {
call.useUnnamedCursorOutputAsResultSet();
} else {
call.useNamedCursorOutputAsResultSet(m_queryParameter);
}
// There are multiple cursor output parameters, then do not use the
// cursor as the result set. This will be set to true in the calls
// above so we must do the multiple cursor call before hand.
if (multipleCursors) {
call.setIsCursorOutputProcedure(false);
}
}
}
/**
* INTERNAL:
*/
public void processResult(StoredFunctionCall call, int index) {
process(call, index);
// Process the function parameter
if (hasType()) {
call.setResult(m_name, getJavaClass(m_type));
} else if (hasJdbcType() && hasJdbcTypeName()) {
call.setResult(m_name, m_jdbcType, m_jdbcTypeName);
} else if (hasJdbcType()) {
call.setResult(m_name, m_jdbcType);
} else {
call.setResult(m_name);
}
}
/**
* INTERNAL:
*/
/*
* SAVED
public void process(StoredProcedureCall call, boolean callByIndex, boolean functionReturn, int index) {
// Process the procedure parameter name, defaults to the argument field name.
if (m_name == null || m_name.equals("")) {
if (m_queryParameter == null || m_queryParameter.equals("")) {
// JPA 2.1 make the query parameter positional
callByIndex = true;
m_queryParameter = String.valueOf(index);
} else {
// EclipseLink support, a query parameter is required to be specified.
// TODO: Log a message when defaulting.
m_name = m_queryParameter;
}
}
// There is no such thing as queryParameter in JPA's version.
if (m_queryParameter == null || m_queryParameter.equals("")) {
m_queryParameter = m_name;
}
if ((m_optional != null) && m_optional) {
call.addOptionalArgument(m_queryParameter);
}
String parameterMode = (m_direction == null) ? m_mode : m_direction;
// Process the parameter mode
if (functionReturn) {
if (hasType()) {
((StoredFunctionCall)call).setResult(m_name, getJavaClass(m_type));
} else if (hasJdbcType() && hasJdbcTypeName()) {
((StoredFunctionCall)call).setResult(m_name, m_jdbcType, m_jdbcTypeName);
} else if (hasJdbcType()) {
((StoredFunctionCall)call).setResult(m_name, m_jdbcType);
} else {
((StoredFunctionCall)call).setResult(m_name);
}
} else if (parameterMode == null || parameterMode.equals(ParameterMode.IN.name())) {
// TODO: Log a defaulting message if parameterMode is null.
if (hasType()) {
if (callByIndex) {
call.addUnamedArgument(m_queryParameter, getJavaClass(m_type));
} else {
call.addNamedArgument(m_name, m_queryParameter, getJavaClass(m_type));
}
} else if (hasJdbcType() && hasJdbcTypeName()) {
if (callByIndex) {
call.addUnamedArgument(m_queryParameter, m_jdbcType, m_jdbcTypeName);
} else {
call.addNamedArgument(m_name, m_queryParameter, m_jdbcType, m_jdbcTypeName);
}
} else if (hasJdbcType()) {
if (callByIndex) {
call.addUnamedArgument(m_queryParameter, m_jdbcType);
} else {
call.addNamedArgument(m_name, m_queryParameter, m_jdbcType);
}
} else {
if (callByIndex) {
call.addUnamedArgument(m_queryParameter);
} else {
call.addNamedArgument(m_name, m_queryParameter);
}
}
} else if (parameterMode.equals(ParameterMode.OUT.name())) {
if (hasType()) {
if (callByIndex) {
call.addUnamedOutputArgument(m_queryParameter, getJavaClass(m_type));
} else {
call.addNamedOutputArgument(m_name, m_queryParameter, getJavaClass(m_type));
}
} else if (hasJdbcType() && hasJdbcTypeName()) {
if (callByIndex) {
call.addUnamedOutputArgument(m_queryParameter, m_jdbcType, m_jdbcTypeName);
} else {
call.addNamedOutputArgument(m_name, m_queryParameter, m_jdbcType, m_jdbcTypeName);
}
} else if (hasJdbcType()) {
if (callByIndex) {
call.addUnamedOutputArgument(m_queryParameter, m_jdbcType);
} else {
call.addNamedOutputArgument(m_name, m_queryParameter, m_jdbcType);
}
} else {
if (callByIndex) {
call.addUnamedOutputArgument(m_queryParameter);
} else {
call.addNamedOutputArgument(m_name, m_queryParameter);
}
}
//set the project level settings on the argument's database fields
setDatabaseFieldSettings((DatabaseField)call.getParameters().get(call.getParameters().size() - 1));
} else if (parameterMode.equals(Direction.IN_OUT.name()) || parameterMode.equals(ParameterMode.INOUT.name())) {
if (hasType()) {
if (callByIndex) {
call.addUnamedInOutputArgument(m_queryParameter, m_queryParameter, getJavaClass(m_type));
} else {
call.addNamedInOutputArgument(m_name, m_queryParameter, m_queryParameter, getJavaClass(m_type));
}
} else if (hasJdbcType() && hasJdbcTypeName()) {
if (callByIndex) {
call.addUnamedInOutputArgument(m_queryParameter, m_queryParameter, m_jdbcType, m_jdbcTypeName);
} else {
call.addNamedInOutputArgument(m_name, m_queryParameter, m_queryParameter, m_jdbcType, m_jdbcTypeName);
}
} else if (hasJdbcType()) {
if (callByIndex) {
call.addUnamedInOutputArgument(m_queryParameter, m_queryParameter, m_jdbcType);
} else {
call.addNamedInOutputArgument(m_name, m_queryParameter, m_queryParameter, m_jdbcType);
}
} else {
if (callByIndex) {
call.addUnamedInOutputArgument(m_queryParameter);
} else {
call.addNamedInOutputArgument(m_name, m_queryParameter);
}
}
//set the project level settings on the argument's out database field
Object[] array = (Object[])call.getParameters().get(call.getParameters().size() - 1);
if (array[0] == array[1]){
array[1] = ((DatabaseField)array[1]).clone();
}
setDatabaseFieldSettings((DatabaseField) array[1]);
} else if (parameterMode.equals(Direction.OUT_CURSOR.name()) || parameterMode.equals(ParameterMode.REF_CURSOR.name())) {
boolean multipleCursors = call.getParameterTypes().contains(call.OUT_CURSOR);
if (callByIndex) {
call.useUnnamedCursorOutputAsResultSet();
} else {
call.useNamedCursorOutputAsResultSet(m_queryParameter);
}
// There are multiple cursor output parameters, then do not use the
// cursor as the result set. This will be set to true in the calls
// above so we must do the multiple cursor call before hand.
if (multipleCursors) {
call.setIsCursorOutputProcedure(false);
}
}
}
*/
/**
* INTERNAL:
* set the project level settings on the database fields
*/
protected void setDatabaseFieldSettings(DatabaseField field) {
if (getProject().useDelimitedIdentifier()) {
field.setUseDelimiters(true);
} else if (getProject().getShouldForceFieldNamesToUpperCase() && !field.shouldUseDelimiters()) {
field.useUpperCaseForComparisons(true);
}
}
/**
* INTERNAL:
* Used for OX mapping.
*/
public void setDirection(String direction) {
m_direction = direction;
}
/**
* INTERNAL:
* Used for OX mapping.
*/
public void setJdbcType(Integer jdbcType) {
m_jdbcType = jdbcType;
}
/**
* INTERNAL:
* Used for OX mapping.
*/
public void setJdbcTypeName(String jdbcTypeName) {
m_jdbcTypeName = jdbcTypeName;
}
/**
* INTERNAL:
* Used for OX mapping.
*/
public void setMode(String mode) {
m_mode = mode;
}
/**
* INTERNAL:
* Used for OX mapping.
*/
public void setName(String name) {
m_name = name;
}
/**
* INTERNAL:
* Used for OX mapping.
*/
public void setOptional(Boolean optional) {
m_optional = optional;
}
/**
* INTERNAL:
* Used for OX mapping.
*/
public void setQueryParameter(String queryParameter) {
m_queryParameter = queryParameter;
}
/**
* INTERNAL:
*/
public void setType(MetadataClass type) {
m_type = type;
}
/**
* INTERNAL:
* Used for OX mapping.
*/
public void setTypeName(String typeName) {
m_typeName = typeName;
}
}
|
package com.verce.forwardmodelling;
import java.io.PrintWriter;
import java.io.IOException;
import java.io.FileInputStream;
import java.io.BufferedReader;
import java.io.InputStreamReader;
import java.io.DataOutputStream;
import java.io.DataInputStream;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.InputStream;
import java.io.OutputStream;
import java.io.FileNotFoundException;
import java.io.BufferedInputStream;
import java.io.File;
import java.net.*;
import javax.net.ssl.HttpsURLConnection;
import java.util.zip.*;
import java.util.TimeZone;
import java.util.Enumeration;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.Date;
import java.util.Hashtable;
import java.util.Vector;
import java.util.List;
import java.util.Map;
import java.util.concurrent.ConcurrentHashMap;
import java.util.Properties;
import java.text.SimpleDateFormat;
import java.text.DateFormat;
import java.text.Format;
import javax.portlet.ActionRequest;
import javax.portlet.ActionResponse;
import javax.portlet.PortletException;
import javax.portlet.ResourceRequest;
import javax.portlet.ResourceResponse;
import javax.servlet.http.HttpServletResponse;
import javax.servlet.http.HttpServletRequest;
import javax.mail.Message;
import javax.mail.MessagingException;
import javax.mail.PasswordAuthentication;
import javax.mail.Session;
import javax.mail.Transport;
import javax.mail.internet.InternetAddress;
import javax.mail.internet.MimeMessage;
import org.apache.commons.fileupload.FileItem;
import org.apache.commons.fileupload.FileItemFactory;
import org.apache.commons.fileupload.disk.DiskFileItem;
import com.liferay.portal.kernel.exception.PortalException;
import com.liferay.portal.kernel.exception.SystemException;
import com.liferay.portal.kernel.repository.model.Folder;
import com.liferay.portal.kernel.repository.model.FileEntry;
import com.liferay.portal.kernel.upload.UploadPortletRequest;
import com.liferay.portal.kernel.util.CharPool;
import com.liferay.portal.kernel.util.HttpUtil;
import com.liferay.portal.kernel.util.HtmlUtil;
import com.liferay.portal.kernel.util.FileUtil;
import com.liferay.portal.kernel.util.ParamUtil;
import com.liferay.portal.kernel.servlet.ServletResponseUtil;
import com.liferay.portal.model.User;
import com.liferay.portal.service.ServiceContext;
import com.liferay.portal.util.PortalUtil;
import com.liferay.portlet.documentlibrary.model.DLFileEntry;
import com.liferay.portlet.documentlibrary.model.DLFolderConstants;
import com.liferay.portlet.documentlibrary.service.DLFileEntryLocalServiceUtil;
import com.liferay.portlet.documentlibrary.service.DLAppServiceUtil;
import com.liferay.portlet.documentlibrary.DuplicateFileException;
import com.liferay.util.bridges.mvc.MVCPortlet;
import hu.sztaki.lpds.pgportal.services.asm.ASMJob;
import hu.sztaki.lpds.pgportal.services.asm.ASMService;
import hu.sztaki.lpds.pgportal.services.asm.ASMWorkflow;
import hu.sztaki.lpds.pgportal.services.asm.beans.ASMRepositoryItemBean;
import hu.sztaki.lpds.pgportal.services.asm.beans.WorkflowInstanceBean;
import hu.sztaki.lpds.pgportal.services.asm.beans.RunningJobDetailsBean;
import hu.sztaki.lpds.pgportal.services.asm.constants.RepositoryItemTypeConstants;
import hu.sztaki.lpds.pgportal.services.asm.constants.DownloadTypeConstants;
import hu.sztaki.lpds.pgportal.service.base.data.WorkflowData;
import hu.sztaki.lpds.pgportal.service.base.PortalCacheService;
import hu.sztaki.lpds.dcibridge.client.ResourceConfigurationFace;
import hu.sztaki.lpds.information.local.InformationBase;
import hu.sztaki.lpds.pgportal.service.workflow.RealWorkflowUtils;
import hu.sztaki.lpds.wfs.com.WorkflowConfigErrorBean;
import hu.sztaki.lpds.pgportal.services.asm.constants.StatusConstants;
import hu.sztaki.lpds.information.com.ServiceType;
import hu.sztaki.lpds.wfs.com.RepositoryWorkflowBean;
import hu.sztaki.lpds.repository.service.veronica.commons.RepositoryFileUtils;
import hu.sztaki.lpds.wfs.inf.PortalWfsClient;
import hu.sztaki.lpds.storage.inf.PortalStorageClient;
import com.verce.forwardmodelling.Constants;
import org.json.*;
public class ForwardPortlet extends MVCPortlet{
ASMService asm_service = null;
public void serveResource(ResourceRequest resourceRequest, ResourceResponse resourceResponse) throws PortletException, IOException
{
System.out.println("
if(resourceRequest.getResourceID().equals("uploadFile"))
uploadFile(resourceRequest, resourceResponse);
else if(resourceRequest.getResourceID().equals("submit"))
submit(resourceRequest, resourceResponse);
else if (resourceRequest.getResourceID().equals("downloadOutput"))
downloadOutput(resourceRequest, resourceResponse);
else if (resourceRequest.getResourceID().equals("deleteWorkflow"))
deleteWorkflow(resourceRequest, resourceResponse);
else if (resourceRequest.getResourceID().equals("meshVelocityModelUpload"))
meshVelocityModelUpload(resourceRequest, resourceResponse);
else if (resourceRequest.getResourceID().equals("downloadMeshDetails"))
downloadMeshDetails(resourceRequest, resourceResponse);
else if (resourceRequest.getResourceID().equals("downloadVelocityModelDetails"))
downloadVelocityModelDetails(resourceRequest, resourceResponse);
}
public void getWorkflowList(ActionRequest req, ActionResponse res)
{
try{
asm_service = ASMService.getInstance();
ArrayList<ASMWorkflow> importedWfs = asm_service.getASMWorkflows(req.getRemoteUser());
// ConcurrentHashMap<String, WorkflowData> workflows = PortalCacheService.getInstance().getUser(req.getRemoteUser()).getWorkflows();
String jsWfArray = "{\"list\":[";
for(ASMWorkflow wf : importedWfs)
{
// WorkflowData workflowData = workflows.get(wf.getWorkflowName());
// System.out.println(workflowData.getWorkflowID());
// System.out.println(workflowData.getGraf());
//wf.getWorkflowName() is formated: (submitedName+RandomID)_YYYY-MM-DD-TTTTTT
//wfDate is YYYY-MM-DD
//wfDate2 is YYYY-MM-DD-TTTTTT (used to sort the results)
//wfName is submitedName+RandomID
String wfDate = wf.getWorkflowName().substring(wf.getWorkflowName().lastIndexOf("_")+1, wf.getWorkflowName().lastIndexOf("-"));
String wfDate2 = wf.getWorkflowName().substring(wf.getWorkflowName().lastIndexOf("_")+1);
String wfName = wf.getWorkflowName().substring(0,wf.getWorkflowName().lastIndexOf("_"));
String status = wf.getStatusbean().getStatus();
if (!status.equals("ERROR") && !status.equals("FINISHED")) {
WorkflowInstanceBean wfIB = asm_service.getDetails(req.getRemoteUser(), wf.getWorkflowName());
if (wfIB == null) {
continue;
}
HashMap<String,String> statuses = new HashMap();
StatusConstants statusConstants = new StatusConstants();
for (RunningJobDetailsBean job : wfIB.getJobs()) {
if (job.getInstances().size() <= 0) {
statuses.put(job.getName(), "UNKNOWN");
continue;
}
statuses.put(job.getName(), statusConstants.getStatus(job.getInstances().get(0).getStatus()));
}
System.out.println(statuses);
String computeStatus = statuses.containsKey("COMPUTE") ? statuses.get("COMPUTE") : statuses.containsKey("Job0") ? statuses.get("Job0") : null;
String stageOutStatus = statuses.containsKey("STAGEOUT") ? statuses.get("STAGEOUT") : statuses.containsKey("Job1") ? statuses.get("Job1") : null;
if (statuses.containsValue("ERROR")) {
status = "ERROR";
} else if (computeStatus == null || "UNKNOWN".equals(computeStatus)) {
status = "INIT";
} else if ("PENDING".equals(computeStatus) || "INIT".equals(computeStatus)) {
status = "PENDING";
} else if ("RUNNING".equals(stageOutStatus)) {
status = "STAGE OUT";
} else if ("FINISHED".equals(stageOutStatus)) {
status = "FINISHED";
} else if ("RUNNING".equals(computeStatus)) {
status = "RUNNING";
} else {
// Fallback to overall workflow status
System.out.println("FALLBACK to workflow status");
}
}
jsWfArray += "{\"name\":\""+wfName+"\", \"desc\":\""+wf.getSubmissionText()+"\", \"status\":\""+status+
"\", \"date\":\""+wfDate+"\", \"date2\":\""+wfDate2+"\", \"workflowId\":\""+wf.getWorkflowName()+"\"},";
}
jsWfArray.substring(0, jsWfArray.length()-1);
jsWfArray +="]}";
HttpServletResponse response = PortalUtil.getHttpServletResponse(res);
PrintWriter out = response.getWriter();
out.print(jsWfArray);
out.flush();
out.close();
//System.out.println("[ForwardModellingPortlet.getWorkflowList] "+jsWfArray);
}
catch(Exception e)
{
e.printStackTrace();
System.out.println("[ForwardModellingPortlet.getWorkflowList] Could not update the workflow list");
}
}
public void updateWorkflowDescription(ActionRequest req, ActionResponse res)
{
asm_service = ASMService.getInstance();
String begName = ParamUtil.getString(req, "workflowId");
String newText = ParamUtil.getString(req, "newText");
ArrayList<ASMWorkflow> importedWfs;
importedWfs = asm_service.getASMWorkflows(req.getRemoteUser());
for(ASMWorkflow wf : importedWfs)
{
if(wf.getWorkflowName().startsWith(begName))
{
wf.setSubmissionText(newText);
System.out.println("[ForwardModellingPortlet.updateWorkflowDescription] Description in workflow "+begName+" has been updated to "+newText+" by user "+req.getRemoteUser());
return;
}
}
System.out.println("[ForwardModellingPortlet.updateWorkflowDescription] Error! Workflow "+begName+" could not be found");
}
private void deleteWorkflow(ResourceRequest resourceRequest, ResourceResponse resourceResponse)
{
String userId = resourceRequest.getRemoteUser();
try{
asm_service = ASMService.getInstance();
String wfId = ParamUtil.getString(resourceRequest, "workflowId");
//String status = asm_service.getStatus(userId, wfId);
//if(status.equals("RUNNING")||status.equals("INIT")||status.equals("INIT"))
asm_service.abort(userId, wfId); //TODO: fixme!
asm_service.DeleteWorkflow(userId, wfId);
System.out.println("[ForwardModellingPortlet.delete] workflow "+wfId+" has been deleted by user "+userId);
}
catch(Exception e)
{
catchError(e, resourceResponse, "500", "[ForwardModellingPortlet.delete] Exception catched!! User :"+userId);
}
}
private void submit(ResourceRequest resourceRequest, ResourceResponse resourceResponse) throws PortletException, IOException
{
try {
asm_service = ASMService.getInstance();
User u = PortalUtil.getUser(resourceRequest);
String userSN = u.getScreenName();
String userId = u.getUserId()+"";
String solverType = ParamUtil.getString(resourceRequest, "solver");
String[] jsonContentArray = resourceRequest.getParameterValues("jsonObject");
String workflowId = ParamUtil.getString(resourceRequest, "workflowId");
String workflowName = ParamUtil.getString(resourceRequest, "workflowName");
String ownerId = ParamUtil.getString(resourceRequest, "ownerId");
String stationUrl = ParamUtil.getString(resourceRequest, "stationUrl");
String eventUrl = ParamUtil.getString(resourceRequest, "eventUrl");
String[] runIds = resourceRequest.getParameterValues("runId");
String stFileType = ParamUtil.getString(resourceRequest, "stationType");
String jobName = "Job0";
String submitMessage = ParamUtil.getString(resourceRequest, "submitMessage");
String nProc = ParamUtil.getString(resourceRequest, "nProc");
boolean eventDLFile = eventUrl.contains("documents");
boolean stationDLFile = stationUrl.contains("documents");
File stationFile = null;
File eventFile = null;
String stPublicPath;
String evPublicPath;
long groupId = PortalUtil.getScopeGroupId(resourceRequest);
long repositoryId = DLFolderConstants.getDataRepositoryId(groupId, DLFolderConstants.DEFAULT_PARENT_FOLDER_ID);
ServiceContext serviceContext = new ServiceContext();
serviceContext.setScopeGroupId(groupId);
Format formatter = new SimpleDateFormat("yyyyMMddHHmm");
String portalUrl = PortalUtil.getPortalURL(resourceRequest);
String currentURL = PortalUtil.getCurrentURL(resourceRequest);
String portal = currentURL.substring(0, currentURL.substring(1).indexOf("/")+1);
portalUrl += portal;
String portalUrl2 = PortalUtil.getPortalURL(resourceRequest);
//System.out.println("[ForwardModellingPortlet.submitSolver] Abans: "+portalUrl2);
if(portalUrl2.equals("http:
//System.out.println("[ForwardModellingPortlet.submitSolver] Despres (sencer): "+portalUrl2+stationUrl);
System.out.println("Try to fetch workflow zip from repository for workflow with ID: " + workflowId);
String job0bin = "";
Date job0binModified = new Date(0L);
Hashtable hsh = new Hashtable();
ServiceType st = InformationBase.getI().getService("wfs", "portal", hsh, new Vector());
PortalWfsClient wfsClient = (PortalWfsClient) Class.forName(st.getClientObject()).newInstance();
wfsClient.setServiceURL(st.getServiceUrl());
wfsClient.setServiceID(st.getServiceID());
RepositoryWorkflowBean bean = new RepositoryWorkflowBean();
bean.setId(Long.parseLong(workflowId));
bean.setWorkflowType(RepositoryItemTypeConstants.Application);
Vector wfList = wfsClient.getRepositoryItems(bean);
if (wfList == null) {
throw new Exception("Not valid wf list !");
}
for (Object wfBeanObject : wfList) {
RepositoryWorkflowBean wfBean = (RepositoryWorkflowBean) wfBeanObject;
String relativePath = wfBean.getZipRepositoryPath();
String fullPath = new String(RepositoryFileUtils.getInstance().getRepositoryDir() + relativePath);
ZipFile zipFile = new ZipFile(fullPath);
Enumeration<? extends ZipEntry> entries = zipFile.entries();
while (entries.hasMoreElements()) {
ZipEntry entry = (ZipEntry) entries.nextElement();
System.out.println(entry.getName());
if (entry.getName().indexOf("Job0/execute.bin") >= 0) {
job0bin = inputStreamToString(zipFile.getInputStream(entry));
job0binModified = new Date(entry.getTime());
// System.out.println(job0bin);
break;
}
}
zipFile.close();
}
if(!stationDLFile) //1a. create StationFile and store it
{
stationFile = FileUtil.createTempFile();
URL wsUrl = new URL(portalUrl2+stationUrl);
FileUtil.write(stationFile, wsUrl.openStream());
String stFileName = "stations_"+runIds[0];
stPublicPath = addFileToDL(stationFile, stFileName, groupId, userSN, Constants.WS_TYPE);
stPublicPath = portalUrl + stPublicPath;
System.out.println("[ForwardModellingPortlet.submitSolver] Stations file created in the document library by "+userSN+", accessible in: "+stPublicPath);
stFileType = Constants.STXML_TYPE;
}
else //1b. Retrieve StationFile
{
String[] urlParts = stationUrl.split("/");
long folderId = Long.parseLong(urlParts[urlParts.length - 2]);
String stFileName = urlParts[urlParts.length - 1];
FileEntry fileEntry = DLAppServiceUtil.getFileEntry(groupId, folderId, stFileName);
stationFile = DLFileEntryLocalServiceUtil.getFile(fileEntry.getUserId(), fileEntry.getFileEntryId(), fileEntry.getVersion(), false);
stPublicPath = stationUrl;
}
if(!eventDLFile) //2a. create EventFile and store it
{
eventFile = FileUtil.createTempFile();
URL wsUrl = new URL(portalUrl2+eventUrl);
FileUtil.write(eventFile, wsUrl.openStream());
String evFileName = "events_"+runIds[0];
evPublicPath = addFileToDL(eventFile, evFileName, groupId, userSN, Constants.WS_TYPE);
evPublicPath = portalUrl + evPublicPath;
System.out.println("[ForwardModellingPortlet.submitSolver] Events file created in the document library by "+userSN+", accessible in: "+evPublicPath);
}
else //2b. Retrieve EventFile
{
String[] urlParts = eventUrl.split("/");
long folderId = Long.parseLong(urlParts[urlParts.length - 2]);
String evFileName = urlParts[urlParts.length - 1];
FileEntry fileEntry = DLAppServiceUtil.getFileEntry(groupId, folderId, evFileName);
eventFile = DLFileEntryLocalServiceUtil.getFile(fileEntry.getUserId(), fileEntry.getFileEntryId(), fileEntry.getVersion(), false);
evPublicPath = eventUrl;
}
//3. Generate zip file
String zipName = runIds[0]+".zip";
createZipFile("temp/"+zipName);
File tempZipFile = new File("temp/"+zipName);
String zipPublicPath = addFileToDL(tempZipFile, zipName, groupId, userSN, Constants.ZIP_TYPE);
zipPublicPath = portalUrl + zipPublicPath;
System.out.println("[ForwardModellingPortlet.submitSolver] Zip file created in the document library by "+userSN+", accessible in: "+zipPublicPath);
// //4. Generate Mesh/Model zip file
// String meshModelZipFileName = runIds[0]+"_meshmodel.zip";
// createMeshModelZipFile("temp/"+meshModelZipFileName, "data/mesh", "data/model");
// File meshModelZipFile = new File("temp/"+meshModelZipFileName);
for(int i=0;i<jsonContentArray.length;i++)
{
String jsonContent = jsonContentArray[i];
//4. Import the workflow
String importedWfId = importWorkflow(userId, ownerId, workflowId, runIds[i]);
//5. Create the solver file and store it
File solverFile = FileUtil.createTempFile();
FileUtil.write(solverFile, jsonContent);
String fileName = solverType+"_"+runIds[i]+".json";
String publicPath = addFileToDL(solverFile, fileName, groupId, userSN, Constants.SOLVER_TYPE);
publicPath = portalUrl + publicPath;
System.out.println("[ForwardModellingPortlet.submitSolver] Solver file created in the document library by "+userSN+", accessible in: "+publicPath);
//6. Upload files
asm_service.placeUploadedFile(userId, stationFile, importedWfId, jobName, "0");
asm_service.placeUploadedFile(userId, eventFile, importedWfId, jobName, "1");
asm_service.placeUploadedFile(userId, solverFile, importedWfId, jobName, "2");
asm_service.placeUploadedFile(userId, tempZipFile, importedWfId, jobName, "3");
// asm_service.placeUploadedFile(userId, meshModelZipFile, importedWfId, jobName, "4");
//7. Check for credential errors
//TODO: we should check just once
WorkflowData wfData = PortalCacheService.getInstance().getUser(userId).getWorkflow(importedWfId);
ResourceConfigurationFace rc=(ResourceConfigurationFace)InformationBase.getI().getServiceClient("resourceconfigure", "portal");
List resources = rc.get();
Vector<WorkflowConfigErrorBean> errorVector = (Vector<WorkflowConfigErrorBean>)RealWorkflowUtils.getInstance().getWorkflowConfigErrorVector(resources, userId, wfData);
if(errorVector!=null && !errorVector.isEmpty())
{
for (WorkflowConfigErrorBean er : errorVector) {
System.out.println("[ForwardModellingPortlet.submitSolver] Alert '"+er.getErrorID()+"'! userSN: "+userSN+", runId: "+runIds[i]);
if(er.getErrorID().contains("noproxy") || er.getErrorID().contains("proxyexpired"))
{
catchError(null, resourceResponse, "401", "[ForwardModellingPortlet.submitSolver] Credential Error! Submission stoped");
return;
}
}
}
//8. Change number of MPI nodes
if(solverType.toLowerCase().contains(Constants.SPECFEM_TYPE))
{
System.out.println("[ForwardModellingPortlet.submitSolver] Set number of processors to "+nProc+", by "+userSN);
asm_service.setJobAttribute(userId, importedWfId, jobName, "gt5.keycount", nProc);
}
//9. Submit
asm_service.submit(userId, importedWfId, submitMessage, "Never");
//10. Add run info in the Provenance Repository
updateProvenanceRepository(userSN, runIds[i], submitMessage, workflowName, workflowId, importedWfId, stPublicPath, evPublicPath, publicPath, zipPublicPath, stFileType, job0bin, job0binModified);
System.out.println("[ForwardModellingPortlet.submitSolver] Submission finished: "+userSN+", "+runIds[i]+", "+submitMessage+", "+workflowId+", "+importedWfId);
}
tempZipFile.delete();
}
catch (Exception e)
{
catchError(e, resourceResponse, "500", "[ForwardModellingPortlet.submitSolver] Exception catched!");
}
}
public void downloadOutput(ResourceRequest resourceRequest,
ResourceResponse resourceResponse)
{
asm_service = ASMService.getInstance();
String userId = resourceRequest.getRemoteUser();
String wfId = ParamUtil.getString(resourceRequest, "workflowId");
resourceResponse.setContentType("application/zip");
resourceResponse.setProperty("Content-Disposition", "attachment; filename=\"logs.zip\"");
try{
asm_service.getWorkflowOutputs(userId, wfId, resourceResponse);
}
catch(Exception e)
{
System.out.println("[ForwardModellingPortlet.downloadOutput] Exception caught!!");
e.printStackTrace();
// TODO send error to client
}
}
private void meshVelocityModelUpload(ResourceRequest resourceRequest, ResourceResponse resourceResponse) {
try {
UploadPortletRequest uploadRequest = PortalUtil.getUploadPortletRequest(resourceRequest);
String meshURL = uploadRequest.getParameter("mesh-link");
if (uploadRequest.getFileName("mesh-file") != null && uploadRequest.getFileName("mesh-file").length() > 0) {
meshURL = saveFileUpload(resourceRequest, uploadRequest.getFileAsStream("mesh-file"), uploadRequest.getFileName("mesh-file"), "mesh");
}
System.out.println(meshURL);
if (meshURL == null || meshURL.equals("")) {
resourceResponse.getWriter().write("{ success: false, errors: { \"mesh-file\": \"No mesh file or URL included or included file too large.\" } }");
return;
}
String velocityModelURL = uploadRequest.getParameter("velocity-model-link");
if (uploadRequest.getFileName("velocity-model-file") != null && uploadRequest.getFileName("velocity-model-file").length() > 0) {
velocityModelURL = saveFileUpload(resourceRequest, uploadRequest.getFileAsStream("velocity-model-file"), uploadRequest.getFileName("velocity-model-file"), "velocitymodel");
}
System.out.println(velocityModelURL);
if (velocityModelURL == null || velocityModelURL.equals("")) {
resourceResponse.getWriter().write("{ success: false, errors: { \"velocity-model-file\": \"No velocity model file or URL included or included file too large.\" } }");
return;
}
String minLat = uploadRequest.getParameter("min_lat");
String maxLat = uploadRequest.getParameter("max_lat");
String minLon = uploadRequest.getParameter("min_lon");
String maxLon = uploadRequest.getParameter("max_lon");
Properties props = new Properties();
props.put("mail.smtp.host", "localhost");
props.put("mail.smtp.port", "25");
Session session = Session.getInstance(props);
try {
Message message = new MimeMessage(session);
message.setFrom(InternetAddress.parse("admin@verce.eu")[0]);
// message.setReplyTo(InternetAddress.parse(PortalUtil.getUser(resourceRequest).getDisplayEmailAddress()));
message.setRecipients(Message.RecipientType.TO,
InternetAddress.parse("spinuso@knmi.nl, emanuele.casarotti@ingv.it, federica.magnoni@ingv.it, " + PortalUtil.getUser(resourceRequest).getDisplayEmailAddress()));
message.setRecipients(Message.RecipientType.BCC,
InternetAddress.parse("jonas.matser@knmi.nl"));
message.setSubject("VERCE: Mesh and velocity model submitted");
message.setText(
"User " + PortalUtil.getUser(resourceRequest).getScreenName() + " has submitted a new mesh and velocity model for review.\n" +
"\n" +
"The mesh and velocity model are available at the following links.\n" +
"Mesh: " + meshURL + "\n" +
"Velocity Model: " + velocityModelURL + "\n" +
"\n" +
"The bounds for the mesh are:\n" +
"Minimum latitude: " + minLat + "\n" +
"Maximum latitude: " + maxLat + "\n" +
"Minimum longitude: " + minLon + "\n" +
"Maximum longitude: " + maxLon + "\n" +
"\n" +
"The user also added the following note:\n" +
HtmlUtil.escape(uploadRequest.getParameter("note"))
);
Transport.send(message);
} catch (MessagingException e) {
throw new RuntimeException(e);
}
resourceResponse.getWriter().write("{ success: true }");
} catch (Exception e) {
System.out.println(e);
catchError(e, resourceResponse, "500", e.getMessage());
}
}
private void uploadFile(ResourceRequest resourceRequest, ResourceResponse resourceResponse)
{
resourceResponse.setContentType("text/html");
try {
UploadPortletRequest uploadRequest = PortalUtil.getUploadPortletRequest(resourceRequest);
InputStream inputStream = uploadRequest.getFileAsStream("form-file");
if(inputStream == null){
throw new Exception("[ForwardModellingPortlet.uploadFile] ERROR: FileInput \"form-file\" not found in request.");
}
String name = ParamUtil.getString(uploadRequest, "name");
String filetype = ParamUtil.getString(uploadRequest, "filetype");
String publicPath = saveFileUpload(resourceRequest, inputStream, name, filetype);
String successString = " {'success':'true', 'path':'"+publicPath+"'}";
resourceResponse.getWriter().write(successString);
} catch (Exception e) {
catchError(e, resourceResponse, "500", e.getMessage());
}
}
private String saveFileUpload(ResourceRequest resourceRequest, InputStream inputStream, String name, String filetype)
throws Exception
{
if(PortalUtil.getUser(resourceRequest)==null)
throw new Exception("[ForwardModellingPortlet.uploadFile] No user logged in!");
String userSN = PortalUtil.getUser(resourceRequest).getScreenName();
long groupId = PortalUtil.getScopeGroupId(resourceRequest);
File file = FileUtil.createTempFile(inputStream);
if (file.length() < 1)
{
throw new Exception("[ForwardModellingPortlet.uploadFile] Failed!! The file is empty. User: "+userSN);
}
//try
String publicPath = addFileToDL(file, name, groupId, userSN, filetype);
String portalUrl = PortalUtil.getPortalURL(resourceRequest);
String currentURL = PortalUtil.getCurrentURL(resourceRequest);
String portal = currentURL.substring(0, currentURL.substring(1).indexOf("/")+1);
portalUrl += portal;
publicPath = portalUrl+publicPath;
System.out.println("[ForwardModellingPortlet.uploadFile] File created in the document library by user "+userSN+", accessible in: "+publicPath);
return publicPath;
//catch (Exception e)
// System.out.println(e.getStackTrace());
// throw new Exception("[ForwardModellingPortlet.uploadFile] ERROR: The file could not be saved in the DL. User: "+userSN, e);
}
private String inputStreamToString(InputStream inputStream) throws IOException {
InputStreamReader inputStreamReader = new InputStreamReader(inputStream);
StringBuilder stringBuilder = new StringBuilder();
char[] buffer = new char[1024];
int charsRead = 0;
while ((charsRead = inputStreamReader.read(buffer)) > 0) {
stringBuilder.append(buffer, 0, charsRead);
};
return stringBuilder.toString();
}
private void downloadMeshDetails(ResourceRequest resourceRequest, ResourceResponse resourceResponse) {
try {
String solverName = ParamUtil.getString(resourceRequest, "solver");
String meshName = ParamUtil.getString(resourceRequest, "meshName");
URL url = new URL("http://localhost:8080/j2ep-1.0/prov/solver/" + solverName);
HttpURLConnection con = (HttpURLConnection) url.openConnection();
con.setRequestMethod("GET");
if(con.getResponseCode()!=200) {
System.out.println("[ForwardModellingPortlet.downloadMeshDetails] Error: " + con.getResponseCode());
return;
}
String input = inputStreamToString(con.getInputStream());
JSONObject jsonObject = new JSONObject(input);
JSONArray meshes = jsonObject.getJSONArray("meshes");
JSONObject mesh = null;
for (int ii = 0; ii < meshes.length(); ii++) {
mesh = meshes.getJSONObject(ii);
if (mesh.getString("name").equals(meshName)) {
break;
}
}
if (mesh == null) {
System.out.println("[ForwardModellingPortlet.downloadMeshDetails] Error: Mesh " + meshName + " not found for solver " + solverName);
return;
}
String details = mesh.getString("details");
resourceResponse.setContentType("application/text");
resourceResponse.setProperty("Content-Disposition", "attachment; filename=\"mesh-details.txt\"");
resourceResponse.getWriter().write(details);
} catch (Exception e) {
System.out.println("[ForwardModellingPortlet.downloadMeshDetails] Error: " + e.getStackTrace());
}
}
private void downloadVelocityModelDetails(ResourceRequest resourceRequest, ResourceResponse resourceResponse) {
try {
String solverName = ParamUtil.getString(resourceRequest, "solver");
String meshName = ParamUtil.getString(resourceRequest, "meshName");
String velocityModelName = ParamUtil.getString(resourceRequest, "velocityModelName");
URL url = new URL("http://localhost:8080/j2ep-1.0/prov/solver/" + solverName);
HttpURLConnection con = (HttpURLConnection) url.openConnection();
con.setRequestMethod("GET");
if(con.getResponseCode()!=200)
System.out.println("[ForwardModellingPortlet.downloadVelocityModelDetails] Error: " + con.getResponseCode());
InputStreamReader inputStreamReader = new InputStreamReader(con.getInputStream());
StringBuilder stringBuilder = new StringBuilder();
char[] buffer = new char[1024];
int charsRead = 0;
while ((charsRead = inputStreamReader.read(buffer)) > 0) {
stringBuilder.append(buffer, 0, charsRead);
};
JSONObject jsonObject = new JSONObject(stringBuilder.toString());
JSONArray meshes = jsonObject.getJSONArray("meshes");
JSONObject mesh = null;
for (int ii = 0; ii < meshes.length(); ii++) {
mesh = meshes.getJSONObject(ii);
if (mesh.getString("name").equals(meshName)) {
break;
}
}
if (mesh == null) {
System.out.println("[ForwardModellingPortlet.downloadVelocityModelDetails] Error: Mesh " + meshName + " not found for solver " + solverName);
return;
}
JSONArray velocityModels = mesh.getJSONArray("velmod");
JSONObject velocityModel = null;
for (int ii = 0; ii < velocityModels.length(); ii++) {
velocityModel = velocityModels.getJSONObject(ii);
if (velocityModel.getString("name").equals(velocityModelName)) {
break;
}
}
if (velocityModel == null) {
System.out.println("[ForwardModellingPortlet.downloadVelocityModelDetails] Error: Velocity Model " + velocityModelName + " not found for Mesh " + meshName + " and solver " + solverName);
return;
}
String details = velocityModel.getString("details");
resourceResponse.setContentType("application/text");
resourceResponse.setProperty("Content-Disposition", "attachment; filename=\"velocitymodel-details.txt\"");
resourceResponse.getWriter().write(details);
} catch (Exception e) {
System.out.println("[ForwardModellingPortlet.downloadVelocityModelDetails] Error: " + e.getStackTrace());
}
}
private String addFileToDL(File file, String name, long groupId, String userSN, String filetype)
throws SystemException, PortalException, Exception
{
long repositoryId = DLFolderConstants.getDataRepositoryId(groupId, DLFolderConstants.DEFAULT_PARENT_FOLDER_ID);
String sourceFileName = file.getName();
String mimeType = "text/plain";
String description = Constants.DOC_DESC + userSN;
String changeLog = "1.0";
ServiceContext serviceContext = new ServiceContext();
serviceContext.setScopeGroupId(groupId);
long folderId = getFolderId(repositoryId, userSN, filetype, serviceContext);
// Search for unused file number
// Don't use recursion because of stack limit (although the algorithm shouldn't run that deep)
// Two step algorithm
// 1. Find the first n (2^m) that is not in use be an existing file
// 2. Do a binary search between 2^(m-1) and 2^m for the first non-existing filename
// Define lower and upper bounds for searching
int lowerBound = 0;
int upperBound = 0;
// define midpoint for binary search part
int mid = 0;
// keep track of if we're search upwards or in binary search
boolean up = true;
String filename = name;
do {
try {
if (up) {
filename = name + (upperBound > 0 ? "_"+upperBound : "");
} else {
filename = name + (mid > 0 ? "_"+mid : "");
}
// try if file exists
DLAppServiceUtil.getFileEntry(repositoryId, folderId, filename);
} catch (PortalException e) {
// File doesnt Exist
if (up) {
// lowest n = 2^m found that's not in use
// start binary search
up = false;
continue;
} else {
// continue binary search in [lowerbound-mid]
upperBound = mid;
mid = lowerBound + (upperBound - lowerBound) / 2;
continue;
}
}
// File exists
if (up) {
// look at next n = 2^m if it's in use
lowerBound = Math.max(upperBound, 1);
upperBound = lowerBound * 2;
} else {
// continue binary search in [mid+1-lowerbound]
lowerBound = mid + 1;
mid = lowerBound + (upperBound - lowerBound) / 2;
}
} while (lowerBound != upperBound);
// set final filename
filename = name + (lowerBound > 0 ? "_"+lowerBound : "");
DLAppServiceUtil.addFileEntry(repositoryId, folderId, sourceFileName, mimeType, filename, description, changeLog, file, serviceContext);
System.out.println("[ForwardModellingPortlet.addFileToDL] The file "+filename+" has been created.");
return "/documents/" + groupId + "/" + folderId + "/" + HttpUtil.encodeURL(HtmlUtil.unescape(filename));
}
/*
* get the folderId for the specific user following the directory structure:
* root/Forwar Modelling/userSN/station (XML)
* if it doesn't exist it is created
*/
private long getFolderId(long repositoryId, String userSN, String filetype, ServiceContext serviceContext) throws SystemException, PortalException
{
Folder folder = null;
String lastFolderName = "";
if(filetype.equals(Constants.EVENT_TYPE)) lastFolderName = Constants.EVENT_FOLDER_NAME;
if(filetype.equals(Constants.STXML_TYPE)) lastFolderName = Constants.STXML_FOLDER_NAME;
if(filetype.equals(Constants.STPOINTS_TYPE)) lastFolderName = Constants.STPOINTS_FOLDER_NAME;
if(filetype.equals(Constants.SOLVER_TYPE)) lastFolderName = Constants.SOLVER_FOLDER_NAME;
if(filetype.equals(Constants.WS_TYPE)) lastFolderName = Constants.WS_FOLDER_NAME;
if(lastFolderName.equals("")) lastFolderName = filetype;
try{
folder = DLAppServiceUtil.getFolder(repositoryId, DLFolderConstants.DEFAULT_PARENT_FOLDER_ID, Constants.BASE_FOLDER_NAME);
} catch (PortalException pe) {
folder = DLAppServiceUtil.addFolder(repositoryId, DLFolderConstants.DEFAULT_PARENT_FOLDER_ID, Constants.BASE_FOLDER_NAME, Constants.BASE_FOLDER_DESC, serviceContext);
}
try{
folder = DLAppServiceUtil.getFolder(repositoryId, folder.getFolderId(), userSN);
} catch (PortalException pe) {
folder = DLAppServiceUtil.addFolder(repositoryId, folder.getFolderId(), userSN, Constants.USER_FOLDER_DESC, serviceContext);
}
try{
folder = DLAppServiceUtil.getFolder(repositoryId, folder.getFolderId(), lastFolderName);
} catch (PortalException pe) {
folder = DLAppServiceUtil.addFolder(repositoryId, folder.getFolderId(), lastFolderName, "", serviceContext);
}
return folder.getFolderId();
}
private String getFileAsString(File file) throws FileNotFoundException, IOException{
FileInputStream fis = null;
BufferedInputStream bis = null;
DataInputStream dis = null;
StringBuffer sb = new StringBuffer();
fis = new FileInputStream(file);
bis = new BufferedInputStream(fis);
dis = new DataInputStream(bis);
while (dis.available() != 0) {
sb.append(dis.readLine() + "\n");
}
fis.close();
bis.close();
dis.close();
return sb.toString();
}
private static final byte[] BUFFER = new byte[4096 * 1024];
private static void copy(InputStream input, OutputStream output) throws IOException
{
int bytesRead;
while ((bytesRead = input.read(BUFFER))!= -1) {
output.write(BUFFER, 0, bytesRead);
}
}
private void createZipFile(String fileName) throws IOException
{
ZipFile zipFile = new ZipFile("data/verce-hpc-pe.zip");
ZipOutputStream append = new ZipOutputStream(new FileOutputStream(fileName));
// copy contents from existing war
Enumeration<? extends ZipEntry> entries = zipFile.entries();
while (entries.hasMoreElements()) {
ZipEntry e = entries.nextElement();
append.putNextEntry(e);
if (!e.isDirectory()) {
copy(zipFile.getInputStream(e), append);
}
append.closeEntry();
}
// append new content
//TODO: get new Files from iraklis WS
ZipEntry e = new ZipEntry("newContent");
append.putNextEntry(e);
append.write("This a simple example".getBytes());
append.closeEntry();
// close
zipFile.close();
append.close();
System.out.println("[ForwardModellingPortlet.createZipFile] File created in the server file system: "+fileName);
}
private void createMeshModelZipFile(String fileName, String meshFileName, String modelFileName) throws IOException
{
ZipOutputStream zos = new ZipOutputStream(new FileOutputStream(fileName));
zos.putNextEntry(new ZipEntry("meshfile"));
copy(new FileInputStream(meshFileName), zos);
zos.closeEntry();
zos.putNextEntry(new ZipEntry("modelfile"));
copy(new FileInputStream(modelFileName), zos);
zos.closeEntry();
zos.close();
}
private void updateProvenanceRepository(String userSN, String runId, String submitMessage, String wfName, String wfId, String asmRunId,
String stationUrl, String eventUrl, String solverUrl, String zipUrl, String stationFileType, String job0bin, Date job0binModified)
{
String runType = "workflow_run";
try{
//TODO: put the url in a properties file
URL url = new URL("http://localhost:8080/j2ep-1.0/prov/workflow/insert");
//HttpsURLConnection con = (HttpsURLConnection) url.openConnection();
HttpURLConnection con = (HttpURLConnection) url.openConnection();
con.setRequestMethod("POST");
con.setRequestProperty("Content-type", "application/x-www-form-urlencoded");
con.setRequestProperty("Accept", "application/json");
TimeZone tz = TimeZone.getTimeZone("UTC");
DateFormat df = new SimpleDateFormat("yyyy-MM-dd'T'HH:mmZ");
df.setTimeZone(tz);
String nowAsISO = df.format(new Date());
if(stationFileType.equals(Constants.STPOINTS_TYPE)) stationFileType = Constants.MIMETYPE_PLAIN;
if(stationFileType.equals(Constants.STXML_TYPE)) stationFileType = Constants.MIMETYPE_XML;
JSONObject params = new JSONObject();
params.put("username", userSN)
.put("_id", runId)
.put("type", runType)
.put("description", submitMessage)
.put("workflowName", wfName)
.put("workflowId", wfId)
.put("system_id", asmRunId)
.put("startTime", nowAsISO)
.put("job0bin", job0bin)
.put("job0binModified", new SimpleDateFormat("yyyy-MM-dd'T'HH:mmZ").format(job0binModified));
JSONArray input = new JSONArray();
input.put(new JSONObject().put("mime-type", stationFileType).put("name",Constants.ST_INPUT_NAME).put("url", stationUrl))
.put(new JSONObject().put("mime-type", Constants.MIMETYPE_XML).put("name",Constants.EVENT_INPUT_NAME).put("url", eventUrl))
.put(new JSONObject().put("mime-type", Constants.MIMETYPE_JSON).put("name",Constants.SOLVER_INPUT_NAME).put("url", solverUrl))
.put(new JSONObject().put("mime-type", Constants.MIMETYPE_ZIP).put("name",Constants.ZIP_INPUT_NAME).put("url", zipUrl));
params.put("input", input);
// System.out.println("[updateProvenanceRepository] Params: "+params.toString());
String urlParameters = "prov="+URLEncoder.encode(params.toString(), "ISO-8859-1");
con.setDoOutput(true);
DataOutputStream wr = new DataOutputStream(con.getOutputStream());
wr.writeBytes(urlParameters);
wr.flush();
wr.close();
if(con.getResponseCode()!=200)
System.out.println("[ForwardModellingPortlet.updateProvenanceRepository] Error: " + con.getResponseCode());
BufferedReader in = new BufferedReader(new InputStreamReader(con.getInputStream()));
String inputLine;
StringBuffer response = new StringBuffer();
while ((inputLine = in.readLine()) != null) {
response.append(inputLine);
}
in.close();
System.out.println("[ForwardModellingPortlet.updateProvenanceRepository] User: "+userSN+", Response: "+response.toString());
}
catch(Exception e)
{
// We log the exception but continue the normal flow
System.out.println("[ForwardModellingPortlet.updateProvenanceRepository] Exception catched!!");
e.printStackTrace();
}
}
private String importWorkflow(String userId, String ownerId, String repositoryEntryId, String importedWfName) throws Exception
{
try
{
//asm_service = ASMService.getInstance();
String wfName = asm_service.ImportWorkflow(userId, importedWfName, ownerId, RepositoryItemTypeConstants.Application, repositoryEntryId);
System.out.println("[ForwardModellingPortlet.importWorkflow] Workflow "+repositoryEntryId+"("+ownerId+") with name "+importedWfName+" imported by user "+userId);
return wfName;
}
catch (Exception e) {
System.out.println("[ForwardModellingPortlet.importWorkflow] Exception catched! Could not import workflow "+repositoryEntryId+" from "+ownerId+", with name "+importedWfName);
throw e;
}
}
/*
* Sends the error through the response. Writes logMessage through the logs
* if e is not null prints the stackTrace through the logs
*/
private void catchError(Exception e, ResourceResponse res, String errorCode, String logMessage)
{
res.setContentType("text/html");
System.out.println("[ForwardModellingPortlet.catchError] Preparing response...");
try{
res.getWriter().write("{success: false, msg:\""+logMessage+"\"}"); //Submit call expects json success parameter
}catch(Exception e2)
{
System.out.println("[ForwardModellingPortlet.catchError] Could not write in response...");
}
res.setProperty(res.HTTP_STATUS_CODE, errorCode); //Ajax call expects status code
//res.setProperty("success", "false");
//res.setProperty("msg", logMessage);
//PrintWriter out = res.getWriter();
//out.println(failedString);
//out.close();
System.out.println(logMessage);
if(e!=null) e.printStackTrace();
}
}
|
package io.subutai.core.hubmanager.impl.appscale;
import java.util.Map;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.apache.commons.lang3.StringUtils;
import com.google.common.base.Preconditions;
import io.subutai.common.command.CommandException;
import io.subutai.common.command.CommandResult;
import io.subutai.common.command.RequestBuilder;
import io.subutai.common.peer.ContainerHost;
import io.subutai.common.peer.HostNotFoundException;
import io.subutai.common.peer.LocalPeer;
import io.subutai.common.peer.ResourceHost;
import io.subutai.core.peer.api.PeerManager;
import io.subutai.hub.share.dto.AppScaleConfigDto;
import static java.lang.String.format;
/**
* Dirty copy from io.subutai.plugin.appscale.impl.ClusterConfiguration.
* Should be refactored.
*/
public class AppScaleManager
{
private final Logger log = LoggerFactory.getLogger( getClass() );
private final LocalPeer localPeer;
public AppScaleManager( PeerManager peerManager )
{
this.localPeer = peerManager.getLocalPeer();
}
void installCluster( AppScaleConfigDto config )
{
log.debug( "AppScale installation started" );
Preconditions.checkArgument( config != null, "Null config" );
Preconditions.checkArgument( !StringUtils.isEmpty( config.getUserDomain() ), "User domain is null" );
ContainerHost controllerHost = getContainerHost( config.getClusterName() );
execute( controllerHost, Commands.getCreateLogDir() );
appscaleInitCluster( controllerHost, config );
makeCleanUpPreviousInstallation( controllerHost );
runAfterInitCommands( controllerHost, config );
addKeyPairSH( controllerHost );
int envContainersCount = config.getContainerAddresses().size();
createRunSH ( controllerHost, envContainersCount );
String runShell = Commands.getRunShell() + " " + envContainersCount;
execute( controllerHost, runShell );
createUpShell ( controllerHost );
runInRH ( controllerHost, config );
execute( controllerHost, "echo '127.0.1.1 appscale-image0' >> /etc/hosts" );
execute( controllerHost, Commands.backUpSSH () );
execute( controllerHost, Commands.backUpAppscale () );
log.debug( "AppScale installation done" );
}
private void runInRH ( ContainerHost containerHost, AppScaleConfigDto config )
{
String ipAddress = config.getContainerAddresses().get( config.getClusterName() );
try
{
ResourceHost resourceHostByContainerId = localPeer.getResourceHostByContainerId( containerHost.getId() );
CommandResult resultStr = resourceHostByContainerId
.execute ( new RequestBuilder ( "grep vlan /mnt/lib/lxc/" + config.getClusterName() + "/config" ) );
String stdOut = resultStr.getStdOut ();
String vlanString = stdOut.substring ( 11, 14 );
resourceHostByContainerId.execute ( new RequestBuilder ( "subutai proxy del " + vlanString + " -d" ) );
resourceHostByContainerId.execute ( new RequestBuilder (
"subutai proxy add " + vlanString + " -d \"*." + config.getUserDomain () + "\" -f /mnt/lib/lxc/"
+ config.getClusterName() + "/rootfs/etc/nginx/ssl.pem" ) );
resourceHostByContainerId
.execute ( new RequestBuilder ( "subutai proxy add " + vlanString + " -h " + ipAddress ) );
}
catch ( Exception e )
{
log.error( "Error to set proxy settings: ", e );
}
}
private void createUpShell ( ContainerHost containerHost )
{
String a = "#!/usr/bin/expect -f\n" + "set timeout -1\n" + "set num $argv\n"
+ "spawn /root/appscale-tools/bin/appscale up\n" + "\n"
+ "for {set i 1} {\"$i\" <= \"$num\"} {incr i} {\n"
+ "expect \"Enter your desired admin e-mail address:\"\n" + "send -- \"a@a.com\\n\"\n"
+ "expect \"Enter new password:\"\n" + "send -- \"aaaaaa\\n\"\n" + "expect \"Confirm password:\"\n"
+ "send -- \"aaaaaa\\n\"\n" + "\n" + "}\n" + "\n" + "expect EOD";
try
{
containerHost.execute ( new RequestBuilder ( "touch /root/up.sh" ) );
containerHost.execute ( new RequestBuilder ( "echo '" + a + "' > /root/up.sh" ) );
containerHost.execute ( new RequestBuilder ( "chmod +x /root/up.sh" ) );
}
catch ( CommandException ex )
{
log.error ( "Error on create up shell: " + ex );
}
}
private void createRunSH( ContainerHost containerHost, int envContainersCount )
{
try
{
containerHost.execute ( new RequestBuilder ( "rm /root/run.sh " ) );
containerHost.execute ( new RequestBuilder ( "touch /root/run.sh" ) );
containerHost.execute ( new RequestBuilder ( "echo '" + returnRunSH( envContainersCount ) + "' > /root/run.sh" ) );
containerHost.execute ( new RequestBuilder ( "chmod +x /root/run.sh" ) );
}
catch ( CommandException ex )
{
log.error ( "createRunSSH error" + ex );
}
}
private String returnRunSH ( int envContainersCount )
{
String sh = "#!/usr/bin/expect -f\n"
+ "set timeout -1\n"
+ "set num $argv\n"
+ "spawn /root/appscale-tools/bin/appscale up\n" + "\n";
if ( envContainersCount == 1 )
{
// This works for environment with one container only. With several containers it fails.
sh += "for {set i 1} {\"$i\" <= \"$num\"} {incr i} {\n"
+ " expect \"Are you sure you want to continue connecting (yes/no)?\"\n" + " send -- \"yes\\n\"\n"
+ " expect \" password:\"\n" + " send -- \"a\\n\"\n" + "}\n" + "\n";
}
sh += "expect \"Enter your desired admin e-mail address:\"\n" + "send -- \"a@a.com\\n\"\n"
+ "expect \"Enter new password:\"\n" + "send -- \"aaaaaa\\n\"\n" + "expect \"Confirm password:\"\n"
+ "send -- \"aaaaaa\\n\"\n" + "\n" + "expect EOD";
return sh;
}
private void addKeyPairSH( ContainerHost containerHost )
{
try
{
String add = "#!/usr/bin/expect -f\n"
+ "set timeout -1\n"
+ "set num argv\n"
+ "spawn /root/appscale-tools/bin/appscale-add-keypair --ips ips.yaml --keyname appscale\n"
+ "for {set i 1} {\"$i\" <= \"$num\"} {incr i} {\n"
+ " expect \"Are you sure you want to continue connecting (yes/no)?\"\n"
+ " send -- \"yes\\n\"\n"
+ " expect \" password:\"\n"
+ " send -- \"a\\n\"\n"
+ "}\n"
+ "expect EOD";
containerHost.execute( new RequestBuilder ( "mkdir .ssh" ) );
containerHost.execute( new RequestBuilder ( "rm /root/addKey.sh " ) );
containerHost.execute( new RequestBuilder ( "touch /root/addKey.sh" ) );
containerHost.execute( new RequestBuilder ( "echo '" + add + "' > /root/addKey.sh" ) );
containerHost.execute( new RequestBuilder ( "chmod +x /root/addKey.sh" ) );
}
catch ( CommandException ex )
{
log.error ( ex.toString () );
}
}
private void runAfterInitCommands( ContainerHost containerHost, AppScaleConfigDto config )
{
execute( containerHost, "sed -i 's/{0}:{1}/{1}.{0}/g' /root/appscale/AppDashboard/lib/app_dashboard_data.py" );
execute( containerHost, "echo -e '127.0.0.1 " + config.getUserDomain () + "' >> /etc/hosts" );
execute( containerHost,
"sed -i 's/127.0.0.1 localhost.localdomain localhost/127.0.0.1 localhost.localdomain localhost "
+ config.getUserDomain () + "/g' " + "/root/appscale/AppController/djinn.rb" );
execute( containerHost,
"sed -i 's/127.0.0.1 localhost.localdomain localhost/127.0.0.1 localhost.localdomain localhost "
+ config.getUserDomain () + "/g' " + "/etc/hosts" );
execute( containerHost, "cat /etc/nginx/mykey.pem /etc/nginx/mycert.pem > /etc/nginx/ssl.pem" );
// Modify navigation.html
String addButton = "<li align=\"center\" class=\"tab\"><a class=\"btn btn-info\" href=\"{{ flower_url }}\">TaskQueue Monitor<\\/a><\\/li>";
String replaceString = addButton + "<br><li align=\"center\" class=\"tab\"><a class=\"btn btn-info\" href=\"#\" onClick=\"growEnvironment()\">Add Appengine<\\/a><\\/li>";
execute( containerHost,
"sed -i 's/ " + addButton + "/" + replaceString + "/g' /root/appscale/AppDashboard/templates/shared/navigation.html" );
String changeMonitURL = "sed -i 's/{{ monit_url }}/http:\\/\\/2812." + config.getUserDomain () + "/g' /root/appscale/AppDashboard/templates/shared/navigation.html";
execute( containerHost, changeMonitURL );
String changeFlowerURL = "sed -i 's/{{ flower_url }}/http:\\/\\/5555." + config.getUserDomain () + "/g' /root/appscale/AppDashboard/templates/shared/navigation.html";
execute( containerHost, changeFlowerURL );
String modUrl = "resturl?";
String modUrlChange = "1443." + config.getUserDomain () + "\\/rest\\/appscale\\/growenvironment?containerName="
+ config.getClusterName () + "&";
execute( containerHost,
"sed -i 's/" + modUrl + "/" + modUrlChange + "/g' /root/appscale/AppDashboard/templates/shared/navigation.html" );
// Modify ss_agent.py
String modstr = "thispathtochange = \"\\/rest\\/appscale\\/growenvironment?clusterName=\\\"";
String modstrchange = "thispathtochange = \"\\/rest\\/appscale\\/growenvironment?clusterName=\"" + config.getClusterName ();
execute( containerHost,
"sed -i 's/" + modstr + "/" + modstrchange + "/g' /root/appscale/InfrastructureManager/agents/ss_agent.py" );
String tokenUrl = "subutai:8443";
String tokenUrlChange = "1443." + config.getUserDomain ();
execute( containerHost,
"sed -i 's/" + tokenUrl + "/" + tokenUrlChange + "/g' /root/appscale/InfrastructureManager/agents/ss_agent.py" );
// Modify nginx
String nginx
= "echo 'server {\n" + " listen 80;\n" + " server_name ~^(?<port>.+)\\." + config
.getUserDomain () + "$;\n" + "\n" + " set $appbackend \"127.0.0.1:${port}\";\n" + "\n"
+ " # proxy to AppScale over http\n" + " if ($port = 1443) {\n"
+ " set $appbackend \"appscaledashboard\";\n" + " }\n" + "\n" + " location / {\n"
+ " proxy_pass http://$appbackend;\n"
+ " proxy_set_header X-Real-IP $remote_addr;\n"
+ " proxy_set_header Host $http_host;\n"
+ " proxy_set_header X-Forwarded-For $proxy_add_x_forwarded_for;\n" + "\n" + " }\n"
+ "}' > /etc/nginx/sites-enabled/default";
execute( containerHost, nginx );
}
private void makeCleanUpPreviousInstallation( ContainerHost containerHost )
{
try
{
CommandResult cr = containerHost.execute ( new RequestBuilder ( "ls /root/.ssh" ) );
if ( !cr.toString ().equals ( "" ) )
{
|
package org.safehaus.subutai.core.peer.ui.forms;
import java.security.KeyStore;
import java.util.Iterator;
import java.util.List;
import java.util.UUID;
import javax.ws.rs.core.MediaType;
import javax.ws.rs.core.Response;
import org.safehaus.subutai.common.environment.Environment;
import org.safehaus.subutai.common.peer.ContainerHost;
import org.safehaus.subutai.common.peer.Peer;
import org.safehaus.subutai.common.peer.PeerException;
import org.safehaus.subutai.common.peer.PeerInfo;
import org.safehaus.subutai.common.peer.PeerStatus;
import org.safehaus.subutai.common.security.crypto.keystore.KeyStoreData;
import org.safehaus.subutai.common.security.crypto.keystore.KeyStoreManager;
import org.safehaus.subutai.common.settings.ChannelSettings;
import org.safehaus.subutai.common.settings.SecuritySettings;
import org.safehaus.subutai.common.util.JsonUtil;
import org.safehaus.subutai.common.util.RestUtil;
import org.safehaus.subutai.core.peer.api.ContainerGroup;
import org.safehaus.subutai.core.peer.api.ContainerGroupNotFoundException;
import org.safehaus.subutai.core.peer.api.ResourceHost;
import org.safehaus.subutai.core.peer.ui.PeerManagerPortalModule;
import org.safehaus.subutai.server.ui.component.ConfirmationDialog;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.apache.cxf.jaxrs.client.WebClient;
import org.apache.cxf.jaxrs.ext.form.Form;
import com.google.gson.Gson;
import com.google.gson.GsonBuilder;
import com.google.gson.reflect.TypeToken;
import com.vaadin.annotations.AutoGenerated;
import com.vaadin.data.Property;
import com.vaadin.ui.AbsoluteLayout;
import com.vaadin.ui.Button;
import com.vaadin.ui.CustomComponent;
import com.vaadin.ui.Label;
import com.vaadin.ui.Notification;
import com.vaadin.ui.Table;
import com.vaadin.ui.TextField;
/**
* Registration process should be handled in save manner so no middleware attacks occur. In order to get there peers
* need to exchange with public keys. This will create ssl layer by encrypting all traffic passing through their
* connection. So first initial handshake will be one direction, to pass keys through encrypted channel and register
* them in peers' trust stores. These newly saved keys will be used further for safe communication, with bidirectional
* authentication.
*
*
* TODO here still exists some issues concerned via registration/reject/approve requests. Some of them must pass through
* secure channel such as unregister process. Which already must be in bidirectional auth completed stage.
*/
public class PeerRegisterForm extends CustomComponent
{
private static final Logger LOG = LoggerFactory.getLogger( PeerRegisterForm.class.getName() );
private final Gson gson = new GsonBuilder().setPrettyPrinting().create();
@AutoGenerated
private AbsoluteLayout mainLayout;
@AutoGenerated
private Table peersTable;
@AutoGenerated
private Button showPeersButton;
@AutoGenerated
private Button registerRequestButton;
@AutoGenerated
private TextField ipTextField;
private PeerManagerPortalModule module;
PeerManageActionsComponent.PeerManagerActionsListener listener =
new PeerManageActionsComponent.PeerManagerActionsListener()
{
@Override
public void OnPositiveButtonTrigger( final PeerInfo peer,
PeerManageActionsComponent.PeerManageUpdateViewListener
updateViewListener )
{
switch ( peer.getStatus() )
{
case REQUESTED:
PeerInfo selfPeer = module.getPeerManager().getLocalPeerInfo();
approvePeerRegistration( selfPeer, peer, updateViewListener );
break;
case REGISTERED:
break;
case BLOCKED:
break;
default:
throw new IllegalStateException( peer.getStatus().name(),
new Throwable( "Invalid case." ) );
}
}
@Override
public void OnNegativeButtonTrigger( final PeerInfo peer,
PeerManageActionsComponent.PeerManageUpdateViewListener
updateViewListener )
{
PeerInfo selfPeer = module.getPeerManager().getLocalPeerInfo();
switch ( peer.getStatus() )
{
case REJECTED:
removeMeFromRemote( selfPeer, peer, updateViewListener );
break;
case BLOCKED:
case BLOCKED_PEER:
case REQUESTED:
case REQUEST_SENT:
rejectPeerRegistration( selfPeer, peer, updateViewListener );
break;
case APPROVED:
unregisterMeFromRemote( selfPeer, peer, updateViewListener );
break;
default:
throw new TypeNotPresentException( peer.getStatus().name(),
new Throwable( "Invalid case." ) );
}
}
};
/**
* The constructor should first build the main layout, set the composition root and then do any custom
* initialization. <p/> The constructor will not be automatically regenerated by the visual editor.
*/
public PeerRegisterForm( final PeerManagerPortalModule module )
{
buildMainLayout();
setCompositionRoot( mainLayout );
this.module = module;
showPeersButton.click();
}
@AutoGenerated
private AbsoluteLayout buildMainLayout()
{
// common part: create layout
mainLayout = new AbsoluteLayout();
mainLayout.setImmediate( false );
mainLayout.setWidth( "100%" );
mainLayout.setHeight( "100%" );
// top-level component properties
setWidth( "100.0%" );
setHeight( "100.0%" );
// peerRegisterLayout
final AbsoluteLayout peerRegisterLayout = buildAbsoluteLayout();
mainLayout.addComponent( peerRegisterLayout, "top:20.0px;right:0.0px;bottom:-20.0px;left:0.0px;" );
return mainLayout;
}
@AutoGenerated
private AbsoluteLayout buildAbsoluteLayout()
{
// common part: create layout
AbsoluteLayout absoluteLayout = new AbsoluteLayout();
absoluteLayout.setImmediate( false );
absoluteLayout.setWidth( "100.0%" );
absoluteLayout.setHeight( "100.0%" );
// peerRegistration
final Label peerRegistration = new Label();
peerRegistration.setImmediate( false );
peerRegistration.setWidth( "-1px" );
peerRegistration.setHeight( "-1px" );
peerRegistration.setValue( "Peer registration" );
absoluteLayout.addComponent( peerRegistration, "top:0.0px;left:20.0px;" );
final Label ip = new Label();
ip.setImmediate( false );
ip.setWidth( "-1px" );
ip.setHeight( "-1px" );
ip.setValue( "IP" );
absoluteLayout.addComponent( ip, "top:36.0px;left:20.0px;" );
// ipTextField
ipTextField = new TextField();
ipTextField.setImmediate( false );
ipTextField.setWidth( "-1px" );
ipTextField.setHeight( "-1px" );
ipTextField.setMaxLength( 15 );
absoluteLayout.addComponent( ipTextField, "top:36.0px;left:150.0px;" );
// registerRequestButton
registerRequestButton = createRegisterButton();
absoluteLayout.addComponent( registerRequestButton, "top:160.0px;left:20.0px;" );
registerRequestButton = createRegisterButton();
// showPeersButton
showPeersButton = createShowPeersButton();
absoluteLayout.addComponent( showPeersButton, "top:234.0px;left:20.0px;" );
// peersTable
peersTable = new Table();
peersTable.setCaption( "Peers" );
peersTable.setImmediate( false );
peersTable.setWidth( "1000px" );
peersTable.setHeight( "283px" );
absoluteLayout.addComponent( peersTable, "top:294.0px;left:20.0px;" );
return absoluteLayout;
}
private Button createShowPeersButton()
{
showPeersButton = new Button();
showPeersButton.setCaption( "Show peers" );
showPeersButton.setImmediate( false );
showPeersButton.setWidth( "-1px" );
showPeersButton.setHeight( "-1px" );
showPeersButton.addClickListener( new Button.ClickListener()
{
@Override
public void buttonClick( final Button.ClickEvent clickEvent )
{
populateData();
peersTable.refreshRowCache();
}
} );
return showPeersButton;
}
private void populateData()
{
List<PeerInfo> peers = module.getPeerManager().peers();
peersTable.removeAllItems();
peersTable.addContainerProperty( "ID", UUID.class, null );
peersTable.addContainerProperty( "Name", String.class, null );
peersTable.addContainerProperty( "IP", String.class, null );
peersTable.addContainerProperty( "Status", PeerStatus.class, null );
peersTable.addContainerProperty( "ActionsAdvanced", PeerManageActionsComponent.class, null );
for ( final PeerInfo peer : peers )
{
if ( peer == null || peer.getStatus() == null )
{
continue;
}
/**
* According to peer status perform sufficient action
*/
//TODO perform different actions on peer response
PeerManageActionsComponent component = new PeerManageActionsComponent( module, peer, listener );
peersTable
.addItem( new Object[] { peer.getId(), peer.getName(), peer.getIp(), peer.getStatus(), component },
peer.getId() );
}
}
/**
* Send peer to register on remote peer. To construct secure connection. For now initializer peer doesn't send its
* px2 (public key requiring bidirectional authentication).
*
* @param peerToRegister - initializer peer info for registration process
* @param ip - target peer ip address
*/
private void registerMeToRemote( final PeerInfo peerToRegister, final String ip )
{
new Thread( new Runnable()
{
@Override
public void run()
{
String baseUrl = String.format( "https://%s:%s/cxf", ip, ChannelSettings.SECURE_PORT_X1 );
WebClient client = RestUtil.createTrustedWebClient( baseUrl );//WebClient.create( baseUrl );
client.type( MediaType.MULTIPART_FORM_DATA ).accept( MediaType.APPLICATION_JSON );
Form form = new Form();
form.set( "peer", gson.toJson( peerToRegister ) );
try
{
Response response = client.path( "peer/register" ).form( form );
if ( response.getStatus() == Response.Status.OK.getStatusCode() )
{
Notification.show( String.format( "Request sent to %s!", ip ) );
String responseString = response.readEntity( String.class );
LOG.info( response.toString() );
PeerInfo remotePeerInfo = JsonUtil.from( responseString, new TypeToken<PeerInfo>()
{
}.getType() );
if ( remotePeerInfo != null )
{
remotePeerInfo.setStatus( PeerStatus.REQUEST_SENT );
try
{
module.getPeerManager().register( remotePeerInfo );
}
catch ( PeerException e )
{
Notification.show( "Couldn't register peer. " + e.getMessage(),
Notification.Type.WARNING_MESSAGE );
LOG.error( "Couldn't register peer", e );
}
}
}
else if ( response.getStatus() == Response.Status.CONFLICT.getStatusCode() )
{
String reason = response.readEntity( String.class );
Notification.show( reason, Notification.Type.WARNING_MESSAGE );
LOG.warn( reason );
}
else
{
LOG.warn( "Response for registering peer: " + response.toString() );
}
}
catch ( Exception e )
{
Notification.show( "Please check peer address for correctness", Notification.Type.WARNING_MESSAGE );
LOG.error( "error sending request", e );
}
}
} ).start();
}
private void unregisterMeFromRemote( final PeerInfo peerToUnregister, final PeerInfo remotePeerInfo,
final PeerManageActionsComponent.PeerManageUpdateViewListener
updateViewListener )
{
int relationExists = 0;
for ( final Iterator<Environment> itEnv = module.getEnvironmentManager().getEnvironments().iterator();
itEnv.hasNext() && relationExists == 0; )
{
Environment environment = itEnv.next();
for ( final Iterator<Peer> itPeer = environment.getPeers().iterator();
itPeer.hasNext() && relationExists == 0; )
{
Peer peer = itPeer.next();
if ( peer.getPeerInfo().equals( remotePeerInfo ) )
{
relationExists = 1;
}
}
}
for ( final Iterator<ResourceHost> itResource =
module.getPeerManager().getLocalPeer().getResourceHosts().iterator();
itResource.hasNext() && relationExists == 0; )
{
ResourceHost resourceHost = itResource.next();
for ( final Iterator<ContainerHost> itContainer = resourceHost.getContainerHosts().iterator();
itContainer.hasNext() && relationExists == 0; )
{
ContainerHost containerHost = itContainer.next();
try
{
ContainerGroup containerGroup = module.getPeerManager().getLocalPeer()
.findContainerGroupByContainerId( containerHost.getId() );
if ( containerGroup.getInitiatorPeerId().equals( remotePeerInfo.getId() ) )
{
relationExists = 2;
}
}
catch ( ContainerGroupNotFoundException ignore )
{
// LOG.debug( "Couldn't get container group by container id", ignore );
}
}
}
if ( relationExists != 0 )
{
String msg = "";
switch ( relationExists )
{
case 1:
msg = "Please destroy all cross peer environments, before you proceed!!!";
break;
case 2:
msg = "You cannot unregister Peer, because you are a carrier of Peer's resources!!!"
+ " Contact with Peer to migrate all his data.";
break;
}
ConfirmationDialog alert = new ConfirmationDialog( msg, "Ok", "" );
alert.getOk().addClickListener( new Button.ClickListener()
{
@Override
public void buttonClick( Button.ClickEvent clickEvent )
{
// unregisterPeer( peerToUnregister, remotePeerInfo );
}
} );
getUI().addWindow( alert.getAlert() );
}
else
{
unregisterPeer( peerToUnregister, remotePeerInfo, updateViewListener );
}
}
private void unregisterPeer( final PeerInfo peerToUnregister, final PeerInfo remotePeerInfo,
final PeerManageActionsComponent.PeerManageUpdateViewListener updateViewListener )
{
new Thread( new Runnable()
{
@Override
public void run()
{
String baseUrl =
String.format( "https://%s:%s/cxf", remotePeerInfo.getIp(), ChannelSettings.SECURE_PORT_X2 );
WebClient client = RestUtil.createTrustedWebClientWithAuth( baseUrl,
SecuritySettings.KEYSTORE_PX2_ROOT_ALIAS );// WebClient.create( baseUrl );
try
{
Response response = client.path( "peer/unregister" ).type( MediaType.APPLICATION_JSON )
.accept( MediaType.APPLICATION_JSON )
.query( "peerId", gson.toJson( peerToUnregister.getId().toString() ) )
.delete();
if ( response.getStatus() == Response.Status.OK.getStatusCode() )
{
LOG.info( response.toString() );
Notification.show( String.format( "Request sent to %s!", remotePeerInfo.getName() ) );
/**
* Peer request rejection intented to be handled before they exchange with keys
*
* @param peerToUpdateOnRemote - local peer info to update/send to remote peer
* @param remotePeer - remote peer whose request was rejected
* @param updateViewListener - used to update peers table with relevant buttons captions
*/
private void rejectPeerRegistration( final PeerInfo peerToUpdateOnRemote, final PeerInfo remotePeer,
final PeerManageActionsComponent.PeerManageUpdateViewListener
updateViewListener )
{
new Thread( new Runnable()
{
@Override
public void run()
{
String baseUrl =
String.format( "https://%s:%s/cxf", remotePeer.getIp(), ChannelSettings.SECURE_PORT_X1 );
WebClient client = RestUtil.createTrustedWebClient( baseUrl );// WebClient.create( baseUrl );
client.type( MediaType.APPLICATION_FORM_URLENCODED ).accept( MediaType.APPLICATION_JSON );
Form form = new Form();
form.set( "rejectedPeerId", peerToUpdateOnRemote.getId().toString() );
try
{
Response response = client.path( "peer/reject" ).put( form );
if ( response.getStatus() == Response.Status.NO_CONTENT.getStatusCode() )
{
LOG.info( "Successfully reject peer request" );
Notification.show( String.format( "Request sent to %s!", remotePeer.getName() ) );
//TODO maybe will implement certificates exchange later on initial request, before peer approves
// initializer' request
/**
* Send peer registration request for further handshakes.
*
* @return - vaadin button with request initializing click listener
*/
private Button createRegisterButton()
{
registerRequestButton = new Button();
registerRequestButton.setCaption( "Register" );
registerRequestButton.setImmediate( true );
registerRequestButton.setWidth( "-1px" );
registerRequestButton.setHeight( "-1px" );
registerRequestButton.addClickListener( new Button.ClickListener()
{
@Override
public void buttonClick( final Button.ClickEvent clickEvent )
{
getUI().access( new Runnable()
{
@Override
public void run()
{
String ip = ipTextField.getValue();
LOG.warn( ip );
PeerInfo selfPeer = module.getPeerManager().getLocalPeerInfo();
registerMeToRemote( selfPeer, ip );
showPeersButton.click();
}
} );
}
} );
return registerRequestButton;
}
}
|
package test.Learning;
import static org.junit.Assert.assertTrue;
import static org.junit.Assert.assertFalse;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.List;
import org.junit.Test;
import org.sat4j.specs.TimeoutException;
import automata.sfa.SFA;
import automata.sfa.SFAInputMove;
import automata.sfa.SFAMove;
import learning.sfa.Learner;
import learning.sfa.Oracle;
import learning.sfa.SFAOracle;
import learning_symbolic_ce.sfa.SymbolicLearner;
import learning_symbolic_ce.sfa.SymbolicOracle;
import learning_symbolic_ce.sfa.SinglePathSFAOracle;
import theory.BooleanAlgebra;
import theory.intervals.UnaryCharIntervalSolver;
import theory.characters.CharConstant;
import theory.characters.CharPred;
import theory.ProductAlgebra;
import theory.cartesian.CartesianProduct;
import theory.intervals.BoundedIntegerSolver;
import theory.intervals.IntPred;
import utilities.Pair;
public class TestSymbolicCE {
@Test
public void testSinglePathOracle() throws TimeoutException{
BooleanAlgebra<IntPred, Integer> ba = new BoundedIntegerSolver(0,null);
Integer init = 0;
List<Integer> fin = Arrays.asList(1);
List<SFAMove<IntPred, Integer>> trans = new ArrayList<SFAMove<IntPred, Integer>>();
trans.add(new SFAInputMove<IntPred, Integer>(0, 1, new IntPred(null, null)));
trans.add(new SFAInputMove<IntPred, Integer>(1, 1, new IntPred(1, null)));
trans.add(new SFAInputMove<IntPred, Integer>(1, 0, new IntPred(null, 0)));
SFA<IntPred, Integer> given = SFA.MkSFA(trans, init, fin, ba, false);
SymbolicOracle<IntPred, Integer> o = new SinglePathSFAOracle<IntPred, Integer>(given, ba);
Integer init2 = 0;
List<Integer> fin2 = Arrays.asList(0);
List<SFAMove<IntPred, Integer>> trans2 = new ArrayList<SFAMove<IntPred, Integer>>();
trans2.add(new SFAInputMove<IntPred, Integer>(0, 0, new IntPred(null, null)));
SFA<IntPred, Integer> hyp = SFA.MkSFA(trans2, init2, fin2, ba, false);
List<IntPred> ce = o.checkEquivalence(hyp);
assertTrue(ce.equals(new ArrayList<IntPred>()));
}
@Test
public void testSinglePathOracle2() throws TimeoutException{
BooleanAlgebra<IntPred, Integer> ba = new BoundedIntegerSolver(0,null);
Integer init = 0;
List<Integer> fin = Arrays.asList(0);
List<SFAMove<IntPred, Integer>> trans = new ArrayList<SFAMove<IntPred, Integer>>();
trans.add(new SFAInputMove<IntPred, Integer>(0, 1, new IntPred(0, null)));
trans.add(new SFAInputMove<IntPred, Integer>(1, 1, new IntPred(2, null)));
trans.add(new SFAInputMove<IntPred, Integer>(1, 0, new IntPred(0, 1)));
SFA<IntPred, Integer> given = SFA.MkSFA(trans, init, fin, ba, false);
SymbolicOracle<IntPred, Integer> o = new SinglePathSFAOracle<IntPred, Integer>(given, ba);
Integer init2 = 0;
List<Integer> fin2 = Arrays.asList(0);
List<SFAMove<IntPred, Integer>> trans2 = new ArrayList<SFAMove<IntPred, Integer>>();
trans2.add(new SFAInputMove<IntPred, Integer>(0, 1, new IntPred(10, null)));
trans2.add(new SFAInputMove<IntPred, Integer>(0, 0, new IntPred(0, 9)));
trans2.add(new SFAInputMove<IntPred, Integer>(1, 1, new IntPred(0, null)));
SFA<IntPred, Integer> hyp = SFA.MkSFA(trans2, init2, fin2, ba, false);
hyp = hyp.minimize(ba);
List<IntPred> ce = o.checkEquivalence(hyp);
assertTrue(ce.equals(Arrays.asList(new IntPred(0,9))));
}
@Test
public void testLearning1() throws TimeoutException {
BooleanAlgebra<IntPred, Integer> ba = new BoundedIntegerSolver(0,null);
Integer init = 1;
List<Integer> fin = Arrays.asList(2);
List<SFAMove<IntPred, Integer>> trans = new ArrayList<SFAMove<IntPred, Integer>>();
trans.add(new SFAInputMove<IntPred, Integer>(1, 2, new IntPred(0, null)));
trans.add(new SFAInputMove<IntPred, Integer>(2, 2, new IntPred(10, null)));
trans.add(new SFAInputMove<IntPred, Integer>(2, 1, new IntPred(0, 9)));
SFA<IntPred, Integer> given = SFA.MkSFA(trans, init, fin, ba, false);
SymbolicLearner<IntPred, Integer> ell = new SymbolicLearner<IntPred, Integer>();
SymbolicOracle<IntPred, Integer> o = new SinglePathSFAOracle<IntPred, Integer>(given, ba);
SFA<IntPred, Integer> learned = ell.learn(o, ba);
assertTrue(SFA.areEquivalent(given, learned, ba));
assertTrue(learned.getStates().size() <= given.getStates().size());
}
@Test
public void testLearning2() throws TimeoutException {
BooleanAlgebra<IntPred, Integer> ba = new BoundedIntegerSolver(0,null);
Integer init = 1;
List<Integer> fin = Arrays.asList(2);
List<SFAMove<IntPred, Integer>> trans = new ArrayList<SFAMove<IntPred, Integer>>();
trans.add(new SFAInputMove<IntPred, Integer>(1, 2, new IntPred(0, 5)));
trans.add(new SFAInputMove<IntPred, Integer>(1, 2, new IntPred(6, null)));
trans.add(new SFAInputMove<IntPred, Integer>(2, 2, new IntPred(10, null)));
trans.add(new SFAInputMove<IntPred, Integer>(2, 1, new IntPred(0, 9)));
SFA<IntPred, Integer> given = SFA.MkSFA(trans, init, fin, ba, false);
SymbolicLearner<IntPred, Integer> ell = new SymbolicLearner<IntPred, Integer>();
SymbolicOracle<IntPred, Integer> o = new SinglePathSFAOracle<IntPred, Integer>(given, ba);
SFA<IntPred, Integer> learned = ell.learn(o, ba);
assertTrue(SFA.areEquivalent(given, learned, ba));
assertTrue(learned.getStates().size() <= given.getStates().size());
}
/*
@Test
public void testLearningChar() throws TimeoutException {
UnaryCharIntervalSolver ba = new UnaryCharIntervalSolver();
Integer init = 1;
List<Integer> fin = Arrays.asList(3);
List<SFAMove<CharPred, Character>> trans = new ArrayList<SFAMove<CharPred, Character>>();
trans.add(new SFAInputMove<CharPred, Character>(1, 2, new CharPred('a')));
trans.add(new SFAInputMove<CharPred, Character>(2, 3, new CharPred('b')));
trans.add(new SFAInputMove<CharPred, Character>(3, 1, new CharPred('c')));
SFA<CharPred, Character> given = SFA.MkSFA(trans, init, fin, ba, false);
SymbolicLearner<CharPred, Character> ell = new SymbolicLearner<CharPred, Character>();
SymbolicOracle<CharPred, Character> o = new SinglePathSFAOracle<CharPred, Character>(given, ba);
SFA<CharPred, Character> learned = ell.learn(o, ba);
assertTrue(SFA.areEquivalent(given, learned, ba));
assertTrue(learned.getStates().size() <= given.getStates().size());
}*/
@Test
public void testLearning3() throws TimeoutException {
BooleanAlgebra<IntPred, Integer> ba = new BoundedIntegerSolver(0,null);
Integer init = 1;
List<Integer> fin = Arrays.asList(2);
List<SFAMove<IntPred, Integer>> trans = new ArrayList<SFAMove<IntPred, Integer>>();
trans.add(new SFAInputMove<IntPred, Integer>(1, 2, new IntPred(0, null)));
trans.add(new SFAInputMove<IntPred, Integer>(2, 2, new IntPred(10, null)));
trans.add(new SFAInputMove<IntPred, Integer>(2, 1, new IntPred(0, 9)));
SFA<IntPred, Integer> given = SFA.MkSFA(trans, init, fin, ba, false);
SymbolicLearner<IntPred, Integer> ell = new SymbolicLearner<IntPred, Integer>();
SymbolicOracle<IntPred, Integer> o = new SinglePathSFAOracle<IntPred, Integer>(given, ba);
SFA<IntPred, Integer> learned = ell.learn(o, ba);
assertTrue(SFA.areEquivalent(given, learned, ba));
assertTrue(learned.getStates().size() <= given.getStates().size());
}
@Test
public void testPaperExample() throws TimeoutException {
BooleanAlgebra<IntPred, Integer> ba = new BoundedIntegerSolver(0,null);
Integer init = 1;
List<Integer> fin = Arrays.asList(1);
List<SFAMove<IntPred, Integer>> trans = new ArrayList<SFAMove<IntPred, Integer>>();
trans.add(new SFAInputMove<IntPred, Integer>(1, 1, new IntPred(0, 50)));
trans.add(new SFAInputMove<IntPred, Integer>(1, 1, new IntPred(101, null)));
trans.add(new SFAInputMove<IntPred, Integer>(1, 2, new IntPred(51, 100)));
trans.add(new SFAInputMove<IntPred, Integer>(2, 3, new IntPred(21, null)));
trans.add(new SFAInputMove<IntPred, Integer>(2, 4, new IntPred(0, 20)));
trans.add(new SFAInputMove<IntPred, Integer>(3, 3, new IntPred(null, null)));
trans.add(new SFAInputMove<IntPred, Integer>(4, 1, new IntPred(null, 20)));
trans.add(new SFAInputMove<IntPred, Integer>(4, 3, new IntPred(21, null)));
SFA<IntPred, Integer> given = SFA.MkSFA(trans, init, fin, ba, false);
SymbolicLearner<IntPred, Integer> ell = new SymbolicLearner<IntPred, Integer>();
SinglePathSFAOracle<IntPred, Integer> o = new SinglePathSFAOracle<IntPred, Integer>(given, ba);
SFA<IntPred, Integer> learned = ell.learn(o, ba);
assertTrue(SFA.areEquivalent(given, learned, ba));
assertTrue(learned.getStates().size() <= given.getStates().size());
}
@Test
public void testMMExample() throws TimeoutException {
BooleanAlgebra<IntPred, Integer> ba = new BoundedIntegerSolver(0,null);
Integer init = 1;
List<Integer> fin = Arrays.asList(2, 3);
List<SFAMove<IntPred, Integer>> trans = new ArrayList<SFAMove<IntPred, Integer>>();
trans.add(new SFAInputMove<IntPred, Integer>(1, 2, new IntPred(null, 50)));
trans.add(new SFAInputMove<IntPred, Integer>(1, 4, new IntPred(51, null)));
trans.add(new SFAInputMove<IntPred, Integer>(2, 3, new IntPred(null, 30)));
trans.add(new SFAInputMove<IntPred, Integer>(2, 4, new IntPred(31, null)));
trans.add(new SFAInputMove<IntPred, Integer>(3, 4, new IntPred(null, null)));
trans.add(new SFAInputMove<IntPred, Integer>(4, 1, new IntPred(null, 20)));
trans.add(new SFAInputMove<IntPred, Integer>(4, 2, new IntPred(51, 80)));
trans.add(new SFAInputMove<IntPred, Integer>(4, 3, new IntPred(21, 50)));
trans.add(new SFAInputMove<IntPred, Integer>(4, 4, new IntPred(81, null)));
SFA<IntPred, Integer> given = SFA.MkSFA(trans, init, fin, ba, false);
Learner<IntPred, Integer> ell = new Learner<IntPred, Integer>();
Oracle<IntPred, Integer> o = new SFAOracle<IntPred, Integer>(given, ba);
SFA<IntPred, Integer> learned = ell.learn(o, ba);
assertTrue(SFA.areEquivalent(given, learned, ba));
assertTrue(learned.getStates().size() <= given.getStates().size());
}
@Test
public void testMMPartialOrderExample() throws TimeoutException {
BooleanAlgebra<IntPred, Integer> ba = new BoundedIntegerSolver(0, 100);
ProductAlgebra<IntPred, Integer, IntPred, Integer> prodmeta =
new ProductAlgebra<IntPred, Integer, IntPred, Integer>(ba, ba);
Integer init = 1;
List<Integer> fin = Arrays.asList(2, 3);
List<SFAMove<CartesianProduct<IntPred, IntPred>, Pair<Integer, Integer>>> trans =
new ArrayList<SFAMove<CartesianProduct<IntPred, IntPred>, Pair<Integer, Integer>>>();
//transitions out of state 1
CartesianProduct<IntPred, IntPred> temp = new CartesianProduct<>(Arrays.asList(
new Pair<>(new IntPred(null,45), new IntPred(null,70)),
new Pair<>(new IntPred(null,60), new IntPred(null,50))));
temp.normalize(ba,ba);
trans.add(new SFAInputMove<CartesianProduct<IntPred, IntPred>, Pair<Integer, Integer>>(1, 2, temp));
trans.add(new SFAInputMove<CartesianProduct<IntPred, IntPred>, Pair<Integer, Integer>>(1, 4, prodmeta.MkNot(temp)));
//transitions out of state 2
temp = new CartesianProduct<>(Arrays.asList(
new Pair<>(new IntPred(null,30), new IntPred(null,80)),
new Pair<>(new IntPred(null,40), new IntPred(null,40)),
new Pair<>(new IntPred(null,80), new IntPred(null,15))));
temp.normalize(ba,ba);
trans.add(new SFAInputMove<CartesianProduct<IntPred, IntPred>, Pair<Integer, Integer>>(2, 3, temp));
trans.add(new SFAInputMove<CartesianProduct<IntPred, IntPred>, Pair<Integer, Integer>>(2, 4, prodmeta.MkNot(temp)));
//transitions out of state 3
trans.add(new SFAInputMove<CartesianProduct<IntPred, IntPred>, Pair<Integer, Integer>>(3, 4, prodmeta.True()));
//transitions out of state 4
temp = new CartesianProduct<>(new IntPred(null,20), new IntPred(null,30));
trans.add(new SFAInputMove<CartesianProduct<IntPred, IntPred>, Pair<Integer, Integer>>(4, 1, temp));
temp = new CartesianProduct<>(Arrays.asList(
new Pair<>(new IntPred(null,55), new IntPred(31,50)),
new Pair<>(new IntPred(21,70), new IntPred(null,35))));
temp.normalize(ba, ba);
trans.add(new SFAInputMove<CartesianProduct<IntPred, IntPred>, Pair<Integer, Integer>>(4, 3, temp));
temp = new CartesianProduct<>(Arrays.asList(
new Pair<>(new IntPred(null,60), new IntPred(51,90)),
new Pair<>(new IntPred(56,70), new IntPred(36,70)),
new Pair<>(new IntPred(71,90), new IntPred(null,50))));
temp.normalize(ba, ba);
trans.add(new SFAInputMove<CartesianProduct<IntPred, IntPred>, Pair<Integer, Integer>>(4, 2, temp));
temp = new CartesianProduct<>(Arrays.asList(
new Pair<>(new IntPred(null,null), new IntPred(91,null)),
new Pair<>(new IntPred(61,null), new IntPred(71,null)),
new Pair<>(new IntPred(71,null), new IntPred(51,null)),
new Pair<>(new IntPred(91,null), new IntPred(null,null))));
temp.normalize(ba, ba);
trans.add(new SFAInputMove<CartesianProduct<IntPred, IntPred>, Pair<Integer, Integer>>(4, 4, temp));
SFA<CartesianProduct<IntPred, IntPred>, Pair<Integer, Integer>> given =
SFA.MkSFA(trans, init, fin, prodmeta, false);
Learner<CartesianProduct<IntPred, IntPred>, Pair<Integer, Integer>> ell =
new Learner<CartesianProduct<IntPred, IntPred>, Pair<Integer, Integer>>();
// test learning using our product algebra meta-separating-predicates
Oracle<CartesianProduct<IntPred, IntPred>, Pair<Integer, Integer>> o1 =
new SFAOracle<CartesianProduct<IntPred, IntPred>, Pair<Integer, Integer>>(given, prodmeta);
SFA<CartesianProduct<IntPred, IntPred>, Pair<Integer, Integer>> learned1 = ell.learn(o1, prodmeta);
assertTrue(SFA.areEquivalent(given, learned1, prodmeta));
assertTrue(learned1.getStates().size() <= given.getStates().size());
// test learning using MM-style cones for separating predicates
ProductAlgebra<IntPred, Integer, IntPred, Integer> prodcone = new MMConeAlgebra(ba);
Oracle<CartesianProduct<IntPred, IntPred>, Pair<Integer, Integer>> o2 =
new SFAOracle<CartesianProduct<IntPred, IntPred>, Pair<Integer, Integer>>(given, prodcone);
SFA<CartesianProduct<IntPred, IntPred>, Pair<Integer, Integer>> learned2 = ell.learn(o2, prodcone);
assertTrue(SFA.areEquivalent(given, learned2, prodmeta));
assertTrue(learned2.getStates().size() <= given.getStates().size());
// for sanity, ensure that these did not give different results
assertTrue(SFA.areEquivalent(learned1, learned2, prodmeta));
assertTrue(learned1.getStates().size() == learned2.getStates().size());
}
}
|
// -*- mode:java; encoding:utf-8 -*-
// vim:set fileencoding=utf-8:
// @homepage@
package example;
import java.awt.*;
import java.net.URL;
import javax.swing.*;
import javax.swing.text.EditorKit;
import javax.swing.text.html.HTMLEditorKit;
import javax.swing.text.html.StyleSheet;
public final class MainPanel extends JPanel {
private MainPanel() {
super(new GridLayout(2, 1));
String html = "<html><h2>H2</h2>text<ul><li>list: %s</li></ul></html>";
JEditorPane editor0 = makeEditorPane();
editor0.setText(String.format(html, "Default"));
ClassLoader cl = Thread.currentThread().getContextClassLoader();
URL url = cl.getResource("example/bullet.png");
JEditorPane editor1 = makeEditorPane();
EditorKit kit = editor1.getEditorKit();
if (kit instanceof HTMLEditorKit && url != null) {
HTMLEditorKit htmlEditorKit = (HTMLEditorKit) kit;
StyleSheet styleSheet = htmlEditorKit.getStyleSheet();
styleSheet.addRule(String.format("ul{list-style-image:url(%s);margin:0px 20px;}", url));
// styleSheet.addRule("ul{list-style-type:circle;margin:0px 20px;}");
// styleSheet.addRule("ul{list-style-type:disc;margin:0px 20px;}");
// styleSheet.addRule("ul{list-style-type:square;margin:0px 20px;}");
// styleSheet.addRule("ul{list-style-type:decimal;margin:0px 20px;}");
// Pseudo-element is not supported in javax.swing.text.html.CSS
// styleSheet.addRule("ul{list-style-type:none;margin:0px 20px;}");
// styleSheet.addRule("ul li:before{content: "\u00BB";}");
}
editor1.setText(String.format(html, "bullet.png"));
add(new JScrollPane(editor0));
add(new JScrollPane(editor1));
setPreferredSize(new Dimension(320, 240));
}
private static JEditorPane makeEditorPane() {
JEditorPane editorPane = new JEditorPane();
editorPane.setContentType("text/html");
editorPane.setEditable(false);
return editorPane;
}
public static void main(String[] args) {
EventQueue.invokeLater(MainPanel::createAndShowGui);
}
private static void createAndShowGui() {
try {
UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
} catch (ClassNotFoundException | InstantiationException | IllegalAccessException | UnsupportedLookAndFeelException ex) {
ex.printStackTrace();
Toolkit.getDefaultToolkit().beep();
}
JFrame frame = new JFrame("@title@");
frame.setDefaultCloseOperation(WindowConstants.EXIT_ON_CLOSE);
frame.getContentPane().add(new MainPanel());
frame.pack();
frame.setLocationRelativeTo(null);
frame.setVisible(true);
}
}
|
package uk.ac.ebi.quickgo.client.service.loader.presets.evidence;
import uk.ac.ebi.quickgo.client.service.loader.presets.ff.RawNamedPresetColumnsBuilder;
import java.util.Comparator;
import java.util.stream.Stream;
/**
* A specialisation of {@link RawEvidenceNamedPresetColumnsBuilder} used to create
* {@link RawEvidenceNamedPresetColumnsImpl}
* instances, which capture information about the column indices relating to a {@link RawEvidenceNamedPreset}.
*
* Created 05/03/18
* @author Tony Wardell
*/
class RawEvidenceNamedPresetColumnsBuilder extends RawNamedPresetColumnsBuilder {
private int goEvidencePosition;
private RawEvidenceNamedPresetColumnsBuilder(int namePosition) {
super(namePosition);
this.goEvidencePosition = UNINITIALIZED_POSITION;
}
@Override
public RawEvidenceNamedPresetColumnsImpl build() {
return new RawEvidenceNamedPresetColumnsImpl(this);
}
public RawEvidenceNamedPresetColumnsBuilder withGoEvidence(int goEvidencePosition) {
checkColumnPosition(goEvidencePosition);
this.goEvidencePosition = goEvidencePosition;
return this;
}
@Override
public RawEvidenceNamedPresetColumnsBuilder withIdPosition(int idPosition) {
super.withIdPosition(idPosition);
return this;
}
@Override
public RawEvidenceNamedPresetColumnsBuilder withRelevancyPosition(int relevancyPosition) {
super.withRelevancyPosition(relevancyPosition);
return this;
}
static RawEvidenceNamedPresetColumnsBuilder createWithNamePosition(int namePosition) {
return new RawEvidenceNamedPresetColumnsBuilder(namePosition);
}
protected static class RawEvidenceNamedPresetColumnsImpl extends RawNamedPresetColumnsImpl {
private final int goEvidencePosition;
RawEvidenceNamedPresetColumnsImpl(RawEvidenceNamedPresetColumnsBuilder builder) {
super(builder);
this.goEvidencePosition = builder.goEvidencePosition;
}
public int getGoEvidencePosition() {
return goEvidencePosition;
}
@Override public int getMaxRequiredColumnCount() {
if (maxRequiredColumnPosition == MAX_REQUIRED_COLUMN_POSITION_NOT_INITIALIZED) {
maxRequiredColumnPosition =
Stream.of(
getDescriptionPosition(),
getIdPosition(),
getNamePosition(),
getRelevancyPosition(),
getAssociationPosition(),
getGoEvidencePosition()
).max(Comparator.naturalOrder())
.map(columnPosition -> columnPosition + 1)
.orElse(DEFAULT_COLUMN_POSITION_NOT_INITIALIZED);
}
return maxRequiredColumnPosition;
}
}
}
|
package org.carlspring.strongbox.providers.storage;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.nio.file.FileSystem;
import java.nio.file.Files;
import java.nio.file.Path;
import java.nio.file.Paths;
import java.security.NoSuchAlgorithmException;
import java.util.List;
import javax.annotation.PostConstruct;
import org.carlspring.commons.http.range.ByteRange;
import org.carlspring.commons.io.reloading.ReloadableInputStreamHandler;
import org.carlspring.strongbox.artifact.coordinates.ArtifactCoordinates;
import org.carlspring.strongbox.io.RepositoryFileSystem;
import org.carlspring.strongbox.io.RepositoryPath;
import org.carlspring.strongbox.io.ArtifactInputStream;
import org.carlspring.strongbox.io.ArtifactOutputStream;
import org.carlspring.strongbox.io.ArtifactPath;
import org.carlspring.strongbox.io.FileSystemWrapper;
import org.carlspring.strongbox.storage.repository.Repository;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Component;
/**
* @author carlspring
*/
@Component("filesystemStorageProvider")
public class FileSystemStorageProvider extends AbstractStorageProvider
{
private static final Logger logger = LoggerFactory.getLogger(FileSystemStorageProvider.class);
private static final String ALIAS = "file-system";
@Autowired
private StorageProviderRegistry storageProviderRegistry;
@Override
public String getAlias()
{
return ALIAS;
}
@PostConstruct
@Override
public void register()
{
storageProviderRegistry.addProvider(getAlias(), this);
logger.info("Registered storage provider '" + getClass().getCanonicalName() + "' with alias '" + ALIAS + "'.");
}
@Override
public ArtifactInputStream getInputStreamImplementation(ReloadableInputStreamHandler handler,
List<ByteRange> byteRanges)
throws IOException,
NoSuchAlgorithmException
{
return new ArtifactInputStream(handler, byteRanges);
}
@Override
public ArtifactInputStream getInputStreamImplementation(ReloadableInputStreamHandler handler,
ByteRange byteRange)
throws IOException,
NoSuchAlgorithmException
{
return new ArtifactInputStream(handler, byteRange);
}
@Override
public ArtifactInputStream getInputStreamImplementation(InputStream is)
throws NoSuchAlgorithmException
{
return new ArtifactInputStream(is);
}
@Override
public ArtifactOutputStream getOutputStreamImplementation(ArtifactPath artifactPath)
throws IOException
{
OutputStream os = Files.newOutputStream(artifactPath);
return new ArtifactOutputStream(os, artifactPath.getCoordinates());
}
@Override
public OutputStream getOutputStreamImplementation(RepositoryPath repositoryPath,
String path)
throws IOException
{
return Files.newOutputStream(repositoryPath.resolve(path));
}
@Override
public ArtifactInputStream getInputStreamImplementation(ArtifactPath artifactPath)
throws IOException,
NoSuchAlgorithmException
{
return new ArtifactInputStream(Files.newInputStream(artifactPath));
}
@Override
public ArtifactInputStream getInputStreamImplementation(InputStream is,
String[] algorithms)
throws NoSuchAlgorithmException
{
return new ArtifactInputStream(is, algorithms);
}
@Override
public ArtifactInputStream getInputStreamImplementation(ArtifactCoordinates coordinates,
InputStream is)
throws NoSuchAlgorithmException
{
ArtifactInputStream ais = new ArtifactInputStream(is);
ais.setArtifactCoordinates(coordinates);
return ais;
}
@Override
public ArtifactPath resolve(Repository repository,
ArtifactCoordinates coordinates)
throws IOException
{
Path targetPath = getArtifactPath(repository.getBasedir(), coordinates.toPath());
// Override FileSystem root to Repository base directory;
return new ArtifactPath(coordinates, targetPath,
getRepositoryFileSystem(repository));
}
@Override
public RepositoryPath resolve(Repository repository)
throws IOException
{
Path path = Paths.get(repository.getBasedir());
return new RepositoryPath(path, getRepositoryFileSystem(repository));
}
private RepositoryFileSystem getRepositoryFileSystem(Repository repository)
{
FileSystem storageFileSystem = new FileSystemWrapper(Paths.get(repository.getBasedir()).getFileSystem())
{
@Override
public Path getRootDirectory()
{
return Paths.get(repository.getBasedir());
}
};
RepositoryFileSystem repoFileSystem = new RepositoryFileSystem(repository, storageFileSystem);
return repoFileSystem;
}
private Path getArtifactPath(String basePath,
String artifactPath)
throws IOException
{
Path path = Paths.get(basePath).resolve(artifactPath);
if (!Files.exists(path))
{
Files.createDirectories(path);
}
return path;
}
}
|
package org.cytoscape.view.vizmap.gui.internal.editor.propertyeditor;
import java.awt.Color;
import java.awt.Component;
import java.awt.event.ActionEvent;
import java.awt.event.ActionListener;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
import java.util.Set;
import java.util.SortedSet;
import java.util.TreeSet;
import javax.swing.JComboBox;
import javax.swing.JList;
import javax.swing.plaf.basic.BasicComboBoxRenderer;
import org.cytoscape.application.CyApplicationManager;
import org.cytoscape.model.CyIdentifiable;
import org.cytoscape.model.CyNetwork;
import org.cytoscape.model.CyNetworkManager;
import org.cytoscape.view.vizmap.gui.editor.ListEditor;
import org.cytoscape.view.vizmap.gui.internal.AttributeSet;
import org.cytoscape.view.vizmap.gui.internal.AttributeSetManager;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
* Tracking the list of columns. By default, three instances of this should be
* created (for NODE, EDGE, and NETWORK).
*
* Export this as an OSGi service!
*/
public final class AttributeComboBoxPropertyEditor extends CyComboBoxPropertyEditor implements ListEditor {
private static final Logger logger = LoggerFactory.getLogger(AttributeComboBoxPropertyEditor.class);
private final Class<? extends CyIdentifiable> graphObjectType;
private final AttributeSetManager attrManager;
private final CyNetworkManager networkManager;
private Map<String, Class<?>> currentColumnMap;
public AttributeComboBoxPropertyEditor(final Class<? extends CyIdentifiable> type,
final AttributeSetManager attrManager, final CyApplicationManager appManager,
final CyNetworkManager networkManager) {
super();
this.attrManager = attrManager;
this.graphObjectType = type;
this.networkManager = networkManager;
currentColumnMap = new HashMap<String, Class<?>>();
final JComboBox comboBox = (JComboBox) editor;
comboBox.setRenderer(new AttributeComboBoxCellRenderer());
comboBox.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent arg0) {
updateComboBox(appManager.getCurrentNetwork());
}
});
}
@Override
public Class<?> getTargetObjectType() {
return graphObjectType;
}
private void updateComboBox(final CyNetwork currentNetwork) {
final JComboBox box = (JComboBox) editor;
final Object selected = box.getSelectedItem();
box.removeAllItems();
if (currentNetwork == null)
return;
final AttributeSet compatibleColumns = attrManager.getAttributeSet(currentNetwork, graphObjectType);
currentColumnMap = compatibleColumns.getAttrMap();
final AttributeSet targetSet = attrManager.getAttributeSet(currentNetwork, graphObjectType);
if (targetSet == null)
return;
final SortedSet<String> sortedName = new TreeSet<String>();
final Set<CyNetwork> networks = networkManager.getNetworkSet();
for (CyNetwork net : networks) {
final AttributeSet currentSet = this.attrManager.getAttributeSet(net, graphObjectType);
for (Entry<String, Class<?>> entry: currentSet.getAttrMap().entrySet())
if (columnIsAllowed(entry.getKey(), entry.getValue()))
sortedName.add(entry.getKey());
}
for (final String attrName : sortedName)
box.addItem(attrName);
// Add new name if not in the list.
box.setSelectedItem(selected);
logger.debug(graphObjectType + " Column Name Combobox Updated: New Names = "
+ targetSet.getAttrMap().keySet());
}
private boolean columnIsAllowed(String name, Class<?> type) {
if (!Long.class.equals(type) && !List.class.equals(type)) {
return true;
}
return !CyIdentifiable.SUID.equals(name) && !name.endsWith(".SUID");
}
private final class AttributeComboBoxCellRenderer extends BasicComboBoxRenderer {
private static final long serialVersionUID = 6828337202195089669L;
@Override
public Component getListCellRendererComponent(JList list, Object value, int index, boolean isSelected,
boolean cellHasFocus) {
if (value == null)
return this;
this.setText(value.toString());
if (isSelected) {
this.setForeground(Color.RED);
this.setBackground(list.getSelectionBackground());
} else {
this.setForeground(Color.BLACK);
this.setBackground(list.getBackground());
}
final Set<String> keys = currentColumnMap.keySet();
String valueString = value.toString();
if (keys != null && keys.contains(valueString) == false) {
this.setEnabled(false);
this.setFocusable(false);
this.setForeground(Color.LIGHT_GRAY);
this.setToolTipText("This column does not exist in current network's table.");
} else {
this.setEnabled(true);
this.setFocusable(true);
this.setToolTipText("Column Data Type: " + currentColumnMap.get(valueString).getSimpleName());
}
return this;
}
}
}
|
package org.eclipse.birt.report.item.crosstab.internal.ui;
import org.eclipse.birt.report.designer.core.DesignerConstants;
import org.eclipse.birt.report.designer.core.model.SessionHandleAdapter;
import org.eclipse.birt.report.designer.internal.ui.dialogs.DataColumnBindingDialog;
import org.eclipse.birt.report.designer.internal.ui.dnd.DNDLocation;
import org.eclipse.birt.report.designer.internal.ui.dnd.DNDService;
import org.eclipse.birt.report.designer.internal.ui.dnd.IDropAdapter;
import org.eclipse.birt.report.designer.internal.ui.util.ExceptionHandler;
import org.eclipse.birt.report.designer.ui.newelement.DesignElementFactory;
import org.eclipse.birt.report.designer.util.DEUtil;
import org.eclipse.birt.report.item.crosstab.core.ICrosstabCellConstants;
import org.eclipse.birt.report.item.crosstab.core.de.CrosstabCellHandle;
import org.eclipse.birt.report.item.crosstab.internal.ui.editors.editparts.CrosstabCellEditPart;
import org.eclipse.birt.report.item.crosstab.internal.ui.editors.model.CrosstabCellAdapter;
import org.eclipse.birt.report.item.crosstab.internal.ui.editors.model.ICrosstabCellAdapterFactory;
import org.eclipse.birt.report.model.api.CellHandle;
import org.eclipse.birt.report.model.api.CommandStack;
import org.eclipse.birt.report.model.api.DataItemHandle;
import org.eclipse.gef.EditPart;
import org.eclipse.gef.commands.Command;
import org.eclipse.gef.requests.CreateRequest;
import org.eclipse.jface.window.Window;
/**
* AggregationDropAdapter
*/
public class AggregationDropAdapter implements IDropAdapter
{
public int canDrop( Object transfer, Object target, int operation,
DNDLocation location )
{
if ( transfer.equals( "DATA_AGG" ) //$NON-NLS-1$
&& target instanceof CrosstabCellEditPart )
{
CrosstabCellAdapter adapter = (CrosstabCellAdapter) ( (CrosstabCellEditPart) target ).getModel( );
if ( adapter.getCrosstabCellHandle( ) != null
&& DEUtil.isReferenceElement( adapter.getCrosstabCellHandle( )
.getCrosstabHandle( ) ) )
return DNDService.LOGIC_FALSE;
String posType = adapter.getPositionType( );
if ( ICrosstabCellAdapterFactory.CELL_MEASURE_AGGREGATION.equals( posType )
|| ICrosstabCellAdapterFactory.CELL_MEASURE.equals( posType ) )
{
return DNDService.LOGIC_TRUE;
}
}
return DNDService.LOGIC_UNKNOW;
}
public boolean performDrop( Object transfer, Object target, int operation,
DNDLocation location )
{
if(target instanceof EditPart)
{
EditPart editPart = (EditPart)target;
CommandStack stack = SessionHandleAdapter.getInstance( )
.getCommandStack( );
stack.startTrans( "Add Aggregation" ); //$NON-NLS-1$
DataItemHandle dataHandle = DesignElementFactory.getInstance( )
.newDataItem( null );
CrosstabCellHandle cellHandle = ( (CrosstabCellAdapter) ( (CrosstabCellEditPart) target ).getModel( ) ).getCrosstabCellHandle( );
try
{
cellHandle.addContent( dataHandle, CellHandle.CONTENT_SLOT );
DataColumnBindingDialog dialog = new DataColumnBindingDialog( true );
dialog.setInput( dataHandle, null, cellHandle );
dialog.setAggreate( true );
if ( dialog.open( ) == Window.OK )
{
CreateRequest request = new CreateRequest( );
request.getExtendedData( )
.put( DesignerConstants.KEY_NEWOBJECT, dataHandle );
request.setLocation( location.getPoint( ) );
Command command = editPart.getCommand( request );
if ( command != null && command.canExecute( ) )
{
dataHandle.setResultSetColumn( dialog.getBindingColumn( )
.getName( ) );
editPart.getViewer( )
.getEditDomain( )
.getCommandStack( )
.execute( command );
stack.commit( );
}else
{
stack.rollback( );
}
}
else
{
stack.rollback( );
}
}
catch ( Exception e )
{
stack.rollback( );
ExceptionHandler.handle( e );
}
}
return true;
}
// public boolean performDrop( Object transfer, Object target, int operation,
// DNDLocation location )
// if(target instanceof EditPart)
// EditPart editPart = (EditPart)target;
// CommandStack stack = SessionHandleAdapter.getInstance( )
// .getCommandStack( );
// stack.startTrans( "Add Aggregation" ); //$NON-NLS-1$
// DataItemHandle dataHandle = DesignElementFactory.getInstance( )
// .newDataItem( null );
// CrosstabCellHandle cellHandle = ( (CrosstabCellAdapter) ( (CrosstabCellEditPart) target ).getModel( ) ).getCrosstabCellHandle( );
// try
// cellHandle.addContent( dataHandle, CellHandle.CONTENT_SLOT );
// DataColumnBindingDialog dialog = new DataColumnBindingDialog( true );
// dialog.setInput( dataHandle, null, cellHandle );
// dialog.setAggreate( true );
// if ( dialog.open( ) == Window.OK )
// cellHandle.getModelHandle( ).getPropertyHandle( ICrosstabCellConstants.CONTENT_PROP ).removeItem( dataHandle );
// CreateRequest request = new CreateRequest( );
// request.getExtendedData( )
// .put( DesignerConstants.KEY_NEWOBJECT, dataHandle );
// request.setLocation( location.getPoint( ) );
// Command command = editPart.getCommand( request );
// if ( command != null && command.canExecute( ) )
// dataHandle.setResultSetColumn( dialog.getBindingColumn( )
// .getName( ) );
// editPart.getViewer( )
// .getEditDomain( )
// .getCommandStack( )
// .execute( command );
// stack.commit( );
// }else
// stack.rollback( );
// else
// stack.rollback( );
// catch ( Exception e )
// stack.rollback( );
// ExceptionHandler.handle( e );
// return true;
}
|
package org.csstudio.config.ioconfig.editorparts;
import java.text.SimpleDateFormat;
import java.util.ArrayList;
import java.util.Date;
import java.util.Formatter;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import javax.annotation.CheckForNull;
import javax.annotation.Nonnull;
import javax.annotation.Nullable;
import org.apache.log4j.Logger;
import org.csstudio.config.ioconfig.config.view.INodeConfig;
import org.csstudio.config.ioconfig.config.view.helper.ConfigHelper;
import org.csstudio.config.ioconfig.config.view.helper.DocumentationManageView;
import org.csstudio.config.ioconfig.config.view.helper.GSDLabelProvider;
import org.csstudio.config.ioconfig.config.view.helper.ShowFileSelectionListener;
import org.csstudio.config.ioconfig.editorinputs.NodeEditorInput;
import org.csstudio.config.ioconfig.model.AbstractNodeDBO;
import org.csstudio.config.ioconfig.model.FacilityDBO;
import org.csstudio.config.ioconfig.model.GSDFileTypes;
import org.csstudio.config.ioconfig.model.IDocumentable;
import org.csstudio.config.ioconfig.model.PersistenceException;
import org.csstudio.config.ioconfig.model.Repository;
import org.csstudio.config.ioconfig.model.pbmodel.GSDFileDBO;
import org.csstudio.config.ioconfig.model.pbmodel.MasterDBO;
import org.csstudio.config.ioconfig.model.pbmodel.SlaveDBO;
import org.csstudio.config.ioconfig.view.MainView;
import org.csstudio.config.ioconfig.view.ProfiBusTreeView;
import org.csstudio.platform.logging.CentralLogger;
import org.csstudio.platform.security.SecurityFacade;
import org.csstudio.platform.security.User;
import org.csstudio.platform.ui.util.CustomMediaFactory;
import org.eclipse.core.runtime.IProgressMonitor;
import org.eclipse.core.runtime.Status;
import org.eclipse.jface.dialogs.ErrorDialog;
import org.eclipse.jface.dialogs.InputDialog;
import org.eclipse.jface.dialogs.MessageDialog;
import org.eclipse.jface.layout.GridDataFactory;
import org.eclipse.jface.layout.TableColumnLayout;
import org.eclipse.jface.viewers.ArrayContentProvider;
import org.eclipse.jface.viewers.ISelectionChangedListener;
import org.eclipse.jface.viewers.SelectionChangedEvent;
import org.eclipse.jface.viewers.StructuredSelection;
import org.eclipse.jface.viewers.TableViewer;
import org.eclipse.jface.viewers.Viewer;
import org.eclipse.jface.viewers.ViewerSorter;
import org.eclipse.jface.window.Window;
import org.eclipse.swt.SWT;
import org.eclipse.swt.events.KeyAdapter;
import org.eclipse.swt.events.KeyEvent;
import org.eclipse.swt.events.ModifyEvent;
import org.eclipse.swt.events.ModifyListener;
import org.eclipse.swt.events.MouseAdapter;
import org.eclipse.swt.events.MouseEvent;
import org.eclipse.swt.events.SelectionEvent;
import org.eclipse.swt.events.SelectionListener;
import org.eclipse.swt.graphics.Color;
import org.eclipse.swt.graphics.Font;
import org.eclipse.swt.layout.GridData;
import org.eclipse.swt.layout.GridLayout;
import org.eclipse.swt.widgets.Button;
import org.eclipse.swt.widgets.Combo;
import org.eclipse.swt.widgets.Composite;
import org.eclipse.swt.widgets.Control;
import org.eclipse.swt.widgets.Display;
import org.eclipse.swt.widgets.Group;
import org.eclipse.swt.widgets.Label;
import org.eclipse.swt.widgets.Menu;
import org.eclipse.swt.widgets.MenuItem;
import org.eclipse.swt.widgets.Shell;
import org.eclipse.swt.widgets.Spinner;
import org.eclipse.swt.widgets.TabFolder;
import org.eclipse.swt.widgets.TabItem;
import org.eclipse.swt.widgets.Text;
import org.eclipse.swt.widgets.TreeItem;
import org.eclipse.ui.IEditorInput;
import org.eclipse.ui.IEditorPart;
import org.eclipse.ui.IEditorSite;
import org.eclipse.ui.ISharedImages;
import org.eclipse.ui.IViewSite;
import org.eclipse.ui.PartInitException;
import org.eclipse.ui.PlatformUI;
import org.eclipse.ui.handlers.IHandlerService;
import org.eclipse.ui.part.EditorPart;
public abstract class AbstractNodeEditor extends EditorPart implements
INodeConfig {
private static final Logger LOG = CentralLogger.getInstance().getLogger(
AbstractNodeEditor.class);
private final class CancelSelectionListener implements SelectionListener {
public CancelSelectionListener() {
// Default Constructor
}
private void doCancle() {
// if (getNode().isPersistent()) {
if (!isNew()) {
cancel();
DocumentationManageView documentationManageView = getDocumentationManageView();
if (documentationManageView != null) {
documentationManageView.cancel();
}
setSaveButtonSaved();
} else {
AbstractNodeDBO node = getNode();
final boolean openQuestion = MessageDialog.openQuestion(
getShell(), "Cancel", "You dispose this "
+ node.getClass().getSimpleName() + "?");
if (openQuestion) {
setSaveButtonSaved();
// hrickens (01.10.2010): Beim Cancel einer neuen Facility
// macht nur Perfrom close Sinn.
AbstractNodeDBO parent = node.getParent();
if(parent!=null) {
parent.removeChild(node);
}
perfromClose();
}
}
}
@Override
public void widgetDefaultSelected(@Nonnull final SelectionEvent e) {
doCancle();
}
@Override
public void widgetSelected(@Nonnull final SelectionEvent e) {
doCancle();
}
}
private final class GSDFileChangeListener implements
ISelectionChangedListener {
private final Button _fileSelect;
/**
* Constructor.
*
* @param fileSelect
*/
protected GSDFileChangeListener(@Nonnull final Button fileSelect) {
_fileSelect = fileSelect;
}
@Override
public void selectionChanged(@Nonnull final SelectionChangedEvent event) {
final StructuredSelection selection = (StructuredSelection) event
.getSelection();
if (selection == null || selection.isEmpty()) {
_fileSelect.setEnabled(false);
return;
}
final GSDFileDBO file = (GSDFileDBO) selection.getFirstElement();
_fileSelect
.setEnabled(getNode().needGSDFile() == GSDFileTypes.Master == file
.isMasterNonHN());
}
}
private final class GSDFileRemoveListener implements SelectionListener {
private final TableViewer _tableViewer;
/**
* Constructor.
*
* @param tableViewer
*/
protected GSDFileRemoveListener(@Nonnull final TableViewer tableViewer) {
_tableViewer = tableViewer;
}
@Override
public void widgetDefaultSelected(@Nonnull final SelectionEvent e) {
// TODO:
}
@Override
public void widgetSelected(@Nonnull final SelectionEvent e) {
final StructuredSelection selection = (StructuredSelection) _tableViewer.getSelection();
final GSDFileDBO removeFile = (GSDFileDBO) selection.getFirstElement();
if (removeFile != null) {
if (MessageDialog.openQuestion(getShell(),
"Lsche Datei aus der Datenbank",
"Sind sie sicher das sie die Datei "
+ removeFile.getName() + " lschen mchten")) {
Repository.removeGSDFiles(removeFile);
List<GSDFileDBO> gsdFiles = getGsdFiles();
if (gsdFiles != null) {
gsdFiles.remove(removeFile);
}
_tableViewer.setInput(gsdFiles);
}
}
}
}
private final class GSDFileSelectionListener implements SelectionListener {
private final TableViewer _tableViewer;
private final Text _tSelected;
/**
* Constructor.
*
* @param tableViewer
* @param tSelected
*/
protected GSDFileSelectionListener(
@Nonnull final TableViewer tableViewer,
@Nonnull final Text tSelected) {
_tableViewer = tableViewer;
_tSelected = tSelected;
}
private void doFileAdd() {
setGsdFile((GSDFileDBO) ((StructuredSelection) _tableViewer
.getSelection()).getFirstElement());
if (fill(getGsdFile())) {
_tSelected.setText(getGsdFile().getName());
setSavebuttonEnabled("GSDFile", true);
}
}
@Override
public void widgetDefaultSelected(@Nullable final SelectionEvent e) {
doFileAdd();
}
@Override
public void widgetSelected(@Nullable final SelectionEvent e) {
doFileAdd();
}
}
private final class NodeConfigModifyListener implements ModifyListener {
public NodeConfigModifyListener() {
// Default Constructor.
}
@Override
public void modifyText(@Nonnull final ModifyEvent e) {
if (e.widget instanceof Text) {
final Text text = (Text) e.widget;
setSavebuttonEnabled("ModifyListenerText:" + text.hashCode(),
!text.getText().equals(text.getData()));
} else if (e.widget instanceof Combo) {
final Combo combo = (Combo) e.widget;
if (combo.getData() instanceof Integer) {
final Integer value = (Integer) combo.getData();
if (value == null) {
setSavebuttonEnabled(
"ModifyListenerCombo" + combo.hashCode(), false);
} else {
setSavebuttonEnabled(
"ModifyListenerCombo" + combo.hashCode(),
value != combo.getSelectionIndex());
}
}
} else if (e.widget instanceof Spinner) {
final Spinner spinner = (Spinner) e.widget;
try {
setSavebuttonEnabled(
"ModifyListenerCombo" + spinner.hashCode(),
(Short) spinner.getData() != spinner.getSelection());
} catch (final ClassCastException cce) {
LOG.error(spinner.toString(), cce);
}
}
}
}
private final class SaveSelectionListener implements SelectionListener {
public SaveSelectionListener() {
// Default Constructor
}
@Override
public void widgetDefaultSelected(@Nonnull final SelectionEvent e) {
getEditorSite().getActionBars()
.getGlobalActionHandler("org.eclipse.ui.file.save").run();
// TODO:need a IProgressMonitor? Yes!
doSave(null);
}
@Override
public void widgetSelected(@Nonnull final SelectionEvent e) {
perfromSave();
}
}
private final class ViewerSorterExtension extends ViewerSorter {
public ViewerSorterExtension() {
// default constructor
}
@Override
public int compare(@Nullable final Viewer viewer,
@Nullable final Object e1, @Nullable final Object e2) {
if (e1 instanceof GSDFileDBO && e2 instanceof GSDFileDBO) {
final GSDFileDBO file1 = (GSDFileDBO) e1;
final GSDFileDBO file2 = (GSDFileDBO) e2;
// sort wrong files to back.
if (!(file1.isMasterNonHN() || file1.isSlaveNonHN())
&& (file2.isMasterNonHN() || file2.isSlaveNonHN())) {
return -1;
} else if ((file1.isMasterNonHN() || file1.isSlaveNonHN())
&& !(file2.isMasterNonHN() || file2.isSlaveNonHN())) {
return 1;
}
// if master -> master file to top
switch (getNode().needGSDFile()) {
case Master:
if (file1.isMasterNonHN() && !file2.isMasterNonHN()) {
return -1;
} else if (!file1.isMasterNonHN() && file2.isMasterNonHN()) {
return 1;
}
break;
case Slave:
// if slave -> slave file to top
if (file1.isSlaveNonHN() && !file2.isSlaveNonHN()) {
return -1;
} else if (!file1.isSlaveNonHN() && file2.isSlaveNonHN()) {
return 1;
}
break;
default:
// do nothing
}
return file1.getName().compareToIgnoreCase(file2.getName());
}
return super.compare(viewer, e1, e2);
}
}
/**
* The warn background color (SWT.COLOR_RED) of the index Spinner.
*/
protected static final Color WARN_BACKGROUND_COLOR = CustomMediaFactory
.getInstance().getColor(CustomMediaFactory.COLOR_RED);
private static Font _FONT;
private static GridDataFactory _LABEL_GRID_DATA = GridDataFactory
.fillDefaults();
private static GridDataFactory _TEXT_GRID_DATA = GridDataFactory
.fillDefaults().grab(true, false);
private static void createGSDFileActions(@Nonnull final TableViewer viewer) {
final Menu menu = new Menu(viewer.getControl());
final MenuItem showItem = new MenuItem(menu, SWT.PUSH);
showItem.addSelectionListener(new ShowFileSelectionListener(viewer));
showItem.setText("&Show");
showItem.setImage(PlatformUI.getWorkbench().getSharedImages()
.getImage(ISharedImages.IMG_OBJ_FOLDER));
// MenuItem saveAsItem = new MenuItem(menu, SWT.PUSH);
// saveAsItem.addSelectionListener(new SaveAsSelectionListener(viewer));
// saveAsItem.setText("&Show");
// saveAsItem.setImage(PlatformUI.getWorkbench().getSharedImages()
// .getImage(ISharedImages.IMG_ETOOL_SAVEAS_EDIT));
viewer.getTable().setMenu(menu);
}
@Nonnull
private static Label getNewLabel(@Nonnull final Composite header,
@Nonnull final String string) {
final Label newLabel = new Label(header, SWT.NONE);
newLabel.setLayoutData(_LABEL_GRID_DATA.create());
newLabel.setText(string);
return newLabel;
}
@Nonnull
private static Text getNewText(@Nonnull final Composite header,
@Nonnull final String text) {
final Text newText = new Text(header, SWT.NONE);
newText.setLayoutData(_TEXT_GRID_DATA.create());
newText.setEditable(false);
newText.setText(text);
return newText;
}
protected static void resetString(@Nonnull Text textField) {
String text = (String) textField.getData();
if (text != null) {
textField.setText(text);
}
}
/**
* A ModifyListener that set the save button enable to store the changes.
* Works with {@link Text}, {@link Combo} and {@link Spinner}.
*/
private final ModifyListener _mLSB = new NodeConfigModifyListener();
/**
* Contain all different events that have change a Value and the status of
* the change. The status means is the new Value a differnt from the origin
* Value.
*/
private final HashMap<String, Boolean> _saveButtonEvents = new HashMap<String, Boolean>();
private final Map<HeaderFields, Text> headerFields = new HashMap<HeaderFields, Text>();
/**
* The Button to cancel Changes.
*/
private Button _cancelButton;
private Text _descText;
/**
* The Tabview to Manage the documentation of Node.
*/
private DocumentationManageView _documentationManageView;
// Node Editor View
private GSDFileDBO _gsdFile;
private List<GSDFileDBO> _gsdFiles;
/**
* The Spinner for the channel index.
*/
private Spinner _indexSpinner;
/**
* The text field for the name of the node.
*/
private Text _nameText;
// Node Editor View
/**
* if true an new SubNet a created also modified _slave.
*/
private boolean _new = false;
private AbstractNodeDBO _node;
// Node Editor View
private Composite _parent;
/**
* The Button to save Changes.
*/
private Button _saveButton;
/**
* The Tabfolder for a config view.
*/
private TabFolder _tabFolder;
public AbstractNodeEditor() {
// TODO Auto-generated constructor stub
}
public AbstractNodeEditor(final boolean nevv) {
// super(parent, SWT.NONE);
setNew(nevv);
// ActionFactory.SAVE.create(this.get);
// setGlobalActionHandler(IWorkbenchActionConstants.,
// goIntoAction);
// setBackgroundComposite(headline, node);
}
// Node Editor View
public void cancel() {
Text descText = getDescText();
if (descText != null && descText.getData() != null
&& descText.getData() instanceof String) {
setDesc((String) descText.getData());
}
if (getNode() != null) {
getNode().setDirty(false);
}
}
@SuppressWarnings("unused")
private void createButtonArea(@Nonnull final TabFolder tabFolder,
@Nonnull final Composite comp, @Nonnull final Text selectedText,
@Nonnull final TableViewer gsdFileTableViewer) {
new Label(comp, SWT.NONE);
final Button fileSelect = new Button(comp, SWT.PUSH);
fileSelect.setText("Select");
fileSelect.setLayoutData(new GridData(SWT.FILL, SWT.FILL, false, false,
1, 1));
fileSelect.addSelectionListener(new GSDFileSelectionListener(
gsdFileTableViewer, selectedText));
new Label(comp, SWT.NONE);
new Label(comp, SWT.NONE);
final Button fileAdd = new Button(comp, SWT.PUSH);
fileAdd.setLayoutData(new GridData(SWT.FILL, SWT.FILL, false, false, 1,
1));
fileAdd.setText("Add File");
fileAdd.addSelectionListener(new GSDFileAddListener(this, tabFolder,
gsdFileTableViewer, comp));
final Button fileRemove = new Button(comp, SWT.PUSH);
fileRemove.setLayoutData(new GridData(SWT.FILL, SWT.FILL, false, false,
1, 1));
fileRemove.setText("Remove File");
fileRemove.addSelectionListener(new GSDFileRemoveListener(
gsdFileTableViewer));
gsdFileTableViewer
.addSelectionChangedListener(new GSDFileChangeListener(
fileSelect));
new Label(comp, SWT.NONE);
}
/**
* @param columnNum
* @param comp
* @return
*/
@Nonnull
private TableViewer createChooserArea(final int columnNum,
@Nonnull final Composite comp) {
final Group gAvailable = new Group(comp, SWT.NONE);
gAvailable.setText("Available GSD File:");
gAvailable.setLayoutData(new GridData(SWT.FILL, SWT.FILL, true, true,
columnNum, 1));
gAvailable.setLayout(new GridLayout(1, false));
final TableColumnLayout tableColumnLayout = new TableColumnLayout();
final Composite tableComposite = new Composite(gAvailable, SWT.BORDER);
GridDataFactory.fillDefaults().grab(true, true).applyTo(tableComposite);
tableComposite.setLayout(tableColumnLayout);
final TableViewer gsdFileTableViewer = new TableViewer(tableComposite,
SWT.H_SCROLL | SWT.V_SCROLL | SWT.MULTI | SWT.FULL_SELECTION);
gsdFileTableViewer.setContentProvider(new ArrayContentProvider());
gsdFileTableViewer.setSorter(new ViewerSorterExtension());
gsdFileTableViewer.setLabelProvider(new GSDLabelProvider(getNode()
.needGSDFile()));
gsdFileTableViewer.getTable().setHeaderVisible(false);
gsdFileTableViewer.getTable().setLinesVisible(false);
GridDataFactory.fillDefaults().grab(true, true)
.applyTo(gsdFileTableViewer.getTable());
setGsdFiles(Repository.load(GSDFileDBO.class));
if (getGsdFiles() == null) {
setGsdFiles(new ArrayList<GSDFileDBO>());
} else if (!getGsdFiles().isEmpty()) {
gsdFileTableViewer.setInput(getGsdFiles().toArray(
new GSDFileDBO[getGsdFiles().size()]));
}
return gsdFileTableViewer;
}
/**
* (@inheritDoc)
*/
@Override
public void createPartControl(@Nonnull final Composite parent) {
_parent = parent;
setBackgroundComposite();
if (getTabFolder() != null
&& getNode().needGSDFile() != GSDFileTypes.NONE) {
makeGSDFileChooser(getTabFolder(), "GSD File List");
}
documents();
}
@Nonnull
private Text createSelectionArea(final int columnNum,
@Nonnull final Composite comp) {
final Text tSelected;
final Group gSelected = new Group(comp, SWT.NONE);
gSelected.setText("Selected GSD File:");
gSelected.setLayoutData(new GridData(SWT.FILL, SWT.FILL, true, false,
columnNum, 1));
gSelected.setLayout(new GridLayout(1, false));
tSelected = new Text(gSelected, SWT.SINGLE | SWT.BORDER);
tSelected.setLayoutData(new GridData(SWT.FILL, SWT.FILL, true, false,
1, 1));
if (getGsdFile() != null) {
setGsdFile(getGsdFile());
tSelected.setText(getGsdFile().getName());
}
return tSelected;
}
/**
*
* {@inheritDoc}
*/
@Override
public void dispose() {
super.dispose();
setSaveButton(null);
if (_saveButtonEvents != null) {
_saveButtonEvents.clear();
}
getProfiBusTreeView().removeOpenEditor(this);
}
/**
* set the documents and Icon tab item.
*/
private void documents() {
final String head = "Documents";
final TabItem item = new TabItem(getTabFolder(), SWT.NO_SCROLL);
item.setText(head);
// TODO: refactor DocumentationManageView
_documentationManageView = new DocumentationManageView(getTabFolder(),
SWT.NONE, this);
item.setControl(_documentationManageView);
getTabFolder().addSelectionListener(new SelectionListener() {
private void docTabSelectionAction(@Nonnull final SelectionEvent e) {
if (e.item.equals(item)) {
getDocumentationManageView().onActivate();
}
}
@Override
public void widgetDefaultSelected(@Nonnull final SelectionEvent e) {
docTabSelectionAction(e);
}
@Override
public void widgetSelected(@Nonnull final SelectionEvent e) {
docTabSelectionAction(e);
}
});
}
@Override
public void doSave(@Nullable final IProgressMonitor monitor) {
// Header
final Date now = new Date();
final SimpleDateFormat df = new SimpleDateFormat(
"yyyy-MM-dd HH:mm:ss.S");
final Text text = getHeaderField(HeaderFields.VERSION);
int i = -1;
try {
i = Integer.valueOf(text.getText());
} catch (final NumberFormatException nfe) {
i = 0;
}
getNode().setVersion(i);
getNode().setUpdatedBy(ConfigHelper.getUserName());
getNode().setUpdatedOn(now);
getNode().setDescription(getDesc());
if (getDescText() != null) {
getDescText().setData(getDesc());
}
// update Header
getHeaderField(HeaderFields.MODIFIED_ON).setText(df.format(now));
getHeaderField(HeaderFields.MODIFIED_BY).setText(
ConfigHelper.getUserName());
getHeaderField(HeaderFields.DB_ID).setText("" + getNode().getId());
// df = null;
// now = null;
}
// Node Editor View
/**
* (@inheritDoc)
*/
@Override
public void doSaveAs() {
// save as not supported
}
/**
* Fill the View whit data from GSDFile.
*
* @param gsdFile
* the GSDFile whit the data.
* @return true when set the data ok.
*/
public abstract boolean fill(@Nullable GSDFileDBO gsdFile);
/**
* @return the cancelButton
*/
@CheckForNull
protected final Button getCancelButton() {
return _cancelButton;
}
@Nonnull
public String getDesc() {
if (getDescText() == null || getDescText().getText() == null) {
return "";
}
return getDescText().getText();
}
@CheckForNull
protected Text getDescText() {
return _descText;
}
// Node Editor View
/**
*
* @return the node which was configured with this View.
*/
@Override
@Nonnull
public IDocumentable getDocumentableObject() {
return _node;
}
/**
*
* @return The Documentation Manage View.
*/
@CheckForNull
protected final DocumentationManageView getDocumentationManageView() {
return _documentationManageView;
}
@CheckForNull
protected List<GSDFileDBO> getGsdFiles() {
return _gsdFiles;
}
@Nonnull
public Text getHeaderField(@Nonnull final HeaderFields field) {
return headerFields.get(field);
}
/**
* @return the indexSpinner
*/
@CheckForNull
protected final Spinner getIndexSpinner() {
return _indexSpinner;
}
/**
* A ModifyListener that set the save button enable to store the changes.
* Works wiht {@link Text}, {@link Combo} and {@link Spinner}.
*
* @return the ModifyListener.
*/
@Nonnull
public final ModifyListener getMLSB() {
return _mLSB;
}
/**
*
* @return the Node Name description field.
*/
@CheckForNull
protected final Text getNameWidget() {
return _nameText;
}
/**
* @param head
* The Tab text.
* @param rows
* row number for the grid.
* @return The Composite of the generated TabItem.
*/
@Nonnull
protected final Composite getNewTabItem(@Nonnull final String head,
final int rows) {
final TabItem item = new TabItem(getTabFolder(), SWT.NONE, 0);
item.setText(head);
final Composite comp = new Composite(getTabFolder(), SWT.NONE);
comp.setLayout(new GridLayout(rows, false));
item.setControl(comp);
comp.setBackground(Display.getDefault().getSystemColor(
SWT.COLOR_WIDGET_BACKGROUND));
return comp;
}
/**
* {@inheritDoc}
*/
@Override
@Nonnull
public AbstractNodeDBO getNode() {
return _node;
}
/**
* @return the parent
*/
@CheckForNull
protected Composite getParent() {
return _parent;
}
/**
* @return the profiBusTreeView
*/
@Nonnull
protected final ProfiBusTreeView getProfiBusTreeView() {
return ((MainView) getEditorSite().getPage().findView(MainView.ID))
.getProfiBusTreeView();
}
@CheckForNull
protected Button getSaveButton() {
return _saveButton;
}
@CheckForNull
protected Shell getShell() {
if (this.getEditorSite() != null) {
return this.getEditorSite().getShell();
}
return null;
}
/**
* @return the tabFolder
*/
@Nonnull
protected final TabFolder getTabFolder() {
assert _tabFolder != null : "Tab folder not avaible!";
return _tabFolder;
}
/**
* (@inheritDoc)
*/
@Override
public void init(@Nonnull final IEditorSite site,
@Nonnull final IEditorInput input) throws PartInitException {
setSite(site);
setInput(input);
// getProfiBusTreeView().closeOpenEditor();
_node = ((NodeEditorInput) input).getNode();
setNew(((NodeEditorInput) input).isNew());
setPartName(_node.getName());
getProfiBusTreeView().setOpenEditor(this);
}
/**
*
* @return only true when the node has on or more changes.
*/
@Override
public final boolean isDirty() {
if (getNode() != null) {
return getNode().isDirty();
}
return true;
}
@Override
public boolean isSaveAsAllowed() {
return false; // save as not supported
}
@Nonnull
private Group makeBackgroundGroup(final int columnNum) {
final Group header = new Group(getParent(), SWT.H_SCROLL);
header.setLayoutData(new GridData(SWT.FILL, SWT.TOP, true, false,
columnNum, 1));
header.setLayout(new GridLayout(7, false));
header.setText("General Information");
header.setTabList(new Control[0]);
return header;
}
protected void makeDescGroup(@Nonnull final Composite comp, final int hSize) {
final Group gDesc = new Group(comp, SWT.NONE);
gDesc.setText("Description: ");
final GridDataFactory gdf = GridDataFactory.fillDefaults()
.grab(true, true).span(hSize, 1).minSize(200, 200);
gDesc.setLayoutData(gdf.create());
gDesc.setLayout(new GridLayout(2, false));
final Label shortDescLabel = new Label(gDesc, SWT.NONE);
shortDescLabel.setLayoutData(new GridData(SWT.BEGINNING, SWT.CENTER,
false, false));
shortDescLabel.setText("Short Desc:");
final Text shortDescText = new Text(gDesc, SWT.BORDER | SWT.SINGLE
| SWT.READ_ONLY);
shortDescText.setLayoutData(new GridData(SWT.FILL, SWT.FILL, true,
false, 1, 1));
shortDescText.setEditable(false);
final Text descText = new Text(gDesc, SWT.BORDER | SWT.MULTI);
descText.setLayoutData(new GridData(SWT.FILL, SWT.FILL, true, true, 2,
1));
descText.setEditable(true);
descText.addModifyListener(new ModifyListener() {
@Override
public void modifyText(@Nonnull final ModifyEvent e) {
final String text = descText.getText();
String string = "";
if (text != null) {
final String[] split = text.split("[\r\n]");
if (split.length > 0) {
if (string.length() > 40) {
string = string.substring(0, 40);
} else {
string = split[0];
}
}
}
shortDescText.setText(string);
}
});
setText(descText, getNode().getDescription(), 255);
setDescWidget(descText);
gDesc.setTabList(new Control[] {descText });
}
/**
*
* @param tabFolder
* The Tab Folder to add the Tab Item.
* @param head
* Headline for the Tab.
* @return Tab Item Composite.
*/
@Nonnull
public Composite makeGSDFileChooser(@Nonnull final TabFolder tabFolder,
@Nonnull final String head) {
final int columnNum = 7;
final Composite comp = ConfigHelper.getNewTabItem(head, tabFolder,
columnNum, 520, 200);
final Text selectedText = createSelectionArea(columnNum, comp);
final TableViewer gsdFileTableViewer = createChooserArea(columnNum,
comp);
createButtonArea(tabFolder, comp, selectedText, gsdFileTableViewer);
createGSDFileActions(gsdFileTableViewer);
return comp;
}
/**
* Generate a new Node on his parent with a Name, creator and creation date.
*/
protected boolean newNode() {
return newNode("");
}
protected boolean newNode(@Nullable final String nameOffer) {
final String nodeType = getNode().getClass().getSimpleName();
final InputDialog id = new InputDialog(getShell(), "Create new "
+ nodeType, "Enter the name of the " + nodeType, nameOffer,
null);
id.setBlockOnOpen(true);
if (id.open() == Window.OK) {
getNode().setName(id.getValue());
final User user = SecurityFacade.getInstance().getCurrentUser();
String name = "Unknown";
if (user != null) {
name = user.getUsername();
}
getNode().setCreatedBy(name);
getNode().setCreatedOn(new Date());
getNode().setVersion(-2);
id.close();
final Object obj = ((StructuredSelection) getProfiBusTreeView()
.getTreeViewer().getSelection()).getFirstElement();
if (getNode() instanceof FacilityDBO || obj == null) {
getProfiBusTreeView().getTreeViewer().setInput(getNode());
// TODO neue facility erstellen und speichern..
} else if (obj instanceof AbstractNodeDBO) {
if (getNode().getParent() == null) {
final AbstractNodeDBO nodeParent = (AbstractNodeDBO) obj;
getNode()
.moveSortIndex(
nodeParent
.getfirstFreeStationAddress(AbstractNodeDBO.MAX_STATION_ADDRESS));
nodeParent.addChild(getNode());
}
}
return true;
}
return false;
}
/**
* @param exception
* A exception to show in a Dialog,
*/
protected void openErrorDialog(@Nonnull final Exception exception) {
LOG.error(exception);
final Formatter f = new Formatter();
String message = exception.getLocalizedMessage();
if (message == null) {
message = exception.getMessage();
if (message == null) {
message = "Unknown Exception";
}
}
f.format("The Settings not saved!\n\nDataBase Failure:\n%s", message);
final ErrorDialog errorDialog = new ErrorDialog(Display.getCurrent()
.getActiveShell(), "Data Base Error", f.toString(),
Status.CANCEL_STATUS, 0);
errorDialog.open();
f.close();
}
public void perfromClose() {
final IViewSite site = getProfiBusTreeView().getSite();
site.getPage().closeEditor(this, false);
}
protected void perfromSave() {
final IViewSite site = getProfiBusTreeView().getSite();
final IHandlerService handlerService = (IHandlerService) site
.getService(IHandlerService.class);
try {
handlerService.executeCommand("org.eclipse.ui.file.save", null);
} catch (final Exception ex) {
LOG.error(ex);
}
}
/**
* Save or Update the Node to the Data Base.
*/
final void save() {
try {
if (getNode().getParent() == null) {
getNode().localSave();
} else {
getNode().getParent().localSave();
}
} catch (final PersistenceException e) {
openErrorDialog(e);
}
setSaveButtonSaved();
getSaveButton().setText("&Save");
if (isNew() && !getNode().isRootNode()) {
getProfiBusTreeView().refresh(getNode().getParent());
} else if (isNew() && getNode().isRootNode()) {
getProfiBusTreeView().addFacility(getNode());
getProfiBusTreeView().refresh(getNode());
getProfiBusTreeView().refresh();
} else {
// refresh the View
getProfiBusTreeView().refresh(getNode());
}
setNew(false);
}
@SuppressWarnings("unused")
private void setBackgroundComposite() {
final int columnNum = 5;
final AbstractNodeDBO node = getNode();
if (node == null) {
return;
}
getParent().setLayout(new GridLayout(columnNum, true));
final Label headlineLabel = new Label(getParent(), SWT.NONE);
if (_FONT == null) {
_FONT = headlineLabel.getFont();
}
headlineLabel.setText("Profibus " + node.getClass().getSimpleName()
+ " Configuration");
headlineLabel.setLayoutData(new GridData(SWT.LEFT, SWT.FILL, false,
false, columnNum, 1));
final GridDataFactory labelGridData = GridDataFactory.fillDefaults();
// - Header
final Group header = makeBackgroundGroup(columnNum);
// -- Create by
getNewLabel(header, "Created by:");
/** The description field with the name of the User that make changes. */
String temp = "";
if (isNew()) {
final SecurityFacade securityFacade = SecurityFacade.getInstance();
if (securityFacade != null
&& securityFacade.getCurrentUser() != null
&& securityFacade.getCurrentUser().getUsername() != null) {
temp = securityFacade.getCurrentUser().getUsername();
}
} else if (node != null && node.getCreatedBy() != null) {
temp = node.getCreatedBy();
}
final Text creatByText = getNewText(header, temp);
getParent().setData("creatBy", creatByText);
temp = "";
getNewLabel(header, "Created on:");
/** The description field with the name of the Date of the last change. */
Date now = new Date();
if (isNew()) {
temp = ConfigHelper.getSimpleDateFormat().format(now);
} else if (node != null && node.getCreatedOn() != null) {
now = node.getCreatedOn();
temp = now.toString();
}
final Text creatOnText = getNewText(header, temp);
getParent().setData("date", now);
getParent().setData("creatOn", creatOnText);
temp = "";
// -- Version
getNewLabel(header, "Version:");
/** The description field with the Version from GSD File. */
if (node != null) {
temp = node.getVersion() + "";
}
final Text versionText = getNewText(header, temp);
setHeaderField(HeaderFields.VERSION, versionText);
final Label iconButton = new Label(header, SWT.BORDER);
iconButton.setLayoutData(GridDataFactory.swtDefaults().span(1, 3)
.minSize(40, 40).create());
iconButton.setImage(ConfigHelper.getImageFromNode(node, 30, 60));
iconButton.addMouseListener(new MouseAdapter() {
@Override
public void mouseUp(@Nullable final MouseEvent e) {
final IconChooserDialog chooseIconDialog = new IconChooserDialog(
AbstractNodeEditor.this.getShell(), node);
chooseIconDialog.setBlockOnOpen(true);
if (chooseIconDialog.open() == 0 && node != null) {
node.setIcon(chooseIconDialog.getImage());
}
}
});
getNewLabel(header, "Modified by:");
/** The description field with the name of the User that make changes. */
temp = "";
if (node != null && node.getUpdatedBy() != null) {
temp = node.getUpdatedBy();
}
final Text modifiedBy = getNewText(header, temp);
setHeaderField(HeaderFields.MODIFIED_BY, modifiedBy);
temp = "";
// -- Modifierd on
getNewLabel(header, "Modified on:");
/** The description field with the name of the Date of the last change. */
if (node != null && node.getUpdatedOn() != null) {
temp = node.getUpdatedOn().toString();
}
final Text modifiedOn = getNewText(header, temp);
setHeaderField(HeaderFields.MODIFIED_ON, modifiedOn);
temp = "";
getNewLabel(header, "DataBase ID:");
/** The description field with the Version from GSD File. */
if (node != null) {
temp = node.getId() + "";
}
final Text dbIdText = getNewText(header, temp);
setHeaderField(HeaderFields.DB_ID, dbIdText);
/**
* GSD Version. The description field with the Version from GSD File.
* Only Master and Slave have a GSD File
*/
if (node instanceof MasterDBO || node instanceof SlaveDBO) {
getNewLabel(header, "Version from GSD:");
if (node.getUpdatedOn() != null) {
// TODO: GSD Versionsnummer setzen.
temp = node.getVersion() + "";
}
final Text version = getNewText(header, temp);
getParent().setData("gsdVersion", version);
}
setTabFolder(new TabFolder(getParent(), SWT.H_SCROLL | SWT.V_SCROLL));
getTabFolder().setLayoutData(
new GridData(SWT.FILL, SWT.FILL, true, true, 5, 1));
getTabFolder().setBackgroundMode(SWT.INHERIT_DEFAULT);
// -Footer
new Label(getParent(), SWT.NONE);
setSaveButton(new Button(getParent(), SWT.PUSH));
if (isNew()) {
getSaveButton().setText("Create");
} else {
getSaveButton().setText("&Save");
}
setSavebuttonEnabled(null, !isNew());
getSaveButton().setLayoutData(labelGridData.create());
setSaveButtonSelectionListener(new SaveSelectionListener());
new Label(getParent(), SWT.NONE);
setCancelButton(new Button(getParent(), SWT.PUSH));
getCancelButton().setText("&Cancel");
getCancelButton().setLayoutData(labelGridData.create());
getCancelButton().addSelectionListener(new CancelSelectionListener());
new Label(getParent(), SWT.NONE);
header.setTabList(new Control[0]);
}
/**
* @param cancelButton
* the cancelButton to set
*/
protected final void setCancelButton(@Nullable final Button cancelButton) {
_cancelButton = cancelButton;
}
/**
* Select a text to a {@link Combo} and store the index into Data as origin
* value.
*
* @param comboField
* The Combo field to set the index
* @param value
* The value was select.
*/
final void setCombo(@Nonnull final Combo comboField,
@Nullable final String value) {
String tmp = value;
if (tmp == null) {
tmp = "";
}
final int index = comboField.indexOf(value);
comboField.select(index);
comboField.setData(index);
comboField.addModifyListener(getMLSB());
}
public void setDesc(@CheckForNull final String desc) {
String temp = desc != null ? desc : "";
getDescText().setText(temp);
}
protected void setDescText(@Nullable final Text descText) {
_descText = descText;
}
/**
*
* @param descText
* set the Node Name description field.
*/
protected final void setDescWidget(@Nonnull final Text descText) {
setDescText(descText);
getDescText().addKeyListener(new KeyAdapter() {
@Override
public void keyPressed(@Nonnull final KeyEvent e) {
if (e.keyCode == SWT.CR || e.keyCode == SWT.KEYPAD_CR) {
if (e.stateMask != SWT.MOD1) {
e.doit = false;
getSaveButton().setFocus();
}
}
}
});
}
@CheckForNull
protected void setGsdFiles(@Nullable final List<GSDFileDBO> gsdFiles) {
_gsdFiles = gsdFiles;
}
@Nonnull
public Text setHeaderField(@Nonnull final HeaderFields field,
@Nullable final Text text) {
return headerFields.put(field, text);
}
/**
* @param indexSpinner
* the indexSpinner to set
*/
protected final void setIndexSpinner(@Nullable final Spinner indexSpinner) {
_indexSpinner = indexSpinner;
}
public final void setName(@Nonnull final String name) {
final TreeItem treeItem = getProfiBusTreeView().getTreeViewer()
.getTree().getSelection()[0];
treeItem.setText(name);
_nameText.setText(name);
}
/**
*
* @param nameText
* set the Node Name description field.
*/
protected final void setNameWidget(@Nonnull final Text nameText) {
_nameText = nameText;
_nameText.addKeyListener(new KeyAdapter() {
@Override
public void keyReleased(@Nonnull final KeyEvent e) {
if (e.keyCode == SWT.CR || e.keyCode == SWT.KEYPAD_CR) {
getDescText().setFocus();
}
}
});
}
protected void setSaveButton(@Nullable final Button saveButton) {
_saveButton = saveButton;
}
/**
* Give a change event and his save status.<br>
* Have one or more events the status unsaved then the Save Button was set
* to enable otherwise to disable.
*
* @param event
* the Save Event Id.
* @param enabled
* the Save Enable status for the event.
*/
@Override
public final void setSavebuttonEnabled(@Nullable final String event,
final boolean enabled) {
if (event != null) {
_saveButtonEvents.put(event, enabled);
}
final boolean enab = !getNode().isPersistent()
|| _saveButtonEvents.containsValue(Boolean.valueOf(true));
final boolean changed = enab != getSaveButton().isEnabled();
getSaveButton().setEnabled(enab);
getNode().setDirty(enab);
if (changed) {
firePropertyChange(IEditorPart.PROP_DIRTY);
}
}
/**
* Clear the dirty bit, delete all saveButton events and set the Button
* disable.
*/
@Override
public final void setSaveButtonSaved() {
_saveButtonEvents.clear();
getSaveButton().setEnabled(false);
if (getNode() != null) {
getNode().setDirty(false);
}
firePropertyChange(PROP_DIRTY);
}
/**
*
* @param selectionListener
*/
public final void setSaveButtonSelectionListener(
@Nonnull final SelectionListener selectionListener) {
getSaveButton().addSelectionListener(selectionListener);
}
/**
* @param tabFolder
* the tabFolder to set
*/
protected final void setTabFolder(@Nullable final TabFolder tabFolder) {
_tabFolder = tabFolder;
}
/**
* Set a int as text to a {@link Text} and store the text into Data as
* origin value.
*
* @param textField
* The Text field to set the text
* @param textValue
* The int was set.
*/
final void setText(@Nonnull final Text textField, final int textValue,
final int limit) {
setText(textField, Integer.toString(textValue), limit);
}
/**
* Set a text to a {@link Text} and store the text into Data as origin
* value.
*
* @param textField
* The Text-field to set the text
* @param text
* The text was set.
* @param limit
* The maximum text length for the Text-field. (Text.LIMIT for
* maximum)
*/
final void setText(@Nonnull final Text textField,
@Nullable final String text, final int limit) {
String tmp = text;
if (tmp == null) {
tmp = "";
}
textField.setText(tmp);
textField.setData(tmp);
textField.setTextLimit(limit);
// Formatter f = new Formatter();
// f.format("The maximum text length is %s character", limit);
textField.setToolTipText("");
textField.addModifyListener(getMLSB());
}
protected void setGsdFile(@Nullable GSDFileDBO gsdFile) {
_gsdFile = gsdFile;
}
@CheckForNull
protected GSDFileDBO getGsdFile() {
return _gsdFile;
}
protected static void resetSelection(@Nonnull Combo combo) {
Integer index = (Integer) combo.getData();
if (index != null) {
combo.select(index);
}
}
protected void setNew(boolean nevv) {
_new = nevv;
}
protected boolean isNew() {
return _new;
}
}
|
package org.ovirt.engine.core.searchbackend;
import org.ovirt.engine.core.common.AuditLogSeverity;
import org.ovirt.engine.core.common.businessentities.DateEnumForSearch;
import org.ovirt.engine.core.compat.StringHelper;
public class AuditLogConditionFieldAutoCompleter extends BaseConditionFieldAutoCompleter {
public AuditLogConditionFieldAutoCompleter() {
super();
// Building the basic vervs Dict
mVerbs.put("TYPE", "TYPE");
mVerbs.put("SEVERITY", "SEVERITY");
mVerbs.put("MESSAGE", "MESSAGE");
mVerbs.put("TIME", "TIME");
mVerbs.put("USRNAME", "USRNAME");
mVerbs.put("EVENT_HOST", "EVENT_HOST");
mVerbs.put("EVENT_VM", "EVENT_VM");
mVerbs.put("EVENT_TEMPLATE", "EVENT_TEMPLATE");
mVerbs.put("EVENT_STORAGE", "EVENT_STORAGE");
mVerbs.put("EVENT_DATACENTER", "EVENT_DATACENTER");
mVerbs.put("EVENT_VOLUME", "EVENT_VOLUME");
mVerbs.put("CORRELATION_ID", "CORRELATION_ID");
buildCompletions();
// These search options remain hidden from the autocompletion
// but still available for the user interface
mVerbs.put("_EVENT_VM_ID", "_EVENT_VM_ID");
mVerbs.put("_EVENT_TEMPLATE_ID", "_EVENT_TEMPLATE_ID");
mVerbs.put("_EVENT_STORAGE_ID", "_EVENT_STORAGE_ID");
mVerbs.put("_EVENT_HOST_ID", "_EVENT_HOST_ID");
mVerbs.put("_EVENT_DATACENTER_ID", "_EVENT_DATACENTER_ID");
mVerbs.put("_EVENT_QUOTA_ID", "_EVENT_QUOTA_ID");
mVerbs.put("USRID", "USRID");
// Building the autoCompletion Dict
// Building the types dict
getTypeDictionary().put("TYPE", Integer.class);
getTypeDictionary().put("SEVERITY", AuditLogSeverity.class);
getTypeDictionary().put("MESSAGE", String.class);
getTypeDictionary().put("TIME", java.util.Date.class);
getTypeDictionary().put("USRNAME", String.class);
getTypeDictionary().put("EVENT_HOST", String.class);
getTypeDictionary().put("EVENT_VM", String.class);
getTypeDictionary().put("EVENT_TEMPLATE", String.class);
getTypeDictionary().put("EVENT_STORAGE", String.class);
getTypeDictionary().put("EVENT_DATACENTER", String.class);
getTypeDictionary().put("USRID", String.class);
getTypeDictionary().put("_EVENT_HOST_ID", String.class);
getTypeDictionary().put("_EVENT_VM_ID", String.class);
getTypeDictionary().put("_EVENT_TEMPLATE_ID", String.class);
getTypeDictionary().put("_EVENT_STORAGE_ID", String.class);
getTypeDictionary().put("_EVENT_DATACENTER_ID", String.class);
getTypeDictionary().put("_EVENT_QUOTA_ID", String.class);
getTypeDictionary().put("EVENT_VOLUME", String.class);
getTypeDictionary().put("_EVENT_VOLUME_ID", String.class);
getTypeDictionary().put("CORRELATION_ID", String.class);
// building the ColumnName Dict
mColumnNameDict.put("TYPE", "log_type");
mColumnNameDict.put("SEVERITY", "severity");
mColumnNameDict.put("MESSAGE", "message");
mColumnNameDict.put("TIME", "log_time");
mColumnNameDict.put("USRNAME", "user_name");
mColumnNameDict.put("USRID", "user_id::varchar");
mColumnNameDict.put("EVENT_HOST", "vds_name");
mColumnNameDict.put("_EVENT_HOST_ID", "vds_id::varchar");
mColumnNameDict.put("EVENT_VM", "vm_name");
mColumnNameDict.put("_EVENT_VM_ID", "vm_id::varchar");
mColumnNameDict.put("EVENT_TEMPLATE", "vm_template_name");
mColumnNameDict.put("_EVENT_TEMPLATE_ID", "vm_template_id::varchar");
mColumnNameDict.put("EVENT_STORAGE", "storage_domain_name");
mColumnNameDict.put("_EVENT_STORAGE_ID", "storage_domain_id::varchar");
mColumnNameDict.put("EVENT_DATACENTER", "storage_pool_name");
mColumnNameDict.put("_EVENT_DATACENTER_ID", "storage_pool_id::varchar");
mColumnNameDict.put("_EVENT_QUOTA_ID", "quota_id::varchar");
mColumnNameDict.put("EVENT_VOLUME", "gluster_volume_name");
mColumnNameDict.put("_EVENT_VOLUME_ID", "gluster_volume_id::varchar");
mColumnNameDict.put("CORRELATION_ID", "correlation_id::varchar");
// Building the validation dict
buildBasicValidationTable();
}
@Override
public IAutoCompleter getFieldRelationshipAutoCompleter(final String fieldName) {
if (StringHelper.EqOp(fieldName, "SEVERITY")) {
return NumericConditionRelationAutoCompleter.INSTANCE;
}
else if (StringHelper.EqOp(fieldName, "TIME")) {
return TimeConditionRelationAutoCompleter.INSTANCE;
}
else if (StringHelper.EqOp(fieldName, "TYPE") || StringHelper.EqOp(fieldName, "MESSAGE")
|| StringHelper.EqOp(fieldName, "USRNAME") || StringHelper.EqOp(fieldName, "EVENT_HOST")
|| StringHelper.EqOp(fieldName, "_EVENT_HOST_ID")
|| StringHelper.EqOp(fieldName, "EVENT_VM") || StringHelper.EqOp(fieldName, "_EVENT_VM_ID")
|| StringHelper.EqOp(fieldName, "EVENT_TEMPLATE") || StringHelper.EqOp(fieldName, "_EVENT_TEMPLATE_ID")
|| StringHelper.EqOp(fieldName, "EVENT_STORAGE") || StringHelper.EqOp(fieldName, "EVENT_DATACENTER")
|| StringHelper.EqOp(fieldName, "_EVENT_DATACENTER_ID")
|| StringHelper.EqOp(fieldName, "_EVENT_QUOTA_ID")
|| StringHelper.EqOp(fieldName, "EVENT_VOLUME") || StringHelper.EqOp(fieldName, "_EVENT_VOLUME_ID") ||
StringHelper.EqOp(fieldName, "CORRELATION_ID")) {
return StringConditionRelationAutoCompleter.INSTANCE;
} else {
return null;
}
}
@Override
public IConditionValueAutoCompleter getFieldValueAutoCompleter(String fieldName) {
if (StringHelper.EqOp(fieldName, "SEVERITY")) {
return new EnumValueAutoCompleter(AuditLogSeverity.class);
}
else if (StringHelper.EqOp(fieldName, "TIME")) {
return new DateEnumValueAutoCompleter(DateEnumForSearch.class);
} else {
return null;
}
}
}
|
package net.safedata.springboot.training.d04.s01.service;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.stereotype.Service;
import java.util.concurrent.CompletableFuture;
import java.util.concurrent.ExecutionException;
import java.util.concurrent.Future;
@Service
@SuppressWarnings("unused")
public class ProductService {
private static final Logger LOGGER = LoggerFactory.getLogger(ProductService.class);
private final AsyncComponent asyncComponent;
@Autowired
public ProductService(final AsyncComponent asyncComponent) {
this.asyncComponent = asyncComponent;
}
public void voidAsyncCall(final String firstParameter, final String secondParameter) {
asyncComponent.voidAsyncCall(firstParameter, secondParameter);
}
public void getFuture() {
final Future<String> future = asyncComponent.getFuture();
try {
getAndDisplayValue(future, "Future");
} catch (final ExecutionException | InterruptedException e) {
handleException(e);
}
}
public void getCompletableFuture() {
final CompletableFuture<String> completableFuture = asyncComponent.getCompletableFuture();
try {
getAndDisplayValue(completableFuture, "CompletableFuture");
} catch (final ExecutionException | InterruptedException e) {
handleException(e);
}
}
private void getAndDisplayValue(final Future<String> futureValue, final String className)
throws ExecutionException, InterruptedException {
if (futureValue.isDone()) {
LOGGER.info("The {} value is '{}'", className, futureValue.get());
} else {
System.out.println(futureValue.isCancelled());
System.out.println(futureValue.get());
}
}
private void handleException(final Exception ex) {
ex.printStackTrace();
}
}
|
package org.eclipse.birt.report.engine.emitter.excel;
import java.io.IOException;
import java.io.OutputStream;
import java.util.Collection;
import java.util.Iterator;
import java.util.Locale;
import java.util.logging.Level;
import java.util.logging.Logger;
import org.eclipse.birt.core.exception.BirtException;
import org.eclipse.birt.report.engine.api.EngineException;
import org.eclipse.birt.report.engine.api.IExcelRenderOption;
import org.eclipse.birt.report.engine.api.IHTMLActionHandler;
import org.eclipse.birt.report.engine.api.IRenderOption;
import org.eclipse.birt.report.engine.api.IReportRunnable;
import org.eclipse.birt.report.engine.api.RenderOption;
import org.eclipse.birt.report.engine.api.script.IReportContext;
import org.eclipse.birt.report.engine.content.IAutoTextContent;
import org.eclipse.birt.report.engine.content.ICellContent;
import org.eclipse.birt.report.engine.content.IContainerContent;
import org.eclipse.birt.report.engine.content.IContent;
import org.eclipse.birt.report.engine.content.IDataContent;
import org.eclipse.birt.report.engine.content.IForeignContent;
import org.eclipse.birt.report.engine.content.IHyperlinkAction;
import org.eclipse.birt.report.engine.content.IImageContent;
import org.eclipse.birt.report.engine.content.ILabelContent;
import org.eclipse.birt.report.engine.content.IListBandContent;
import org.eclipse.birt.report.engine.content.IListContent;
import org.eclipse.birt.report.engine.content.IPageContent;
import org.eclipse.birt.report.engine.content.IReportContent;
import org.eclipse.birt.report.engine.content.IRowContent;
import org.eclipse.birt.report.engine.content.IStyle;
import org.eclipse.birt.report.engine.content.ITableContent;
import org.eclipse.birt.report.engine.content.ITextContent;
import org.eclipse.birt.report.engine.css.engine.value.DataFormatValue;
import org.eclipse.birt.report.engine.emitter.ContentEmitterAdapter;
import org.eclipse.birt.report.engine.emitter.EmitterUtil;
import org.eclipse.birt.report.engine.emitter.IEmitterServices;
import org.eclipse.birt.report.engine.emitter.excel.layout.ColumnsInfo;
import org.eclipse.birt.report.engine.emitter.excel.layout.ContainerSizeInfo;
import org.eclipse.birt.report.engine.emitter.excel.layout.ExcelContext;
import org.eclipse.birt.report.engine.emitter.excel.layout.ExcelLayoutEngine;
import org.eclipse.birt.report.engine.emitter.excel.layout.LayoutUtil;
import org.eclipse.birt.report.engine.emitter.excel.layout.PageDef;
import org.eclipse.birt.report.engine.ir.DataItemDesign;
import org.eclipse.birt.report.engine.ir.DimensionType;
import org.eclipse.birt.report.engine.ir.MapDesign;
import org.eclipse.birt.report.engine.ir.SimpleMasterPageDesign;
import org.eclipse.birt.report.engine.layout.pdf.util.HTML2Content;
import org.eclipse.birt.report.engine.presentation.ContentEmitterVisitor;
import com.ibm.icu.util.TimeZone;
import com.ibm.icu.util.ULocale;
public class ExcelEmitter extends ContentEmitterAdapter
{
protected static Logger logger = Logger.getLogger( ExcelEmitter.class
.getName( ) );
protected IEmitterServices service = null;
protected OutputStream out = null;
protected ExcelLayoutEngine engine;
ContentEmitterVisitor contentVisitor = new ContentEmitterVisitor( this );
protected IExcelWriter writer;
public ExcelContext context = new ExcelContext( );
private String orientation = null;
protected String pageHeader;
protected String pageFooter;
private boolean outputInMasterPage = false;
protected boolean isRTLSheet = false;
private int sheetIndex = 1;
public String getOutputFormat( )
{
return "xls";
}
public void initialize( IEmitterServices service ) throws EngineException
{
this.service = service;
if ( service != null )
{
this.out = EmitterUtil.getOuputStream( service, "report."
+ getOutputFormat( ) );
}
context.setTempFileDir( service.getReportEngine( ).getConfig( )
.getTempDir( ) );
IReportContext reportContext = service.getReportContext( );
if ( reportContext != null )
{
Locale locale = reportContext.getLocale( );
if ( locale != null )
{
context.setLocale( ULocale.forLocale( locale ) );
}
else
context.setLocale( ULocale.getDefault( ) );
}
}
public void start( IReportContent report )
{
setupRenderOptions( );
// We can the page size from the design, maybe there is a better way
// to get the page definition.
String reportOrientation = report.getDesign( ).getReportDesign( )
.getBidiOrientation( );
if ( "rtl".equalsIgnoreCase( reportOrientation ) )
isRTLSheet = true;
IStyle style = report.getRoot( ).getComputedStyle( );
SimpleMasterPageDesign master = (SimpleMasterPageDesign) report
.getDesign( ).getPageSetup( ).getMasterPage( 0 );
engine = createLayoutEngine( context, this );
engine.initalize( new PageDef( master, style ) );
createWriter( );
}
protected ExcelLayoutEngine createLayoutEngine( ExcelContext context,
ExcelEmitter emitter )
{
return new ExcelLayoutEngine( context, emitter );
}
private void setupRenderOptions()
{
IRenderOption renderOptions = service.getRenderOption( );
Object textWrapping = renderOptions.getOption(IExcelRenderOption.WRAPPING_TEXT);
if(textWrapping!=null && textWrapping instanceof Boolean)
{
context.setWrappingText((Boolean)textWrapping);
}
else
{
context.setWrappingText( ( Boolean )true);
}
Object officeVersion = renderOptions.getOption(IExcelRenderOption.OFFICE_VERSION);
if(officeVersion!=null && officeVersion instanceof String)
{
if(officeVersion.equals( "office2007" ))
{
context.setOfficeVersion("office2007" );
}
}
else
{
context.setOfficeVersion( "office2003" );
}
}
public void startPage( IPageContent page ) throws BirtException
{
if ( orientation == null )
{
orientation = capitalize( page.getOrientation( ) );
}
if(needOutputInMasterPage(page.getPageHeader( ))&& needOutputInMasterPage(page.getPageFooter( )))
{
outputInMasterPage = true;
pageHeader = formatHeaderFooter( page.getPageHeader( ),true );
pageFooter = formatHeaderFooter( page.getPageFooter( ),false );
}
if ( !outputInMasterPage && page.getPageHeader( ) != null )
{
contentVisitor.visitChildren( page.getPageHeader( ), null );
}
engine.setPageStyle( page.getComputedStyle( ) );
}
public void endPage( IPageContent page ) throws BirtException
{
if(!outputInMasterPage && page.getPageFooter( ) != null)
{
contentVisitor.visitChildren( page.getPageFooter( ), null );
}
}
public void startTable( ITableContent table )
{
ContainerSizeInfo sizeInfo = engine.getCurrentContainer( ).getSizeInfo( );
int width = sizeInfo.getWidth( );
int[] columns = LayoutUtil.createTable( table, LayoutUtil
.getElementWidth( table, width ) );
ColumnsInfo info = new ColumnsInfo( columns );
String caption = table.getCaption( );
if(caption != null)
{
engine.addCaption( caption );
}
engine.addTable( table, info, sizeInfo );
}
public void startRow( IRowContent row )
{
engine.addRow( row.getComputedStyle( ) );
}
public void endRow( IRowContent row )
{
DimensionType height = row.getHeight( );
double rowHeight = height != null ? ExcelUtil.covertDimensionType(
height, 0 ) : 0;
engine.endRow( rowHeight );
}
public void startCell( ICellContent cell )
{
IStyle style = cell.getComputedStyle( );
engine.addCell( cell, cell.getColumn( ), cell.getColSpan( ), cell
.getRowSpan( ), style );
}
public void endCell( ICellContent cell )
{
engine.endCell( );
}
public void endTable( ITableContent table )
{
engine.endTable();
}
public void startList( IListContent list )
{
ContainerSizeInfo size = engine.getCurrentContainer( ).getSizeInfo( );
ColumnsInfo table = LayoutUtil.createTable( list, size.getWidth( ) );
engine.addTable( list, table, size );
if(list.getChildren( ) == null)
{
HyperlinkDef link = parseHyperLink(list);
BookmarkDef bookmark = getBookmark( list );
engine.addData( ExcelLayoutEngine.EMPTY,
list.getComputedStyle( ), link, bookmark );
}
}
public void startListBand( IListBandContent listBand )
{
engine.addCell( 0, 1, 0, listBand.getComputedStyle( ) );
}
public void endListBand( IListBandContent listBand )
{
engine.endContainer( );
}
public void endList( IListContent list )
{
engine.endTable( );
}
public void startForeign( IForeignContent foreign ) throws BirtException
{
if ( IForeignContent.HTML_TYPE.equalsIgnoreCase( foreign.getRawType( ) ) )
{
HTML2Content.html2Content( foreign );
HyperlinkDef link = parseHyperLink(foreign);
engine.addContainer( foreign.getComputedStyle( ), link );
contentVisitor.visitChildren( foreign, null );
engine.endContainer( );
}
}
public void startText( ITextContent text )
{
HyperlinkDef url = parseHyperLink( text );
BookmarkDef bookmark = getBookmark( text );
engine.addData( text.getText( ), text.getComputedStyle( ), url,
bookmark );
}
public void startData( IDataContent data )
{
addDataContent( data );
}
protected Data addDataContent( IDataContent data )
{
HyperlinkDef url = parseHyperLink( data );
BookmarkDef bookmark = getBookmark( data );
Data excelData = null;
Object generateBy = data.getGenerateBy( );
IStyle style = data.getComputedStyle( );
DataFormatValue dataformat = style.getDataFormat( );
MapDesign map = null;
if(generateBy instanceof DataItemDesign )
{
DataItemDesign design = (DataItemDesign) generateBy;
map = design.getMap( );
}
if ( map != null && map.getRuleCount( ) > 0
&& data.getLabelText( ) != null )
{
excelData = engine.addData( data.getLabelText( ).trim( ), style,
url, bookmark );
}
else
{
String locale = null;
int type = ExcelUtil.getType( data.getValue( ) );
if ( type == SheetData.STRING )
{
if ( dataformat != null )
{
locale = dataformat.getStringLocale( );
}
excelData = engine.addData( data.getText( ), style, url,
bookmark, locale );
}
else if ( type == Data.NUMBER )
{
if ( dataformat != null )
{
locale = dataformat.getNumberLocale( );
}
excelData = engine.addData( data.getValue( ), style, url,
bookmark, locale );
}
else
{
if ( dataformat != null )
{
locale = dataformat.getDateTimeLocale( );
}
excelData = engine.addDateTime( data, style, url, bookmark, locale );
}
}
return excelData;
}
public void startImage( IImageContent image )
{
IStyle style = image.getComputedStyle( );
HyperlinkDef url = parseHyperLink( image );
BookmarkDef bookmark = getBookmark( image );
engine.addImageData( image, style, url, bookmark );
}
public void startLabel( ILabelContent label )
{
Object design = label.getGenerateBy( );
IContent container = label;
while ( design == null )
{
container = (IContent) container.getParent( );
design = ( (IContent) container ).getGenerateBy( );
}
HyperlinkDef url = parseHyperLink( label );
BookmarkDef bookmark = getBookmark( label );
// If the text is BR and it generated by foreign,
// ignore it
if ( !( "\n".equalsIgnoreCase( label.getText( ) ) &&
container instanceof IForeignContent ) )
{
engine.addData( label.getText( ), label.getComputedStyle( ), url, bookmark );
}
}
public void startAutoText( IAutoTextContent autoText )
{
HyperlinkDef link = parseHyperLink( autoText );
BookmarkDef bookmark = getBookmark( autoText );
engine.addData( autoText.getText( ) ,
autoText.getComputedStyle( ), link, bookmark );
}
public void outputSheet( )
{
engine.cacheBookmarks( sheetIndex );
engine.complete( );
try
{
outputCacheData( );
}
catch ( IOException e )
{
logger.log( Level.SEVERE, e.getLocalizedMessage( ), e );
}
sheetIndex++;
}
public void end( IReportContent report )
{
// Make sure the engine already calculates all data in cache.
engine.cacheBookmarks( sheetIndex );
engine.complete( );
try
{
writer.start( report, engine.getStyleMap( ), engine
.getAllBookmarks( ) );
outputCacheData( );
writer.end( );
}
catch ( IOException e )
{
logger.log( Level.SEVERE, e.getLocalizedMessage( ), e );
}
}
protected void createWriter( )
{
writer = new ExcelWriter( out, context, isRTLSheet );
}
/**
* @throws IOException
*
*/
public void outputCacheData( ) throws IOException
{
writer.startSheet( engine.getCoordinates( ), pageHeader, pageFooter );
Iterator<RowData> it = engine.getIterator( );
while ( it.hasNext( ) )
{
outputRowData( it.next( ) );
}
writer.endSheet( orientation );
}
protected void outputRowData( RowData rowData ) throws IOException
{
writer.startRow( rowData.getHeight( ) );
SheetData[] data = rowData.getRowdata( );
for ( int i = 0; i < data.length; i++ )
{
writer.outputData( data[i] );
}
writer.endRow( );
}
public HyperlinkDef parseHyperLink( IContent content )
{
HyperlinkDef hyperlink = null;
IHyperlinkAction linkAction = content.getHyperlinkAction( );
if ( linkAction != null )
{
String tooltip = linkAction.getTooltip( );
String bookmark = linkAction.getBookmark( );
IReportRunnable reportRunnable = service.getReportRunnable( );
IReportContext reportContext = service.getReportContext( );
IHTMLActionHandler actionHandler = (IHTMLActionHandler) service
.getOption( RenderOption.ACTION_HANDLER );
switch ( linkAction.getType( ) )
{
case IHyperlinkAction.ACTION_BOOKMARK :
hyperlink = new HyperlinkDef( bookmark,
IHyperlinkAction.ACTION_BOOKMARK, tooltip );
break;
case IHyperlinkAction.ACTION_HYPERLINK :
String url = EmitterUtil.getHyperlinkUrl( linkAction,
reportRunnable, actionHandler, reportContext );
hyperlink = new HyperlinkDef( url,
IHyperlinkAction.ACTION_HYPERLINK, tooltip );
break;
case IHyperlinkAction.ACTION_DRILLTHROUGH :
url = EmitterUtil.getHyperlinkUrl( linkAction,
reportRunnable, actionHandler, reportContext );
hyperlink = new HyperlinkDef( url,
IHyperlinkAction.ACTION_DRILLTHROUGH, tooltip );
break;
}
}
return hyperlink;
}
protected BookmarkDef getBookmark( IContent content )
{
String bookmarkName = content.getBookmark( );
if (bookmarkName == null)
return null;
BookmarkDef bookmark=new BookmarkDef(content.getBookmark( ));
if ( !ExcelUtil.isValidBookmarkName( bookmarkName ) )
{
bookmark.setGeneratedName( engine
.getGenerateBookmark( bookmarkName ) );
}
// !( content.getBookmark( ).startsWith( "__TOC" ) ) )
// bookmark starting with "__TOC" is not OK?
return bookmark;
}
public String capitalize( String orientation )
{
if ( orientation.equalsIgnoreCase( "landscape" ) )
{
return "Landscape";
}
if(orientation.equalsIgnoreCase( "portrait" ))
{
return "Portrait";
}
return null;
}
public String formatHeaderFooter( IContent headerFooter, boolean isHeader )
{
StringBuffer headfoot = new StringBuffer( );
if ( headerFooter != null )
{
Collection list = headerFooter.getChildren( );
Iterator iter = list.iterator( );
while ( iter.hasNext( ) )
{
Object child = iter.next( );
if ( child instanceof ITableContent )
{
headfoot.append( getTableValue( (ITableContent) child ) );
}
else
processText( headfoot, child );
}
return headfoot.toString( );
}
return null;
}
private void processText( StringBuffer buffer, Object child )
{
if ( child instanceof IAutoTextContent )
{
buffer.append( getAutoText( (IAutoTextContent) child ) );
}
else if ( child instanceof ITextContent )
{
buffer.append( ( (ITextContent) child ).getText( ) );
}
else if ( child instanceof IForeignContent )
{
buffer.append( ( (IForeignContent) child ).getRawValue( ) );
}
}
public boolean needOutputInMasterPage( IContent headerFooter )
{
if ( headerFooter != null )
{
Collection list = headerFooter.getChildren( );
Iterator iter = list.iterator( );
while ( iter.hasNext( ) )
{
Object child = iter.next( );
if ( child instanceof ITableContent )
{
int columncount = ( (ITableContent) child )
.getColumnCount( );
int rowcount = ( (ITableContent) child ).getChildren( )
.size( );
if ( columncount > 3 || rowcount > 1 )
{
logger
.log(
Level.WARNING,
"Excel page header or footer only accept a table no more than 1 row and 3 columns." );
return false;
}
if ( isEmbededTable( (ITableContent) child ) )
{
logger
.log( Level.WARNING,
"Excel page header and footer don't support embeded grid." );
return false;
}
}
if ( isHtmlText( child ) )
{
logger
.log( Level.WARNING,
"Excel page header and footer don't support html text." );
return false;
}
}
}
return true;
}
private boolean isHtmlText( Object child )
{
return child instanceof IForeignContent
&& IForeignContent.HTML_TYPE
.equalsIgnoreCase( ( (IForeignContent) child )
.getRawType( ) );
}
public String getTableValue( ITableContent table )
{
StringBuffer tableValue = new StringBuffer( );
Collection list = table.getChildren( );
Iterator iter = list.iterator( );
while ( iter.hasNext( ) )
{
Object child = iter.next( );
tableValue.append( getRowValue( (IRowContent) child ) );
}
return tableValue.toString( );
}
public String getRowValue( IRowContent row )
{
StringBuffer rowValue = new StringBuffer( );
Collection list = row.getChildren( );
Iterator iter = list.iterator( );
int cellCount = list.size( );
int currentCellCount = 0;
while ( iter.hasNext( ) )
{
currentCellCount++;
Object child = iter.next( );
switch ( currentCellCount )
{
case 1 :
rowValue.append( "&L" );
break;
case 2 :
rowValue.append( "&C" );
break;
case 3 :
rowValue.append( "&R" );
break;
default :
break;
}
rowValue.append( getCellValue( (ICellContent) child ) );
}
return rowValue.toString( );
}
public String getCellValue( ICellContent cell )
{
StringBuffer cellValue = new StringBuffer( );
Collection list = cell.getChildren( );
Iterator iter = list.iterator( );
while ( iter.hasNext( ) )
{
processText( cellValue, iter.next( ) );
}
return cellValue.toString( );
}
private String getAutoText( IAutoTextContent autoText )
{
String result = null;
int type = autoText.getType( );
if ( type == IAutoTextContent.PAGE_NUMBER )
{
result = "&P";
}
else if ( type == IAutoTextContent.TOTAL_PAGE )
{
result = "&N";
}
return result;
}
private boolean isEmbededTable(ITableContent table)
{
boolean isEmbeded = false;
Collection list = table.getChildren( );
Iterator iterRow = list.iterator( );
while ( iterRow.hasNext( ) )
{
Object child = iterRow.next( );
Collection listCell = ( (IRowContent) child ).getChildren( );
Iterator iterCell = listCell.iterator( );
while ( iterCell.hasNext( ) )
{
Object cellChild = iterCell.next( );
Collection listCellChild = ( (ICellContent) cellChild )
.getChildren( );
Iterator iterCellChild = listCellChild.iterator( );
while ( iterCellChild.hasNext( ) )
{
Object cellchild = iterCellChild.next( );
if ( cellchild instanceof ITableContent )
{
isEmbeded = true;
}
}
}
}
return isEmbeded;
}
public TimeZone getTimeZone()
{
if ( service != null )
{
IReportContext reportContext = service.getReportContext( );
if ( reportContext != null )
{
return reportContext.getTimeZone( );
}
}
return TimeZone.getDefault( );
}
public void endContainer( IContainerContent container )
{
engine.removeContainerStyle( );
}
public void startContainer( IContainerContent container )
{
engine.addContainerStyle( container.getComputedStyle( ) );
}
}
|
package org.eclipse.persistence.testing.tests.queries;
import org.eclipse.persistence.testing.models.employee.domain.*;
import org.eclipse.persistence.exceptions.DatabaseException;
import org.eclipse.persistence.expressions.*;
import org.eclipse.persistence.queries.*;
import org.eclipse.persistence.testing.framework.*;
import org.eclipse.persistence.sessions.server.*;
/**
* This test verifies if a transaction is committed while using read & write
* connections in same client session with cursored stream used in read.
*/
public class CursoredStreamReadWriteClientSessionTest extends TestCase {
protected Server serverSession;
protected ClientSession clientSession;
protected int addressId = 0;
protected Exception caughtException = null;
/**
* CursoredStreamReadWriteClientSessionTest constructor.
*/
public CursoredStreamReadWriteClientSessionTest() {
setDescription("Verifies if a transaction is committed while using read & write connections in same client session with cursored stream used in read.");
}
public void reset() {
this.clientSession.release();
this.serverSession.logout();
}
public void setup() {
org.eclipse.persistence.sessions.Project proj =
new org.eclipse.persistence.testing.models.employee.relational.EmployeeProject();
proj.setDatasourceLogin(getSession().getDatasourceLogin().clone());
// Set initial & min size of connection in pool to ZERO.
this.serverSession = proj.createServerSession(0, 0, 1);
this.serverSession.setSessionLog(getSession().getSessionLog());
this.serverSession.login();
this.clientSession = this.serverSession.acquireClientSession();
// Fetch a address Id from database.
Employee emp = (Employee) getSession().readObject(Employee.class);
this.addressId = emp.getAddress().getId().intValue();
}
public void test() {
clientSession.beginTransaction();
try {
// Fetch Address object to update.
ReadObjectQuery objquery = new ReadObjectQuery();
objquery.setReferenceClass(Address.class);
ExpressionBuilder objquerybuilder = new ExpressionBuilder();
Expression objexpr = objquerybuilder.get("id").equal(this.addressId);
objquery.setSelectionCriteria(objexpr);
Address address = (Address) clientSession.executeQuery(objquery);
// This seems to be a very bad test, it is corrupting the database state,
// Changing the address is not required anyway as this test does no verify,
// and since it is not using a UnitOfWork, the update will update verything anyway.
//address.setStreet("Lawrence Street");
UpdateObjectQuery updateQuery = new UpdateObjectQuery();
updateQuery.setObject(address);
clientSession.executeQuery(updateQuery);
ReadAllQuery query = new ReadAllQuery();
query.setReferenceClass(Employee.class);
query.useCursoredStream(1, 1);
CursoredStream stream = (CursoredStream)clientSession.executeQuery(query);
Object result = null;
while (stream.hasNext()) {
result = stream.next();
}
clientSession.commitTransaction();
} catch(Exception ex) {
caughtException = ex;
} finally {
try {
clientSession.rollbackTransaction();
} catch (Exception ex) {
// ignore
}
}
}
public void verify() {
if (caughtException == null) {
return;
}
if (caughtException instanceof DatabaseException) {
throw new TestErrorException("incorrect if the exception is thrown due to a closed connection");
}
}
}
|
package com.excilys.liferay.gatling;
import java.io.IOException;
import java.io.OutputStream;
import java.io.PrintWriter;
import java.util.ArrayList;
import java.util.Date;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.zip.ZipEntry;
import java.util.zip.ZipOutputStream;
import javax.portlet.ActionRequest;
import javax.portlet.ActionResponse;
import javax.portlet.PortletException;
import javax.portlet.ReadOnlyException;
import javax.portlet.RenderRequest;
import javax.portlet.RenderResponse;
import javax.portlet.ResourceRequest;
import javax.portlet.ResourceResponse;
import javax.portlet.ValidatorException;
import com.excilys.liferay.gatling.exception.EmptySimulation;
import com.excilys.liferay.gatling.model.Request;
import com.excilys.liferay.gatling.model.Scenario;
import com.excilys.liferay.gatling.model.Simulation;
import com.excilys.liferay.gatling.mustache.ScriptGeneratorGatling;
import com.excilys.liferay.gatling.service.RequestLocalServiceUtil;
import com.excilys.liferay.gatling.service.ScenarioLocalServiceUtil;
import com.excilys.liferay.gatling.service.SimulationLocalServiceUtil;
import com.excilys.liferay.gatling.util.DisplayItem;
import com.excilys.liferay.gatling.util.DisplayItemUtil;
import com.excilys.liferay.gatling.util.GatlingUtil;
import com.github.mustachejava.DefaultMustacheFactory;
import com.github.mustachejava.Mustache;
import com.github.mustachejava.MustacheFactory;
import com.liferay.portal.kernel.exception.PortalException;
import com.liferay.portal.kernel.exception.SystemException;
import com.liferay.portal.kernel.log.Log;
import com.liferay.portal.kernel.log.LogFactoryUtil;
import com.liferay.portal.kernel.servlet.HttpHeaders;
import com.liferay.portal.kernel.util.ParamUtil;
import com.liferay.portal.kernel.util.WebKeys;
import com.liferay.portal.model.Group;
import com.liferay.portal.model.Layout;
import com.liferay.portal.model.PortletPreferences;
import com.liferay.portal.service.GroupLocalServiceUtil;
import com.liferay.portal.service.LayoutLocalServiceUtil;
import com.liferay.portal.theme.ThemeDisplay;
import com.liferay.util.bridges.mvc.MVCPortlet;
/**
* Portlet implementation class GatlingPortlet.
*/
public class GatlingPortlet extends MVCPortlet {
/**
* attribute mustacheFoctory.
*/
private MustacheFactory mf = new DefaultMustacheFactory();
/**
* logging.
*/
private static final Log LOG = LogFactoryUtil.getLog(GatlingPortlet.class);
/**
* pages of portlet.
*/
protected String jspListSimulation, jspEditSimulation, jspEditScenario, jspFormFirstScenario, jspHelp;
/**
* get all name page
* @throws PortletException
*/
@Override
public void init() throws PortletException {
jspListSimulation = getInitParameter("list-simulation-jsp");
jspEditSimulation = getInitParameter("edit-simulation-jsp");
jspEditScenario = getInitParameter("edit-scenario-jsp");
jspFormFirstScenario = getInitParameter("form-first-scenario-jsp");
jspHelp = getInitParameter("help-jsp");
super.init();
}
/**
* Adds a new Simulation to the database.
*
* @param request
* @param response
* @throws Exception
*/
public void addSimulation(final ActionRequest request, final ActionResponse response) throws Exception {
Simulation simulation = SimulationLocalServiceUtil.addSimulationFromRequest(request);
if (simulation != null) {
response.setRenderParameter("simulationId", Long.toString(simulation.getSimulation_id()));
// If new simulation the redirect to add First scenario page else edit simulation page
LOG.info("Simulation added");
response.setRenderParameter("page", jspEditSimulation);
} else {
LOG.debug("Simulation fails to add");
response.setRenderParameter("page", jspListSimulation);
}
}
/**
* edit simulation method
*
* @param request
* @param response
* @throws Exception
*/
public void editSimulation(ActionRequest request, ActionResponse response) throws Exception {
long simulationId = ParamUtil.getLong(request, "simulationId");
LOG.info("edit Simulation with id : " + simulationId);
Simulation simulation = SimulationLocalServiceUtil.getSimulation(simulationId);
simulation.setName(ParamUtil.getString(request, "simulationName"));
String variable = GatlingUtil.createVariableName("Simulation", GatlingUtil.createVariableName("simulation", simulation.getName()));
simulation.setVariableName(variable);
SimulationLocalServiceUtil.updateSimulation(simulation);
response.setRenderParameter("simulationId", Long.toString(simulationId));
response.setRenderParameter("page", jspEditSimulation);
}
/**
* remove simulation method
*
* @param request
* @param response
* @throws Exception
*/
public void removeSimulation(ActionRequest request, ActionResponse response) throws Exception {
long simulationId = ParamUtil.getLong(request, "simulationId");
if (LOG.isDebugEnabled()) {
LOG.debug("remove Simulation with id : " + simulationId);
}
SimulationLocalServiceUtil.removeSimulationCascade(simulationId);
response.setRenderParameter("page", jspListSimulation);
}
/**
* Add a new Scenario to the database.
* @param request
* @param response
* @throws Exception
*/
public void addScenario(final ActionRequest request, final ActionResponse response) throws Exception {
Scenario scenario = ScenarioLocalServiceUtil.addScenarioFromRequest(request);
String first = ParamUtil.getString(request, "first");
if (scenario != null) {
// redirect to editScenario
response.setRenderParameter("scenarioId", Long.toString(scenario.getScenario_id()));
response.setRenderParameter("page", jspEditScenario);
} else {
response.setRenderParameter("simulationId", Long.toString(ParamUtil.getLong(request, "simulationId")));
response.setRenderParameter("page", !first.equals("") ? jspFormFirstScenario : jspEditSimulation);
response.setRenderParameter("page", jspEditSimulation);
}
}
/**
* edit scenario.
*
* @param request
* @param response
* @throws SystemException
* @throws PortalException
*/
public void editScenario(final ActionRequest request, final ActionResponse response) throws SystemException, PortalException {
LOG.debug("edit scenario controler");
Scenario scenario = ScenarioLocalServiceUtil.editScenarioFromRequest(request);
response.setRenderParameter("page", scenario != null ? jspEditSimulation : jspListSimulation);
if (scenario != null) {
response.setRenderParameter("simulationId", Long.toString(scenario.getSimulation_id()));
}
}
/**
* Remove scenario from database.
* @param request
* @param response
* @throws PortalException
* @throws SystemException
*/
public void removeScenario(final ActionRequest request, final ActionResponse response)
throws PortalException, SystemException {
long scenarioId = ParamUtil.getLong(request, "scenarioId");
long simulationId = ParamUtil.getLong(request, "simulationId");
if (LOG.isDebugEnabled()){
LOG.debug("remove Scenario with id : " + scenarioId);
}
// cascade delete
ScenarioLocalServiceUtil.removeByIdCascade(scenarioId);
response.setRenderParameter("simulationId", Long.toString(simulationId));
response.setRenderParameter("page", jspEditSimulation);
}
/**
* Remove request from database.
* @param request
* @param response
* @throws PortalException
* @throws SystemException
*/
public void removeRequest(final ActionRequest request, final ActionResponse response) throws PortalException, SystemException {
long requestId = Long.parseLong(request.getParameter("requestId"));
RequestLocalServiceUtil.deleteRequest(requestId);
LOG.debug("request deleted succefully ");
}
/**
* get the scenario state, if completed or not yet.
* @param scenario
* @return
*/
private int scenarioState(Scenario scenario) {
try {
int count = RequestLocalServiceUtil.countByScenarioIdAndUsed(scenario.getScenario_id());
if (count != 0 && scenario.getDuration() != 0 && scenario.getUsers_per_seconds() != 0) {
// completed scenario = case if all minimal information are
// completed
return 2;
} else if (count != 0 && (scenario.getDuration() == 0 || scenario.getUsers_per_seconds() == 0)) {
// incomplete scenario = case if one or more information detail of
// scenario are not completed but there is request selected
return 1;
}
} catch (SystemException e) {
if (LOG.isErrorEnabled()){
LOG.error("enable to determine Scenario state " + e.getMessage());
}
}
// case if not request selected to that scenario = empty scenario
return 0;
}
/**
* get the simulation state, if all scenario are completed or not yet.
* @param simulation
* @return
*/
public int simulationState(final Simulation simulation) {
try {
List<Scenario> scenariosList = ScenarioLocalServiceUtil.findBySimulationId(simulation.getSimulation_id());
int checkNumberCompleted = 0;
for (Scenario scenario : scenariosList) {
if (scenarioState(scenario) == 2) {
checkNumberCompleted++;
}
}
if ((checkNumberCompleted == 0) || (scenariosList.size() == 0)) {
//if no one scenario is completed = simulation empty
return 0;
} else if (checkNumberCompleted == scenariosList.size()) {
//if all scenario completed = simulation complited
return 2;
} else {
//other case = simulation incompleted
return 1;
}
} catch (SystemException e) {
if (LOG.isErrorEnabled()) {
LOG.error("enable to determine Simulation state " + e.getMessage());
}
return 0;
}
}
/**
* View method : redirect to requested page and send necessary parameters.
*/
@Override
public void doView(final RenderRequest renderRequest, final RenderResponse renderResponse) throws IOException, PortletException {
/* get the path for next jsp or by default jspListSimulation */
String page = ParamUtil.get(renderRequest, "page", jspListSimulation);
//view.jsp => list of the simulations
if (page.equals(jspListSimulation)) {
LOG.debug("DoView : List Simulation");
List<Simulation> simulationList = new ArrayList<Simulation>();
Map<Simulation, Integer[]> simulationMap = new HashMap<Simulation, Integer[]>();
try {
simulationList = SimulationLocalServiceUtil.getSimulations(0, SimulationLocalServiceUtil.getSimulationsCount());
for (Simulation simulation : simulationList) {
Integer[] simulationInfos = new Integer[2];
simulationInfos[0] = ScenarioLocalServiceUtil.countBySimulationId(simulation.getSimulation_id());
simulationInfos[1] = simulationState(simulation);
simulationMap.put(simulation, simulationInfos);
}
} catch (SystemException e) {
throw new RuntimeException("error with getSimulation with localServiceUtil " + e.getMessage());
}
String JSListName = GatlingUtil.createJSListOfSimulationName(simulationList);
final javax.portlet.PortletPreferences prefs = renderRequest.getPreferences();
String gatlingVersionString;
gatlingVersionString = prefs.getValue("gatlingVersion", null);
renderRequest.setAttribute("gatlingVersion", gatlingVersionString);
renderRequest.setAttribute("listOfSimulationName", JSListName);
renderRequest.setAttribute("listSimulation", simulationList);
renderRequest.setAttribute("MapSimulation", simulationMap);
} else if (page.equals(jspEditSimulation) || page.equals(jspFormFirstScenario)) {
/*
* Edit simulation, get and send scenarios list to jsp page
*/
LOG.debug("DoView : Edit Simulation");
Long id = (Long) ParamUtil.getLong(renderRequest, "simulationId");
if(id==null)
throw new NullPointerException("simulation id is null");
Simulation simulation;
try {
simulation = SimulationLocalServiceUtil.getSimulation(id);
int scenarioListSize = ScenarioLocalServiceUtil.countBySimulationId(simulation.getSimulation_id());
renderRequest.setAttribute("simulation", simulation);
// If empty go to form first scenario
if(scenarioListSize == 0)
throw new EmptySimulation();
// List of Scenario
List<Scenario> scenarioList = ScenarioLocalServiceUtil.findBySimulationId(simulation.getSimulation_id());
// map <scenario, scenarioInfo>
Map<Scenario, Number[]> scenariosMap = new HashMap<Scenario, Number[]>();
for (Scenario scenario : scenarioList) {
Number[] info = new Number[3];
info[2] = scenarioState(scenario);
info[0] = RequestLocalServiceUtil.countByScenarioIdAndUsed(scenario.getScenario_id());
info[1] = RequestLocalServiceUtil.countByScenarioId(scenario.getScenario_id());
scenariosMap.put(scenario, info);
}
String JSListName = GatlingUtil.createJSListOfScenarioName(scenarioList);
renderRequest.setAttribute("listOfScenarioName", JSListName);
/*
* get list of simulation (for edit name)
*/
List<Simulation> listSimulations = SimulationLocalServiceUtil.getSimulations(0,
SimulationLocalServiceUtil.getSimulationsCount());
String JSListSimName = GatlingUtil.createJSListOfSimulationName(listSimulations);
renderRequest.setAttribute("listOfSimulationName", JSListSimName);
renderRequest.setAttribute("listScenario", scenarioList);
renderRequest.setAttribute("MapScenario", scenariosMap);
} catch (SystemException | PortalException e) {
throw new RuntimeException("error with get scenario list with localServiceUtil " + e.getMessage());
} catch (EmptySimulation e) {
LOG.info("Empty simulation ... redirect");
page = jspFormFirstScenario;
}
// List of Sites
List<Group> listGroups = GatlingUtil.getListOfSites();
renderRequest.setAttribute("listGroup", listGroups);
}else if (page.equals(jspEditScenario)) {
/*
* Edit scenario -> request list send to jsp page
*/
LOG.debug("DoView : Edit Scenario");
if (ParamUtil.getLong(renderRequest, "scenarioId") == 0) {
throw new NullPointerException("scenario id is null");
}
try {
// get scenario
Scenario scenario = ScenarioLocalServiceUtil.getScenario(ParamUtil.getLong(renderRequest, "scenarioId"));
Simulation simulation = SimulationLocalServiceUtil.getSimulation(scenario.getSimulation_id());
//update friendlyUrl of site if changed
String oldFriendlyURL = scenario.getUrl_site();
final ThemeDisplay themeDisplay = (ThemeDisplay)renderRequest.getAttribute(WebKeys.THEME_DISPLAY);
String currentFriendlyURL = GroupLocalServiceUtil.fetchGroup(scenario.getGroup_id()).getIconURL(themeDisplay);
StringBuilder sb = new StringBuilder(currentFriendlyURL.split("/")[0]);
sb.append("//").append(currentFriendlyURL.split("/")[2]).append("/web").append(GroupLocalServiceUtil.fetchGroup(scenario.getGroup_id()).getFriendlyURL());
currentFriendlyURL = sb.toString();
if (! oldFriendlyURL.equals(currentFriendlyURL)) {
//update site url
scenario.setUrl_site(currentFriendlyURL);
ScenarioLocalServiceUtil.updateScenario(scenario);
}
//get public layout list
long groupId = scenario.getGroup_id();
List<Layout> listPublicLayouts = LayoutLocalServiceUtil.getLayouts(groupId, false, 0);
//get private layout list
List<Layout> listPrivateLayouts = LayoutLocalServiceUtil.getLayouts(groupId, true, 0);
//get site name
String siteName = GroupLocalServiceUtil.getGroup(groupId).getName();
//create DisplayLayoutList with actuel layout of the site and old layout added from requests
List<DisplayItem> displayLayoutList = new ArrayList<DisplayItem>();
DisplayItemUtil.addLayoutToDisplayItemList(displayLayoutList, listPublicLayouts);
DisplayItemUtil.addLayoutToDisplayItemList(displayLayoutList, listPrivateLayouts );
//get list of request to add the old page to DisplayLayout
List<Request> listRequests = RequestLocalServiceUtil.findByScenarioId(ParamUtil.get(renderRequest, "scenarioId", 0));
//Merge Layout and Request in DisplayLayout List
displayLayoutList = DisplayItemUtil.addRequestToDisplayItemList(displayLayoutList, listRequests);
// Get list of used names
List<Scenario> scenariolist = ScenarioLocalServiceUtil.getScenarios(0, ScenarioLocalServiceUtil.getScenariosCount());
String JSListName = GatlingUtil.createJSListOfScenarioName(scenariolist);
//add private and public url of site
String publicURL = scenario.getUrl_site();
/*
* create header list
*/
String[] headerList = new String[] {simulation.getName(), scenario.getName(), siteName};
renderRequest.setAttribute("headerList", headerList);
//add request parameters
renderRequest.setAttribute("scenario", scenario);
renderRequest.setAttribute("listPages", displayLayoutList);
renderRequest.setAttribute("siteName", siteName);
renderRequest.setAttribute("publicURL", publicURL);
renderRequest.setAttribute("listOfScenarioName", JSListName);
} catch (SystemException | PortalException e) {
throw new RuntimeException("connot get layout list: " + e.getMessage());
}
}
/* redirect to jsp page */
include(page, renderRequest, renderResponse);
}
@Override
public void serveResource(final ResourceRequest request, final ResourceResponse response) {
/*
* Get template from version
*/
int gatlingVersion = ParamUtil.getInteger(request, "gatlingVersion");
//add user preference
final PortletPreferences prefs = (PortletPreferences) request.getPreferences();
try {
((javax.portlet.PortletPreferences) prefs).setValue("gatlingVersion", Integer.toString(gatlingVersion));
((javax.portlet.PortletPreferences) prefs).store();
} catch (ReadOnlyException | ValidatorException | IOException e) {
throw new RuntimeException("connot add user preferences for gatling version " + e.getMessage());
}
//scripting Gatling
String template;
switch (gatlingVersion) {
case 1:
template = "resources/templateGatling1.5.mustache";
break;
case 2:
template = "resources/templateGatling2.0.M3a.mustache";
break;
case 3:
template = "resources/templateGatling2.0.RC2.mustache";
break;
default:
template = "resources/templateGatling2.0.RC2.mustache";
break;
}
/*
* Get simulations ids
*/
long[] simulationsIds = ParamUtil.getLongValues(request, "export");
Simulation simulation;
Date date = new Date();
Mustache mustache = mf.compile(template);
if (simulationsIds.length > 1) {
response.setContentType("application/zip");
response.addProperty("Content-Disposition", "attachment; filename = GatlingSimulations" + date.getTime() + ".zip");
try {
ZipOutputStream zipOutputStream = new ZipOutputStream(response.getPortletOutputStream());
for (long id : simulationsIds) {
if (id > 0) {
simulation = SimulationLocalServiceUtil.getSimulation(id);
zipOutputStream.putNextEntry(new ZipEntry("Simulation" + simulation.getName() + date.getTime() + ".scala"));
mustache.execute(new PrintWriter(zipOutputStream), new ScriptGeneratorGatling(id)).flush();
zipOutputStream.closeEntry();
}
}
zipOutputStream.close();
} catch (Exception e) {
throw new RuntimeException("cannot export zip for scenario(s) " + e.getMessage());
}
} else if (simulationsIds.length == 1 && simulationsIds[0] > 0) {
//create and export only one file with scenario script for this simulation id
response.setContentType("application/x-wais-source");
try {
simulation = SimulationLocalServiceUtil.getSimulation(simulationsIds[0]);
response.addProperty("Content-Disposition", "attachment; filename=Simulation" + simulation.getName() + date.getTime() + ".scala");
OutputStream out = response.getPortletOutputStream();
mustache.execute(new PrintWriter(out), new ScriptGeneratorGatling(simulationsIds[0])).flush();
out.close();
} catch (Exception e) {
throw new RuntimeException("cannot export script file " + e.getMessage());
}
} else {
//if no one valide simulation id received then error
throw new NullPointerException("nothing to export");
}
response.addProperty(HttpHeaders.CACHE_CONTROL, "max-age=3600, must-revalidate");
}
}
|
package org.example;
import javax.ejb.ActivationConfigProperty;
import javax.ejb.MessageDriven;
import io.vertx.core.eventbus.Message;
import io.vertx.resourceadapter.inflow.VertxListener;
import org.jboss.ejb3.annotation.ResourceAdapter;
@MessageDriven(name = "VertxMonitor",
messageListenerInterface = VertxListener.class,
activationConfig = {
@ActivationConfigProperty(propertyName = "address", propertyValue = "tacos"),
@ActivationConfigProperty(propertyName = "clusterHost", propertyValue = "localhost"),
@ActivationConfigProperty(propertyName = "clusterPort", propertyValue = "0"),
})
@ResourceAdapter("vertx-ra")
public class MyListener implements VertxListener{
@Override
public <String> void onMessage(Message<String> message) {
System.out.println("MESSAGE: "+message.body());
}
}
|
package gov.nih.nci.cacore.workbench.common;
/**
* Constants used in the caCORE Workbench Portal
*
* @author <A HREF="MAILTO:dumitrud@mail.nih.gov">Daniel Dumitru </A>
* @author <A HREF="MAILTO:patelsat@mail.nih.gov">Satish Patel </A>
*/
public abstract class CacoreWorkbenchConstants {
// Workbench specific constants
public static final String WORKBENCH_VERSION_PROPERTY = "cacore.workbench.version";
public static final String WORKBENCH_ENGINE_PROPERTIES = "cacore.workbench.engine.properties";
public static final String WORKBENCH_HELP_URL = "cacore.workbench.help.url";
public static final String WORKBENCH_TOOLS_SITE_URL = "cacore.workbench.tools.site.url";
public static final String SDK_GUIDE_URL = "cacore.sdk.programmers.guide";
public static final String WORKBENCH_GUIDE_URL = "cacore.workbench.user.guide";
//Create Grid Service Workflow
public static final String LAUNCH_INTRODUCE_URL = "cacore.workbench.launch.introduce.url";
//Create UML Model Workflow
public static final String LAUNCH_ARGO_UML_WEB_START_URL = "cacore.workbench.launch.argo.uml.web.start.url";
public static final String DOWNLOAD_ENTERPRISE_ARCHITECT_URL = "cacore.workbench.download.ea.url";
//Semantic Integration Workflow
public static final String LAUNCH_SIW_URL = "cacore.workbench.launch.siw.url";
public static final String LAUNCH_CDE_BROWSER_URL = "cacore.workbench.launch.cde.browser.url";
public static final String LAUNCH_UML_MODEL_BROWSER_URL = "cacore.workbench.launch.uml.model.browser.url";
public static final String LAUNCH_CDE_CURATION_TOOL_URL = "cacore.workbench.launch.cde.curation.tool.url";
//Model Mapping Workflow
public static final String LAUNCH_CAADAPTER_URL = "cacore.workbench.launch.caadapter.url";
private CacoreWorkbenchConstants() {
// prevents instantiation
}
}
|
package com.azure.messaging.eventhubs.implementation;
import com.azure.core.amqp.AmqpEndpointState;
import com.azure.core.amqp.AmqpRetryPolicy;
import com.azure.core.amqp.implementation.AmqpReceiveLink;
import com.azure.core.util.logging.ClientLogger;
import org.apache.qpid.proton.message.Message;
import org.reactivestreams.Subscription;
import reactor.core.CoreSubscriber;
import reactor.core.Disposable;
import reactor.core.Disposables;
import reactor.core.Exceptions;
import reactor.core.publisher.FluxProcessor;
import reactor.core.publisher.Mono;
import reactor.core.publisher.Operators;
import java.time.Duration;
import java.util.Deque;
import java.util.Objects;
import java.util.concurrent.ConcurrentLinkedDeque;
import java.util.concurrent.atomic.AtomicBoolean;
import java.util.concurrent.atomic.AtomicInteger;
import java.util.concurrent.atomic.AtomicLongFieldUpdater;
import java.util.concurrent.atomic.AtomicReference;
import java.util.concurrent.atomic.AtomicReferenceFieldUpdater;
/**
* Processes AMQP receive links into a stream of AMQP messages.
*/
public class AmqpReceiveLinkProcessor extends FluxProcessor<AmqpReceiveLink, Message> implements Subscription {
private final ClientLogger logger = new ClientLogger(AmqpReceiveLinkProcessor.class);
private final Object lock = new Object();
private final AtomicBoolean isTerminated = new AtomicBoolean();
private final AtomicInteger retryAttempts = new AtomicInteger();
private final Deque<Message> messageQueue = new ConcurrentLinkedDeque<>();
private final AtomicBoolean hasFirstLink = new AtomicBoolean();
private final AtomicBoolean linkCreditsAdded = new AtomicBoolean();
private final AtomicReference<CoreSubscriber<? super Message>> downstream = new AtomicReference<>();
private final AtomicInteger wip = new AtomicInteger();
private final int prefetch;
private final AmqpRetryPolicy retryPolicy;
private final Disposable parentConnection;
private volatile Throwable lastError;
private volatile boolean isCancelled;
private volatile AmqpReceiveLink currentLink;
private volatile Disposable currentLinkSubscriptions;
private volatile Disposable retrySubscription;
// Opting to use AtomicReferenceFieldUpdater because Project Reactor provides utility methods that calculates
// backpressure requests, sets the upstream correctly, and reports its state.
private volatile Subscription upstream;
private static final AtomicReferenceFieldUpdater<AmqpReceiveLinkProcessor, Subscription> UPSTREAM =
AtomicReferenceFieldUpdater.newUpdater(AmqpReceiveLinkProcessor.class, Subscription.class,
"upstream");
private volatile long requested;
private static final AtomicLongFieldUpdater<AmqpReceiveLinkProcessor> REQUESTED =
AtomicLongFieldUpdater.newUpdater(AmqpReceiveLinkProcessor.class, "requested");
public AmqpReceiveLinkProcessor(int prefetch, AmqpRetryPolicy retryPolicy, Disposable parentConnection) {
this.retryPolicy = Objects.requireNonNull(retryPolicy, "'retryPolicy' cannot be null.");
this.parentConnection = Objects.requireNonNull(parentConnection, "'parentConnection' cannot be null.");
if (prefetch < 0) {
throw logger.logExceptionAsError(new IllegalArgumentException("'prefetch' cannot be less than 0."));
}
this.prefetch = prefetch;
}
/**
* Gets the error associated with this processor.
*
* @return Error associated with this processor. {@code null} if there is no error.
*/
@Override
public Throwable getError() {
return lastError;
}
/**
* Gets whether or not the processor is terminated.
*
* @return {@code true} if the processor has terminated; false otherwise.
*/
@Override
public boolean isTerminated() {
return isTerminated.get() || isCancelled;
}
/**
* When a subscription is obtained from upstream publisher.
*
* @param subscription Subscription to upstream publisher.
*/
@Override
public void onSubscribe(Subscription subscription) {
Objects.requireNonNull(subscription, "'subscription' cannot be null");
if (!Operators.setOnce(UPSTREAM, this, subscription)) {
throw logger.logExceptionAsError(new IllegalStateException("Cannot set upstream twice."));
}
requestUpstream();
}
@Override
public int getPrefetch() {
return prefetch;
}
/**
* When the next AMQP link is fetched.
*
* @param next The next AMQP receive link.
*/
@Override
public void onNext(AmqpReceiveLink next) {
Objects.requireNonNull(next, "'next' cannot be null.");
if (isTerminated()) {
logger.warning("linkName[{}] entityPath[{}]. Got another link when we have already terminated processor.",
next.getLinkName(), next.getEntityPath());
Operators.onNextDropped(next, currentContext());
return;
}
final String linkName = next.getLinkName();
final String entityPath = next.getEntityPath();
logger.info("linkName[{}] entityPath[{}]. Setting next AMQP receive link.", linkName, entityPath);
final AmqpReceiveLink oldChannel;
final Disposable oldSubscription;
synchronized (lock) {
oldChannel = currentLink;
oldSubscription = currentLinkSubscriptions;
currentLink = next;
// The first time, add the prefetch to the link as credits.
if (!hasFirstLink.getAndSet(true)) {
linkCreditsAdded.set(true);
next.addCredits(prefetch);
}
next.setEmptyCreditListener(() -> getCreditsToAdd());
currentLinkSubscriptions = Disposables.composite(
next.getEndpointStates().subscribe(
state -> {
// Connection was successfully opened, we can reset the retry interval.
if (state == AmqpEndpointState.ACTIVE) {
retryAttempts.set(0);
}
},
error -> {
currentLink = null;
logger.warning("linkName[{}] entityPath[{}]. Error occurred in link.", linkName, entityPath);
onError(error);
},
() -> {
if (parentConnection.isDisposed() || isTerminated()
|| upstream == Operators.cancelledSubscription()) {
logger.info("Terminal state reached. Disposing of link processor.");
dispose();
} else {
logger.info("Receive link endpoint states are closed. Requesting another.");
final AmqpReceiveLink existing = currentLink;
currentLink = null;
if (existing != null) {
existing.dispose();
}
requestUpstream();
}
}),
next.receive().subscribe(message -> {
messageQueue.add(message);
drain();
}));
}
if (oldChannel != null) {
oldChannel.dispose();
}
if (oldSubscription != null) {
oldSubscription.dispose();
}
}
@Override
public void subscribe(CoreSubscriber<? super Message> actual) {
Objects.requireNonNull(actual, "'actual' cannot be null.");
final boolean terminateSubscriber = isTerminated()
|| (currentLink == null && upstream == Operators.cancelledSubscription());
if (isTerminated()) {
final AmqpReceiveLink link = currentLink;
final String linkName = link != null ? link.getLinkName() : "n/a";
final String entityPath = link != null ? link.getEntityPath() : "n/a";
logger.info("linkName[{}] entityPath[{}]. AmqpReceiveLink is already terminated.", linkName, entityPath);
} else if (currentLink == null && upstream == Operators.cancelledSubscription()) {
logger.info("There is no current link and upstream is terminated.");
}
if (terminateSubscriber) {
actual.onSubscribe(Operators.emptySubscription());
if (hasError()) {
actual.onError(lastError);
} else {
actual.onComplete();
}
return;
}
if (downstream.compareAndSet(null, actual)) {
actual.onSubscribe(this);
drain();
} else {
Operators.error(actual, logger.logExceptionAsError(new IllegalStateException(
"There is already one downstream subscriber.'")));
}
}
/**
* When an error occurs from the upstream publisher. If the {@code throwable} is a transient failure, another AMQP
* element is requested if the {@link AmqpRetryPolicy} allows. Otherwise, the processor closes.
*
* @param throwable Error that occurred in upstream publisher.
*/
@Override
public void onError(Throwable throwable) {
Objects.requireNonNull(throwable, "'throwable' is required.");
if (isTerminated() || isCancelled) {
logger.info("AmqpReceiveLinkProcessor is terminated. Cannot process another error.", throwable);
Operators.onErrorDropped(throwable, currentContext());
return;
}
final int attempt = retryAttempts.incrementAndGet();
final Duration retryInterval = retryPolicy.calculateRetryDelay(throwable, attempt);
final AmqpReceiveLink link = currentLink;
final String linkName = link != null ? link.getLinkName() : "n/a";
final String entityPath = link != null ? link.getEntityPath() : "n/a";
if (retryInterval != null && !parentConnection.isDisposed() && upstream != Operators.cancelledSubscription()) {
logger.warning("linkName[{}] entityPath[{}]. Transient error occurred. Attempt: {}. Retrying after {} ms.",
linkName, entityPath, attempt, retryInterval.toMillis(), throwable);
retrySubscription = Mono.delay(retryInterval).subscribe(i -> requestUpstream());
return;
}
if (parentConnection.isDisposed()) {
logger.info("Parent connection is disposed. Not reopening on error.");
}
logger.warning("linkName[{}] entityPath[{}]. Non-retryable error occurred in AMQP receive link.",
linkName, entityPath, throwable);
lastError = throwable;
isTerminated.set(true);
final CoreSubscriber<? super Message> subscriber = downstream.get();
if (subscriber != null) {
subscriber.onError(throwable);
}
onDispose();
}
/**
* When the upstream publisher has no more items to emit.
*/
@Override
public void onComplete() {
this.upstream = Operators.cancelledSubscription();
}
@Override
public void dispose() {
if (isTerminated.getAndSet(true)) {
return;
}
drain();
onDispose();
}
/**
* When downstream subscriber makes a back-pressure request.
*/
@Override
public void request(long request) {
if (!Operators.validate(request)) {
logger.warning("Invalid request: {}", request);
return;
}
Operators.addCap(REQUESTED, this, request);
final AmqpReceiveLink link = currentLink;
if (link != null && !linkCreditsAdded.getAndSet(true)) {
int credits = getCreditsToAdd();
logger.verbose("Link credits not yet added. Adding: {}", credits);
link.addCredits(credits);
}
drain();
}
/**
* When downstream subscriber cancels their subscription.
*/
@Override
public void cancel() {
if (isCancelled) {
return;
}
isCancelled = true;
drain();
}
/**
* Requests another receive link from upstream.
*/
private void requestUpstream() {
if (isTerminated()) {
logger.info("Processor is terminated. Not requesting another link.");
return;
} else if (upstream == null) {
logger.info("There is no upstream. Not requesting another link.");
return;
} else if (upstream == Operators.cancelledSubscription()) {
logger.info("Upstream is cancelled or complete. Not requesting another link.");
return;
}
synchronized (lock) {
if (currentLink != null) {
logger.info("Current link exists. Not requesting another link.");
return;
}
}
logger.info("Requesting a new AmqpReceiveLink from upstream.");
upstream.request(1L);
}
private void onDispose() {
if (retrySubscription != null && !retrySubscription.isDisposed()) {
retrySubscription.dispose();
}
if (currentLink != null) {
currentLink.dispose();
}
currentLink = null;
if (currentLinkSubscriptions != null) {
currentLinkSubscriptions.dispose();
}
Operators.onDiscardQueueWithClear(messageQueue, currentContext(), null);
}
private void drain() {
// If someone is already in this loop, then we are already clearing the queue.
if (!wip.compareAndSet(0, 1)) {
return;
}
try {
drainQueue();
} finally {
if (wip.decrementAndGet() != 0) {
logger.warning("There is another worker in drainLoop. But there should only be 1 worker.");
}
}
}
private void drainQueue() {
final CoreSubscriber<? super Message> subscriber = downstream.get();
if (subscriber == null || checkAndSetTerminated()) {
return;
}
long numberRequested = requested;
boolean isEmpty = messageQueue.isEmpty();
while (numberRequested != 0L && !isEmpty) {
if (checkAndSetTerminated()) {
break;
}
long numberEmitted = 0L;
while (numberRequested != numberEmitted) {
if (isEmpty && checkAndSetTerminated()) {
break;
}
Message message = messageQueue.poll();
if (message == null) {
break;
}
if (isCancelled) {
Operators.onDiscard(message, subscriber.currentContext());
Operators.onDiscardQueueWithClear(messageQueue, subscriber.currentContext(), null);
return;
}
try {
subscriber.onNext(message);
} catch (Exception e) {
logger.error("Exception occurred while handling downstream onNext operation.", e);
throw logger.logExceptionAsError(Exceptions.propagate(
Operators.onOperatorError(upstream, e, message, subscriber.currentContext())));
}
numberEmitted++;
isEmpty = messageQueue.isEmpty();
}
if (requested != Long.MAX_VALUE) {
numberRequested = REQUESTED.addAndGet(this, -numberEmitted);
}
}
}
private boolean checkAndSetTerminated() {
if (!isTerminated()) {
return false;
}
final CoreSubscriber<? super Message> subscriber = downstream.get();
final Throwable error = lastError;
if (error != null) {
subscriber.onError(error);
} else {
subscriber.onComplete();
}
if (currentLink != null) {
currentLink.dispose();
}
messageQueue.clear();
return true;
}
private int getCreditsToAdd() {
final CoreSubscriber<? super Message> subscriber = downstream.get();
final long r = requested;
if (subscriber == null || r == 0) {
logger.verbose("Not adding credits. No downstream subscribers or items requested.");
linkCreditsAdded.set(false);
return 0;
}
linkCreditsAdded.set(true);
// If there is no back pressure, always add 1. Otherwise, add whatever is requested.
return r == Long.MAX_VALUE ? 1 : Long.valueOf(r).intValue();
}
}
|
import java.io.*;
import java.util.Arrays;
import java.util.Random;
/**
* This class loads the file corpus.txt, reads the file line by line up to the nr of lines provided in args[0].
* Each line is processed according to a set of rules, and the resuls are written to ppCorpus.txt, line by line.
* After next it reads the following lines args[0]+1 to args[0]+args[1] and preprocesses them for testing,
* saving the results in testSentences.txt
*
*
* @author Jasmin Suljkic
*/
public class CorpusPreprocessUK {
/**
* No arguments are taken in account.
* Statically configured file corpus.txt is read and ppCorpus.txt as well as testSentences.txt is created and written to.
* @param args -> X Y, (X: lines to for learning, Y: lines for testing)
*/
public static void main(String[] args) {
//args[0] -> Amount of lines to preprocess for learning
//args[1] -> Amount of lines to preprocess for testing
String corpusStringPath = "corpus.txt";
String testSentenceStringPath = "testSentences";
String testSentencesCorrectionStringPath = "testSentencesCorrection";
// TODO Auto-generated method stub
BufferedReader br;
BufferedWriter bufferedWriterCorpus;
BufferedWriter bufferedWriterTest;
BufferedWriter bufferedWriterTestCorrection;
StringBuffer sb = new StringBuffer();
StringBuffer sbt = new StringBuffer();
int nrLines=0;
int toLearn = Integer.MAX_VALUE>>3;
int toTest = Integer.MAX_VALUE>>3;
if(args.length>=2) {
toLearn = Integer.parseInt(args[0]);
toTest = Integer.parseInt(args[1]);
}
try {
//br = new BufferedReader(new FileReader("corpus.txt"));
//br = new BufferedReader(new InputStreamReader(new FileInputStream("corpus.txt"), "UTF-8"));
br = new BufferedReader(new InputStreamReader(new FileInputStream(corpusStringPath)));
//bufferedWriterCorpus = new BufferedWriter(new FileWriter("ppCorpus.txt"));
bufferedWriterCorpus = new BufferedWriter(new OutputStreamWriter(new FileOutputStream("ppCorpus.txt"), "UTF-16BE"));
//bufferedWriterTest = new BufferedWriter(new FileWriter("testSentences.txt"));
//bufferedWriterTestCorrection = new BufferedWriter(new FileWriter("testScentencesCorrect.txt"));
String line;
char[] lc;
//Go trough the corpus and count the amount of lines present
while ((line=br.readLine()) != null) {
nrLines++;
}
br.close();
if((toLearn+toTest)>nrLines){
System.err.println("Request invalid: Number of lines requested > nr of lines available in corpus.\nThere are "+nrLines+" number of lines.");
System.err.println("toLearn = "+toLearn);
System.err.println("toTest = "+toTest);
return;
}
br=new BufferedReader(new FileReader("corpus.txt"));
//Read a line from file (as long as there are lines in the file)
//Process the line
//Write the result to output file.
int current = 0;
boolean testing = false;
OutputStreamWriter writeToTest[] = new OutputStreamWriter[1];
OutputStreamWriter writeToTestCorrection[] = new OutputStreamWriter[1];
for(int i = 0; i < writeToTest.length; i++) {
writeToTest[i] = new OutputStreamWriter(new FileOutputStream(testSentenceStringPath+i+".txt"), "UTF-16BE");
writeToTestCorrection[i] = new OutputStreamWriter(new FileOutputStream(testSentencesCorrectionStringPath+i+".txt"), "UTF-16BE");
//writeToTest[i] = new OutputStreamWriter(new FileOutputStream("testSentences"+i+".txt"));
//writeToTestCorrection[i] = new OutputStreamWriter(new FileOutputStream("testSentencesCorrection"+i+".txt"));
}
int corpusSentences = 0;
int trainingSentences = 0;
int index = 0;
int length = 0;
String buffer[] = new String[10];
while ((line=br.readLine()) != null) {
line = line.toLowerCase().replaceAll("[-,]", "").replaceAll("( )*[.!?]+( )*", " .PERIOD ").replaceAll("( )+", " ").replaceAll("(.PERIOD )+", ".PERIOD ").trim();
//System.err.println(line);
int really = line.split(" ").length;
int previous = length;
if(really>1) {
length+=really;
System.err.println(length);
}
if(length<=10) {
buffer[index]=line;
System.err.println(line);
index++;
} else if(length>=3&&previous<=10) {
if(toLearn>corpusSentences) {
bufferedWriterCorpus.write("START ");
for(int i = 0; i < index; i++) {
//System.err.println(buffer[i]);
bufferedWriterCorpus.write(buffer[i]);
System.err.println(buffer[i]);
}
System.err.println();
bufferedWriterCorpus.append(" ¿EOL");
//bufferedWriterCorpus.newLine();
corpusSentences++;
} else if(trainingSentences<toTest) {
writeToTestCorrection[0].write("START ");
writeToTest[0].write("START ");
for(int i = 0; i < index; i++) {
writeToTestCorrection[0].write(buffer[i]);
writeToTest[0].write(buffer[i].replaceAll("( )*.PERIOD( )*", " "));
}
writeToTestCorrection[0].write(" ¿EOL");
writeToTestCorrection[0].write('\n');
writeToTest[0].write(" ¿EOL");
writeToTest[0].write('\n');
trainingSentences++;
} else {
break;
}
index = 0;
length = 0;
} else {
index = 0;
length = 0;
}
}
br.close();
bufferedWriterCorpus.close();
//bufferedWriterTest.close();
System.err.println("Using encoding: "+writeToTest[0].getEncoding());
System.err.println(corpusSentences+" sentences in corpus.");
System.err.println(trainingSentences+" sentences in training.");
for(int k = 0; k < writeToTest.length; k++) {
writeToTest[k].close();
writeToTestCorrection[k].close();
}
} catch (FileNotFoundException e) {
e.printStackTrace();
} catch (IOException e) {
e.printStackTrace();
}
}
}
|
package fr.imie.cdi13.dav.test;
public class B extends A {
private String a = "test a";
@Override
public AInterface function1(String value) {
// new commentaire
return new B();
}
@Override
public String toString() {
return this.a + ' ' + super.toString();
}
}
|
package ch.idsia.benchmark.tasks;
import ch.idsia.tools.EvaluationInfo;
import ch.idsia.tools.MarioAIOptions;
import java.text.DecimalFormat;
public class GamePlayTask extends BasicTask implements Task
{
private static final DecimalFormat df = new DecimalFormat("
private EvaluationInfo localEvaluationInfo;
public GamePlayTask(MarioAIOptions marioAIOptions)
{
super(marioAIOptions);
localEvaluationInfo = new EvaluationInfo();
localEvaluationInfo.setTaskName("GamePlayTask");
localEvaluationInfo.distancePassedCells = 0;
localEvaluationInfo.distancePassedPhys = 0;
localEvaluationInfo.flowersDevoured = 0;
localEvaluationInfo.killsTotal = 0;
localEvaluationInfo.killsByFire = 0;
localEvaluationInfo.killsByShell = 0;
localEvaluationInfo.killsByStomp = 0;
localEvaluationInfo.marioMode = 0;
localEvaluationInfo.marioStatus = 0;
localEvaluationInfo.mushroomsDevoured = 0;
localEvaluationInfo.coinsGained = 0;
localEvaluationInfo.timeLeft = 0;
localEvaluationInfo.timeSpent = 0;
localEvaluationInfo.hiddenBlocksFound = 0;
localEvaluationInfo.totalNumberOfCoins = 0;
localEvaluationInfo.totalNumberOfCreatures = 0;
localEvaluationInfo.totalNumberOfFlowers = 0;
localEvaluationInfo.totalNumberOfMushrooms = 0;
localEvaluationInfo.totalNumberOfHiddenBlocks = 0;
localEvaluationInfo.collisionsWithCreatures = 0;
localEvaluationInfo.levelLength = 0;
}
private void updateEvaluationInfo(EvaluationInfo evInfo)
{
localEvaluationInfo.distancePassedCells += evInfo.distancePassedCells;
localEvaluationInfo.distancePassedPhys += evInfo.distancePassedPhys;
localEvaluationInfo.flowersDevoured += evInfo.flowersDevoured;
localEvaluationInfo.killsTotal += evInfo.killsTotal;
localEvaluationInfo.killsByFire += evInfo.killsByFire;
localEvaluationInfo.killsByShell += evInfo.killsByShell;
localEvaluationInfo.killsByStomp += evInfo.killsByStomp;
localEvaluationInfo.marioMode += evInfo.marioMode;
localEvaluationInfo.marioStatus += evInfo.marioStatus;
localEvaluationInfo.mushroomsDevoured += evInfo.mushroomsDevoured;
localEvaluationInfo.coinsGained += evInfo.coinsGained;
localEvaluationInfo.timeLeft += evInfo.timeLeft;
localEvaluationInfo.timeSpent += evInfo.timeSpent;
localEvaluationInfo.hiddenBlocksFound += evInfo.hiddenBlocksFound;
localEvaluationInfo.totalNumberOfCoins += evInfo.totalNumberOfCoins;
localEvaluationInfo.totalNumberOfCreatures += evInfo.totalNumberOfCreatures;
localEvaluationInfo.totalNumberOfFlowers += evInfo.totalNumberOfFlowers;
localEvaluationInfo.totalNumberOfMushrooms += evInfo.totalNumberOfMushrooms;
localEvaluationInfo.totalNumberOfHiddenBlocks += evInfo.totalNumberOfHiddenBlocks;
localEvaluationInfo.collisionsWithCreatures += evInfo.collisionsWithCreatures;
localEvaluationInfo.levelLength += evInfo.levelLength;
}
public void doEpisodes(final int amount, final boolean verbose, final int repetitionsOfSingleEpisode)
{
for (int i = 0; i < amount; ++i)
{
options.setLevelLength((200 + (i * 128) + (options.getLevelRandSeed() % (i + 1))) % 512);
options.setLevelType(i % 3);
options.setLevelRandSeed(options.getLevelRandSeed() + i);
options.setLevelDifficulty(i % 10);
options.setGapsCount(i % 3 == 0);
options.setCannonsCount(i % 3 != 0);
options.setCoinsCount(i % 5 != 0);
options.setBlocksCount(i % 4 != 0);
options.setHiddenBlocksCount(i % 6 != 0);
options.setDeadEndsCount(i % 10 == 0);
options.setLevelLadder(i % 10 == 2);
options.setFrozenCreatures(i % 3 == 1);
this.reset();
this.runSingleEpisode(repetitionsOfSingleEpisode);
updateEvaluationInfo(environment.getEvaluationInfo());
if (verbose)
System.out.println(environment.getEvaluationInfoAsString());
}
}
public EvaluationInfo getEvaluationInfo()
{
return localEvaluationInfo;
}
public void printStatistics()
{
System.out.println("\n[MarioAI] ~ Evaluation Results for Task: " + localEvaluationInfo.getTaskName() +
"\n Weighted Fitness : " + df.format(localEvaluationInfo.computeWeightedFitness()) +
"\n Mario Status : " + localEvaluationInfo.marioStatus +
"\n Mario Mode : " + localEvaluationInfo.marioMode +
"\nCollisions with creatures : " + localEvaluationInfo.collisionsWithCreatures +
"\n Passed (Cells, Phys) : " + localEvaluationInfo.distancePassedCells + " of " + localEvaluationInfo.levelLength + ", " + df.format(localEvaluationInfo.distancePassedPhys) + " of " + df.format(localEvaluationInfo.levelLength * 16) + " (" + localEvaluationInfo.distancePassedCells * 100 / localEvaluationInfo.levelLength + "% passed)" +
"\n Time Spent(marioseconds) : " + localEvaluationInfo.timeSpent +
"\n Time Left(marioseconds) : " + localEvaluationInfo.timeLeft +
"\n Coins Gained : " + localEvaluationInfo.coinsGained + " of " + localEvaluationInfo.totalNumberOfCoins + " (" + localEvaluationInfo.coinsGained * 100 / (localEvaluationInfo.totalNumberOfCoins == 0 ? 1 : localEvaluationInfo.totalNumberOfCoins) + "% collected)" +
"\n Hidden Blocks Found : " + localEvaluationInfo.hiddenBlocksFound + " of " + localEvaluationInfo.totalNumberOfHiddenBlocks + " (" + localEvaluationInfo.hiddenBlocksFound * 100 / (localEvaluationInfo.totalNumberOfHiddenBlocks == 0 ? 1 : localEvaluationInfo.totalNumberOfHiddenBlocks) + "% found)" +
"\n Mushrooms Devoured : " + localEvaluationInfo.mushroomsDevoured + " of " + localEvaluationInfo.totalNumberOfMushrooms + " found (" + localEvaluationInfo.mushroomsDevoured * 100 / (localEvaluationInfo.totalNumberOfMushrooms == 0 ? 1 : localEvaluationInfo.totalNumberOfMushrooms) + "% collected)" +
"\n Flowers Devoured : " + localEvaluationInfo.flowersDevoured + " of " + localEvaluationInfo.totalNumberOfFlowers + " found (" + localEvaluationInfo.flowersDevoured * 100 / (localEvaluationInfo.totalNumberOfFlowers == 0 ? 1 : localEvaluationInfo.totalNumberOfFlowers) + "% collected)" +
"\n kills Total : " + localEvaluationInfo.killsTotal + " of " + localEvaluationInfo.totalNumberOfCreatures + " found (" + localEvaluationInfo.killsTotal * 100 / (localEvaluationInfo.totalNumberOfCreatures == 0 ? 1 : localEvaluationInfo.totalNumberOfCreatures) + "%)" +
"\n kills By Fire : " + localEvaluationInfo.killsByFire +
"\n kills By Shell : " + localEvaluationInfo.killsByShell +
"\n kills By Stomp : " + localEvaluationInfo.killsByStomp);
// System.out.println(localEvaluationInfo.toString());
// System.out.println("Mario status sum: " + localEvaluationInfo.marioStatus);
// System.out.println("Mario mode sum: " + localEvaluationInfo.marioMode);
}
}
|
package ch.minipowerpc.emulator.ui;
import java.awt.BorderLayout;
import java.awt.Container;
import java.util.Observable;
import java.util.Observer;
import javax.swing.JFrame;
import javax.swing.UIManager;
import ch.minipowerpc.emulator.Emulator;
public class MainWindow extends JFrame implements Observer {
private static final long serialVersionUID = 6829224920697585349L;
private IEmulatorModel model;
// UI controls
private InstructionMemoryPanel instructionMemoryPanel;
private DataMemoryPanel dataMemoryPanel;
private EmulatorControlPanel emulatorControlPanel;
private ControlUnitPanel controlUnitPanel;
public MainWindow(IEmulatorModel model) {
this.model = model;
((Observable)model).addObserver(this);
initialize();
}
private void initialize() {
setTitle("MiniPowerPC emulator");
setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
try {
// Set System L&F
UIManager.setLookAndFeel(UIManager.getSystemLookAndFeelClassName());
}
catch(Exception ex) {
}
Container content = getContentPane();
// Program memory
/*
programMemory = new ProgramMemory(emulator);
content.add(programMemory, BorderLayout.CENTER);
*/
instructionMemoryPanel = new InstructionMemoryPanel(model);
content.add(instructionMemoryPanel, BorderLayout.CENTER);
dataMemoryPanel = new DataMemoryPanel(model);
content.add(dataMemoryPanel, BorderLayout.LINE_END);
/*
JButton button = new JButton("Toggle base");
button.addActionListener(new ActionListener() {
@Override
public void actionPerformed(ActionEvent e) {
base = (base == 2) ? 10 : 2;
programMemory.setBase(base);
programMemory.setPosition(programMemory.getPosition() + 2);
tableModel.setBase(base);
tableModel.fireTableDataChanged();
}
});
content.add(button, BorderLayout.PAGE_END);
*/
emulatorControlPanel = new EmulatorControlPanel(model);
content.add(emulatorControlPanel, BorderLayout.PAGE_END);
// Registers and so on
controlUnitPanel = new ControlUnitPanel(model);
content.add(controlUnitPanel, BorderLayout.LINE_START);
update(null, null);
setSize(950, 500);
}
@Override
public void update(Observable o, Object arg) {
instructionMemoryPanel.refresh();
dataMemoryPanel.refresh();
emulatorControlPanel.refresh();
controlUnitPanel.refresh();
}
public static void main(String[] args) {
if(args.length != 1) System.exit(-1);
Emulator emulator = new Emulator();
// HACK: Change configuration for special Aufgabe4
if(args[0].equals("Aufgabe4")) {
emulator.getConfiguration().setInstructionRangeTo((short)199);
emulator.getConfiguration().setDataRangeFrom((short)200);
emulator.getConfiguration().setDataRangeTo((short)299);
}
try {
emulator.loadProgram(args[0]);
emulator.loadMemory(args[0]);
}
catch(Exception ex) {
System.out.println(ex.getMessage());
System.exit(-2);
}
MainWindow window = new MainWindow(new EmulatorModel(emulator));
window.setVisible(true);
}
}
|
package org.csstudio.alarm.diirt.datasource;
import static org.diirt.util.concurrent.Executors.namedPool;
import java.net.URI;
import java.net.URLDecoder;
import java.net.URLEncoder;
import java.util.ArrayList;
import java.util.Collections;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.concurrent.CompletableFuture;
import java.util.concurrent.Executor;
import java.util.concurrent.ExecutorService;
import java.util.concurrent.Executors;
import java.util.concurrent.atomic.AtomicInteger;
import java.util.function.Consumer;
import java.util.logging.Level;
import java.util.logging.Logger;
import org.csstudio.alarm.beast.client.AlarmTreeItem;
import org.csstudio.alarm.beast.client.AlarmTreePV;
import org.csstudio.alarm.beast.ui.clientmodel.AlarmClientModel;
import org.csstudio.alarm.beast.ui.clientmodel.AlarmClientModelConfigListener;
import org.csstudio.alarm.beast.ui.clientmodel.AlarmClientModelListener;
import org.diirt.datasource.ChannelHandler;
import org.diirt.datasource.DataSource;
import org.diirt.datasource.vtype.DataTypeSupport;
import org.eclipse.core.runtime.Platform;
/**
* @author Kunal Shroff
*
*/
public class BeastDataSource extends DataSource implements AlarmClientModelConfigListener {
private static final Logger log = Logger.getLogger(BeastDataSource.class.getName());
private static final String PREF_QUALIFIER = "org.csstudio.alarm.diirt.datasource";
private static final String PREF_KEY_COMPOSITE = "composite.model.name";
private static final String PREF_DEFAULT_COMPOSITE_MODEL_NAME = "Composite";
// The model, activeAlarms and acknowledgedAlarms is shared by the entire
// datasource, the benefit of does this at the datasource level instead of
// in each channel is that they need to be computed only once and only a single
// copy needs to be maintained.
private AlarmClientModel model;
private Map<String, List<Consumer>> channelConsumers = Collections.synchronizedMap(new HashMap<String, List<Consumer>>());
private Map<String, AlarmClientModel> models = Collections.synchronizedMap(new HashMap<String, AlarmClientModel>());
private AtomicInteger loaded;
private AtomicInteger toLoad;
private Executor executor = Executors.newScheduledThreadPool(4);
private final ExecutorService exec = Executors.newSingleThreadExecutor(namedPool("RemoveChannel " + getClass().getSimpleName() + " Worker "));
private BeastTypeSupport typeSupport;
private BeastDataSourceConfiguration configuration;
private BeastAlarmClientModelListener modelListener;
private CompositeAlarmClientModel compositeModel;
static {
// Install type support for the types it generates.
DataTypeSupport.install();
}
private class BeastAlarmClientModelListener implements AlarmClientModelListener{
private BeastDataSource parent;
BeastAlarmClientModelListener(BeastDataSource parent) {
this.parent = parent;
}
@Override
public void newAlarmConfiguration(AlarmClientModel model) {
log.config("beast datasource: new alarm configuration --- " + model);
// new model loaded
parent.loaded.incrementAndGet();
if (!parent.compositeModel.equals(model)) parent.compositeModel.addAlarmClientModel(model);
if (parent.loaded.get() == parent.toLoad.get()) {
parent.compositeModel.setAllLoaded(true);
log.log(Level.FINE, "All models loaded - notifying Composite model listeners.");
parent.compositeModel.compositeModelsLoaded();
}
synchronized (parent.channelConsumers) {
for (String channelName : parent.channelConsumers.keySet()) {
BeastChannelHandler channel = (BeastChannelHandler) getChannels()
.get(channelHandlerLookupName(channelName));
channel.reconnect();
}
}
notifyCompositeBeastChannelListeners();
}
@Override
public void serverTimeout(AlarmClientModel model) {
log.warning("beast datasource: server timeout (server alive: " + model.isServerAlive() + ")");
synchronized (parent.channelConsumers) {
for (String channelName : parent.channelConsumers.keySet()) {
BeastChannelHandler channel = (BeastChannelHandler) getChannels()
.get(channelHandlerLookupName(channelName));
// notify the ChannelHandler that we lost connection
// (causes ConnectionChanged event + Listeners' PVReader.isConnected() will return the correct state)
channel.connectionStateChanged(false);
}
}
}
@Override
public void serverModeUpdate(AlarmClientModel model, boolean maintenance_mode) {
log.fine("beast datasource: server mode update");
}
@SuppressWarnings({ "rawtypes", "unchecked" })
@Override
public void newAlarmState(AlarmClientModel alarmModel, AlarmTreePV pv, boolean parent_changed) {
if (pv != null) {
log.fine(pv.getPathName());
synchronized (parent.channelConsumers) {
parent.channelConsumers.forEach((key, pathHandlers) -> {
if (BeastTypeSupport.getStrippedChannelName(key).equals(pv.getPathName().substring(1))
|| BeastTypeSupport.getStrippedChannelName(key).equals(pv.getName())) {
if (pathHandlers != null) {
for (Consumer consumer : pathHandlers) {
consumer.accept(pv);
}
}
}
});
}
// Notify parent nodes (regardless of parent_changed - because the parents' AlarmPVsCount)
AlarmTreeItem parent = pv.getParent();
while (parent != null) {
final String parentPath = parent.getPathName();
synchronized (this.parent.channelConsumers) {
this.parent.channelConsumers.forEach((key, pathHandlers) -> {
if (BeastTypeSupport.getStrippedChannelName(key).equals(parentPath.substring(1))) {
if (pathHandlers != null) {
for (Consumer consumer : pathHandlers) {
try {
consumer.accept(getState(parentPath));
} catch (Exception e) {
e.printStackTrace();
}
}
}
}
});
}
parent = parent.getParent();
}
} else {
// The AlarmClientModel has recovered from a disconnection or is notifying us that the first
// messages have been received after initial connection.
synchronized (parent.channelConsumers) {
for (String channelName : parent.channelConsumers.keySet()) {
BeastChannelHandler channel = (BeastChannelHandler) getChannels()
.get(channelHandlerLookupName(channelName));
if (channel!=null)
channel.reconnect(); // will send connection state + current AlarmTreeItem state
}
}
}
notifyCompositeBeastChannelListeners();
}
private void notifyCompositeBeastChannelListeners() {
synchronized (parent.channelConsumers) {
final BeastChannelHandler compositeChannel = (BeastChannelHandler) getChannels()
.get(channelHandlerLookupName(parent.compositeModel.getConfigurationName()));
if (compositeChannel != null) {
// there is an actual connection to the composite root
log.fine("Sending message to the composite tree channel.");
parent.compositeModel.getConfigTree().maximizeSeverity();
compositeChannel.accept(parent.compositeModel.getConfigTree());
}
}
}
}
public BeastDataSource(BeastDataSourceConfiguration configuration) {
super(true);
this.configuration = configuration;
loaded = new AtomicInteger(0);
toLoad = new AtomicInteger(-1);
final String compositeModelName = Platform.getPreferencesService().
getString(PREF_QUALIFIER, PREF_KEY_COMPOSITE, PREF_DEFAULT_COMPOSITE_MODEL_NAME, null);
log.log(Level.CONFIG, () -> String.format("Using '%s' as the composite alarm model name.", compositeModelName));
compositeModel = new CompositeAlarmClientModel(compositeModelName);
compositeModel.registerWithClientModels();
// one global listener for all models
modelListener = new BeastAlarmClientModelListener(this);
try {
// Create an instance to the AlarmClientModel
final CompletableFuture<Void> future = CompletableFuture
.supplyAsync(() -> initialize(configuration), executor)
.thenAccept((model) -> {
this.model = model;
this.models.put(model.getConfigurationName(), model);
this.model.addListener(modelListener);
});
typeSupport = new BeastTypeSupport();
compositeModel.addListener(modelListener);
} catch (Exception e) {
e.printStackTrace();
}
}
private AlarmClientModel initialize(BeastDataSourceConfiguration configuration) {
AlarmClientModel alarmModel;
try {
if (configuration.getConfigName() != null && !configuration.getConfigName().isEmpty()) {
alarmModel = AlarmClientModel.getInstance(configuration.getConfigName(), this);
} else {
alarmModel = AlarmClientModel.getInstance(this);
}
return alarmModel;
} catch (Exception e) {
return null;
}
}
@Override
protected ChannelHandler createChannel(String channelName) {
return new BeastChannelHandler(channelName, BeastTypeSupport.getChannelType(channelName), this);
}
@Override
public void close() {
super.close();
if (!models.isEmpty()) {
for (final AlarmClientModel aModel : models.values()) aModel.release();
} else {
model.release();
}
}
/**
* Override of default channelHandlerLookupName.
* This implementation makes a leading and trailing forward slash ("/") optional.
* All four of these will resolve to the same channel:
* "/demo/test/", "/demo/test", "demo/test/" & "demo/test".
*
* @see org.diirt.datasource.DataSource#channelHandlerLookupName(java.lang.String)
*/
@Override
protected String channelHandlerLookupName(String channelName) {
String channel = channelName;
if (channel != null && !channel.equals("/") && !channel.isEmpty()) {
if (channel.endsWith("/"))
channel = channel.substring(0, channel.length() - 1);
if (channel.startsWith("/"))
channel = channel.substring(1);
}
return channel;
}
@SuppressWarnings("rawtypes")
protected void add(String channelName, Consumer beastChannelHandler) {
exec.execute(new Runnable() {
@Override
public void run() {
String beastChannel = channelHandlerLookupName(channelName);
synchronized (channelConsumers) {
List<Consumer> list = channelConsumers.get(beastChannel);
if (list == null) {
list = new ArrayList<>();
channelConsumers.put(beastChannel, list);
}
list.add(beastChannelHandler);
}
}
});
}
@SuppressWarnings("rawtypes")
protected void remove(String channelName, Consumer beastChannelHandler) {
exec.execute(new Runnable() {
@Override
public void run() {
String beastChannel = channelHandlerLookupName(channelName);
synchronized (channelConsumers) {
if (channelConsumers.containsKey(beastChannel)) {
channelConsumers.get(beastChannel).remove(beastChannelHandler);
}
}
}
});
}
protected AlarmTreeItem getState(String channelName) throws Exception {
URI uri = URI.create(URLEncoder.encode(BeastTypeSupport.getStrippedChannelName(channelName), "UTF-8"));
String pvName = uri.getPath().substring(uri.getPath().lastIndexOf("/") + 1);
AlarmClientModel aModel = selectModel(uri);
int actualRetries = 0;
final int maxRetries = 5;
while (aModel == null && actualRetries < maxRetries) {
log.warning("Waiting for model initialization of " + channelName + " (retrying: " + (actualRetries+1) + " of " + maxRetries + ")");
Thread.sleep(1000);
aModel = selectModel(uri);
actualRetries++;
}
if (aModel != null) {
AlarmTreePV alarmTreePV = aModel.findPV(pvName);
if (alarmTreePV != null) {
return alarmTreePV;
} else {
String path = URLDecoder.decode(uri.getPath(), "UTF-8");
AlarmTreeItem alarmTreeItem = aModel.getConfigTree().getItemByPath(path);
return alarmTreeItem;
}
} else {
throw new Exception("Model hasn't been created yet: " + uri.getPath());
}
}
private AlarmClientModel selectModel(URI uri) throws Exception {
if (model == null) {
log.warning("No default model.");
return null;
}
final String decodedUri = URLDecoder.decode(uri.getPath(), "UTF-8");
log.log(Level.FINE, () -> "decodedUri: " + decodedUri);
if (uri.getPath().contains("/")) {
// Alarm root defined
final String lookupName = channelHandlerLookupName(decodedUri);
//log.log(Level.INFO, "With root: " + lookupName);
final String root;
if (lookupName.contains("/"))
root = lookupName.substring(0, lookupName.indexOf('/'));
else
root = lookupName;
log.log(Level.FINE, () -> "root: " + root);
if (model.getConfigurationName().equals(root)) {
log.fine("Returning default model.");
return model;
}
if (models.containsKey(root)) {
log.fine("Returning named model.");
return models.get(root);
}
if (root.equals(compositeModel.getConfigurationName())) {
log.fine("Returning composite model.");
return compositeModel;
}
log.log(Level.WARNING, () -> String.format("Root not found: %s", root));
return null;
} else {
// PV only - search models in the DIIRT defined order, but search default first.
final String pvName = decodedUri.substring(decodedUri.lastIndexOf("/") + 1);
//log.log(Level.INFO, "no root. pvName: " + pvName);
if (model.findPV(pvName) != null) return model;
for (final String configName : configuration.getConfigNames()) {
final AlarmClientModel aModel = models.get(configName);
if ((aModel != null) && (aModel.findPV(pvName) != null)) return aModel;
}
// PV not found anywhere!!! Return default.
return model;
}
}
protected boolean isConnected() {
if (model != null) {
return model.isServerAlive();
} else {
return false;
}
}
protected boolean isWriteAllowed() {
// this is governed by the org.csstudio.alarm.beast.Preferences so it is the same for all models
if (model != null) {
return model.isServerAlive() && model.isWriteAllowed();
} else {
return false;
}
}
protected void acknowledge(String channelName, boolean acknowledge) throws Exception {
getState(channelName).acknowledge(acknowledge);
}
// implementing the enable disable mechanism using the example of the DisableComponentAction
protected void enable(String channelName, boolean enable) throws Exception {
AlarmTreeItem item = getState(channelName);
final List<AlarmTreePV> pvs = new ArrayList<>();
final CompletableFuture<Void> future = CompletableFuture
.runAsync(() -> addPVs(pvs, item, enable), executor)
.thenRun(() -> {
for (AlarmTreePV alarmTreePV : pvs) {
try {
model.enable(alarmTreePV, enable);
} catch (Exception e) {
new Exception("Failed to enable/disable : " + ((AlarmTreePV) item).getName(), e);
}
}
});
}
/** @param pvs List where PVs to enable/disable will be added
* @param item Item for which to locate PVs, recursively
*/
private void addPVs(final List<AlarmTreePV> pvs, final AlarmTreeItem item, boolean enable) {
if (item instanceof AlarmTreePV) {
final AlarmTreePV pv = (AlarmTreePV) item;
if (pv.isEnabled() != enable)
pvs.add(pv);
} else {
final int N = item.getChildCount();
for (int i=0; i<N; ++i)
addPVs(pvs, item.getChild(i), enable);
}
}
public BeastTypeSupport getTypeSupport() {
return typeSupport;
}
@Override
public void newAlarmConfiguration(AlarmClientModel model) {
// initial model loaded
// store the default model in a list of all models
log.log(Level.CONFIG, () -> "Default alarm client model loaded: " + model.getConfigurationName());
// now obtain all roots from it, and then see if you have anything else in the DIIRT configuration
final String[] confNames = model.getConfigurationNames();
toLoad.set(confNames.length);
if (confNames.length == 1) compositeModel.setAllLoaded(true); // there is only one model, and that one was just loaded.
final List<String> diirtConfNames = new ArrayList<>(configuration.getConfigNames()); // original is unmodifiable
for (final String confName : confNames) {
try {
if (!models.containsKey(confName)) {
log.log(Level.FINER, () -> "Loading model: " + confName);
final AlarmClientModel aModel = AlarmClientModel.getInstance(confName, modelListener);
models.put(confName, aModel);
}
diirtConfNames.remove(confName);
} catch (final Exception e) {
// Log warning if not debugging
if (!log.isLoggable(Level.FINER)) log.log(Level.WARNING, "Error loading alarm Client Model: " + confName);
log.log(Level.FINER, "Error loading alarm Client Model.", e);
}
}
if (!diirtConfNames.isEmpty()) {
log.log(Level.WARNING,
"DIIRT beast configuration defines alarm models not configured in the database: "
+ diirtConfNames.toString());
}
}
}
|
package net.tomp2p.connection;
import io.netty.channel.ChannelHandler.Sharable;
import io.netty.channel.ChannelHandlerContext;
import io.netty.channel.ChannelInboundHandlerAdapter;
import java.util.concurrent.atomic.AtomicInteger;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
* This is a soft limit, as there is no way to drop a connection before creating
* a socket from Java. This handler counts the incoming connections and drops the
* connection if a certain limit is reached.
*
* @author Thomas Bocek
*
*/
@Sharable
public class DropConnectionInboundHandler extends ChannelInboundHandlerAdapter {
private static final Logger LOG = LoggerFactory.getLogger(DropConnectionInboundHandler.class);
private final AtomicInteger counter = new AtomicInteger();
final int limit;
public DropConnectionInboundHandler(int limit) {
this.limit = limit;
}
@Override
public void channelRegistered(ChannelHandlerContext ctx) throws Exception {
int current = -1;
if ((current = counter.incrementAndGet()) > limit) {
ctx.channel().close();
LOG.warn("dropped connection because: " + current +" > " + limit +" connections active");
} else {
ctx.fireChannelRegistered();
}
}
@Override
public void channelInactive(ChannelHandlerContext ctx) throws Exception {
counter.decrementAndGet();
ctx.fireChannelInactive();
}
}
|
package king.flow.net;
import io.netty.bootstrap.Bootstrap;
import io.netty.buffer.ByteBuf;
import io.netty.channel.AdaptiveRecvByteBufAllocator;
import io.netty.channel.ChannelFuture;
import io.netty.channel.ChannelHandler;
import io.netty.channel.ChannelHandlerContext;
import io.netty.channel.ChannelInboundHandlerAdapter;
import io.netty.channel.ChannelInitializer;
import io.netty.channel.ChannelOption;
import io.netty.channel.EventLoopGroup;
import io.netty.channel.FixedRecvByteBufAllocator;
import io.netty.channel.nio.NioEventLoopGroup;
import io.netty.channel.socket.SocketChannel;
import io.netty.channel.socket.nio.NioSocketChannel;
import io.netty.handler.codec.DelimiterBasedFrameDecoder;
import io.netty.handler.codec.Delimiters;
import io.netty.handler.codec.FixedLengthFrameDecoder;
import io.netty.handler.codec.LengthFieldPrepender;
import io.netty.handler.codec.MessageToByteEncoder;
import io.netty.handler.codec.bytes.ByteArrayDecoder;
import io.netty.handler.codec.string.StringDecoder;
import io.netty.handler.codec.string.StringEncoder;
import java.util.concurrent.TimeUnit;
import java.util.logging.Level;
import java.util.logging.Logger;
import javax.xml.bind.JAXBException;
import king.flow.common.CommonConstants;
import static king.flow.data.TLSResult.PRS_CODE;
import king.flow.design.TLSProcessor;
import king.flow.test.net.MockClientReq;
/**
*
* @author Administrator
*/
public class P2PTunnel implements Tunnel {
private final String host;
private final int port;
private final int timeout;
private String responseMSG = null;
public P2PTunnel(String hostName, int portNumber, int channelTimeout) {
this.host = hostName;
this.port = portNumber;
this.timeout = channelTimeout;
}
@Override
public String connect() {
connectAndSend(null, null);
return this.responseMSG;
}
@Override
public String connect(int commmand, String message) {
connectAndSend(commmand, message);
return this.responseMSG;
}
private void connectAndSend(Integer command, String message) {
EventLoopGroup workerGroup = new NioEventLoopGroup();
try {
Bootstrap b = new Bootstrap();
b.group(workerGroup);
b.channel(NioSocketChannel.class);
b.option(ChannelOption.SO_KEEPALIVE, true);
b.option(ChannelOption.MAX_MESSAGES_PER_READ,
CommonConstants.MAX_MESSAGES_PER_READ);
// b.option(ChannelOption.RCVBUF_ALLOCATOR,
// new FixedRecvByteBufAllocator(CommonConstants.MAX_RECEIVED_BUFFER_SIZE));
b.option(ChannelOption.RCVBUF_ALLOCATOR,
new AdaptiveRecvByteBufAllocator(
CommonConstants.MIN_RECEIVED_BUFFER_SIZE,
CommonConstants.RECEIVED_BUFFER_SIZE,
CommonConstants.MAX_RECEIVED_BUFFER_SIZE));
if (command == null || message == null) {
b.handler(new ChannelInitializerImpl());
} else {
b.handler(new ChannelInitializerImpl(command, message));
}
// Start the client.
ChannelFuture f = b.connect(host, port).sync();
// Wait until the connection is closed.
//f.channel().closeFuture().sync();
boolean completed = f.channel().closeFuture().await(timeout, TimeUnit.SECONDS);
if (!completed) {
String PRSCODE_PREFIX = "<" + PRS_CODE + ">";
String PRSCODE_AFFIX = "</" + PRS_CODE + ">";
String prsCode = "[Unkonwn prscode]";
if (message == null) {
} else {
int start = message.indexOf(PRSCODE_PREFIX);
int end = message.indexOf(PRSCODE_AFFIX) + PRSCODE_AFFIX.length();
prsCode = (start == -1 || end == -1) ? prsCode : message.substring(start, end);
}
Logger.getLogger(P2PTunnel.class.getName()).log(Level.WARNING,
"[{0}] operation exceeds {1}seconds and is timeout, channel is forcily closed",
new Object[]{prsCode, timeout});
//forcily close channel to avoid connection leak
//acutally if no forcible channel close calling, connection still will be closed.
//but for comprehensive consideration, I call channel close again
f.channel().close().sync();
}
} catch (InterruptedException ex) {
Logger.getLogger(P2PTunnel.class.getName()).log(Level.SEVERE,
"channel management hits a problem, due to\n{0}", ex);
} finally {
workerGroup.shutdownGracefully();
}
}
private class MessageClientHandler extends ChannelInboundHandlerAdapter {
private String message = null;
private StringBuilder sb = null;
public MessageClientHandler() {
}
public MessageClientHandler(String msg) {
this.message = msg;
this.sb = new StringBuilder();
}
public MessageClientHandler setMessage(String message) {
this.message = message;
return this;
}
@Override
public void channelActive(ChannelHandlerContext ctx) throws Exception {
ctx.writeAndFlush(this.message);
}
@Override
public void channelRead(ChannelHandlerContext ctx, Object msg) {
Logger.getLogger(MessageClientHandler.class.getName()).log(Level.CONFIG, msg.toString());
sb.append(msg);
}
@Override
public void channelReadComplete(ChannelHandlerContext ctx) throws Exception {
P2PTunnel.this.responseMSG = sb.toString();
ctx.disconnect();
}
@Override
public void exceptionCaught(ChannelHandlerContext ctx, Throwable cause) {
Logger.getLogger(MessageClientHandler.class.getName()).log(Level.SEVERE, cause.getMessage(), cause);
ctx.close();
}
}
private class ByteMessageClientHandler extends ChannelInboundHandlerAdapter {
private String message = null;
private byte[] content = null;
public ByteMessageClientHandler() {
}
public ByteMessageClientHandler(String msg) {
this.message = msg;
}
public ByteMessageClientHandler setMessage(String message) {
this.message = message;
return this;
}
@Override
public void channelActive(ChannelHandlerContext ctx) throws Exception {
ctx.writeAndFlush(this.message);
}
@Override
public void channelRead(ChannelHandlerContext ctx, Object msg) {
byte[] block = (byte[]) msg;
if (content == null) {
content = block;
} else {
byte[] enlarge = new byte[content.length + block.length];
System.arraycopy(content, 0, enlarge, 0, content.length);
System.arraycopy(block, 0, enlarge, content.length, block.length);
content = enlarge;
}
}
@Override
public void channelReadComplete(ChannelHandlerContext ctx) throws Exception {
P2PTunnel.this.responseMSG = new String((content == null ? new byte[0] : content), CommonConstants.UTF8);
ctx.disconnect();
}
@Override
public void exceptionCaught(ChannelHandlerContext ctx, Throwable cause) {
Logger.getLogger(MessageClientHandler.class.getName()).log(Level.SEVERE, cause.getMessage(), cause);
ctx.close();
}
}
public static void main(String... args) throws JAXBException {
// Parse options.
String host = "127.0.0.1";
int port = 8080;
int code = 1;
String msg = new TLSProcessor().init().createRegistryMsg("1", "sanlogin", "token");
if (args != null && args.length >= 2) {
host = args[0];
port = Integer.parseInt(args[1]);
if (args.length >= 4) {
code = Integer.parseInt(args[2]);
msg = args[3];
}
}
Tunnel tunnel = TunnelBuilder.getTunnelBuilder().setHostName(host).setPortNumber(port).createTunnel();
tunnel.connect(code, msg);
System.out.println("0000000000000000 : " + ((P2PTunnel) tunnel).responseMSG);
tunnel.connect(300, MockClientReq.mockBasicReq());
// System.out.println("33333333330000000 : " + ((P2PTunnel)tunnel).responseMSG);
tunnel.connect(400, MockClientReq.mockBasicReq());
}
private class ChannelInitializerImpl extends ChannelInitializer<SocketChannel> {
private ChannelHandler[] handler_list = null;
public ChannelInitializerImpl() {
this.handler_list = new ChannelHandler[]{new CMDFieldPrepender(1), new LengthFieldPrepender(4),
new StringEncoder(CommonConstants.UTF8), new StringDecoder(CommonConstants.UTF8),
new MessageClientHandler("This is echo message")};
}
public ChannelInitializerImpl(int command, String message) {
this.handler_list = new ChannelHandler[]{new CMDFieldPrepender(command), new LengthFieldPrepender(4),
//new StringEncoder(CommonConstants.UTF8), new StringDecoder(CommonConstants.UTF8),
new StringEncoder(CommonConstants.UTF8), new ByteArrayDecoder(),
//new MessageClientHandler(message)};
new ByteMessageClientHandler(message)};
//new DelimiterBasedFrameDecoder(2048, Delimiters.lineDelimiter()),
}
public ChannelInitializerImpl(ChannelHandler... ch) {
this.handler_list = ch;
}
@Override
public void initChannel(SocketChannel ch) throws Exception {
ch.pipeline().addLast(handler_list);
}
}
private class CMDFieldPrepender extends MessageToByteEncoder<ByteBuf> {
private int command = -1;
public CMDFieldPrepender(int commandCode) {
this.command = commandCode;
}
@Override
protected void encode(ChannelHandlerContext ctx, ByteBuf msg, ByteBuf out) throws Exception {
out.writeInt(this.command);
out.writeBytes(msg, msg.readerIndex(), msg.readableBytes());
}
}
}
|
import javax.swing.JPanel;
import javax.swing.JEditorPane;
import javax.swing.event.HyperlinkListener;
import java.net.URL;
import javax.swing.event.HyperlinkEvent;
import javax.swing.text.html.HTMLFrameHyperlinkEvent;
public class Browser{
public JEditorPane displayEditorPane;
public Browser(){
displayEditorPane = new JEditorPane();
displayEditorPane.setContentType("text/html");
displayEditorPane.setEditable(false);
try{displayEditorPane.setPage(new URL("http://"+Repository.host+":"+Repository.getHTTPServerPort()+"/report"));}
catch(Exception e){System.out.println("could not get "+Repository.host+":"+Repository.getHTTPServerPort());}
displayEditorPane.addHyperlinkListener(new HyperlinkListener(){
public void hyperlinkUpdate(HyperlinkEvent e){
HyperlinkEvent.EventType eventType = e.getEventType();
if (eventType == HyperlinkEvent.EventType.ACTIVATED) {
if (!(e instanceof HTMLFrameHyperlinkEvent)){
try{displayEditorPane.setPage(e.getURL());}
catch(Exception ex){System.out.println("Could not get to:"+e.getURL());}}}}});}}
|
package org.apereo.cas.support.saml.web.idp.profile.builders;
import org.apereo.cas.support.saml.services.SamlRegisteredService;
import org.apereo.cas.support.saml.services.idp.metadata.SamlRegisteredServiceServiceProviderMetadataFacade;
import org.apereo.cas.support.saml.util.AbstractSaml20ObjectBuilder;
import org.jasig.cas.client.validation.Assertion;
import org.apereo.cas.support.saml.SamlException;
import org.opensaml.saml.saml2.core.AuthnRequest;
import org.opensaml.saml.saml2.core.NameID;
import org.opensaml.saml.saml2.core.Subject;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Qualifier;
import org.springframework.beans.factory.annotation.Value;
import org.springframework.cloud.context.config.annotation.RefreshScope;
import org.springframework.stereotype.Component;
import java.time.ZoneOffset;
import java.time.ZonedDateTime;
import javax.servlet.http.HttpServletRequest;
import javax.servlet.http.HttpServletResponse;
/**
* This is {@link SamlProfileSamlSubjectBuilder}.
*
* @author Misagh Moayyed
* @since 5.0.0
*/
@RefreshScope
@Component("samlProfileSamlSubjectBuilder")
public class SamlProfileSamlSubjectBuilder extends AbstractSaml20ObjectBuilder implements SamlProfileObjectBuilder<Subject> {
private static final long serialVersionUID = 4782621942035583007L;
@Autowired
@Qualifier("samlProfileSamlNameIdBuilder")
private SamlProfileSamlNameIdBuilder ssoPostProfileSamlNameIdBuilder;
@Value("${cas.samlidp.response.skewAllowance:0}")
private int skewAllowance;
@Override
public Subject build(final AuthnRequest authnRequest, final HttpServletRequest request, final HttpServletResponse response,
final Assertion assertion, final SamlRegisteredService service,
final SamlRegisteredServiceServiceProviderMetadataFacade adaptor)
throws SamlException {
return buildSubject(request, response, authnRequest, assertion, service, adaptor);
}
private Subject buildSubject(final HttpServletRequest request,
final HttpServletResponse response,
final AuthnRequest authnRequest, final Assertion assertion,
final SamlRegisteredService service,
final SamlRegisteredServiceServiceProviderMetadataFacade adaptor) throws SamlException {
final NameID nameID = this.ssoPostProfileSamlNameIdBuilder.build(authnRequest, request, response, assertion, service, adaptor);
final ZonedDateTime validFromDate = ZonedDateTime.ofInstant(assertion.getValidFromDate().toInstant(), ZoneOffset.UTC);
final Subject subject = newSubject(nameID.getFormat(), nameID.getValue(),
authnRequest.getAssertionConsumerServiceURL(),
validFromDate.plusSeconds(this.skewAllowance),
authnRequest.getID());
subject.setNameID(nameID);
return subject;
}
}
|
package org.mskcc.cbio.oncokb.quest;
import java.io.BufferedReader;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileNotFoundException;
import java.io.FileWriter;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.PrintWriter;
import java.util.ArrayList;
import java.util.Collections;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
import org.dom4j.Document;
import org.dom4j.DocumentException;
import org.dom4j.Node;
import org.dom4j.io.SAXReader;
import org.mskcc.cbio.oncokb.bo.GeneBo;
import org.mskcc.cbio.oncokb.model.Alteration;
import org.mskcc.cbio.oncokb.model.AlterationType;
import org.mskcc.cbio.oncokb.model.Gene;
import org.mskcc.cbio.oncokb.util.AlterationUtils;
import org.mskcc.cbio.oncokb.util.ApplicationContextSingleton;
import org.mskcc.cbio.oncokb.util.FileUtils;
import org.mskcc.cbio.oncokb.util.GeneUtils;
import org.mskcc.cbio.oncokb.util.TumorTypeUtils;
import org.springframework.stereotype.Controller;
/**
*
* @author jgao
*/
@Controller
public final class VariantAnnotationXMLV2 {
public static void main(String[] args) throws FileNotFoundException {
String input = args[0];
InputStream is = new FileInputStream(input);
String annotation = getVariantAnnotation(is);
String output;
if (args.length>1) {
output = args[1];
} else {
output = input.substring(0, input.length()-4)+".oncokb.xml";
}
try (PrintWriter writer = new PrintWriter(output)) {
writer.append(annotation);
}
}
public static String getVariantAnnotation(InputStream isXml) {
try {
Map<Alteration, String> mapAlterationXml = new LinkedHashMap<Alteration, String>();
SAXReader reader = new SAXReader();
Document document = reader.read(isXml);
// sample id
String sampleId = document.selectSingleNode("//xml/sample_id").getText();
// test id
String testId = document.selectSingleNode("//xml/test_id").getText();
// diagnosis
String diagnosis = document.selectSingleNode("//xml/diagnosis").getText();
// Somatic variants
List<Node> vcfNodes = document.selectNodes("//xml/somatic_variants/data");
if (!vcfNodes.isEmpty()) {
runVcf2Maf(document.asXML(), mapAlterationXml, diagnosis);
}
// for (Node vcfNode : vcfNodes) {
// handleSomaticVariants(vcfNode, alterations, alterationXmls, diagnosis);
// Copy number alterations
List<Node> cnaNodes = document.selectNodes("//xml/copy_number_alterations/copy_number_alteration");
for (Node cnaNode : cnaNodes) {
handleCNA(cnaNode, mapAlterationXml, diagnosis);
}
// fusions
List<Node> fusionNodes = document.selectNodes("//xml/fusion_genes/fusion_gene");
for (Node fusionNode : fusionNodes) {
handleFusion(fusionNode, mapAlterationXml, diagnosis);
}
List<Node> entrezNodes = document.selectNodes("//xml/sequencing_panel/genes/gene/entrez_gene_id");
ArrayList<Gene> sequencedGenes = new ArrayList<Gene>();
//use entrezGeneID, which is more stable than hugoSymbol, to fetch Gene instance
for(int i = 0;i < entrezNodes.size();i++){
sequencedGenes.add(GeneUtils.getGene(Integer.parseInt(entrezNodes.get(i).getText()), null));
}
// identify other related variants such as KRAS wildtype
identifyAdditionalVariants(mapAlterationXml, diagnosis, sequencedGenes);
List<Alteration> alterations = getAlterationOrderByLevelOfEvidence(mapAlterationXml);
// exporting
StringBuilder sb = new StringBuilder();
// meta
sb.append("<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"no\" ?>\n");
sb.append("<document>\n");
sb.append("<date_generated>2015-01-09</date_generated>\n");
sb.append("<oncokb_api_version>0.2</oncokb_api_version>\n");
sb.append("<ensembl_version>79</ensembl_version>\n");
sb.append("<sample>\n");
sb.append("<sample_id>").append(sampleId).append("</sample_id>\n");
sb.append("<diagnosis>").append(diagnosis).append("</diagnosis>\n");
sb.append("<test>\n");
sb.append("<test_id>").append(testId).append("</test_id>\n");
// variants
sb.append(exportVariants(alterations, mapAlterationXml));
// variant_interation
// end
sb.append("</test>\n");
sb.append("</sample>\n");
sb.append("</document>");
return sb.toString();
} catch (Exception ex) {
ex.printStackTrace();
return "<document>Failed to upload file.</document>";
}
}
private static void handleSomaticVariants(Node vcfNode, Map<Alteration, String> mapAlterationXml, String diagnosis) {
// do it here
}
/**
* This is a hacky way to run VEP. We should switch to web service once that is ready.
*/
private static void runVcf2Maf(String inputXml, Map<Alteration, String> mapAlterationXml, String diagnosis) throws IOException, DocumentException, InterruptedException {
File tmpFile = File.createTempFile("temp-oncokb-input-", ".xml");
tmpFile.deleteOnExit();
String inputPath = tmpFile.getAbsolutePath();
String outputPath = inputPath.substring(0,inputPath.length()-3) + "oncokb.xml";
FileWriter writer = new FileWriter(tmpFile);
writer.append(inputXml);
writer.close();
String vepMafXmlPl = System.getenv("VEP_MAF_XML_PL");
if (null==vepMafXmlPl) {
throw new IOException("VEP_MAF_XML_PL was not defined");
}
Process proc = Runtime.getRuntime().exec(new String[]{"perl",vepMafXmlPl,inputPath});
proc.waitFor();
InputStream stderr = proc.getErrorStream();
InputStreamReader isr = new InputStreamReader(stderr);
BufferedReader br = new BufferedReader(isr);
String line = null;
System.out.println("<ERROR>");
while ( (line = br.readLine()) != null)
System.out.println(line);
System.out.println("</ERROR>");
int exitVal = proc.waitFor();
System.out.println("Process exitValue: " + exitVal);
SAXReader reader = new SAXReader();
Document document = reader.read(outputPath);
List<Node> variantNodes = document.selectNodes("//document/sample/test/variant");
for (Node node : variantNodes) {
String alterationXml = "<variant_type>small_nucleotide_variant</variant_type>\n"
+ node.selectSingleNode("genomic_locus").asXML()
+ node.selectSingleNode("allele").asXML();
String geneSymbol = node.selectSingleNode("allele/transcript/hgnc_symbol").getText();
GeneBo geneBo = ApplicationContextSingleton.getGeneBo();
Gene gene = geneBo.findGeneByHugoSymbol(geneSymbol);
String proteinChange = node.selectSingleNode("allele/transcript/hgvs_p_short").getText();
Alteration alteration = new Alteration();
alteration.setAlterationType(AlterationType.MUTATION);
alteration.setGene(gene);
alteration.setName(proteinChange);
AlterationUtils.annotateAlteration(alteration, proteinChange);
mapAlterationXml.put(alteration, alterationXml);
}
}
private static void handleCNA(Node cnaNode, Map<Alteration, String> mapAlterationXml, String diagnosis) {
Gene gene = parseGene(cnaNode, "gene");
if (gene==null) {
return;
}
String type = cnaNode.selectSingleNode("type").getText();
Alteration alteration = new Alteration();
alteration.setGene(gene);
alteration.setAlteration(type);
alteration.setAlterationType(AlterationType.MUTATION); // TODO: this needs to be fixed
StringBuilder sb = new StringBuilder();
sb.append("<variant_type>copy_number_alteration</variant_type>\n");
sb.append(cnaNode.asXML()).append("\n");
sb.append(VariantAnnotationXML.annotate(alteration, diagnosis));
mapAlterationXml.put(alteration, sb.toString());
}
private static void handleFusion(Node fusionNode, Map<Alteration, String> mapAlterationXml, String diagnosis) {
StringBuilder sb = new StringBuilder();
sb.append("<variant_type>fusion_gene</variant_type>\n");
sb.append(fusionNode.asXML()).append("\n");
Gene gene1 = parseGene(fusionNode, "gene_1");
Gene gene2 = parseGene(fusionNode, "gene_2");
// String type = fusionNode.selectSingleNode("type").getText();
String fusion = gene1.getHugoSymbol()+"-"+gene2.getHugoSymbol()+" fusion";
Alteration alteration = new Alteration();
alteration.setGene(gene2);
alteration.setAlteration(fusion);
alteration.setAlterationType(AlterationType.MUTATION); // TODO: this needs to be fixed
sb.append(VariantAnnotationXML.annotate(alteration, diagnosis));
mapAlterationXml.put(alteration, sb.toString());
}
private static void identifyAdditionalVariants(Map<Alteration, String> mapAlterationXml, String diagnosis, ArrayList<Gene> sequencedGenes) {
List<String> lines;
try {
ArrayList<Alteration> alterations = new ArrayList<Alteration>(mapAlterationXml.keySet());
ArrayList<Gene> genesWithMutation = new ArrayList<Gene>();
for(int i = 0;i < alterations.size();i++){
genesWithMutation.add(alterations.get(i).getGene());
}
lines = FileUtils.readTrimedLinesStream(TumorTypeUtils.class.getResourceAsStream("/data/wildtype-alterations.txt"));
String[] parts = new String[2];
Alteration tempAlteration = new Alteration();
Gene tempGene = new Gene();
for (String line : lines) {
if (line.startsWith("
continue;
}
parts = line.split("\t");
tempGene = GeneUtils.getGene(null, parts[0]);
if(sequencedGenes.contains(tempGene) && diagnosis.equals(parts[1]) && !genesWithMutation.contains(tempGene)){
tempAlteration.setGene(tempGene);
tempAlteration.setAlteration("Wildtype");
tempAlteration.setAlterationType(AlterationType.MUTATION);
StringBuilder sb = new StringBuilder();
sb.append("<variant_type>wildtype</variant_type>\n");
sb.append(VariantAnnotationXML.annotate(tempAlteration, diagnosis));
mapAlterationXml.put(tempAlteration, sb.toString());
}
}
} catch (IOException e) {
e.printStackTrace();
}
}
private static List<Alteration> getAlterationOrderByLevelOfEvidence(Map<Alteration, String> mapAlterationXml) {
return new ArrayList<Alteration>(mapAlterationXml.keySet());
}
private static Gene parseGene(Node node, String genePath) {
GeneBo geneBo = ApplicationContextSingleton.getGeneBo();
Gene gene = null;
Node entrezGeneIdNode = node.selectSingleNode(genePath+"/entrez_gene_id");
Node hugoSymbolNode = node.selectSingleNode(genePath+"/hgnc_symbol");
if (entrezGeneIdNode!=null) {
int entrezId = Integer.parseInt(entrezGeneIdNode.getText());
gene = geneBo.findGeneByEntrezGeneId(entrezId);
}
if (gene==null && hugoSymbolNode!=null) {
String symbol = hugoSymbolNode.getText();
gene = geneBo.findGeneByHugoSymbol(symbol);
}
if (gene==null) {
// a gene not in system
gene = new Gene();
gene.setEntrezGeneId(Integer.parseInt(entrezGeneIdNode.getText()));
gene.setHugoSymbol(hugoSymbolNode.getText());
}
return gene;
}
private static String exportVariants(List<Alteration> alterations, Map<Alteration, String> mapAlterationXml) {
StringBuilder sb = new StringBuilder();
for (int i=0; i<alterations.size(); i++) {
Alteration alt = alterations.get(i);
String xml = mapAlterationXml.get(alt);
sb.append("<variant no=\"").append(i+1).append("\">\n").append(xml).append("</variant>\n");
}
return sb.toString();
}
}
|
package org.openhealthtools.mdht.uml.ui.navigator.actions;
import java.util.ArrayList;
import java.util.Collection;
import java.util.List;
import org.eclipse.emf.common.command.Command;
import org.eclipse.emf.common.command.IdentityCommand;
import org.eclipse.emf.common.command.UnexecutableCommand;
import org.eclipse.emf.edit.domain.EditingDomain;
import org.eclipse.emf.edit.domain.IEditingDomainProvider;
import org.eclipse.emf.edit.ui.EMFEditUIPlugin;
import org.eclipse.emf.edit.ui.action.CommandActionHandler;
import org.eclipse.ui.IWorkbenchPart;
import org.eclipse.uml2.common.edit.command.ChangeCommand;
import org.eclipse.uml2.uml.Association;
import org.eclipse.uml2.uml.Class;
import org.eclipse.uml2.uml.Element;
import org.eclipse.uml2.uml.NamedElement;
import org.eclipse.uml2.uml.Property;
import org.openhealthtools.mdht.uml.common.ui.saveable.ModelDocument;
import org.openhealthtools.mdht.uml.common.ui.saveable.ModelManager;
public class DeleteUMLAction extends CommandActionHandler {
protected List<Element> elements;
public DeleteUMLAction(EditingDomain domain) {
super(domain, EMFEditUIPlugin.INSTANCE.getString("_UI_Delete_menu_item"));
}
public DeleteUMLAction(EditingDomain domain, String label) {
super(domain, label);
}
public void setActiveWorkbenchPart(IWorkbenchPart workbenchPart) {
if (workbenchPart instanceof IEditingDomainProvider) {
domain = ((IEditingDomainProvider) workbenchPart).getEditingDomain();
}
}
@Override
public Command createCommand(Collection<?> selection) {
elements = new ArrayList<Element>();
for (Object object : selection) {
if (object instanceof Element && ((Element) object).getOwner() != null) {
if (object instanceof Class) {
Class umlClass = (Class) object;
// delete associations for owned attributes
for (Property property : umlClass.getOwnedAttributes()) {
if (property.getAssociation() != null) {
elements.addAll(property.getAssociation().getMemberEnds());
elements.add(property.getAssociation());
}
}
// delete associations when umlClass is the target
// List<DirectedRelationship> specializations = umlClass.getTargetDirectedRelationships(UMLPackage.Literals.ASSOCIATION);
// for (DirectedRelationship relationship : specializations) {
for (Association association : umlClass.getAssociations()) {
elements.addAll(association.getMemberEnds());
elements.add(association);
}
// delete the class
elements.add(umlClass);
} else if (object instanceof Association) {
Association association = (Association) object;
elements.addAll(association.getMemberEnds());
elements.add(association);
} else {
elements.add((Element) object);
}
}
}
if (elements.size() > 0) {
return IdentityCommand.INSTANCE;
}
return UnexecutableCommand.INSTANCE;
}
@Override
public void run() {
if (command != UnexecutableCommand.INSTANCE) {
String label = elements.get(0) instanceof NamedElement &&
((NamedElement) elements.get(0)).getName() != null
? "Delete " + ((NamedElement) elements.get(0)).getName()
: "Delete Element";
if (elements.size() > 1) {
label += " (+" + (elements.size() - 1) + ")";
}
domain.getCommandStack().execute(new ChangeCommand(domain, new Runnable() {
public void run() {
for (Element element : elements) {
if (element.eResource() != null) {
// mark resource dirty so that it can be saved
ModelDocument sourceDocument = ModelManager.getManager().manage(element.eResource());
if (sourceDocument != null) {
sourceDocument.setDirty(true);
}
}
element.destroy();
}
}
}, label));
}
}
}
|
package com.backendless;
import com.backendless.commons.DeviceType;
import com.backendless.exceptions.BackendlessException;
import com.backendless.exceptions.ExceptionMessage;
import java.util.Hashtable;
import java.util.Map;
class AndroidHeadersManager implements IHeadersManager
{
private static volatile AndroidHeadersManager instance;
static AndroidHeadersManager getInstance() throws BackendlessException
{
if( instance == null )
synchronized( AndroidHeadersManager.class )
{
if( instance == null )
{
instance = new AndroidHeadersManager();
}
}
return instance;
}
protected final Object headersLock = new Object();
protected final Hashtable<String, String> headers = new Hashtable<>();
AndroidHeadersManager()
{
if( Backendless.getApplicationId() == null || Backendless.getSecretKey() == null )
{
throw new IllegalStateException( ExceptionMessage.NOT_INITIALIZED );
}
initialFill();
}
private void initialFill()
{
addHeader( HeadersManager.HeadersEnum.APP_ID_NAME, Backendless.getApplicationId() );
addHeader( HeadersManager.HeadersEnum.SECRET_KEY_NAME, Backendless.getSecretKey() );
addHeader( HeadersManager.HeadersEnum.APP_TYPE_NAME, DeviceType.ANDROID.name() );
addHeader( HeadersManager.HeadersEnum.API_VERSION, "1.0" );
addHeaders( Backendless.getHeaders() );
}
public void cleanHeaders()
{
synchronized( headersLock )
{
headers.clear();
initialFill();
}
}
public void addHeader( HeadersManager.HeadersEnum headersEnum, String value )
{
synchronized( headersLock )
{
headers.put( headersEnum.getHeader(), value );
}
}
public void addHeaders( Map<String, String> headers )
{
if( headers == null || headers.isEmpty() )
return;
synchronized( headersLock )
{
this.headers.putAll( headers );
}
}
public void removeHeader( HeadersManager.HeadersEnum headersEnum )
{
synchronized( headersLock )
{
headers.remove( headersEnum.getHeader() );
}
}
public Hashtable<String, String> getHeaders() throws BackendlessException
{
synchronized( headersLock )
{
if( headers == null || headers.isEmpty() )
throw new IllegalStateException( ExceptionMessage.NOT_INITIALIZED );
return headers;
}
}
public void setHeaders( Map<String, String> headers )
{
synchronized( headersLock )
{
this.headers.putAll( headers );
}
}
public String getHeader( HeadersManager.HeadersEnum headersEnum ) throws BackendlessException
{
synchronized( headersLock )
{
if( headers == null || headers.isEmpty() )
throw new IllegalStateException( ExceptionMessage.NOT_INITIALIZED );
String header = headers.get( headersEnum );
if( header == null )
header = headers.get( headersEnum.getHeader() );
return header;
}
}
}
|
package org.objectweb.proactive.ic2d.jmxmonitoring.data;
import java.io.IOException;
import java.util.Collection;
import java.util.Comparator;
import java.util.List;
import java.util.concurrent.CopyOnWriteArrayList;
import javax.management.AttributeNotFoundException;
import javax.management.InstanceNotFoundException;
import javax.management.MBeanException;
import javax.management.MBeanServerInvocationHandler;
import javax.management.NotificationListener;
import javax.management.ObjectName;
import javax.management.ReflectionException;
import org.objectweb.proactive.core.UniqueID;
import org.objectweb.proactive.core.body.migration.MigrationException;
import org.objectweb.proactive.core.debug.stepbystep.BreakpointType;
import org.objectweb.proactive.core.debug.stepbystep.DebugInfo;
import org.objectweb.proactive.core.jmx.mbean.BodyWrapperMBean;
import org.objectweb.proactive.core.jmx.naming.FactoryName;
import org.objectweb.proactive.core.jmx.util.JMXNotificationManager;
import org.objectweb.proactive.ic2d.console.Console;
import org.objectweb.proactive.ic2d.jmxmonitoring.Activator;
import org.objectweb.proactive.ic2d.jmxmonitoring.data.listener.ActiveObjectListener;
import org.objectweb.proactive.ic2d.jmxmonitoring.util.MVCNotification;
import org.objectweb.proactive.ic2d.jmxmonitoring.util.MVCNotificationTag;
import org.objectweb.proactive.ic2d.jmxmonitoring.util.State;
/**
* Class for the active object representation in the IC2D model.
*/
public final class ActiveObject extends AbstractData<ProActiveNodeObject, AbstractData<?, ?>> {
public static final String ACTIVE_OBJECT_TYPE = "active object";
/** The parent object !! CAN CHANGE because of migration !! */
private ProActiveNodeObject parent;
/**
* Forwards methods in an MBean's management interface through the MBean
* server to the BodyWrapperMBean. !! CAN CHANGE because of migration !!
*/
private BodyWrapperMBean proxyMBean;
/**
* ID used to identify the active object globally, even in case of
* migration.
*/
private final UniqueID id;
/**
* A string version of the id that is used as a key
*/
private final String key;
/** Name of the class used to created the active object. */
private final String className;
/** The object's name (ex: ao#2) */
private final String name;
/**
* The JMX Notification listener that will be subscribed to the
* JMXNotificationManager *
*/
private final NotificationListener listener;
/**
* State of the object defined as a constant of the enum
* {@link org.objectweb.proactive.ic2d.jmxmonitoring.util.State}
*/
private State currentState = State.UNKNOWN;
/** request queue length */
private int requestQueueLength = -1; // -1 = not known
/**
* List of outgoing communications such as for each communication in the
* list, this active object is the source.
*/
protected final List<Communication> outgoingCommunications;
/**
* List of incoming communications such as for each communication in the
* list, this active object is the target.
*/
protected final List<Communication> incomingCommunications;
/**
* The destination node url used during migration !! CAN CHANGE because of
* migration !!
*/
private String destNodeURLOnMigration;
/**
* A volatile variable used to handle or not the communications concerned by
* this active object.
* <p>
* This volatile variable is used to provide thread-safety since it can be
* accessed by several threads at the same time during the reset
* communications user action.
*/
protected volatile boolean canHandleCommunications = true;
/**
* Creates and returns new instance of ActiveObject from an ObjectName. All
* operations related to the creation of an ActiveObject representation in
* IC2D should be done in its class, NOT elsewhere !
* <p>
* The parent NodeObject MUST NOT contain an active object with same key
* (string of unique id) !
*
* @param objectName
* The JMX object name associated to this ActiveObject
* @param parent
* The parent NodeObject
* @return A new instance of ActiveObject class
*/
public static ActiveObject createActiveObjectFrom(final ObjectName objectName,
final ProActiveNodeObject parent) {
// First create the mbean proxy to get all information about the active
// object
final BodyWrapperMBean proxyMBean = ActiveObject.createMBeanProxy(parent, objectName);
// Since the id is already contained as a String in the ObjectName
// the proxyMBean.getID() call can be avoid if the UniqueID can be built
// from a string
return new ActiveObject(parent, objectName, proxyMBean.getID(), proxyMBean.getName(), proxyMBean);
}
/**
* Creates a new proxy to the possibly remote
* {@link org.objectweb.proactive.core.jmx.mbean.BodyWrapperMBean} from a
* connection provided by a NodeObject and the object name associated with
* the mbean.
*
* @param parent
* The connection with the remote mbean server
* @param objectName
* The name associated with the mbean
* @return A new proxy to the possibly remote mbean.
*/
private static final BodyWrapperMBean createMBeanProxy(final ProActiveNodeObject parent,
final ObjectName objectName) {
return (BodyWrapperMBean) MBeanServerInvocationHandler.newProxyInstance(parent
.getProActiveConnection(), objectName, BodyWrapperMBean.class, false);
}
/**
* Creates and returns new instance of ActiveObject from an ObjectName. All
* operations related to the creation of an ActiveObject representation in
* IC2D should be done in its class, NOT elsewhere !
* <p>
* The parent NodeObject MUST NOT contain an active object with same key
* (string of unique id) !
*
* @param id
* The UniqueID of the ActiveObject
* @param className
* The name of the reified object class
* @param parent
* The parent NodeObject
* @return A new instance of ActiveObject class
*/
public static ActiveObject createActiveObjectFrom(final UniqueID id, final String className,
final ProActiveNodeObject parent) {
// Create the ObjectName from the id
final ObjectName objectName = FactoryName.createActiveObjectName(id);
// From the ObjectName create the MBeanProxy
final BodyWrapperMBean proxyMBean = ActiveObject.createMBeanProxy(parent, objectName);
return new ActiveObject(parent, objectName, id, className, proxyMBean);
}
/**
* Creates a new instance of ActiveObject from an ObjectName. Use static
* methods to create an ActiveObject.
*
* @param parent
* The parent NodeObject
* @param objectName
* The JMX object name associated to this ActiveObject
* @param id
* The UniqueID of the ActiveObject
* @param className
* The name of the reified object class
* @param proxyMBean
* The JMX proxy to the mbean of the body
*/
private ActiveObject(final ProActiveNodeObject parent, final ObjectName objectName, final UniqueID id,
final String className, final BodyWrapperMBean proxyMBean) {
super(objectName, null);
this.parent = parent;
this.proxyMBean = proxyMBean;
this.id = id;
this.key = id.toString();
this.className = className;
this.name = NamesFactory.getInstance().associateName(this.id, this.className);
this.listener = new ActiveObjectListener(this);
this.subscribeListener();
// CopyOnWriteArrayList is used since traversal operations vastly
// outnumbers mutations
// See addInCommunication and addOutCommunication methods of this class
this.outgoingCommunications = new CopyOnWriteArrayList<Communication>();
this.incomingCommunications = new CopyOnWriteArrayList<Communication>();
// // LOG TO REMOVE
// System.out.println("ActiveObject.ActiveObject() --> creating ao : " + this.name );
// if (parent.containsChild(this.key)
// || parent.getWorldObject().findActiveObject(key) != null) {
// System.out
// + this.name
// + " on NODE : "
// + this.getParent().getName()
// + "Current Thread : "
// + Thread.currentThread().getName());
// Thread.dumpStack();
// Used to have good performances. TODO : Check if the performances are
// as good as its said
this.getWorldObject().addActiveObject(this);
}
/**
* Change the current state
*
* @param newState
* The new state of this active object
*/
public synchronized void setState(final State newState) {
if (newState.equals(currentState)) {
return;
}
switch (newState) {
case WAITING_BY_NECESSITY:
if (currentState == State.SERVING_REQUEST) {
currentState = State.WAITING_BY_NECESSITY_WHILE_SERVING;
} else {
currentState = State.WAITING_BY_NECESSITY_WHILE_ACTIVE;
}
break;
case RECEIVED_FUTURE_RESULT:
if (currentState == State.WAITING_BY_NECESSITY_WHILE_SERVING) {
currentState = State.SERVING_REQUEST;
} else {
currentState = State.ACTIVE;
}
break;
default:
currentState = newState;
break;
}
setChanged();
notifyObservers(new MVCNotification(MVCNotificationTag.STATE_CHANGED, this.currentState));
}
/**
* Returns the current state of this active object.
*
* @return The current state.
*/
public synchronized State getState() {
return this.currentState;
}
/**
* Returns true if this active object is migrating false otherwise.
*
* @return true if this active object is migrating false otherwise
*/
public synchronized boolean isMigrating() {
return this.currentState == State.MIGRATING;
}
/**
* Sends a migration request to this object to migrate to another node. This
* method uses the mbean proxy to send an asynchronous request of migration.
*
* @param targetNode
* The target node object
* @return true if it has successfully migrated, false otherwise.
*/
public synchronized boolean migrateTo(final ProActiveNodeObject targetNode) {
final Console console = Console.getInstance(Activator.CONSOLE_NAME);
final String nodeTargetURL = targetNode.getUrl();
try {
// Migrate
this.proxyMBean.migrateTo(nodeTargetURL);
} catch (Exception e) {
console.err("Couldn't migrate " + this.getName() + " to " + nodeTargetURL + " Reason : " +
e.getMessage());
return false;
}
console.log("Successfully sent a request of migration of " + this + " to " + nodeTargetURL);
return true;
}
/**
* Prepares this active object to migrate, sets the current state to
* {@link org.objectweb.proactive.ic2d.jmxmonitoring.util.State.MIGRATING}.
*
* @param destinationNodeURL
* The url of the destination node
*/
public void prepareToMigrate(final String destinationNodeURL) {
this.destNodeURLOnMigration = destinationNodeURL;
this.setState(State.MIGRATING);
}
/**
* Finishes the migration. Refreshes current parent and the mbean proxy of
* this active object.
* <p>
* This method is
* <code>synchronized</p> because sometimes it can be called by 2 different threads
* at the same time.
*
* @param destinationRuntimeURL
* The <code>URL</code> of the destination runtime
*/
public synchronized void finishMigration(final String destinationRuntimeURL) {
// First if its not a migrating object or destNodeURLOnMigration is null we can't finish migration
if (this.currentState != State.MIGRATING || this.destNodeURLOnMigration == null) {
return;
}
// Get the console for the output
final Console console = Console.getInstance(Activator.CONSOLE_NAME);
// Try to locate the destination runtime object from its url
// First locate the destination host from the given URL
// The next code extracts proto://addr:port/ from
// proto://addr:port/runtime_name
final String destHostURL = destinationRuntimeURL.substring(0,
destinationRuntimeURL.lastIndexOf('/') + 1);
final HostObject destHostObject = (HostObject) this.getParent().getWorldObject()
.getChild(destHostURL);
if (destHostObject == null) {
console.log("Cannot finish migration of the active object : " + this.name +
". Trying to migrate to an unknown host : " + destHostURL);
return;
}
// Second locate the destination runtime by its URL
final RuntimeObject destRuntimeObject = (RuntimeObject) destHostObject
.getChild(destinationRuntimeURL);
if (destRuntimeObject == null) {
console.log("Cannot finish migration of the active object : " + this.name +
". Trying to migrate to an unknown runtime : " + destinationRuntimeURL);
return;
}
// Third locate the destination node by its URL
final ProActiveNodeObject destNodeObject = (ProActiveNodeObject) destRuntimeObject
.getChild(this.destNodeURLOnMigration);
if (destNodeObject == null) {
console.log("Cannot finish migration of the active object : " + this.name +
". Trying to migrate to an unknown node : " + this.destNodeURLOnMigration);
return;
}
// Update the mbean proxy (recreate one from the ProActiveConnection
// provided by
// the new node object)
this.proxyMBean = ActiveObject.createMBeanProxy(destNodeObject, this.objectName);
// WARNING !!! DO NOT REMOVE COMMUNICATIONS HERE !!!
// Communications are represented by outgoingCommunications and
// incomingCommunications list attributes of this class.
// Representation of a migration concerns only edit parts NOT MODELS !
// Since the active object model is NOT DELETED.
// Remove this from current parent node
this.parent.removeChild(this);
// Update the new parent
this.parent = destNodeObject;
// Add this to new parent
this.parent.addChild(this);
// Restore a standard state
this.setState(State.WAITING_FOR_REQUEST);
this.destNodeURLOnMigration = null;
}
/**
* Say to the model that a MigrationException occurred during a migration of
* this active object.
*
* @param migrationException
*/
public void migrationFailed(MigrationException migrationException) {
Console.getInstance(Activator.CONSOLE_NAME).logException(
"The active object " + this + " didn't migrate!", migrationException);
}
/**
* Returns the unique id of the active object.
*
* @return An unique id.
*/
public UniqueID getUniqueID() {
return this.id;
}
/**
* Returns the name of the class given in parameter to the constructor.
*
* @return The class name
*/
public String getClassName() {
return this.className;
}
/**
* Returns a JMX Notification listener.
*
* @return a JMX Notification listener.
*/
public NotificationListener getListener() {
return this.listener;
}
/**
* Returns a direct reference on the list of outgoing communications.
*
* @return A list of outgoing communications
*/
public List<Communication> getOutgoingCommunications() {
return this.outgoingCommunications;
}
/**
* Returns a direct reference on the list of incoming communications.
*
* @return A list of incoming communications
*/
public List<Communication> getIncomingCommunications() {
return this.incomingCommunications;
}
/**
* Adds a communication from this active object to another active object
* Warning: This active object is the source of the communication.
*
* @param destinationID
* The unique id of the destination of the communication.
*/
public void addOutCommunication(final UniqueID destinationID) {
if (!this.canHandleCommunications)
return;
// First seek through all known outgoing communications
for (final Communication c : this.outgoingCommunications) {
if (c.getTarget().getUniqueID().equals(destinationID)) {
c.addOneCall();
return;
}
}
final ActiveObject destAO = getWorldObject().findActiveObject(destinationID.getCanonString());
// If the destination ao is not known or this has no observers return
// silently
if (destAO == null || this.countObservers() == 0 || destAO.countObservers() == 0) {
return;
}
// If it's an unknown outgoing communication create one
new Communication(this, destAO);
}
/**
* Adds a communication to this active object from another active object
* Warning: This active object is the target of the communication.
*
* @param sourceID
* The unique id of the source of the communication.
*/
public void addInCommunication(final UniqueID sourceID) {
if (!this.canHandleCommunications)
return;
// First seek through all known incoming communications
for (final Communication c : this.incomingCommunications) {
if (c.getSource().getUniqueID().equals(sourceID)) {
c.addOneCall();
return;
}
}
final ActiveObject srcAO = getWorldObject().findActiveObject(sourceID.getCanonString());
// If the source ao in not known or this has no observers return
// silently
if (srcAO == null || this.countObservers() == 0 || srcAO.countObservers() == 0) {
return;
}
// If the communication was not found create one
new Communication(srcAO, this);
}
/**
* Removes all outgoing and incoming communications of this active object.
* For each removed communication a notification is fired to the observers
* of this active object.
*
* @param softly
* If true then the communications will be removed soflty (ie
* through
* {@link org.objectweb.proactive.ic2d.jmxmonitoring.data.Communication#disconnect()})
* method that can slower otherwise a rough method that consists
* of simply clearing the lists of communications is used.
*
*/
public void removeAllCommunications(boolean softly) {
// Soft method
if (softly) {
// Remove all outgoing
for (Communication c : this.outgoingCommunications) {
c.disconnect();
}
// Remove all incoming
for (Communication c : this.incomingCommunications) {
c.disconnect();
}
return;
}
this.outgoingCommunications.clear();
// Fire remove event
this.setChanged();
notifyObservers(new MVCNotification(
MVCNotificationTag.ACTIVE_OBJECT_REMOVE_ALL_OUTGOING_COMMUNICATION, null));
this.incomingCommunications.clear();
// Fire remove event
this.setChanged();
notifyObservers(new MVCNotification(
MVCNotificationTag.ACTIVE_OBJECT_REMOVE_ALL_INCOMING_COMMUNICATION, null));
}
@Override
public void destroy() {
this.internalDestroy();
// The destroy method of the super-class will remove this object from
// the parents children
super.destroy();
}
/**
* Remove the jmx listener, removes this from world then removes communications
*/
protected void internalDestroy() {
// First unsubscribe JMX listener
this.unsubscribeListener();
// Remove this object from world
super.getWorldObject().removeActiveObject(this.key);
// Second remove all communications
this.removeAllCommunications(true);
}
public boolean subscribeListener() {
// Subscribe to the jmx listener
try {
JMXNotificationManager.getInstance().subscribe(super.objectName, this.listener,
this.parent.getParent().getUrl());
return true;
} catch (Exception e) {
Console.getInstance(Activator.CONSOLE_NAME).log(
"Cannot subscribe the JMX listener of " + getType() + " " + getName());
return false;
}
}
public void unsubscribeListener() {
try {
// Remove the JMX Listener
JMXNotificationManager.getInstance().unsubscribe(super.objectName, this.listener);
} catch (Exception e) {
Console.getInstance(Activator.CONSOLE_NAME).log(
"Cannot unsubscribe the JMX listener of " + getType() + " " + getName());
}
}
/**
* Adds an outgoing communication to this active object and fires an
* {@link org.objectweb.proactive.ic2d.jmxmonitoring.util.MVCNotificationTag.ACTIVE_OBJECT_ADD_OUTGOING_COMMUNICATION}
* WARNING ! This method MUST be called ONLY from
* {@link org.objectweb.proactive.ic2d.jmxmonitoring.data.Communication#connect()}
* method.
*
* @param outgoingCommunication
* The outgoing communication to add
*/
void internalAddOutgoingCommunication(final Communication outgoingCommunication) {
this.outgoingCommunications.add(outgoingCommunication);
// Fire a notification
this.setChanged();
notifyObservers(new MVCNotification(MVCNotificationTag.ACTIVE_OBJECT_ADD_OUTGOING_COMMUNICATION,
outgoingCommunication));
}
/**
* Adds an incoming communication to this active object and fires an
* {@link org.objectweb.proactive.ic2d.jmxmonitoring.util.MVCNotificationTag.ACTIVE_OBJECT_ADD_INCOMING_COMMUNICATION}
* WARNING ! This method MUST be called ONLY from
* {@link org.objectweb.proactive.ic2d.jmxmonitoring.data.Communication#connect()}
* method.
*
* @param incomingCommunication
* The incoming communication to add
*/
void internalAddIncomingCommunication(final Communication incomingCommunication) {
this.incomingCommunications.add(incomingCommunication);
// Fire a notification
this.setChanged();
notifyObservers(new MVCNotification(MVCNotificationTag.ACTIVE_OBJECT_ADD_INCOMING_COMMUNICATION,
incomingCommunication));
}
/**
* Removes an outgoing communication of this active object and fires an
* {@link org.objectweb.proactive.ic2d.jmxmonitoring.util.MVCNotificationTag.ACTIVE_OBJECT_REMOVE_OUTGOING_COMMUNICATION}
* WARNING ! This method MUST be called ONLY from
* {@link org.objectweb.proactive.ic2d.jmxmonitoring.data.Communication#disconnect()}
* method.
*
* @param outgoingCommunication
* The outgoing communication to remove
*/
void internalRemoveOutgoingCommunication(final Communication outgoingCommunication) {
// Fire a notification
this.setChanged();
notifyObservers(new MVCNotification(MVCNotificationTag.ACTIVE_OBJECT_REMOVE_OUTGOING_COMMUNICATION,
outgoingCommunication));
this.outgoingCommunications.remove(outgoingCommunication);
}
/**
* Removes an incoming communication to this active object and fires an
* {@link org.objectweb.proactive.ic2d.jmxmonitoring.util.MVCNotificationTag.ACTIVE_OBJECT_REMOVE_INCOMING_COMMUNICATION}
* WARNING ! This method MUST be called ONLY from
* {@link org.objectweb.proactive.ic2d.jmxmonitoring.data.Communication#disconnect()}
* method.
*
* @param incomingCommunication
* The incoming communication to remove
*/
void internalRemoveIncomingCommunication(final Communication incomingCommunication) {
// Fire a notification
this.setChanged();
notifyObservers(new MVCNotification(MVCNotificationTag.ACTIVE_OBJECT_REMOVE_INCOMING_COMMUNICATION,
incomingCommunication));
this.incomingCommunications.remove(incomingCommunication);
}
/**
* The monitored active object adds a request, increments the request queue
* length.
*/
public void addRequest() {
this.requestQueueLength++;
setChanged();
notifyObservers(new MVCNotification(MVCNotificationTag.ACTIVE_OBJECT_REQUEST_QUEUE_LENGHT_CHANGED,
requestQueueLength));
}
/**
* The monitored active object removes a request, decrements the request
* queue length.
*/
public void removeRequest() {
this.requestQueueLength
setChanged();
notifyObservers(new MVCNotification(MVCNotificationTag.ACTIVE_OBJECT_REQUEST_QUEUE_LENGHT_CHANGED,
requestQueueLength));
}
public void setRequestQueueLength(int requestQueueLength) {
if (this.requestQueueLength != requestQueueLength) {
this.requestQueueLength = requestQueueLength;
setChanged();
notifyObservers(new MVCNotification(
MVCNotificationTag.ACTIVE_OBJECT_REQUEST_QUEUE_LENGHT_CHANGED, requestQueueLength));
}
}
/**
* Returns the length of the monitored active object request queue.
*
* @return The length of the request queue
*/
public int getRequestQueueLength() {
return this.requestQueueLength;
}
public String getJobId() {
return this.getParent().getJobId();
}
/**
* Returns the name of this active object. (Example: ao#3)
*
* @return The name of this active object.
*/
@Override
public String getName() {
return this.name;
}
@SuppressWarnings("unchecked")
@Override
public ProActiveNodeObject getParent() {
return this.parent;
}
@Override
public String getKey() {
return this.key;
}
@Override
public String getType() {
return ActiveObject.ACTIVE_OBJECT_TYPE;
}
@Override
public void explore() {
}
@Override
public String toString() {
return this.name;
}
public void enableStepByStep() {
setChanged();
proxyMBean.enableStepByStep();
}
public void disableStepByStep() {
setChanged();
proxyMBean.disableStepByStep();
}
public void nextStep() {
proxyMBean.nextStep();
}
public void nextStep(long id) {
proxyMBean.nextStep(id);
}
public void nextStep(Collection<Long> ids) {
proxyMBean.nextStep(ids);
}
public DebugInfo getDebugInfo() {
try {
return (DebugInfo) getProActiveConnection().getAttribute(getObjectName(), "DebugInfo");
} catch (AttributeNotFoundException e) {
e.printStackTrace();
} catch (InstanceNotFoundException e) {
e.printStackTrace();
} catch (MBeanException e) {
e.printStackTrace();
} catch (ReflectionException e) {
e.printStackTrace();
} catch (IOException e) {
e.printStackTrace();
}
return null;
}
public void slowMotion(long slowMotionDelay) {
setChanged();
proxyMBean.slowMotion(slowMotionDelay);
}
public void initBreakpointTypes() {
proxyMBean.initBreakpointTypes();
}
public void enableBreakpointTypes(BreakpointType[] types) {
proxyMBean.enableBreakpointTypes(types);
}
public void disableBreakpointTypes(BreakpointType[] types) {
proxyMBean.disableBreakpointTypes(types);
}
public static final class ActiveObjectComparator implements Comparator<String> {
/**
* Compare two active objects. (For Example: ao#3 and ao#5 give -1
* because ao#3 has been discovered before ao#5.)
*
* @return -1, 0, or 1 as the first argument is less than, equal to, or
* greater than the second.
*/
public int compare(final String ao1Name, final String ao2Name) {
return -(ao1Name.compareTo(ao2Name));
}
}
}
|
package org.innovateuk.ifs.application;
import org.innovateuk.ifs.BaseControllerMockMVCTest;
import org.innovateuk.ifs.application.constant.ApplicationStatusConstants;
import org.innovateuk.ifs.application.form.ApplicantInviteForm;
import org.innovateuk.ifs.application.form.ApplicationTeamUpdateForm;
import org.innovateuk.ifs.application.populator.ApplicationTeamManagementModelPopulator;
import org.innovateuk.ifs.application.resource.ApplicationResource;
import org.innovateuk.ifs.application.viewmodel.ApplicationTeamManagementApplicantRowViewModel;
import org.innovateuk.ifs.application.viewmodel.ApplicationTeamManagementViewModel;
import org.innovateuk.ifs.invite.resource.ApplicationInviteResource;
import org.innovateuk.ifs.invite.resource.InviteOrganisationResource;
import org.innovateuk.ifs.invite.resource.InviteResultsResource;
import org.innovateuk.ifs.user.resource.OrganisationResource;
import org.innovateuk.ifs.user.resource.UserResource;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.mockito.InOrder;
import org.mockito.InjectMocks;
import org.mockito.Spy;
import org.mockito.runners.MockitoJUnitRunner;
import org.springframework.http.MediaType;
import org.springframework.test.context.TestPropertySource;
import org.springframework.test.web.servlet.MvcResult;
import org.springframework.validation.BindingResult;
import java.util.List;
import java.util.Map;
import static java.lang.String.format;
import static java.util.Arrays.asList;
import static org.innovateuk.ifs.application.builder.ApplicationResourceBuilder.newApplicationResource;
import static org.innovateuk.ifs.application.constant.ApplicationStatusConstants.OPEN;
import static org.innovateuk.ifs.commons.rest.RestResult.restSuccess;
import static org.innovateuk.ifs.invite.builder.ApplicationInviteResourceBuilder.newApplicationInviteResource;
import static org.innovateuk.ifs.invite.builder.InviteOrganisationResourceBuilder.newInviteOrganisationResource;
import static org.innovateuk.ifs.invite.constant.InviteStatus.OPENED;
import static org.innovateuk.ifs.invite.constant.InviteStatus.SENT;
import static org.innovateuk.ifs.user.builder.OrganisationResourceBuilder.newOrganisationResource;
import static org.innovateuk.ifs.user.builder.ProcessRoleResourceBuilder.newProcessRoleResource;
import static org.innovateuk.ifs.user.builder.UserResourceBuilder.newUserResource;
import static org.innovateuk.ifs.util.CollectionFunctions.simpleToMap;
import static org.junit.Assert.assertEquals;
import static org.junit.Assert.assertTrue;
import static org.mockito.Mockito.*;
import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.get;
import static org.springframework.test.web.servlet.request.MockMvcRequestBuilders.post;
import static org.springframework.test.web.servlet.result.MockMvcResultMatchers.*;
@RunWith(MockitoJUnitRunner.class)
@TestPropertySource(locations = "classpath:application.properties")
public class ApplicationTeamManagementControllerTest extends BaseControllerMockMVCTest<ApplicationTeamManagementController> {
@Spy
@InjectMocks
private ApplicationTeamManagementModelPopulator applicationTeamManagementModelPopulator;
@Override
protected ApplicationTeamManagementController supplyControllerUnderTest() {
return new ApplicationTeamManagementController();
}
@Test
public void getUpdateLeadTeam_loggedInUserIsLead() throws Exception {
Map<String, OrganisationResource> organisationsMap = setupOrganisationResources();
ApplicationResource applicationResource = setupApplicationResource(organisationsMap);
Map<String, UserResource> usersMap = setupUserResources();
List<InviteOrganisationResource> inviteOrganisationList = setupOrganisationInvitesWithInviteForLeadOrg(applicationResource.getId(), usersMap, organisationsMap);
Long applicationInviteId = inviteOrganisationList.get(2).getInviteResources().get(0).getId();
UserResource leadApplicant = setupLeadApplicant(applicationResource, usersMap);
OrganisationResource expectedOrganisation = organisationsMap.get("Empire Ltd");
List<ApplicationTeamManagementApplicantRowViewModel> expectedApplicants = asList(
new ApplicationTeamManagementApplicantRowViewModel("Steve Smith", "steve.smith@empire.com", true, false, false),
new ApplicationTeamManagementApplicantRowViewModel(applicationInviteId,"Paul Davidson", "paul.davidson@empire.com", false, false, true));
ApplicationTeamManagementViewModel expectedViewModel = new ApplicationTeamManagementViewModel(
applicationResource.getId(),
"Application name",
expectedOrganisation.getId(),
expectedOrganisation.getName(),
true,
true,
expectedApplicants);
setLoggedInUser(leadApplicant);
MvcResult mockResult = mockMvc.perform(get("/application/{applicationId}/team/update?organisation={organisationId}", applicationResource.getId(), expectedOrganisation.getId()))
.andExpect(status().isOk())
.andExpect(model().attribute("model", expectedViewModel))
.andExpect(view().name("application-team/edit-org"))
.andReturn();
ApplicationTeamManagementViewModel viewModelResult = (ApplicationTeamManagementViewModel) mockResult.getModelAndView().getModel().get("model");
InOrder inOrder = inOrder(applicationService, inviteRestService, userService);
inOrder.verify(applicationService).getById(applicationResource.getId());
inOrder.verify(applicationService).getLeadOrganisation(applicationResource.getId());
inOrder.verify(inviteRestService).getInvitesByApplication(applicationResource.getId());
inOrder.verify(applicationService).getById(applicationResource.getId());
inOrder.verify(userService).getLeadApplicantProcessRoleOrNull(applicationResource);
inOrder.verify(userService).findById(leadApplicant.getId());
inOrder.verifyNoMoreInteractions();
}
@Test
public void getUpdateNonLeadTeam_loggedInUserIsLead() throws Exception {
Map<String, OrganisationResource> organisationsMap = setupOrganisationResources();
ApplicationResource applicationResource = setupApplicationResource(organisationsMap);
Map<String, UserResource> usersMap = setupUserResources();
List<InviteOrganisationResource> inviteOrganisationList = setupOrganisationInvitesWithInviteForLeadOrg(applicationResource.getId(), usersMap, organisationsMap);
Long applicationInviteId1 = inviteOrganisationList.get(0).getInviteResources().get(0).getId();
Long applicationInviteId2 = inviteOrganisationList.get(0).getInviteResources().get(1).getId();
UserResource leadApplicant = setupLeadApplicant(applicationResource, usersMap);
OrganisationResource expectedOrganisation = organisationsMap.get("Ludlow");
List<ApplicationTeamManagementApplicantRowViewModel> expectedApplicants = asList(
new ApplicationTeamManagementApplicantRowViewModel(applicationInviteId1,"Jessica Doe", "jessica.doe@ludlow.com", false, false, true),
new ApplicationTeamManagementApplicantRowViewModel(applicationInviteId2,"Ryan Dell", "ryan.dell@ludlow.com", false, true, true));
ApplicationTeamManagementViewModel expectedViewModel = new ApplicationTeamManagementViewModel(
applicationResource.getId(),
"Application name",
expectedOrganisation.getId(),
expectedOrganisation.getName(),
false,
true,
expectedApplicants);
setLoggedInUser(leadApplicant);
MvcResult mockResult = mockMvc.perform(get("/application/{applicationId}/team/update?organisation={organisationId}", applicationResource.getId(), expectedOrganisation.getId()))
.andExpect(status().isOk())
.andExpect(model().attribute("model", expectedViewModel))
.andExpect(view().name("application-team/edit-org"))
.andReturn();
ApplicationTeamManagementViewModel viewModelResult = (ApplicationTeamManagementViewModel) mockResult.getModelAndView().getModel().get("model");
InOrder inOrder = inOrder(applicationService, inviteRestService, userService);
inOrder.verify(applicationService).getById(applicationResource.getId());
inOrder.verify(applicationService).getLeadOrganisation(applicationResource.getId());
inOrder.verify(inviteRestService).getInvitesByApplication(applicationResource.getId());
inOrder.verify(applicationService).getById(applicationResource.getId());
inOrder.verify(userService).getLeadApplicantProcessRoleOrNull(applicationResource);
inOrder.verify(userService).findById(leadApplicant.getId());
inOrder.verifyNoMoreInteractions();
}
@Test
public void getUpdateNonLeadTeam_loggedInUserIsNonLead() throws Exception {
Map<String, OrganisationResource> organisationsMap = setupOrganisationResources();
ApplicationResource applicationResource = setupApplicationResource(organisationsMap);
Map<String, UserResource> usersMap = setupUserResources();
List<InviteOrganisationResource> inviteOrganisationList = setupOrganisationInvitesWithInviteForLeadOrg(applicationResource.getId(), usersMap, organisationsMap);
Long applicationInviteId1 = inviteOrganisationList.get(0).getInviteResources().get(0).getId();
Long applicationInviteId2 = inviteOrganisationList.get(0).getInviteResources().get(1).getId();
UserResource leadApplicant = setupLeadApplicant(applicationResource, usersMap);
OrganisationResource expectedOrganisation = organisationsMap.get("Ludlow");
List<ApplicationTeamManagementApplicantRowViewModel> expectedApplicants = asList(
new ApplicationTeamManagementApplicantRowViewModel(applicationInviteId1,"Jessica Doe", "jessica.doe@ludlow.com", false, false, false),
new ApplicationTeamManagementApplicantRowViewModel(applicationInviteId2,"Ryan Dell", "ryan.dell@ludlow.com", false, true, true));
ApplicationTeamManagementViewModel expectedViewModel = new ApplicationTeamManagementViewModel(
applicationResource.getId(),
"Application name",
expectedOrganisation.getId(),
expectedOrganisation.getName(),
false,
false,
expectedApplicants);
setLoggedInUser(usersMap.get("jessica.doe@ludlow.com"));
MvcResult mockResult = mockMvc.perform(get("/application/{applicationId}/team/update?organisation={organisationId}", applicationResource.getId(), expectedOrganisation.getId()))
.andExpect(status().isOk())
.andExpect(model().attribute("model", expectedViewModel))
.andExpect(view().name("application-team/edit-org"))
.andReturn();
ApplicationTeamManagementViewModel viewModelResult = (ApplicationTeamManagementViewModel) mockResult.getModelAndView().getModel().get("model");
InOrder inOrder = inOrder(applicationService, inviteRestService, userService);
inOrder.verify(applicationService).getById(applicationResource.getId());
inOrder.verify(applicationService).getLeadOrganisation(applicationResource.getId());
inOrder.verify(inviteRestService).getInvitesByApplication(applicationResource.getId());
inOrder.verify(applicationService).getById(applicationResource.getId());
inOrder.verify(userService).getLeadApplicantProcessRoleOrNull(applicationResource);
inOrder.verify(userService).findById(leadApplicant.getId());
inOrder.verifyNoMoreInteractions();
}
@Test
public void getUpdateNewTeam_loggedInUserIsLead() throws Exception {
Map<String, OrganisationResource> organisationsMap = setupOrganisationResources();
ApplicationResource applicationResource = setupApplicationResource(organisationsMap);
Map<String, UserResource> usersMap = setupUserResources();
List<InviteOrganisationResource> inviteOrganisationList = setupOrganisationInvitesWithInviteForLeadOrg(applicationResource.getId(), usersMap, organisationsMap);
Long applicationInviteId1 = inviteOrganisationList.get(0).getInviteResources().get(0).getId();
Long applicationInviteId2 = inviteOrganisationList.get(0).getInviteResources().get(1).getId();
UserResource leadApplicant = setupLeadApplicant(applicationResource, usersMap);
OrganisationResource expectedOrganisation = organisationsMap.get("Ludlow");
List<ApplicationTeamManagementApplicantRowViewModel> expectedApplicants = asList(
new ApplicationTeamManagementApplicantRowViewModel(applicationInviteId1, "Jessica Doe", "jessica.doe@ludlow.com", false, false, true),
new ApplicationTeamManagementApplicantRowViewModel(applicationInviteId2,"Ryan Dell", "ryan.dell@ludlow.com", false, true, true));
ApplicationTeamManagementViewModel expectedViewModel = new ApplicationTeamManagementViewModel(
applicationResource.getId(),
"Application name",
expectedOrganisation.getId(),
expectedOrganisation.getName(),
false,
true,
expectedApplicants);
setLoggedInUser(leadApplicant);
MvcResult mockResult = mockMvc.perform(get("/application/{applicationId}/team/update?organisationName={organisationName}", applicationResource.getId(), expectedOrganisation.getName()))
.andExpect(status().isOk())
.andExpect(model().attribute("model", expectedViewModel))
.andExpect(view().name("application-team/edit-org"))
.andReturn();
ApplicationTeamManagementViewModel viewModelResult = (ApplicationTeamManagementViewModel) mockResult.getModelAndView().getModel().get("model");
InOrder inOrder = inOrder(applicationService, inviteRestService, userService);
inOrder.verify(applicationService).getById(applicationResource.getId());
inOrder.verify(applicationService).getLeadOrganisation(applicationResource.getId());
inOrder.verify(inviteRestService).getInvitesByApplication(applicationResource.getId());
inOrder.verify(applicationService).getById(applicationResource.getId());
inOrder.verify(userService).getLeadApplicantProcessRoleOrNull(applicationResource);
inOrder.verify(userService).findById(leadApplicant.getId());
inOrder.verifyNoMoreInteractions();
}
@Test
public void submitUpdateLeadOrganisation_loggedInUserIsLead() throws Exception {
Map<String, OrganisationResource> organisationsMap = setupOrganisationResources();
ApplicationResource applicationResource = setupApplicationResource(organisationsMap);
Map<String, UserResource> usersMap = setupUserResources();
setupOrganisationInvitesWithInviteForLeadOrg(applicationResource.getId(), usersMap, organisationsMap);
UserResource leadApplicant = setupLeadApplicant(applicationResource, usersMap);
OrganisationResource organisation = organisationsMap.get("Empire Ltd");
ApplicationTeamUpdateForm expectedForm = new ApplicationTeamUpdateForm();
List<ApplicantInviteForm> applicants = asList(
new ApplicantInviteForm("Fred Brown", "fred.brown@empire.com")
);
expectedForm.setApplicants(applicants);
ApplicationInviteResource applicationInvite = new ApplicationInviteResource(applicants.get(0).getName(), applicants.get(0).getEmail(), applicationResource.getId());
InviteResultsResource inviteResultsResource = new InviteResultsResource();
inviteResultsResource.setInvitesSendSuccess(1);
when(inviteRestService.createInvitesByOrganisation(organisation.getId(), asList(applicationInvite))).thenReturn(restSuccess(inviteResultsResource));
setLoggedInUser(leadApplicant);
MvcResult mockResult = mockMvc.perform(post("/application/{applicationId}/team/update?organisation={organisationId}", applicationResource.getId(), organisation.getId())
.contentType(MediaType.APPLICATION_FORM_URLENCODED)
.param("applicants[0].name", applicants.get(0).getName())
.param("applicants[0].email", applicants.get(0).getEmail()))
.andExpect(model().attribute("form", expectedForm))
.andExpect(status().is3xxRedirection())
.andExpect(redirectedUrl(format("/application/%s/team", applicationResource.getId())))
.andReturn();
InOrder inOrder = inOrder(applicationService, inviteRestService);
inOrder.verify(applicationService).getById(applicationResource.getId());
inOrder.verify(inviteRestService).createInvitesByOrganisation(organisation.getId(), asList(applicationInvite));
inOrder.verifyNoMoreInteractions();
}
@Test
public void submitUpdateNewOrganisation_loggedInUserIsLead() throws Exception {
Map<String, OrganisationResource> organisationsMap = setupOrganisationResources();
ApplicationResource applicationResource = setupApplicationResource(organisationsMap);
Map<String, UserResource> usersMap = setupUserResources();
setupOrganisationInvitesWithInviteForLeadOrg(applicationResource.getId(), usersMap, organisationsMap);
UserResource leadApplicant = setupLeadApplicant(applicationResource, usersMap);
OrganisationResource organisation = organisationsMap.get("Org X");
ApplicationTeamUpdateForm expectedForm = new ApplicationTeamUpdateForm();
List<ApplicantInviteForm> applicants = asList(
new ApplicantInviteForm("Fred Brown", "fred.brown@orgx.com")
);
expectedForm.setApplicants(applicants);
ApplicationInviteResource applicationInvite = new ApplicationInviteResource(applicants.get(0).getName(), applicants.get(0).getEmail(), applicationResource.getId());
InviteResultsResource inviteResultsResource = new InviteResultsResource();
inviteResultsResource.setInvitesSendSuccess(1);
when(inviteRestService.createInvitesByInviteOrganisation(organisation.getName(), asList(applicationInvite))).thenReturn(restSuccess(inviteResultsResource));
setLoggedInUser(leadApplicant);
MvcResult mockResult = mockMvc.perform(post("/application/{applicationId}/team/update?organisationName={organisationName}", applicationResource.getId(), organisation.getName())
.contentType(MediaType.APPLICATION_FORM_URLENCODED)
.param("applicants[0].name", applicants.get(0).getName())
.param("applicants[0].email", applicants.get(0).getEmail()))
.andExpect(model().attribute("form", expectedForm))
.andExpect(status().is3xxRedirection())
.andExpect(redirectedUrl(format("/application/%s/team", applicationResource.getId())))
.andReturn();
InOrder inOrder = inOrder(applicationService, inviteRestService);
inOrder.verify(applicationService).getById(applicationResource.getId());
inOrder.verify(inviteRestService).createInvitesByInviteOrganisation(organisation.getName(), asList(applicationInvite));
inOrder.verifyNoMoreInteractions();
}
@Test
public void submitUpdateNonLeadOrganisation_loggedInUserIsLead() throws Exception {
Map<String, OrganisationResource> organisationsMap = setupOrganisationResources();
ApplicationResource applicationResource = setupApplicationResource(organisationsMap);
Map<String, UserResource> usersMap = setupUserResources();
setupOrganisationInvitesWithInviteForLeadOrg(applicationResource.getId(), usersMap, organisationsMap);
UserResource leadApplicant = setupLeadApplicant(applicationResource, usersMap);
OrganisationResource organisation = organisationsMap.get("Ludlow");
ApplicationTeamUpdateForm expectedForm = new ApplicationTeamUpdateForm();
List<ApplicantInviteForm> applicants = asList(
new ApplicantInviteForm("Joe Smith", "joe.smith@empire.com")
);
expectedForm.setApplicants(applicants);
ApplicationInviteResource applicationInvite = new ApplicationInviteResource(applicants.get(0).getName(), applicants.get(0).getEmail(), applicationResource.getId());
InviteResultsResource inviteResultsResource = new InviteResultsResource();
inviteResultsResource.setInvitesSendSuccess(1);
when(inviteRestService.createInvitesByOrganisation(organisation.getId(), asList(applicationInvite))).thenReturn(restSuccess(inviteResultsResource));
setLoggedInUser(leadApplicant);
MvcResult mockResult = mockMvc.perform(post("/application/{applicationId}/team/update?organisation={organisationId}", applicationResource.getId(), organisation.getId())
.contentType(MediaType.APPLICATION_FORM_URLENCODED)
.param("applicants[0].name", applicants.get(0).getName())
.param("applicants[0].email", applicants.get(0).getEmail()))
.andExpect(model().attribute("form", expectedForm))
.andExpect(status().is3xxRedirection())
.andExpect(redirectedUrl(format("/application/%s/team", applicationResource.getId())))
.andReturn();
InOrder inOrder = inOrder(applicationService, inviteRestService);
inOrder.verify(applicationService).getById(applicationResource.getId());
inOrder.verify(inviteRestService).createInvitesByOrganisation(organisation.getId(), asList(applicationInvite));
inOrder.verifyNoMoreInteractions();
}
@Test
public void submitUpdateNonLeadOrganisation_loggedInUserIsNonLead() throws Exception {
Map<String, OrganisationResource> organisationsMap = setupOrganisationResources();
ApplicationResource applicationResource = setupApplicationResource(organisationsMap);
Map<String, UserResource> usersMap = setupUserResources();
setupOrganisationInvitesWithInviteForLeadOrg(applicationResource.getId(), usersMap, organisationsMap);
OrganisationResource organisation = organisationsMap.get("Ludlow");
ApplicationTeamUpdateForm expectedForm = new ApplicationTeamUpdateForm();
List<ApplicantInviteForm> applicants = asList(
new ApplicantInviteForm("Joe Smith", "joe.smith@empire.com")
);
expectedForm.setApplicants(applicants);
ApplicationInviteResource applicationInvite = new ApplicationInviteResource(applicants.get(0).getName(), applicants.get(0).getEmail(), applicationResource.getId());
InviteResultsResource inviteResultsResource = new InviteResultsResource();
inviteResultsResource.setInvitesSendSuccess(1);
when(inviteRestService.createInvitesByOrganisation(organisation.getId(), asList(applicationInvite))).thenReturn(restSuccess(inviteResultsResource));
setLoggedInUser(usersMap.get("jessica.doe@ludlow.com"));
MvcResult mockResult = mockMvc.perform(post("/application/{applicationId}/team/update?organisation={organisationId}", applicationResource.getId(), organisation.getId())
.contentType(MediaType.APPLICATION_FORM_URLENCODED)
.param("applicants[0].name", applicants.get(0).getName())
.param("applicants[0].email", applicants.get(0).getEmail()))
.andExpect(model().attribute("form", expectedForm))
.andExpect(status().is3xxRedirection())
.andExpect(redirectedUrl(format("/application/%s/team", applicationResource.getId())))
.andReturn();
InOrder inOrder = inOrder(applicationService, inviteRestService);
inOrder.verify(applicationService).getById(applicationResource.getId());
inOrder.verify(inviteRestService).createInvitesByOrganisation(organisation.getId(), asList(applicationInvite));
inOrder.verifyNoMoreInteractions();
}
@Test
public void submitUpdateLeadOrganisation_loggedInUserIsLead_invalid() throws Exception {
Map<String, OrganisationResource> organisationsMap = setupOrganisationResources();
ApplicationResource applicationResource = setupApplicationResource(organisationsMap);
Map<String, UserResource> usersMap = setupUserResources();
setupOrganisationInvitesWithInviteForLeadOrg(applicationResource.getId(), usersMap, organisationsMap);
UserResource leadApplicant = setupLeadApplicant(applicationResource, usersMap);
OrganisationResource organisation = organisationsMap.get("Empire Ltd");
List<ApplicantInviteForm> applicants = asList(
new ApplicantInviteForm("Joe Smith", "joe.smith@empire.com")
);
setLoggedInUser(leadApplicant);
MvcResult result = mockMvc.perform(post("/application/{applicationId}/team/update?organisation={organisationId}", applicationResource.getId(), organisation.getId())
.contentType(MediaType.APPLICATION_FORM_URLENCODED)
.param("applicants[0].name", applicants.get(0).getName()))
.andExpect(status().isOk())
.andExpect(model().hasErrors())
.andExpect(model().attributeHasFieldErrors("form", "applicants[0].email"))
.andExpect(view().name("application-team/edit-org"))
.andReturn();
ApplicationTeamUpdateForm form = (ApplicationTeamUpdateForm) result.getModelAndView().getModel().get("form");
BindingResult bindingResult = form.getBindingResult();
assertEquals(0, bindingResult.getGlobalErrorCount());
assertEquals(1, bindingResult.getFieldErrorCount());
assertTrue(bindingResult.hasFieldErrors("applicants[0].email"));
assertEquals("Please enter an email address.", bindingResult.getFieldError("applicants[0].email").getDefaultMessage());
InOrder inOrder = inOrder(applicationService, userService);
inOrder.verify(applicationService, times(3)).getById(applicationResource.getId());
inOrder.verify(userService).getLeadApplicantProcessRoleOrNull(applicationResource);
inOrder.verify(userService).findById(leadApplicant.getId());
inOrder.verifyNoMoreInteractions();
}
@Test
public void addApplicantLeadOrganisation_loggedInUserIsLead() throws Exception {
Map<String, OrganisationResource> organisationsMap = setupOrganisationResources();
ApplicationResource applicationResource = setupApplicationResource(organisationsMap);
Map<String, UserResource> usersMap = setupUserResources();
setupOrganisationInvitesWithInviteForLeadOrg(applicationResource.getId(), usersMap, organisationsMap);
UserResource leadApplicant = setupLeadApplicant(applicationResource, usersMap);
OrganisationResource organisation = organisationsMap.get("Empire Ltd");
ApplicationTeamUpdateForm expectedForm = new ApplicationTeamUpdateForm();
List<ApplicantInviteForm> applicants = asList(
new ApplicantInviteForm("Fred Brown", "fred.brown@empire.com")
);
expectedForm.setApplicants(applicants);
ApplicationInviteResource applicationInvite = new ApplicationInviteResource(applicants.get(0).getName(), applicants.get(0).getEmail(), applicationResource.getId());
InviteResultsResource inviteResultsResource = new InviteResultsResource();
inviteResultsResource.setInvitesSendSuccess(1);
when(inviteRestService.createInvitesByOrganisation(organisation.getId(), asList(applicationInvite))).thenReturn(restSuccess(inviteResultsResource));
setLoggedInUser(leadApplicant);
MvcResult mockResult = mockMvc.perform(post("/application/{applicationId}/team/update/?organisation={organisationId}&addApplicant=true", applicationResource.getId(), organisation.getId())
.contentType(MediaType.APPLICATION_FORM_URLENCODED)
.param("applicants[0].name", applicants.get(0).getName())
.param("applicants[0].email", applicants.get(0).getEmail()))
.andExpect(status().isOk())
.andExpect(view().name("application-team/edit-org"))
.andReturn();
InOrder inOrder = inOrder(applicationService);
inOrder.verify(applicationService, times(3)).getById(applicationResource.getId());
inOrder.verifyNoMoreInteractions();
}
@Test
public void addApplicantNewOrganisation_loggedInUserIsLead() throws Exception {
Map<String, OrganisationResource> organisationsMap = setupOrganisationResources();
ApplicationResource applicationResource = setupApplicationResource(organisationsMap);
Map<String, UserResource> usersMap = setupUserResources();
setupOrganisationInvitesWithInviteForLeadOrg(applicationResource.getId(), usersMap, organisationsMap);
UserResource leadApplicant = setupLeadApplicant(applicationResource, usersMap);
OrganisationResource organisation = organisationsMap.get("Org X");
ApplicationTeamUpdateForm expectedForm = new ApplicationTeamUpdateForm();
List<ApplicantInviteForm> applicants = asList(
new ApplicantInviteForm("Fred Brown", "fred.brown@orgx.com")
);
expectedForm.setApplicants(applicants);
ApplicationInviteResource applicationInvite = new ApplicationInviteResource(applicants.get(0).getName(), applicants.get(0).getEmail(), applicationResource.getId());
InviteResultsResource inviteResultsResource = new InviteResultsResource();
inviteResultsResource.setInvitesSendSuccess(1);
when(inviteRestService.createInvitesByOrganisation(organisation.getId(), asList(applicationInvite))).thenReturn(restSuccess(inviteResultsResource));
setLoggedInUser(leadApplicant);
MvcResult mockResult = mockMvc.perform(post("/application/{applicationId}/team/update/?organisationName={organisationName}&addApplicant=true", applicationResource.getId(), organisation.getName())
.contentType(MediaType.APPLICATION_FORM_URLENCODED)
.param("applicants[0].name", applicants.get(0).getName())
.param("applicants[0].email", applicants.get(0).getEmail()))
.andExpect(status().isOk())
.andExpect(view().name("application-team/edit-org"))
.andReturn();
InOrder inOrder = inOrder(applicationService);
inOrder.verify(applicationService, times(3)).getById(applicationResource.getId());
inOrder.verifyNoMoreInteractions();
}
@Test
public void removeApplicantLeadOrganisation_loggedInUserIsLead() throws Exception {
Map<String, OrganisationResource> organisationsMap = setupOrganisationResources();
ApplicationResource applicationResource = setupApplicationResource(organisationsMap);
Map<String, UserResource> usersMap = setupUserResources();
setupOrganisationInvitesWithInviteForLeadOrg(applicationResource.getId(), usersMap, organisationsMap);
UserResource leadApplicant = setupLeadApplicant(applicationResource, usersMap);
OrganisationResource organisation = organisationsMap.get("Empire Ltd");
ApplicationTeamUpdateForm expectedForm = new ApplicationTeamUpdateForm();
List<ApplicantInviteForm> applicants = asList(
new ApplicantInviteForm("Fred Brown", "fred.brown@empire.com")
);
expectedForm.setApplicants(applicants);
ApplicationInviteResource applicationInvite = new ApplicationInviteResource(applicants.get(0).getName(), applicants.get(0).getEmail(), applicationResource.getId());
InviteResultsResource inviteResultsResource = new InviteResultsResource();
inviteResultsResource.setInvitesSendSuccess(1);
when(inviteRestService.createInvitesByOrganisation(organisation.getId(), asList(applicationInvite))).thenReturn(restSuccess(inviteResultsResource));
setLoggedInUser(leadApplicant);
MvcResult mockResult = mockMvc.perform(post("/application/{applicationId}/team/update/?organisation={organisationId}&removeApplicant=0", applicationResource.getId(), organisation.getId())
.contentType(MediaType.APPLICATION_FORM_URLENCODED)
.param("applicants[0].name", applicants.get(0).getName())
.param("applicants[0].email", applicants.get(0).getEmail()))
.andExpect(status().isOk())
.andExpect(view().name("application-team/edit-org"))
.andReturn();
InOrder inOrder = inOrder(applicationService);
inOrder.verify(applicationService, times(3)).getById(applicationResource.getId());
inOrder.verifyNoMoreInteractions();
}
@Test
public void removeApplicantNewOrganisation_loggedInUserIsLead() throws Exception {
Map<String, OrganisationResource> organisationsMap = setupOrganisationResources();
ApplicationResource applicationResource = setupApplicationResource(organisationsMap);
Map<String, UserResource> usersMap = setupUserResources();
setupOrganisationInvitesWithInviteForLeadOrg(applicationResource.getId(), usersMap, organisationsMap);
UserResource leadApplicant = setupLeadApplicant(applicationResource, usersMap);
OrganisationResource organisation = organisationsMap.get("Org X");
ApplicationTeamUpdateForm expectedForm = new ApplicationTeamUpdateForm();
List<ApplicantInviteForm> applicants = asList(
new ApplicantInviteForm("Fred Brown", "fred.brown@orgx.com")
);
expectedForm.setApplicants(applicants);
ApplicationInviteResource applicationInvite = new ApplicationInviteResource(applicants.get(0).getName(), applicants.get(0).getEmail(), applicationResource.getId());
InviteResultsResource inviteResultsResource = new InviteResultsResource();
inviteResultsResource.setInvitesSendSuccess(1);
when(inviteRestService.createInvitesByOrganisation(organisation.getId(), asList(applicationInvite))).thenReturn(restSuccess(inviteResultsResource));
setLoggedInUser(leadApplicant);
MvcResult mockResult = mockMvc.perform(post("/application/{applicationId}/team/update/?organisationName={organisationName}&removeApplicant=0", applicationResource.getId(), organisation.getName())
.contentType(MediaType.APPLICATION_FORM_URLENCODED)
.param("applicants[0].name", applicants.get(0).getName())
.param("applicants[0].email", applicants.get(0).getEmail()))
.andExpect(status().isOk())
.andExpect(view().name("application-team/edit-org"))
.andReturn();
InOrder inOrder = inOrder(applicationService);
inOrder.verify(applicationService, times(3)).getById(applicationResource.getId());
inOrder.verifyNoMoreInteractions();
}
@Test
public void markApplicantLeadOrganisation_loggedInUserIsLead() throws Exception {
Map<String, OrganisationResource> organisationsMap = setupOrganisationResources();
ApplicationResource applicationResource = setupApplicationResource(organisationsMap);
Map<String, UserResource> usersMap = setupUserResources();
List<InviteOrganisationResource> inviteOrganisationList = setupOrganisationInvitesWithInviteForLeadOrg(applicationResource.getId(), usersMap, organisationsMap);
Long applicationInviteId = inviteOrganisationList.get(2).getInviteResources().get(0).getId();
UserResource leadApplicant = setupLeadApplicant(applicationResource, usersMap);
OrganisationResource organisation = organisationsMap.get("Empire Ltd");
ApplicationTeamUpdateForm expectedForm = new ApplicationTeamUpdateForm();
List<ApplicantInviteForm> applicants = asList(
new ApplicantInviteForm("Fred Brown", "fred.brown@empire.com")
);
expectedForm.setApplicants(applicants);
setLoggedInUser(leadApplicant);
MvcResult mockResult = mockMvc.perform(post("/application/{applicationId}/team/update/?organisation={organisationId}&markForRemoval={applicationInviteId}", applicationResource.getId(), organisation.getId(), applicationInviteId)
.contentType(MediaType.APPLICATION_FORM_URLENCODED)
.param("applicants[0].name", applicants.get(0).getName())
.param("applicants[0].email", applicants.get(0).getEmail()))
.andExpect(status().isOk())
.andExpect(view().name("application-team/edit-org"))
.andReturn();
InOrder inOrder = inOrder(applicationService);
inOrder.verify(applicationService, times(3)).getById(applicationResource.getId());
inOrder.verifyNoMoreInteractions();
}
@Test
public void markApplicantNewOrganisation_loggedInUserIsLead() throws Exception {
Map<String, OrganisationResource> organisationsMap = setupOrganisationResources();
ApplicationResource applicationResource = setupApplicationResource(organisationsMap);
Map<String, UserResource> usersMap = setupUserResources();
List<InviteOrganisationResource> inviteOrganisationList = setupOrganisationInvitesWithAnUnconfirmedOrganisation(applicationResource.getId(), usersMap, organisationsMap);
Long applicationInviteId = inviteOrganisationList.get(0).getInviteResources().get(0).getId();
UserResource leadApplicant = setupLeadApplicant(applicationResource, usersMap);
OrganisationResource organisation = organisationsMap.get("Ludlow");
ApplicationTeamUpdateForm expectedForm = new ApplicationTeamUpdateForm();
List<ApplicantInviteForm> applicants = asList(
new ApplicantInviteForm("Fred Brown", "fred.brown@ludlow.com")
);
expectedForm.setApplicants(applicants);
setLoggedInUser(leadApplicant);
MvcResult mockResult = mockMvc.perform(post("/application/{applicationId}/team/update/?organisationName={organisationName}&markForRemoval={applicationInviteId}", applicationResource.getId(), organisation.getName(), applicationInviteId)
.contentType(MediaType.APPLICATION_FORM_URLENCODED)
.param("applicants[0].name", applicants.get(0).getName())
.param("applicants[0].email", applicants.get(0).getEmail()))
.andExpect(status().isOk())
.andExpect(view().name("application-team/edit-org"))
.andReturn();
InOrder inOrder = inOrder(applicationService);
inOrder.verify(applicationService, times(3)).getById(applicationResource.getId());
inOrder.verifyNoMoreInteractions();
}
private ApplicationResource setupApplicationResource(Map<String, OrganisationResource> organisationsMap) {
return setupApplicationResource(organisationsMap, OPEN);
}
private ApplicationResource setupApplicationResource(Map<String, OrganisationResource> organisationsMap, ApplicationStatusConstants applicationStatus) {
ApplicationResource applicationResource = newApplicationResource()
.withName("Application name")
.withApplicationStatus(applicationStatus)
.build();
when(applicationService.getById(applicationResource.getId())).thenReturn(applicationResource);
when(applicationService.getLeadOrganisation(applicationResource.getId())).thenReturn(organisationsMap.get("Empire Ltd"));
return applicationResource;
}
private Map<String, UserResource> setupUserResources() {
List<UserResource> userResources = newUserResource()
.withFirstName("Jessica", "Paul", "Steve", "Paul")
.withLastName("Doe", "Tom", "Smith", "Davidson")
.withEmail("jessica.doe@ludlow.com", "paul.tom@egg.com", "steve.smith@empire.com", "paul.davidson@empire.com")
.build(4);
return simpleToMap(userResources, UserResource::getEmail);
}
private UserResource setupLeadApplicant(ApplicationResource applicationResource, Map<String, UserResource> usersMap) {
UserResource leadApplicant = usersMap.get("steve.smith@empire.com");
when(userService.getLeadApplicantProcessRoleOrNull(applicationResource)).thenReturn(newProcessRoleResource()
.withUser(leadApplicant)
.build());
when(userService.findById(leadApplicant.getId())).thenReturn(leadApplicant);
return leadApplicant;
}
private Map<String, OrganisationResource> setupOrganisationResources() {
List<OrganisationResource> organisationResources = newOrganisationResource()
.withName("Ludlow", "EGGS", "Empire Ltd", "Org X")
.build(4);
return simpleToMap(organisationResources, OrganisationResource::getName);
}
private List<InviteOrganisationResource> setupOrganisationInvitesWithInviteForLeadOrg(long applicationId,
Map<String, UserResource> usersMap,
Map<String, OrganisationResource> organisationsMap) {
UserResource user1 = usersMap.get("jessica.doe@ludlow.com");
UserResource user2 = usersMap.get("paul.tom@egg.com");
UserResource user3 = usersMap.get("paul.davidson@empire.com");
List<ApplicationInviteResource> invitesOrg1 = newApplicationInviteResource()
.withUsers(user1.getId(), null)
.withNameConfirmed(user1.getName(), null)
.withName("Jess Doe", "Ryan Dell")
.withEmail(user1.getEmail(), "ryan.dell@ludlow.com")
.withStatus(OPENED, SENT)
.build(2);
List<ApplicationInviteResource> invitesOrg2 = newApplicationInviteResource()
.withUsers(user2.getId())
.withNameConfirmed(user2.getName())
.withName(user2.getName())
.withEmail(user2.getEmail())
.withStatus(OPENED)
.build(1);
List<ApplicationInviteResource> invitesOrg3 = newApplicationInviteResource()
.withUsers(user3.getId())
.withNameConfirmed(user3.getName())
.withName(user3.getName())
.withEmail(user3.getEmail())
.withStatus(OPENED)
.build(1);
OrganisationResource org1 = organisationsMap.get("Ludlow");
OrganisationResource org2 = organisationsMap.get("EGGS");
OrganisationResource org3 = organisationsMap.get("Empire Ltd");
OrganisationResource org4 = organisationsMap.get("Org X");
List<InviteOrganisationResource> inviteOrganisationResources = newInviteOrganisationResource()
.withOrganisation(org1.getId(), org2.getId(), org3.getId(), org4.getId())
.withOrganisationName(org1.getName(), org2.getName(), org3.getName(), org4.getName())
.withOrganisationNameConfirmed(org1.getName(), org2.getName(), org3.getName(), org4.getName())
.withInviteResources(invitesOrg1, invitesOrg2, invitesOrg3, null)
.build(4);
when(inviteRestService.getInvitesByApplication(applicationId)).thenReturn(restSuccess(inviteOrganisationResources));
return inviteOrganisationResources;
}
private List<InviteOrganisationResource> setupOrganisationInvitesWithoutInvitesForLeadOrg(long applicationId,
Map<String, UserResource> usersMap,
Map<String, OrganisationResource> organisationsMap) {
UserResource user1 = usersMap.get("jessica.doe@ludlow.com");
UserResource user2 = usersMap.get("paul.tom@egg.com");
List<ApplicationInviteResource> invitesOrg1 = newApplicationInviteResource()
.withUsers(user1.getId(), null)
.withNameConfirmed(user1.getName(), null)
.withName("Jess Doe", "Ryan Dell")
.withEmail(user1.getEmail(), "ryan.dell@ludlow.com")
.withStatus(OPENED, SENT)
.build(2);
List<ApplicationInviteResource> invitesOrg2 = newApplicationInviteResource()
.withUsers(user2.getId())
.withNameConfirmed(user2.getName())
.withName(user2.getName())
.withEmail(user2.getEmail())
.withStatus(OPENED)
.build(1);
OrganisationResource org1 = organisationsMap.get("Ludlow");
OrganisationResource org2 = organisationsMap.get("EGGS");
List<InviteOrganisationResource> inviteOrganisationResources = newInviteOrganisationResource()
.withOrganisation(org1.getId(), org2.getId())
.withOrganisationName(org1.getName(), org2.getName())
.withOrganisationNameConfirmed(org1.getName(), org2.getName())
.withInviteResources(invitesOrg1, invitesOrg2)
.build(2);
when(inviteRestService.getInvitesByApplication(applicationId)).thenReturn(restSuccess(inviteOrganisationResources));
return inviteOrganisationResources;
}
private List<InviteOrganisationResource> setupOrganisationInvitesWithAnUnconfirmedOrganisation(long applicationId,
Map<String, UserResource> usersMap,
Map<String, OrganisationResource> organisationsMap) {
UserResource user1 = usersMap.get("jessica.doe@ludlow.com");
UserResource user2 = usersMap.get("paul.tom@egg.com");
UserResource user3 = usersMap.get("paul.davidson@empire.com");
List<ApplicationInviteResource> invitesOrg1 = newApplicationInviteResource()
.withUsers(user1.getId(), null)
.withNameConfirmed(user1.getName(), null)
.withName("Jess Doe", "Ryan Dell")
.withEmail(user1.getEmail(), "ryan.dell@ludlow.com")
.withStatus(SENT, SENT)
.build(2);
List<ApplicationInviteResource> invitesOrg2 = newApplicationInviteResource()
.withUsers(user2.getId())
.withNameConfirmed(user2.getName())
.withName(user2.getName())
.withEmail(user2.getEmail())
.withStatus(OPENED)
.build(1);
List<ApplicationInviteResource> invitesOrg3 = newApplicationInviteResource()
.withUsers(user3.getId())
.withNameConfirmed(user3.getName())
.withName(user3.getName())
.withEmail(user3.getEmail())
.withStatus(OPENED)
.build(1);
OrganisationResource org2 = organisationsMap.get("EGGS");
OrganisationResource org3 = organisationsMap.get("Empire Ltd");
List<InviteOrganisationResource> inviteOrganisationResources = newInviteOrganisationResource()
.withOrganisation(null, org2.getId(), org3.getId())
.withOrganisationName("Ludlow", org2.getName(), org3.getName())
.withOrganisationNameConfirmed(null, org2.getName(), org3.getName())
.withInviteResources(invitesOrg1, invitesOrg2, invitesOrg3)
.build(3);
when(inviteRestService.getInvitesByApplication(applicationId)).thenReturn(restSuccess(inviteOrganisationResources));
return inviteOrganisationResources;
}
}
|
package org.collectionspace.chain.csp.schema;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Set;
import org.collectionspace.chain.csp.config.ReadOnlySection;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
/**
*
* @author caret
*
*
*/
public class Record implements FieldParent {
private static final Logger log=LoggerFactory.getLogger(Record.class);
private String id;
private Map<String,Structure> structure=new HashMap<String,Structure>();
private Map<String,Record> subrecords=new HashMap<String,Record>();
private Map<String,FieldSet> fields=new HashMap<String,FieldSet>();
private Map<String,FieldSet> servicefields=new HashMap<String,FieldSet>();
private Map<String,FieldSet> repeatfields=new HashMap<String,FieldSet>();
private Map<String,Instance> instances=new HashMap<String,Instance>();
private Map<String,FieldSet> summarylist=new HashMap<String,FieldSet>();
private Map<String, Map<String, FieldSet>> minidataset=new HashMap<String, Map<String,FieldSet>>();
private Spec spec;
private FieldSet mini_summary,mini_number,display_name;
private Set<String> type;
/* UI Stuff */
private String web_url,terms_used_url,number_selector,row_selector,list_key,ui_url,tab_url,primaryfield;
private boolean in_findedit=false;
private boolean is_multipart=false;
private boolean has_terms_used = false;
private boolean has_refobj_used = true;
private boolean has_delete_method = false;
private String services_search_keyword = "kw";
/* Service stuff */
private String authorization_name,services_url,services_list_path,in_tag,urn_syntax,authority_vocab_type,services_instances_path,services_single_instance_path;
private Set<String> authorization_includes;
private Map<String,String> services_record_paths=new HashMap<String,String>();
private Map<String,Field> services_filter_param=new HashMap<String,Field>();
// XXX utility methods
Record(Spec parent,ReadOnlySection section) {
/* parameters */
// this is what the service layer id defaults to if not specified later
// standard = singular form of the concept
id=(String)section.getValue("/@id");
// record,authority,compute-displayname can have multiple types using commas
type=Util.getSetOrDefault(section,"/@type",new String[]{"record"});
//specified that it is included in the findedit uispec
in_findedit=Util.getBooleanOrDefault(section,"/@in-findedit",false);
//config whether service layer needs call as multipart or not
is_multipart=Util.getBooleanOrDefault(section,"/is-multipart",true);
//config whether record type has termsUsed or not (returns empty array in Json if = false )
has_terms_used = Util.getBooleanOrDefault(section,"/terms-used",true);
//config whether record type has relatedObj/procs or not (returns empty array in Json if = false )
has_refobj_used = Util.getBooleanOrDefault(section,"/refobj-used",true);
//config the keyword to use for searching
services_search_keyword = Util.getStringOrDefault(section,"/services-search-keyword","kw");
// Used to differentiate between authority and vocabulary on create
in_tag=Util.getStringOrDefault(section,"/membership-tag","inAuthority");
/* UI Layer helpers */
//ui layer path
web_url=Util.getStringOrDefault(section,"/web-url",id);
// specify url if not nameAuthority
terms_used_url=Util.getStringOrDefault(section,"/terms-used-url","nameAuthority");
//ui layer json row
number_selector=Util.getStringOrDefault(section,"/number-selector",".csc-entry-number");
//ui layer json used in list views
row_selector=Util.getStringOrDefault(section,"/row-selector",".csc-recordList-row:");
list_key=Util.getStringOrDefault(section,"/list-key","procedures"+id.substring(0,1).toUpperCase()+id.substring(1));
//ui layer path: defaults to web_url if not specified
ui_url=Util.getStringOrDefault(section,"/ui-url",web_url+".html");
//ui layer path
tab_url=Util.getStringOrDefault(section,"/tab-url",web_url+"-tab");
/* Service layer helpers */
//path that the service layer uses to access this record
services_url=Util.getStringOrDefault(section,"/services-url",id);
//authorization name
authorization_name = Util.getStringOrDefault(section,"/authorization-name",id);
if(type.contains("record")){
authorization_includes = Util.getSetOrDefault(section,"/authorization-includes",new String[]{services_url, "/"+services_url+"/*/authorityrefs/"});
}
else if(type.contains("authority")){
authorization_includes = Util.getSetOrDefault(section,"/authorization-includes",new String[]{services_url,services_url+"/*/items/", "/"+services_url+"/*/items/*/authorityrefs/", "/"+services_url+"/*/items/*/refobjs/", "/"+services_url+"/*/items/*/contacts/"});
}
else if(type.contains("id")){
authorization_includes = Util.getSetOrDefault(section,"/authorization-includes",new String[]{id,"idgenerators", "/idgenerators/*/ids/"});
}
else {
authorization_includes = Util.getSetOrDefault(section,"/authorization-includes",new String[]{});
}
//service layer paths to list data for this record type
services_list_path=Util.getStringOrDefault(section,"/services-list-path",services_url+"-common-list/"+services_url+"-list-item");
//used by service layer to construct authority names
urn_syntax=Util.getStringOrDefault(section,"/urn-syntax","urn:cspace.org.collectionspace.demo."+id+":name({vocab}):"+id+":name({entry})'{display}'");
authority_vocab_type = Util.getStringOrDefault(section, "/authority-vocab-type", "PersonAuthority");
services_instances_path=Util.getStringOrDefault(section,"/services-instances-path",
services_url+"_common:http://collectionspace.org/services/"+services_url+","+services_url+"-common-list/"+services_url+"-list-item");
services_single_instance_path=Util.getStringOrDefault(section,"/services-single-instance-path",
services_url+"_common:http://collectionspace.org/services/"+services_url+","+services_url+"-common");
primaryfield = Util.getStringOrDefault(section, "/primaryfield","");
has_delete_method = Util.getBooleanOrDefault(section, "/hasdeletemethod", false);
spec=parent;
}
public String getID() { return id; }
public String getWebURL() { return web_url; }
public String getUIURL() { return ui_url; }
public String getTabURL() { return tab_url; }
public boolean isType(String k) { return type.contains(k); }
public Spec getSpec() { return spec; }
public FieldSet[] getAllServiceFields() { return servicefields.values().toArray(new FieldSet[0]); }
public FieldSet[] getAllFields() { return fields.values().toArray(new FieldSet[0]); }
public FieldSet getField(String id) { return fields.get(id); }
public FieldSet[] getAllRepeatFields() { return repeatfields.values().toArray(new FieldSet[0]); }
/*
* includes all the fields that are children of repeats as well as top level fields.
*/
public FieldSet getRepeatField(String id) { return repeatfields.get(id); }
public Structure getStructure(String id) { return structure.get(id); }
public Record getSubrecord(String id) { return subrecords.get(id); }
public Record[] getAllSubRecords(){
if(subrecords.values().isEmpty()){
for(FieldSet fs : this.getAllRepeatFields()){
if(fs.usesRecord()){
this.addSubRecord(fs.usesRecordId());
}
}
}
return subrecords.values().toArray(new Record[0]);
}
public String getPrimaryField(){ return primaryfield; };
public Boolean hasPrimaryField(){ if(primaryfield.equals("")){return false;} else {return true;}}
public String getTermsUsedURL() { return terms_used_url; }
public String getNumberSelector() { return number_selector; }
public String getRowSelector() { return row_selector; }
public String getListKey() { return list_key; }
public boolean isInFindEdit() { return in_findedit; }
public boolean isMultipart() { return is_multipart; }
public boolean hasTermsUsed() { return has_terms_used; }
public boolean hasRefObjUsed() { return has_refobj_used; }
public boolean hasDeleteMethod() { return has_delete_method; }
public String getServicesSearchKeyword(){ return services_search_keyword; }
public String getInTag() { return in_tag; }
public String getURNSyntax() { return urn_syntax; }
public String getVocabType() {return authority_vocab_type; }
public Instance[] getAllInstances() { return instances.values().toArray(new Instance[0]); }
public Instance getInstance(String key) { return instances.get(key); }
public String getServicesURL() { return services_url; }
public String getServicesListPath() { return services_list_path; }
public String getServicesInstancesPath() { return services_instances_path; }
public String getServicesSingleInstancePath() { return services_single_instance_path; }
public String[] getServicesRecordPaths() { return services_record_paths.keySet().toArray(new String[0]); }
public String getServicesRecordPath(String name) { return services_record_paths.get(name); }
void setMiniNumber(Field f) { mini_number=f; }
void setMiniSummary(Field f) { mini_summary=f; }
void setMiniNumber(Repeat f) { mini_number=f; }
void setMiniSummary(Repeat f) { mini_summary=f; }
void setDisplayName(Field f) { display_name=f; }
void setServicesRecordPath(String section,String path) { services_record_paths.put(section,path); }
void setServicesFilterParam(String param,Field field) { services_filter_param.put(param,field); }
public FieldSet getMiniNumber() { return mini_number; }
public FieldSet getMiniSummary() { return mini_summary; }
public FieldSet[] getAllMiniSummaryList() { return summarylist.values().toArray(new FieldSet[0]); }
public FieldSet getMiniSummaryList(String key) { return summarylist.get(key); }
public FieldSet getDisplayNameField() { return display_name; }
public Field getFieldByServicesFilterParam(String param) { return services_filter_param.get(param); }
//authorization
public String getAuthorizationName(){ return authorization_name; }
public String[] getAllAuthorizationTypes(){ return authorization_includes.toArray(new String[0]) ; }
public Boolean isAuthorizationType(String name){
return authorization_includes.contains(name);
}
public void addField(FieldSet f) {
fields.put(f.getID(),f);
if(f.isInServices()){
servicefields.put(f.getID(),f);
}
}
public void addAllField(FieldSet f) {
repeatfields.put(f.getID(),f);
}
public void addStructure(Structure s) {
structure.put(s.getID(),s);
}
public void addSubRecord(Record r) {
subrecords.put(r.getID(),r);
}
public void addInstance(Instance n) {
instances.put(n.getID(),n);
spec.addInstance(n);
}
//obsolete?
public void addMiniSummaryList(FieldSet f){
summarylist.put(f.getID(), f);
}
public void addMiniDataSet(FieldSet f, String s){
//s:{ name: field, name: field, name: field }
if(!minidataset.containsKey(s)){
Map<String,FieldSet> subdata=new HashMap<String,FieldSet>();
minidataset.put(s, subdata);
}
minidataset.get(s).put(f.getID(), f);
}
public void addMiniDataSet(Repeat r, String s){
//s:{ name: field, name: field, name: field }
if(!minidataset.containsKey(s)){
Map<String,FieldSet> subdata=new HashMap<String,FieldSet>();
minidataset.put(s, subdata);
}
minidataset.get(s).put(r.getID(), r);
}
public FieldSet[] getMiniDataSetByName(String s){
if(minidataset.containsKey(s)){
return minidataset.get(s).values().toArray(new FieldSet[0]);
}
return new FieldSet[0];
}
public String[] getAllMiniDataSets(){
if(minidataset.isEmpty()){
return new String[0];
}
return minidataset.keySet().toArray(new String[0]);
}
void dump(StringBuffer out) {
out.append(" record id="+id+"\n");
out.append(" web_url="+web_url+"\n");
out.append(" type="+type+"\n");
}
public Record getRecord() { return this; }
public void config_finish(Spec spec) {
for(Instance n : instances.values())
n.config_finish(spec);
for(FieldSet fs : fields.values())
fs.config_finish(spec);
}
}
|
package org.eclipse.persistence.testing.oxm.mappings.binarydatacollection;
import java.io.ByteArrayInputStream;
import java.io.IOException;
import java.util.Vector;
import javax.activation.DataHandler;
import org.eclipse.persistence.internal.helper.ConversionManager;
import org.eclipse.persistence.internal.oxm.conversion.Base64;
public class EmployeeWithByteArrayObject {
public static final int DEFAULT_ID = 123;
private int id;
private Vector photos;
public EmployeeWithByteArrayObject() {
super();
}
public EmployeeWithByteArrayObject(int id) {
super();
this.id = id;
}
public EmployeeWithByteArrayObject(int id, Vector photos) {
super();
this.id = id;
this.photos = photos;
}
public static Employee example1() {
Vector photos = new Vector();
byte[] bytes = MyAttachmentUnmarshaller.PHOTO_BASE64.getBytes();
Byte[] objectBytes = new Byte[bytes.length];
for (int index = 0; index < bytes.length; index++) {
objectBytes[index] = new Byte(bytes[index]);
}
photos.addElement(objectBytes);
photos.addElement(objectBytes);
photos.addElement(objectBytes);
return new Employee(DEFAULT_ID, photos);
}
public int getID() {
return id;
}
public void setID(int newId) {
id = newId;
}
public Vector getPhotos() {
return photos;
}
public void setPhotos(Vector vectorOfPhotos) {
photos = vectorOfPhotos;
}
public String toString() {
String returnString = "Employee: " + this.getID() + " ";
if (getPhotos() != null) {
returnString += "Photos: ";
for (int i = 0; i < getPhotos().size(); i++) {
Object next = getPhotos().elementAt(i);
if (next != null) {
returnString += (next + "\n" + "-->" + new String(Base64.base64Encode(((byte[])ConversionManager.getDefaultManager().convertObject(next, byte[].class)))));
} else {
returnString += ("null_item" + " ");
}
}
}
return returnString;
}
public boolean equals(Object object) {
if (!(object instanceof EmployeeWithByteArrayObject)) {
return false;
}
EmployeeWithByteArrayObject employeeObject = (EmployeeWithByteArrayObject)object;
if ((this.getPhotos() == null) && (employeeObject.getPhotos() != null)) {
return false;
}
if ((employeeObject.getPhotos() == null) && (this.getPhotos() != null)) {
return false;
}
/**
* Note: do not use Vector.contains() for byte[] arrays since each .getBytes() will return
* a different hash-value and will not pass the embedded (==) during the .contain check.
* You must check each base64 byte in sequence
*/
if ((this.getID() == employeeObject.getID()) && (((this.getPhotos() == null) && (employeeObject.getPhotos() == null)) ||
(this.getPhotos().isEmpty() && employeeObject.getPhotos().isEmpty())) ) {
return true;
}
boolean equal = true;
// hash equality changes
for (int i = 0; i < getPhotos().size(); i++) {
try{
equal = equal && equalByteArrays((Byte[])getPhotos().get(i), (Byte[])employeeObject.getPhotos().get(i));
}catch(ClassCastException e){
equal = equal && equalDataHandlers((DataHandler)getPhotos().get(i), (DataHandler)employeeObject.getPhotos().get(i));
}
}
return equal;
}
private boolean equalDataHandlers(DataHandler data, DataHandler data2){
if(!data.getContentType().equals(data2.getContentType())){
return false;
}
try {
Object obj1 = data.getContent();
Object obj2 = data2.getContent();
if(data.getContent() instanceof ByteArrayInputStream && data2.getContent() instanceof ByteArrayInputStream){
ByteArrayInputStream controlStream = ((ByteArrayInputStream)data.getContent());
ByteArrayInputStream testStream = ((ByteArrayInputStream)data2.getContent());
if(controlStream.available() != testStream.available()){
return false;
}
Byte[] controlBytes = new Byte[controlStream.available()];
Byte[] testBytes = new Byte[testStream.available()];
if(!equalByteArrays(controlBytes, testBytes)){
return false;
}
}else{
if(!data.getContent().equals(data2.getContent())){
return false;
}
}
} catch (IOException e) {
e.printStackTrace();
return false;
}
return true;
}
// override the contains check on a Vector of byte[] arrays - see TypeDirectMappingTestSuite
private boolean equalByteArrays(Byte[] array1, Byte[] array2) {
if (array1.length != array2.length) {
return false;
}
// check each base64 byte in sequence
for (int i = 0; i < array1.length; i++) {
if (!(array1[i].equals(array2[i]))) {
return false;
}
}
return true;
}
}
|
package com.ethlo.dachs;
import java.util.ArrayList;
import java.util.Collection;
import java.util.LinkedList;
import java.util.List;
import java.util.stream.Collectors;
@EntityListenerIgnore
public class MutableEntityDataChangeSet implements EntityDataChangeSet
{
private final Collection<EntityDataChange> created;
private final Collection<EntityDataChange> updated;
private final Collection<EntityDataChange> deleted;
public MutableEntityDataChangeSet()
{
this.created = new LinkedList<>();
this.updated = new LinkedList<>();
this.deleted = new LinkedList<>();
}
public static EntityDataChangeSet clone(EntityDataChangeSet cs)
{
final MutableEntityDataChangeSet e = new MutableEntityDataChangeSet();
e.getCreated().addAll(clone(cs.getCreated()));
e.getUpdated().addAll(clone(cs.getUpdated()));
e.getDeleted().addAll(clone(cs.getDeleted()));
return e;
}
private static Collection<? extends EntityDataChange> clone(Collection<EntityDataChange> l)
{
return l.stream().map(i->clone(i)).collect(Collectors.toList());
}
private static EntityDataChange clone(EntityDataChange edc)
{
return new EntityDataChangeImpl(edc.getId(), edc.getEntity(), clonePropChanges(edc.getPropertyChanges()));
}
@SuppressWarnings({ "unchecked", "rawtypes" })
private static Collection<PropertyChange<?>> clonePropChanges(Collection<PropertyChange<?>> propertyChanges)
{
final List<PropertyChange<?>> r = new ArrayList<>();
propertyChanges
.stream()
.forEach(e->r.add(new PropertyChange(e.getPropertyName(), e.getPropertyType(), e.getOldValue(), e.getNewValue())));
return r;
}
@Override
public Collection<EntityDataChange> getCreated()
{
return created;
}
@Override
public Collection<EntityDataChange> getUpdated()
{
return updated;
}
@Override
public Collection<EntityDataChange> getDeleted()
{
return deleted;
}
@Override
public String toString() {
return "ChangeSet [" + created.size() + " created=" + created + ", " + updated.size() + " updated=" + updated + ", " + deleted.size() + " deleted=" + deleted + "]";
}
@Override
public boolean isEmpty()
{
return created.isEmpty() && updated.isEmpty() && deleted.isEmpty();
}
}
|
package com.x.organization.assemble.control.jaxrs.personcard;
import java.io.ByteArrayInputStream;
import java.io.ByteArrayOutputStream;
import java.io.File;
import java.util.List;
import java.awt.image.BufferedImage;
import javax.imageio.ImageIO;
import javax.persistence.EntityManager;
import javax.persistence.criteria.CriteriaBuilder;
import javax.persistence.criteria.CriteriaQuery;
import javax.persistence.criteria.Predicate;
import javax.persistence.criteria.Root;
import com.x.base.core.container.EntityManagerContainer;
import com.x.base.core.container.factory.EntityManagerContainerFactory;
import com.x.base.core.project.exception.ExceptionEntityNotExist;
import com.x.base.core.project.exception.ExceptionPersonNotExist;
import com.x.base.core.project.http.ActionResult;
import com.x.base.core.project.http.EffectivePerson;
import com.x.base.core.project.jaxrs.WoFile;
import com.x.base.core.project.jaxrs.WoId;
import com.x.base.core.project.tools.DateTools;
import com.x.organization.assemble.control.Business;
import com.x.organization.assemble.control.jaxrs.personcard.ActionCreateCode.Wo;
import com.x.organization.assemble.control.staticconfig.FollowConfig;
import com.x.organization.core.entity.Identity;
import com.x.organization.core.entity.Identity_;
import com.x.organization.core.entity.Person;
import com.x.organization.core.entity.Unit;
import com.x.organization.core.entity.UnitDuty;
import com.x.organization.core.entity.UnitDuty_;
import org.apache.commons.codec.binary.Base64;
class ActionPersonCode extends BaseAction {
ActionResult<Wo> personcode(EffectivePerson effectivePerson, String flag) throws Exception {
try (EntityManagerContainer emc = EntityManagerContainerFactory.instance().create()) {
ActionResult<Wo> result = new ActionResult<>();
Business business = new Business(emc);
Person personCard = emc.find(flag, Person.class);
if (null == personCard) {
throw new ExceptionPersonNotExist(flag);
}
String fname = personCard.getId()+".png";
String content = "BEGIN:VCARD\n" +
"VERSION:3.0\n" +
"N:"+personCard.getName()+"\n";
if(personCard.getOfficePhone()!=null && !personCard.getOfficePhone().equals("")){
content = content+"TEL:"+personCard.getOfficePhone()+"\n";
}
if(personCard.getMobile()!=null && !personCard.getMobile().equals("")){
content = content+"TEL;CELL:"+personCard.getMobile()+"\n";
}
/*if(!personCard.getAddress().equals("")){
content = content+"ADR;HOME;POSTAL:;;"+personCard.getAddress()+";;;;\n";
}*/
if(personCard.getMail()!=null && !personCard.getMail().equals("")){
content = content+"EMAIL:"+personCard.getMail()+"\n";
}
if(personCard.getQq()!=null && !personCard.getQq().equals("")){
content = content+"X-QQ:"+personCard.getQq()+"\n";
}
if(personCard.getWeixin()!=null && !personCard.getWeixin().equals("")){
content = content+"NOTE::"+personCard.getWeixin()+"\n";
}
if(personCard.getBirthday()!=null && !personCard.getBirthday().equals("")){
content = content+"BDAY:"+DateTools.formatDate(personCard.getBirthday())+"\n";
}
if(personCard.getId()!=null && !personCard.getId().equals("")){
List<Identity> identityList = referenceIdentity(business,flag);
if(identityList.isEmpty()){
if(!personCard.getTopUnitList().isEmpty()){
String TopUnitId = personCard.getTopUnitList().get(0);
Unit unit = emc.find(flag, Unit.class);
if (null == unit) {
throw new ExceptionEntityNotExist(flag);
}
content = content+"ORG:"+unit.getName()+"\n";
}
}else{
String orgString = "";
String titleString = "";
for (Identity identity : identityList) {
orgString = orgString.equals("")?identity.getUnitLevelName():orgString +";"+identity.getUnitLevelName();
List<UnitDuty> unitdutyList = referenceUnitduty(business,identity.getId());
if(!unitdutyList.isEmpty()){
for(UnitDuty unitduty : unitdutyList){
if(null != unitduty){
titleString = titleString.equals("")?unitduty.getName():titleString +";"+unitduty.getName();
}
}
}
}
if(!orgString.equals("")){
content = content+"ORG:"+orgString+"\n";
}
if(!titleString.equals("")){
content = content+"TITLE:"+titleString+"\n";
}
}
}
content = content+"END:VCARD";
/*
File logoFile = null;
if(personCard.getIconMdpi()!=null && !personCard.getIconMdpi().equals("")){
logoFile = CodeUtil.decoderBase64File(logopath,personCard.getIconMdpi());
}
File QrCodeFile = new File(path);
CodeUtil.drawLogoQRCode(logoFile, QrCodeFile, content, "");*/
BufferedImage logoFile = null;
ByteArrayOutputStream QrCodeFile = new ByteArrayOutputStream();
if(personCard.getIconMdpi()!=null && !personCard.getIconMdpi().equals("")){
//byte[] buffer = new BASE64Decoder().decodeBuffer(personCard.getIconMdpi());
byte[] buffer = Base64.decodeBase64(personCard.getIconMdpi());
ByteArrayInputStream in = new ByteArrayInputStream(buffer);
logoFile = ImageIO.read(in); //inimageinByteArrayInputStream();
}
Wo wo = new Wo(CodeUtil.drawLogoQRCodeByte(logoFile, QrCodeFile, content, ""), this.contentType(false, fname), this.contentDisposition(false, fname));
result.setData(wo);
return result;
}
}
public static class Wo extends WoFile {
public Wo(byte[] bytes, String contentType, String contentDisposition) {
super(bytes, contentType, contentDisposition);
}
}
public List<Identity> referenceIdentity(Business business,String flag) throws Exception {
EntityManager em = business.entityManagerContainer().get(Identity.class);
CriteriaBuilder cb = em.getCriteriaBuilder();
CriteriaQuery<Identity> cq = cb.createQuery(Identity.class);
Root<Identity> root = cq.from(Identity.class);
Predicate p = cb.equal(root.get(Identity_.person), flag);
return em.createQuery(cq.select(root).where(p)).getResultList();
}
public List<UnitDuty> referenceUnitduty(Business business,String flag) throws Exception {
EntityManager em = business.entityManagerContainer().get(UnitDuty.class);
CriteriaBuilder cb = em.getCriteriaBuilder();
CriteriaQuery<UnitDuty> cq = cb.createQuery(UnitDuty.class);
Root<UnitDuty> root = cq.from(UnitDuty.class);
Predicate p = cb.isMember(flag, root.get(UnitDuty_.identityList));
return em.createQuery(cq.select(root).where(p)).getResultList();
}
}
|
package com.irccloud.android;
import java.util.Iterator;
import java.util.Timer;
import java.util.TimerTask;
import java.util.Map.Entry;
import org.json.JSONObject;
import android.annotation.SuppressLint;
import android.content.Context;
import android.content.Intent;
import android.content.SharedPreferences;
import android.util.Log;
import com.google.android.gcm.GCMBaseIntentService;
import com.google.android.gcm.GCMRegistrar;
import com.google.gson.JsonElement;
import com.google.gson.JsonObject;
import com.google.gson.JsonParser;
public class GCMIntentService extends GCMBaseIntentService {
public static final String GCM_ID = "";
@Override
protected void onError(Context context, String errorId) {
Log.e("IRCCloud", "GCM Error: " + errorId);
}
@SuppressLint("NewApi")
@Override
protected void onMessage(Context context, Intent intent) {
Log.i("IRCCloud", "Recieved GCM message!");
if(intent != null && intent.getExtras() != null) {
Log.d("IRCCloud", "GCM K/V pairs: " + intent.getExtras().toString());
try {
String type = intent.getStringExtra("type");
if(type.equalsIgnoreCase("heartbeat_echo")) {
NetworkConnection conn = NetworkConnection.getInstance();
JsonParser parser = new JsonParser();
JsonObject seenEids = parser.parse(intent.getStringExtra("seenEids")).getAsJsonObject();
Iterator<Entry<String, JsonElement>> i = seenEids.entrySet().iterator();
while(i.hasNext()) {
Entry<String, JsonElement> entry = i.next();
JsonObject eids = entry.getValue().getAsJsonObject();
Iterator<Entry<String, JsonElement>> j = eids.entrySet().iterator();
while(j.hasNext()) {
Entry<String, JsonElement> eidentry = j.next();
String bid = eidentry.getKey();
long eid = eidentry.getValue().getAsLong();
if(conn.ready && conn.getState() != NetworkConnection.STATE_CONNECTED)
BuffersDataSource.getInstance().updateLastSeenEid(Integer.valueOf(bid), eid);
Notifications.getInstance().deleteOldNotifications(Integer.valueOf(bid), eid);
Notifications.getInstance().updateLastSeenEid(Integer.valueOf(bid), eid);
}
}
} else {
int cid = Integer.valueOf(intent.getStringExtra("cid"));
int bid = Integer.valueOf(intent.getStringExtra("bid"));
long eid = Long.valueOf(intent.getStringExtra("eid"));
if(Notifications.getInstance().getNotification(eid) != null) {
Log.d("IRCCloud", "A notification for this event already exists in the db, ignoring");
return;
}
String from = intent.getStringExtra("from_nick");
String msg = ColorFormatter.html_to_spanned(ColorFormatter.irc_to_html(intent.getStringExtra("msg"))).toString();
String chan = intent.getStringExtra("chan");
if(chan == null)
chan = "";
String buffer_type = intent.getStringExtra("buffer_type");
String server_name = intent.getStringExtra("server_name");
if(server_name == null || server_name.length() == 0)
server_name = intent.getStringExtra("server_hostname");
String network = Notifications.getInstance().getNetwork(cid);
if(network == null)
Notifications.getInstance().addNetwork(cid, server_name);
Notifications.getInstance().deleteNotification(cid, bid, eid);
Notifications.getInstance().addNotification(cid, bid, eid, from, msg, chan, buffer_type, type);
if(buffer_type.equals("channel"))
Notifications.getInstance().showNotifications(chan + ": <" + from + "> " + msg);
else
Notifications.getInstance().showNotifications(from + ": " + msg);
}
} catch (Exception e) {
e.printStackTrace();
Log.w("IRCCloud", "Unable to parse GCM message");
}
}
}
public static void scheduleRegisterTimer(int delay) {
final int retrydelay = delay;
new Timer().schedule(new TimerTask() {
@Override
public void run() {
if(!GCMRegistrar.isRegistered(IRCCloudApplication.getInstance().getApplicationContext()) || !IRCCloudApplication.getInstance().getApplicationContext().getSharedPreferences("prefs", 0).contains("session_key")) {
Log.w("IRCCloud", "Not logged in, not posting GCM id");
return;
}
if(IRCCloudApplication.getInstance().getApplicationContext().getSharedPreferences("prefs", 0).contains("gcm_registered")) {
Log.w("IRCCloud", "Already POSTed this ID");
return;
}
boolean success = false;
try {
JSONObject result = NetworkConnection.getInstance().registerGCM(GCMRegistrar.getRegistrationId(IRCCloudApplication.getInstance().getApplicationContext()), IRCCloudApplication.getInstance().getApplicationContext().getSharedPreferences("prefs", 0).getString("session_key", ""));
if(result.has("success"))
success = result.getBoolean("success");
} catch (Exception e) {
e.printStackTrace();
}
if(success) {
SharedPreferences.Editor editor = IRCCloudApplication.getInstance().getApplicationContext().getSharedPreferences("prefs", 0).edit();
editor.putBoolean("gcm_registered", true);
editor.commit();
} else {
Log.e("IRCCloud", "Failed to register device ID, will retry in " + ((retrydelay*2)/1000) + " seconds");
scheduleRegisterTimer(retrydelay * 2);
}
}
}, delay);
}
@Override
protected void onRegistered(Context context, String regId) {
Log.i("IRCCloud", "GCM registered, id: " + regId);
scheduleRegisterTimer(30000);
}
@Override
protected void onUnregistered(Context context, String regId) {
Log.i("IRCCloud", "GCM unregistered, id: " + regId);
SharedPreferences.Editor editor = getSharedPreferences("prefs", 0).edit();
editor.remove("gcm_registered");
editor.commit();
}
}
|
package org.ihtsdo.buildcloud.dao;
import com.amazonaws.services.s3.AmazonS3Client;
import com.amazonaws.services.s3.model.*;
import com.hazelcast.core.IQueue;
import org.ihtsdo.buildcloud.dao.helper.ExecutionS3PathHelper;
import org.ihtsdo.buildcloud.entity.Build;
import org.ihtsdo.buildcloud.entity.Execution;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.beans.factory.annotation.Required;
import org.springframework.util.FileCopyUtils;
import org.springframework.util.StreamUtils;
import java.io.*;
import java.util.ArrayList;
import java.util.List;
import java.util.zip.ZipEntry;
import java.util.zip.ZipOutputStream;
public class ExecutionDAOImpl implements ExecutionDAO {
@Autowired
private AmazonS3Client s3Client;
@Autowired
private ExecutionS3PathHelper pathHelper;
@Autowired
private String executionS3BucketName;
private IQueue<String> buildQueue;
private static final String BLANK = "";
private static final Logger LOGGER = LoggerFactory.getLogger(ExecutionDAOImpl.class);
@Override
public void save(Execution execution, String jsonConfig) {
saveToBucket(execution, jsonConfig);
}
@Override
public ArrayList<Execution> findAll(Build build) {
String buildDirectoryPath = pathHelper.getBuildPath(build).toString();
ArrayList<Execution> executions = findExecutions(buildDirectoryPath, build);
return executions;
}
@Override
public Execution find(Build build, String executionId) {
String executionDirectoryPath = pathHelper.getExecutionPath(build, executionId).toString();
ArrayList<Execution> executions = findExecutions(executionDirectoryPath, build);
if (!executions.isEmpty()) {
return executions.get(0);
} else {
return null;
}
}
@Override
public String loadConfiguration(Execution execution) throws IOException {
String configFilePath = pathHelper.getConfigFilePath(execution);
S3Object s3Object = s3Client.getObject(executionS3BucketName, configFilePath);
if (s3Object != null) {
S3ObjectInputStream objectContent = s3Object.getObjectContent();
return FileCopyUtils.copyToString(new InputStreamReader(objectContent));
} else {
return null;
}
}
@Override
public void saveBuildScripts(File sourceDirectory, Execution execution) {
saveFiles(sourceDirectory, pathHelper.getBuildScriptsPath(execution));
}
@Override
public void streamBuildScriptsZip(Execution execution, OutputStream outputStream) throws IOException {
StringBuffer buildScriptsPath = pathHelper.getBuildScriptsPath(execution);
streamS3FilesAsZip(buildScriptsPath.toString(), outputStream);
}
@Override
public void queueForBuilding(Execution execution) {
execution.setStatus(Execution.Status.QUEUED);
saveStatus(execution);
String executionApiUrl = String.format("http://localhost/api/v1/builds/%s/executions/%s/", execution.getBuild().getId(), execution.getId());
buildQueue.add(executionApiUrl);
}
private void saveFiles(File sourceDirectory, StringBuffer targetDirectoryPath) {
File[] files = sourceDirectory.listFiles();
for (File file : files) {
StringBuffer filePath = new StringBuffer(targetDirectoryPath).append(file.getName());
if (file.isFile()) {
s3Client.putObject(executionS3BucketName, filePath.toString(), file);
} else if (file.isDirectory()) {
filePath.append(pathHelper.SEPARATOR);
saveFiles(file, filePath);
}
}
}
private ArrayList<Execution> findExecutions(String buildDirectoryPath, Build build) {
ArrayList<Execution> executions = new ArrayList<>();
LOGGER.info("List s3 objects {}, {}", executionS3BucketName, buildDirectoryPath);
ListObjectsRequest listObjectsRequest = new ListObjectsRequest(executionS3BucketName, buildDirectoryPath, null, null, 100);
ObjectListing objectListing = s3Client.listObjects(listObjectsRequest);
List<S3ObjectSummary> objectSummaries = objectListing.getObjectSummaries();
for (S3ObjectSummary objectSummary : objectSummaries) {
String key = objectSummary.getKey();
LOGGER.debug("Found key {}", key);
if (key.contains("/status:")) {
String[] keyParts = key.split("/");
String dateString = keyParts[2];
String status = keyParts[3].split(":")[1];
Execution execution = new Execution(dateString, status, build);
executions.add(execution);
}
}
LOGGER.debug("Found {} Executions", executions.size());
return executions;
}
private void saveToBucket(Execution execution, String jsonConfig) {
// Save config file
String configPath = pathHelper.getConfigFilePath(execution);
putFile(configPath, jsonConfig);
// Save status file
saveStatus(execution);
}
private void saveStatus(Execution execution) {
String statusFilePath = pathHelper.getStatusFilePath(execution, execution.getStatus().toString());
putFile(statusFilePath, BLANK);
}
private PutObjectResult putFile(String filePath, String contents) {
return s3Client.putObject(executionS3BucketName, filePath,
new ByteArrayInputStream(contents.getBytes()), new ObjectMetadata());
}
private void streamS3FilesAsZip(String buildScriptsPath, OutputStream outputStream) throws IOException {
LOGGER.debug("Serving zip of files in {}", buildScriptsPath);
ObjectListing objectListing = s3Client.listObjects(executionS3BucketName, buildScriptsPath);
int buildScriptsPathLength = buildScriptsPath.length();
ZipOutputStream zipOutputStream = new ZipOutputStream(outputStream);
for (S3ObjectSummary summary : objectListing.getObjectSummaries()) {
String key = summary.getKey();
String relativePath = key.substring(buildScriptsPathLength);
LOGGER.debug("Zip entry. S3Key {}, Entry path {}", key, relativePath);
zipOutputStream.putNextEntry(new ZipEntry(relativePath));
S3Object object = s3Client.getObject(executionS3BucketName, key);
try (InputStream objectContent = object.getObjectContent()) {
StreamUtils.copy(objectContent, zipOutputStream);
}
}
zipOutputStream.close();
}
@Required
public void setBuildQueue(IQueue<String> buildQueue) {
this.buildQueue = buildQueue;
}
public void setS3Client(AmazonS3Client s3Client) {
this.s3Client = s3Client;
}
}
|
package io.oasp.gastronomy.restaurant.salesmanagement.logic.impl;
import io.oasp.gastronomy.restaurant.general.common.AbstractSpringIntegrationTest;
import io.oasp.gastronomy.restaurant.general.common.api.datatype.Money;
import io.oasp.gastronomy.restaurant.salesmanagement.common.api.OrderPosition;
import io.oasp.gastronomy.restaurant.salesmanagement.common.api.datatype.OrderPositionState;
import io.oasp.gastronomy.restaurant.salesmanagement.common.api.datatype.ProductOrderState;
import io.oasp.gastronomy.restaurant.salesmanagement.dataaccess.api.dao.OrderPositionDao;
import io.oasp.gastronomy.restaurant.salesmanagement.logic.api.Salesmanagement;
import io.oasp.gastronomy.restaurant.salesmanagement.logic.api.to.OrderEto;
import io.oasp.gastronomy.restaurant.salesmanagement.logic.api.to.OrderPositionEto;
import io.oasp.gastronomy.restaurant.tablemanagement.logic.api.to.TableEto;
import io.oasp.module.configuration.common.api.ApplicationConfigurationConstants;
import javax.inject.Inject;
import org.junit.Test;
import org.springframework.test.context.ContextConfiguration;
/**
* This is the test-case of {@link Salesmanagement}.
*
* @author hohwille
*/
@ContextConfiguration({ ApplicationConfigurationConstants.BEANS_LOGIC })
public class SalesManagementTest extends AbstractSpringIntegrationTest {
@Inject
private Salesmanagement salesManagement;
@Inject
private OrderPositionDao orderPositionDao;
/**
* Tests if a Bill is persisted correctly. Special focus is on the mapping of {@link Money} and furthermore the query
* of one of the {@link Money} fields is tested.
*/
@Test
public void testSalesmanagement() {
TableEto table = new TableEto();
Long tableId = 1L;
table.setId(tableId);
OrderEto order = this.salesManagement.saveOrder(table);
assertEquals(tableId, Long.valueOf(order.getTableId()));
}
/**
* Tests if the {@link OrderPositionState} is persisted correctly. The test modifies the {@link OrderPositionState}
* through modifying the drinkState {@link ProductOrderState} which is a sub-state of the {@link OrderPosition}
*
*/
@Test
public void testOrderPositionStateChange() {
OrderPositionEto currentOrderPosition = new OrderPositionEto();
Long orderPositionId = 1L;
currentOrderPosition.setId(orderPositionId);
OrderPositionState newState = OrderPositionState.PAYED;
ProductOrderState newDrinkState = ProductOrderState.PREPARED;
this.salesManagement.markOrderPositionDrinkAs(currentOrderPosition, newState, newDrinkState);
OrderPosition orderPosition = this.orderPositionDao.findOne(orderPositionId);
assertEquals(orderPosition.getState(), newState);
}
}
|
package com.jefftharris.passwdsafe;
import java.io.File;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Collections;
import java.util.Comparator;
import java.util.HashMap;
import java.util.Map;
import java.util.TreeMap;
import org.pwsafe.lib.exception.InvalidPassphraseException;
import org.pwsafe.lib.file.PwsRecord;
import android.app.AlertDialog;
import android.app.Dialog;
import android.app.ExpandableListActivity;
import android.app.ProgressDialog;
import android.content.DialogInterface;
import android.content.Intent;
import android.content.SharedPreferences;
import android.content.DialogInterface.OnClickListener;
import android.net.Uri;
import android.os.AsyncTask;
import android.os.Bundle;
import android.preference.PreferenceManager;
import android.view.LayoutInflater;
import android.view.Menu;
import android.view.MenuItem;
import android.view.View;
import android.widget.Button;
import android.widget.EditText;
import android.widget.ExpandableListAdapter;
import android.widget.ExpandableListView;
import android.widget.SimpleExpandableListAdapter;
import android.widget.TextView;
public class PasswdSafe extends ExpandableListActivity {
private static final String TAG = "PasswdSafe";
private static final int DIALOG_GET_PASSWD = 0;
private static final int DIALOG_PROGRESS = 1;
private static final int DIALOG_DETAILS = 2;
private static final int DIALOG_CHANGE_PASSWD = 3;
private static final int MENU_ADD_RECORD = 1;
private static final int MENU_DETAILS = 2;
private static final int MENU_CHANGE_PASSWD = 3;
private static final String RECORD = "record";
private static final String TITLE = "title";
private static final String GROUP = "group";
private static final String NO_GROUP_GROUP = "Records";
private static final int RECORD_VIEW_REQUEST = 0;
private static final int RECORD_ADD_REQUEST = 1;
private File itsFile;
private ActivityPasswdFile itsPasswdFile;
private LoadTask itsLoadTask;
private boolean itsGroupRecords = true;
private boolean itsIsSortCaseSensitive = true;
private final ArrayList<Map<String, String>> itsGroupData =
new ArrayList<Map<String, String>>();
private final ArrayList<ArrayList<HashMap<String, Object>>> itsChildData =
new ArrayList<ArrayList<HashMap<String, Object>>>();
/** Called when the activity is first created. */
@Override
public void onCreate(Bundle savedInstanceState)
{
super.onCreate(savedInstanceState);
PasswdSafeApp.dbginfo(TAG, "onCreate intent:" + getIntent());
itsFile = new File(getIntent().getData().getPath());
PasswdSafeApp app = (PasswdSafeApp)getApplication();
SharedPreferences prefs =
PreferenceManager.getDefaultSharedPreferences(this);
itsGroupRecords = PasswdSafeApp.getGroupRecordsPref(prefs);
itsIsSortCaseSensitive = PasswdSafeApp.getSortCaseSensitivePref(prefs);
itsPasswdFile = app.accessPasswdFile(itsFile, this);
setTitle(PasswdSafeApp.getAppFileTitle(itsFile, this));
if (!itsPasswdFile.isOpen()) {
showDialog(DIALOG_GET_PASSWD);
} else {
showFileData();
}
}
/* (non-Javadoc)
* @see android.app.Activity#onDestroy()
*/
@Override
protected void onDestroy()
{
PasswdSafeApp.dbginfo(TAG, "onDestroy");
super.onDestroy();
if (itsPasswdFile != null) {
itsPasswdFile.release();
}
}
/* (non-Javadoc)
* @see android.app.Activity#onPause()
*/
@Override
protected void onPause()
{
super.onPause();
removeDialog(DIALOG_GET_PASSWD);
if (itsLoadTask != null)
itsLoadTask.cancel(true);
}
/* (non-Javadoc)
* @see android.app.Activity#onResume()
*/
@Override
protected void onResume()
{
super.onResume();
itsPasswdFile.touch();
}
/* (non-Javadoc)
* @see android.app.Activity#onSaveInstanceState(android.os.Bundle)
*/
@Override
protected void onSaveInstanceState(Bundle outState)
{
removeDialog(DIALOG_GET_PASSWD);
removeDialog(DIALOG_PROGRESS);
super.onSaveInstanceState(outState);
}
/* (non-Javadoc)
* @see android.app.Activity#onCreateOptionsMenu(android.view.Menu)
*/
@Override
public boolean onCreateOptionsMenu(Menu menu)
{
MenuItem mi = menu.add(0, MENU_ADD_RECORD, 0, R.string.add_record);
mi.setIcon(android.R.drawable.ic_menu_add);
mi = menu.add(0, MENU_DETAILS, 0, R.string.details);
mi.setIcon(android.R.drawable.ic_menu_info_details);
mi = menu.add(0, MENU_CHANGE_PASSWD, 0, R.string.change_password);
mi.setIcon(android.R.drawable.ic_menu_edit);
return true;
}
/* (non-Javadoc)
* @see android.app.Activity#onPrepareOptionsMenu(android.view.Menu)
*/
@Override
public boolean onPrepareOptionsMenu(Menu menu)
{
MenuItem mi = menu.findItem(MENU_ADD_RECORD);
if (mi != null) {
boolean enabled = false;
if (itsPasswdFile != null) {
PasswdFileData fileData = itsPasswdFile.getFileData();
enabled = (fileData != null) && fileData.canEdit();
}
mi.setEnabled(enabled);
}
return super.onPrepareOptionsMenu(menu);
}
/* (non-Javadoc)
* @see android.app.Activity#onOptionsItemSelected(android.view.MenuItem)
*/
@Override
public boolean onOptionsItemSelected(MenuItem item)
{
boolean rc = true;
switch (item.getItemId()) {
case MENU_ADD_RECORD:
{
startActivityForResult(
new Intent(Intent.ACTION_INSERT, getIntent().getData(),
this, RecordEditActivity.class),
RECORD_ADD_REQUEST);
break;
}
case MENU_DETAILS:
{
showDialog(DIALOG_DETAILS);
break;
}
case MENU_CHANGE_PASSWD:
{
showDialog(DIALOG_CHANGE_PASSWD);
break;
}
default:
{
rc = super.onOptionsItemSelected(item);
break;
}
}
return rc;
}
/* (non-Javadoc)
* @see android.app.Activity#onActivityResult(int, int, android.content.Intent)
*/
@Override
protected void onActivityResult(int requestCode, int resultCode, Intent data)
{
PasswdSafeApp.dbginfo(TAG,
"onActivityResult req: " + requestCode +
", rc: " + resultCode);
if (((requestCode == RECORD_VIEW_REQUEST) ||
(requestCode == RECORD_ADD_REQUEST)) &&
(resultCode == PasswdSafeApp.RESULT_MODIFIED)) {
showFileData();
} else {
super.onActivityResult(requestCode, resultCode, data);
}
}
/* (non-Javadoc)
* @see android.app.Activity#onCreateDialog(int)
*/
@Override
protected Dialog onCreateDialog(int id)
{
Dialog dialog = null;
switch (id) {
case DIALOG_GET_PASSWD:
{
LayoutInflater factory = LayoutInflater.from(this);
final View passwdView =
factory.inflate(R.layout.passwd_entry, null);
AbstractDialogClickListener dlgClick =
new AbstractDialogClickListener()
{
@Override
public void onOkClicked(DialogInterface dialog)
{
EditText passwdInput = (EditText) passwdView
.findViewById(R.id.passwd_edit);
openFile(
new StringBuilder(passwdInput.getText().toString()));
}
@Override
public void onCancelClicked(DialogInterface dialog)
{
cancelFileOpen();
}
};
AlertDialog.Builder alert = new AlertDialog.Builder(this)
.setTitle("Open " + itsFile.getPath())
.setMessage("Enter password:")
.setView(passwdView)
.setPositiveButton("Ok", dlgClick)
.setNegativeButton("Cancel", dlgClick)
.setOnCancelListener(dlgClick);
dialog = alert.create();
break;
}
case DIALOG_PROGRESS:
{
ProgressDialog dlg = new ProgressDialog(this);
dlg.setTitle(PasswdSafeApp.getAppTitle(this));
dlg.setMessage("Loading " + itsFile.getName() + "...");
dlg.setIndeterminate(true);
dlg.setCancelable(true);
dialog = dlg;
break;
}
case DIALOG_DETAILS:
{
LayoutInflater factory = LayoutInflater.from(this);
final View detailsView =
factory.inflate(R.layout.file_details, null);
AlertDialog.Builder alert = new AlertDialog.Builder(this)
.setTitle(itsFile.getName())
.setView(detailsView)
.setNeutralButton(R.string.close, new OnClickListener()
{
public void onClick(DialogInterface dialog, int which)
{
dialog.dismiss();
}
});
dialog = alert.create();
break;
}
case DIALOG_CHANGE_PASSWD:
{
LayoutInflater factory = LayoutInflater.from(this);
View passwdView = factory.inflate(R.layout.change_passwd, null);
final EditText passwdEdit = (EditText)
passwdView.findViewById(R.id.password);
final EditText confirmEdit = (EditText)
passwdView.findViewById(R.id.password_confirm);
AbstractDialogClickListener dlgClick =
new AbstractDialogClickListener()
{
@Override
public void onOkClicked(DialogInterface dialog)
{
StringBuilder passwdText =
new StringBuilder(passwdEdit.getText().toString());
dialog.dismiss();
changePasswd(passwdText);
}
};
AlertDialog.Builder alert = new AlertDialog.Builder(this)
.setTitle(itsFile.getName())
.setView(passwdView)
.setPositiveButton("Ok", dlgClick)
.setNegativeButton("Cancel", dlgClick)
.setOnCancelListener(dlgClick);
AlertDialog alertDialog = alert.create();
final Button okButton =
alertDialog.getButton(AlertDialog.BUTTON_POSITIVE);
dialog = alertDialog;
break;
}
}
return dialog;
}
@Override
protected void onPrepareDialog(int id, Dialog dialog)
{
super.onPrepareDialog(id, dialog);
switch (id)
{
case DIALOG_DETAILS:
{
TextView tv;
tv = (TextView)dialog.findViewById(R.id.file);
tv.setText(itsFile.getPath());
PasswdFileData fileData = itsPasswdFile.getFileData();
tv = (TextView)dialog.findViewById(R.id.permissions);
tv.setText(fileData.canEdit() ?
R.string.read_write : R.string.read_only);
tv = (TextView)dialog.findViewById(R.id.num_groups);
tv.setText(Integer.toString(itsGroupData.size()));
tv = (TextView)dialog.findViewById(R.id.num_records);
tv.setText(Integer.toString(fileData.getRecords().size()));
break;
}
default:
{
break;
}
}
}
/* (non-Javadoc)
* @see android.app.ExpandableListActivity#onChildClick(android.widget.ExpandableListView, android.view.View, int, int, long)
*/
@Override
public boolean onChildClick(ExpandableListView parent,
View v,
int groupPosition,
int childPosition,
long id)
{
PasswdFileData fileData = itsPasswdFile.getFileData();
PwsRecord rec = (PwsRecord)
itsChildData.get(groupPosition).
get(childPosition).
get(RECORD);
Uri.Builder builder = getIntent().getData().buildUpon();
String uuid = fileData.getUUID(rec);
if (uuid != null) {
builder.appendQueryParameter("rec", uuid.toString());
}
Intent intent = new Intent(Intent.ACTION_VIEW, builder.build(),
this, RecordView.class);
startActivityForResult(intent, RECORD_VIEW_REQUEST);
return true;
}
private final void openFile(StringBuilder passwd)
{
removeDialog(DIALOG_GET_PASSWD);
showDialog(DIALOG_PROGRESS);
itsLoadTask = new LoadTask(passwd);
itsLoadTask.execute();
}
private final void changePasswd(StringBuilder passwd)
{
// TODO fill...
}
private final void showFileData()
{
itsGroupData.clear();
itsChildData.clear();
PasswdFileData fileData = itsPasswdFile.getFileData();
ArrayList<PwsRecord> records = fileData.getRecords();
RecordMapComparator comp =
new RecordMapComparator(itsIsSortCaseSensitive);
if (itsGroupRecords) {
TreeMap<String, ArrayList<PwsRecord>> recsByGroup;
if (itsIsSortCaseSensitive) {
recsByGroup = new TreeMap<String, ArrayList<PwsRecord>>();
} else {
recsByGroup = new TreeMap<String, ArrayList<PwsRecord>>(
String.CASE_INSENSITIVE_ORDER);
}
for (PwsRecord rec : records) {
String group = fileData.getGroup(rec);
if ((group == null) || (group.length() == 0)) {
group = NO_GROUP_GROUP;
}
ArrayList<PwsRecord> groupList = recsByGroup.get(group);
if (groupList == null) {
groupList = new ArrayList<PwsRecord>();
recsByGroup.put(group, groupList);
}
groupList.add(rec);
}
for (Map.Entry<String, ArrayList<PwsRecord>> entry :
recsByGroup.entrySet()) {
Map<String, String> groupInfo =
Collections.singletonMap(GROUP, entry.getKey());
itsGroupData.add(groupInfo);
ArrayList<HashMap<String, Object>> children =
new ArrayList<HashMap<String, Object>>();
for (PwsRecord rec : entry.getValue()) {
HashMap<String, Object> recInfo =
new HashMap<String, Object>();
String title = fileData.getTitle(rec);
if (title == null) {
title = "Untitled";
}
recInfo.put(TITLE, title);
recInfo.put(RECORD, rec);
children.add(recInfo);
}
Collections.sort(children, comp);
itsChildData.add(children);
}
} else {
Map<String, String> groupInfo =
Collections.singletonMap(GROUP, NO_GROUP_GROUP);
itsGroupData.add(groupInfo);
ArrayList<HashMap<String, Object>> children =
new ArrayList<HashMap<String, Object>>();
for (PwsRecord rec : records) {
HashMap<String, Object> recInfo = new HashMap<String, Object>();
String title = fileData.getTitle(rec);
if (title == null) {
title = "Untitled";
}
recInfo.put(TITLE, title);
recInfo.put(RECORD, rec);
children.add(recInfo);
}
Collections.sort(children, comp);
itsChildData.add(children);
}
ExpandableListAdapter adapter =
new SimpleExpandableListAdapter(PasswdSafe.this,
itsGroupData,
android.R.layout.simple_expandable_list_item_1,
new String[] { GROUP },
new int[] { android.R.id.text1 },
itsChildData,
android.R.layout.simple_expandable_list_item_1,
new String[] { TITLE },
new int[] { android.R.id.text1 });
setListAdapter(adapter);
if (itsGroupData.size() == 1) {
getExpandableListView().expandGroup(0);
}
}
private final void cancelFileOpen()
{
removeDialog(DIALOG_PROGRESS);
removeDialog(DIALOG_GET_PASSWD);
finish();
}
private final class LoadTask extends AsyncTask<Void, Void, Object>
{
private final StringBuilder itsPasswd;
private LoadTask(StringBuilder passwd)
{
itsPasswd = passwd;
}
/* (non-Javadoc)
* @see android.os.AsyncTask#doInBackground(Params[])
*/
@Override
protected Object doInBackground(Void... params)
{
try {
return new PasswdFileData(itsFile, itsPasswd);
} catch (Exception e) {
return e;
}
}
/* (non-Javadoc)
* @see android.os.AsyncTask#onCancelled()
*/
@Override
protected void onCancelled()
{
PasswdSafeApp.dbginfo(TAG, "LoadTask cancelled");
itsLoadTask = null;
cancelFileOpen();
}
/* (non-Javadoc)
* @see android.os.AsyncTask#onPostExecute(java.lang.Object)
*/
@Override
protected void onPostExecute(Object result)
{
if (isCancelled()) {
onCancelled();
return;
}
PasswdSafeApp.dbginfo(TAG, "LoadTask post execute");
dismissDialog(DIALOG_PROGRESS);
itsLoadTask = null;
if (result instanceof PasswdFileData) {
itsPasswdFile.setFileData((PasswdFileData)result);
showFileData();
} else if (result instanceof Exception) {
Exception e = (Exception)result;
if (((e instanceof IOException) &&
e.getMessage().equals("Invalid password")) ||
(e instanceof InvalidPassphraseException))
PasswdSafeApp.showFatalMsg("Invalid password",
PasswdSafe.this);
else
PasswdSafeApp.showFatalMsg(e, PasswdSafe.this);
}
}
}
private static final class RecordMapComparator implements
Comparator<HashMap<String, Object>>
{
private boolean itsIsSortCaseSensitive;
public RecordMapComparator(boolean sortCaseSensitive)
{
itsIsSortCaseSensitive = sortCaseSensitive;
}
public int compare(HashMap<String, Object> arg0,
HashMap<String, Object> arg1)
{
String title0 = arg0.get(TITLE).toString();
String title1 = arg1.get(TITLE).toString();
if (itsIsSortCaseSensitive) {
return title0.compareTo(title1);
} else {
return title0.compareToIgnoreCase(title1);
}
}
}
}
|
package com.google.training.cpd200.conference;
import com.google.api.server.spi.Constant;
/**
* Contains the client IDs and scopes for allowed clients consuming the conference API.
*/
public class Constants {
public static final String WEB_CLIENT_ID = "replace with your client id";
public static final String EMAIL_SCOPE = Constant.API_EMAIL_SCOPE;
public static final String API_EXPLORER_CLIENT_ID = Constant.API_EXPLORER_CLIENT_ID;
public static final String MEMCACHE_ANNOUNCEMENTS_KEY = "RECENT_ANNOUNCEMENTS";
}
|
package org.opennms.netmgt.provision.support;
import java.net.BindException;
import java.net.InetSocketAddress;
import java.net.SocketAddress;
import java.util.concurrent.Executor;
import java.util.concurrent.Executors;
import org.apache.mina.core.RuntimeIoException;
import org.apache.mina.core.future.CloseFuture;
import org.apache.mina.core.future.ConnectFuture;
import org.apache.mina.core.future.IoFutureListener;
import org.apache.mina.core.service.IoHandler;
import org.apache.mina.core.service.IoProcessor;
import org.apache.mina.core.service.SimpleIoProcessorPool;
import org.apache.mina.core.session.IoSessionInitializer;
import org.apache.mina.transport.socket.SocketConnector;
import org.apache.mina.transport.socket.nio.NioProcessor;
import org.apache.mina.transport.socket.nio.NioSession;
import org.apache.mina.transport.socket.nio.NioSocketConnector;
import org.opennms.core.utils.LogUtils;
/**
* <p>This {@link ConnectionFactory} type will create a new {@link NioSocketConnector}
* for every call to {@link #connect(SocketAddress, SocketAddress, IoSessionInitializer)}.
* This is a naive implementation that does not really take advantage of the asynchronous
* operations in MINA since it is creating new threads for each socket operation.</p>
*
* @author Seth
* @author ranger
* @author Duncan Mackintosh
*/
public class ConnectionFactoryNewConnectorImpl extends ConnectionFactory {
private static final Executor m_executor = Executors.newFixedThreadPool(Runtime.getRuntime().availableProcessors());
private static final IoProcessor<NioSession> m_processor = new SimpleIoProcessorPool<NioSession>(NioProcessor.class, m_executor);
private ThreadLocal<Integer> m_port = new ThreadLocal<Integer>();
private final Object m_portMutex = new Object();
/**
* Create a new factory. Private because one should use {@link #getFactory(int)}
*/
protected ConnectionFactoryNewConnectorImpl(int timeoutInMillis) {
super(timeoutInMillis);
}
private static final NioSocketConnector getSocketConnector(long timeout, IoHandler handler) {
// Create a new NioSocketConnector
NioSocketConnector connector = new NioSocketConnector(m_executor, m_processor);
// Enable SO_REUSEADDR on the socket so that TIMED_WAIT connections that are bound on the
// same port do not block new outgoing connections. If the connections are blocked, then
// the following exception will be thrown under heavy load:
// Caused by: java.net.SocketException: Invalid argument
// at sun.nio.ch.Net.connect(Native Method)
// at sun.nio.ch.SocketChannelImpl.connect(SocketChannelImpl.java:500)
// at org.apache.mina.transport.socket.nio.NioSocketConnector.connect(NioSocketConnector.java:188)
connector.getSessionConfig().setReuseAddress(true);
// Setting SO_LINGER will prevent TIME_WAIT sockets altogether because TCP connections will be
// forcefully terminated with RST packets. However, this doesn't seem to be necessary to maintain
// performance of the outgoing connections. As long as SO_REUSEADDR is set, the operating system
// and Java appear to recycle the ports effectively although some will remain in TIME_WAIT state.
//connector.getSessionConfig().setSoLinger(0);
connector.setHandler(handler);
connector.setConnectTimeoutMillis(timeout);
return connector;
}
/**
* <p>Connect to a remote socket. If org.opennms.netmgt.provision.maxConcurrentConnections
* is set, this may block until a connection slot is available.</p>
*
* <p>You must dispose both the {@link ConnectionFactoryNewConnectorImpl} and {@link ConnectFuture} when done
* by calling {@link #dispose(ConnectionFactoryNewConnectorImpl, ConnectFuture)}.</p>
*
* @param remoteAddress
* Destination address
* @param init
* Initialiser for the IoSession
* @return
* ConnectFuture from a Mina connect call
*/
@Override
public ConnectFuture connect(SocketAddress remoteAddress, IoSessionInitializer<? extends ConnectFuture> init, IoHandler handler) {
SocketConnector connector = getSocketConnector(getTimeout(), handler);
InetSocketAddress localAddress = null;
synchronized (m_portMutex) {
if (m_port.get() == null) {
// Fetch a new ephemeral port
localAddress = new InetSocketAddress(0);
m_port.set(localAddress.getPort());
} else {
localAddress = new InetSocketAddress(m_port.get());
}
}
final ConnectFuture cf = connector.connect(remoteAddress, localAddress, init);
cf.addListener(portSwitcher(connector, remoteAddress, init, handler));
cf.addListener(connectorDisposer(connector));
return cf;
}
private static IoFutureListener<ConnectFuture> connectorDisposer(final SocketConnector connector) {
return new IoFutureListener<ConnectFuture>() {
public void operationComplete(ConnectFuture future) {
try {
// Add a listener to the CloseFuture that will dispose of the connector once the
// conversation is complete
future.getSession().getCloseFuture().addListener(new IoFutureListener<CloseFuture>() {
@Override
public void operationComplete(CloseFuture future) {
LogUtils.debugf(this, "Disposing of connector: %s", Thread.currentThread().getName());
connector.dispose();
}
});
} catch (RuntimeIoException e) {
LogUtils.debugf(this, e, "Exception of type %s caught, disposing of connector: %s", e.getClass().getName(), Thread.currentThread().getName());
// This will be thrown in the event of a ConnectException for example
connector.dispose();
}
}
};
}
private IoFutureListener<ConnectFuture> portSwitcher(final SocketConnector connector, final SocketAddress remoteAddress, final IoSessionInitializer<? extends ConnectFuture> init, final IoHandler handler) {
return new IoFutureListener<ConnectFuture>() {
public void operationComplete(ConnectFuture future) {
try {
Throwable e = future.getException();
// If we failed to bind to the outgoing port...
if (e != null && e instanceof BindException) {
synchronized(m_portMutex) {
// ... then reset the port
LogUtils.warnf(this, "Resetting outgoing TCP port, value was %d", m_port.get());
m_port.set(null);
}
// and reattempt the connection
connect(remoteAddress, init, handler);
}
} catch (RuntimeIoException e) {
LogUtils.debugf(this, e, "Exception of type %s caught, disposing of connector: %s", e.getClass().getName(), Thread.currentThread().getName());
// This will be thrown in the event of a ConnectException for example
connector.dispose();
}
}
};
}
/**
* Delegates completely to {@link #connect(SocketAddress, SocketAddress, IoSessionInitializer, IoHandler)}
* since we are recreating connectors during each invocation.
*
* @param remoteAddress
* @param localAddress
* @param init
* @param handler
*/
@Override
public ConnectFuture reConnect(SocketAddress remoteAddress, IoSessionInitializer<? extends ConnectFuture> init, IoHandler handler) {
return connect(remoteAddress, init, handler);
}
@Override
protected void dispose() {
// Do nothing; we dispose of every NioSocketConnector as soon as a session is complete
}
}
|
package com.google.zxing.client.android;
import java.io.ByteArrayOutputStream;
import java.util.Map;
import android.graphics.Bitmap;
import android.os.Bundle;
import android.os.Handler;
import android.os.Looper;
import android.os.Message;
import android.util.Log;
import com.google.zxing.BinaryBitmap;
import com.google.zxing.DecodeHintType;
import com.google.zxing.MultiFormatReader;
import com.google.zxing.PlanarYUVLuminanceSource;
import com.google.zxing.ReaderException;
import com.google.zxing.Result;
import com.google.zxing.common.HybridBinarizer;
/**
*
*
* @author lijian
* @date 2017-8-27 4:41:36
*/
final class DecodeHandler extends Handler {
private static final String TAG = DecodeHandler.class.getSimpleName();
private final CaptureActivity activity;
private final MultiFormatReader multiFormatReader;
private boolean running = true;
/**
*
*
* @param activity
* @param hints
*
*/
DecodeHandler(CaptureActivity activity, Map<DecodeHintType, Object> hints) {
multiFormatReader = new MultiFormatReader();
multiFormatReader.setHints(hints);
this.activity = activity;
}
@Override
public void handleMessage(Message message) {
if (!running) {
return;
}
switch (message.what) {
case R.id.decode:// (CaptureActivityHandlerhandleMessage)-(cameraManager.requestPreviewFrame)
decode((byte[]) message.obj, message.arg1, message.arg2);
break;
case R.id.quit:// CaptureActivityHandler.quitSynchronously()
running = false;
Looper.myLooper().quit();
break;
}
}
/**
*
*
* @param data
* YUV
* @param width
*
* @param height
*
*/
private void decode(byte[] data, int width, int height) {
long start = System.currentTimeMillis();
Result rawResult = null;
// YUV
PlanarYUVLuminanceSource source = activity.getCameraManager()
.buildLuminanceSource(data, width, height);
if (source != null) {
// BinaryBitmap;HybridBinarizer
BinaryBitmap bitmap = new BinaryBitmap(new HybridBinarizer(source));
try {
rawResult = multiFormatReader.decodeWithState(bitmap);
} catch (ReaderException re) {
// continue
} finally {
multiFormatReader.reset();
}
}
Handler handler = activity.getHandler();
if (rawResult != null) {
// log
long end = System.currentTimeMillis();
Log.d(TAG, " " + (end - start) + " ms");
if (handler != null) {
Message message = Message.obtain(handler,
R.id.decode_succeeded, rawResult);
Bundle bundle = new Bundle();
bundleThumbnail(source, bundle);
message.setData(bundle);
message.sendToTarget();
}
} else {
if (handler != null) {
Message message = Message.obtain(handler, R.id.decode_failed);
message.sendToTarget();
}
}
}
/**
*
*
* @param source
*
* @param bundle
*/
private static void bundleThumbnail(PlanarYUVLuminanceSource source,
Bundle bundle) {
int[] pixels = source.renderThumbnail();
int width = source.getThumbnailWidth();
int height = source.getThumbnailHeight();
Bitmap bitmap = Bitmap.createBitmap(pixels, 0, width, width, height,
Bitmap.Config.ARGB_8888);
ByteArrayOutputStream out = new ByteArrayOutputStream();
// boolean compress(Bitmap.CompressFormat format, int quality,
// OutputStream stream)
// trueBitmapFactory.decodeStream()
// BitmapFactoryalpha(JPEG)
// (color
// depth),(bitdePth),,2n,8bit28
// format
// quality 0-100
// 0100PNGquality
// stream
// true
bitmap.compress(Bitmap.CompressFormat.JPEG, 50, out);
bundle.putByteArray(DecodeThread.BARCODE_BITMAP, out.toByteArray());
bundle.putFloat(DecodeThread.BARCODE_SCALED_FACTOR, (float) width
/ source.getWidth());
}
}
|
package org.osgi.test.cases.deploymentadmin.tc1.tb1.DeploymentAdmin;
import org.osgi.service.deploymentadmin.DeploymentException;
import org.osgi.service.deploymentadmin.DeploymentPackage;
import org.osgi.test.cases.deploymentadmin.tc1.tbc.DeploymentConstants;
import org.osgi.test.cases.deploymentadmin.tc1.tbc.DeploymentTestControl;
import org.osgi.test.cases.deploymentadmin.tc1.tbc.util.TestingDeploymentPackage;
public class InstallPackageThread extends Thread {
private DeploymentTestControl tbc;
private TestingDeploymentPackage testDP;
DeploymentPackage dp = null;
private boolean installed=false;//true if the DP is already installed
private boolean uninstalled=false;//true if the DP is already uninstalled
private boolean uninstall=false;//true if you want to uninstall the DP
private boolean uninstalling=false;//true if the DP is uninstalling
private boolean running=false;//true if this Thread is running
public static final int EXCEPTION_NOT_THROWN = -1;
private int exceptionCodeInstall = EXCEPTION_NOT_THROWN;
private int exceptionCodeUninstall = EXCEPTION_NOT_THROWN;
protected InstallPackageThread(DeploymentTestControl tbc, TestingDeploymentPackage testDP) {
this.tbc = tbc;
this.testDP = testDP;
}
public void uninstallDP(boolean blockDP) {
if (isAlive()) {
uninstall=true;
//If a blocked DP is being uninstalled, you cannot wait until this Thread die, otherwise it waits forever
if (!blockDP) {
try {
this.join(DeploymentConstants.SHORT_TIMEOUT);
} catch (InterruptedException e) {
}
}
}
}
public boolean isInstalled() {
return installed;
}
public boolean isRunning() {
return running;
}
public boolean isUninstalled() {
return uninstalled;
}
public int getDepExceptionCodeInstall() {
return exceptionCodeInstall;
}
public int getDepExceptionCodeUninstall() {
return exceptionCodeUninstall;
}
public DeploymentPackage getDeploymentPackage() {
return dp;
}
public boolean isUninstalling() {
return uninstalling;
}
public synchronized void run() {
try {
try {
running=true;
dp = tbc.installDeploymentPackage(tbc.getWebServer() + testDP.getFilename());
installed=(dp==null?false:true);
} catch (Exception e) {
if (e instanceof DeploymentException) {
exceptionCodeInstall = ((DeploymentException)e).getCode();
}
}
} finally {
while (!uninstall) {
try {
this.wait(100);
} catch (InterruptedException e) { }
}
if (isInstalled()) {
try {
uninstalling = true;
dp.uninstall();
uninstalled=true;
} catch (Exception e) {
if (e instanceof DeploymentException) {
exceptionCodeUninstall = ((DeploymentException)e).getCode();
}
}
}
}
}
}
|
package com.oakesville.mythling;
import java.io.IOException;
import java.net.MalformedURLException;
import java.net.URL;
import java.text.ParseException;
import java.util.Calendar;
import java.util.Map;
import java.util.TimeZone;
import java.util.Timer;
import java.util.TimerTask;
import org.json.JSONException;
import android.app.Activity;
import android.app.AlertDialog;
import android.app.Dialog;
import android.app.ProgressDialog;
import android.content.DialogInterface;
import android.content.Intent;
import android.media.MediaPlayer;
import android.media.MediaPlayer.OnCompletionListener;
import android.net.Uri;
import android.os.AsyncTask;
import android.os.Bundle;
import android.support.v4.app.NavUtils;
import android.util.Log;
import android.view.Menu;
import android.view.MenuItem;
import android.view.View;
import android.widget.ArrayAdapter;
import android.widget.ListView;
import android.widget.ProgressBar;
import android.widget.Toast;
import com.oakesville.mythling.app.AppData;
import com.oakesville.mythling.app.AppSettings;
import com.oakesville.mythling.app.BadSettingsException;
import com.oakesville.mythling.media.Item;
import com.oakesville.mythling.media.LiveStreamInfo;
import com.oakesville.mythling.media.MediaList;
import com.oakesville.mythling.media.MediaSettings;
import com.oakesville.mythling.media.MediaSettings.MediaType;
import com.oakesville.mythling.media.MediaSettings.SortType;
import com.oakesville.mythling.media.MediaSettings.ViewType;
import com.oakesville.mythling.media.Movie;
import com.oakesville.mythling.media.Recording;
import com.oakesville.mythling.media.StorageGroup;
import com.oakesville.mythling.media.TunerInUseException;
import com.oakesville.mythling.media.TvShow;
import com.oakesville.mythling.prefs.PrefsActivity;
import com.oakesville.mythling.util.FrontendPlayer;
import com.oakesville.mythling.util.HttpHelper;
import com.oakesville.mythling.util.MediaListParser;
import com.oakesville.mythling.util.MythTvParser;
import com.oakesville.mythling.util.Recorder;
import com.oakesville.mythling.util.ServiceFrontendPlayer;
import com.oakesville.mythling.util.SocketFrontendPlayer;
import com.oakesville.mythling.util.Transcoder;
/**
* Base class for the two different ways to view collections of MythTV media.
*/
public abstract class MediaActivity extends Activity
{
private static final String TAG = MediaActivity.class.getSimpleName();
protected MediaList mediaList;
private static AppData appData;
public static AppData getAppData() { return appData; }
public static void setAppData(AppData data) { appData = data; }
private AppSettings appSettings;
public AppSettings getAppSettings() { return appSettings; }
private MediaType mediaType;
protected MediaType getMediaType() { return mediaType; }
protected void setMediaType(MediaType mt) { this.mediaType = mt; }
public String getCharSet() { return "UTF-8"; }
private MenuItem mediaMenuItem;
protected MenuItem getMediaMenuItem() { return mediaMenuItem; }
private MenuItem searchMenuItem;
private MenuItem viewMenuItem;
private MenuItem sortMenuItem;
private MenuItem moviesMenuItem;
private MenuItem tvSeriesMenuItem;
private MenuItem musicMenuItem;
private MenuItem mythwebMenuItem;
private static MediaPlayer mediaPlayer;
private ProgressBar progressBar;
private ProgressDialog countdownDialog;
private int count;
private Timer timer;
public abstract void refresh() throws BadSettingsException;
public abstract ListView getListView();
@Override
public void onCreate(Bundle savedInstanceState)
{
super.onCreate(savedInstanceState);
appSettings = new AppSettings(getApplicationContext());
}
protected ProgressBar createProgressBar()
{
progressBar = (ProgressBar)findViewById(R.id.progress);
progressBar.setVisibility(View.GONE);
progressBar.setIndeterminate(true);
progressBar.setScaleX(0.20f);
progressBar.setScaleY(0.20f);
return progressBar;
}
@Override
public boolean onPrepareOptionsMenu(Menu menu)
{
MediaSettings mediaSettings = appSettings.getMediaSettings();
mediaMenuItem = menu.findItem(R.id.menu_media);
if (mediaMenuItem != null)
{
mediaMenuItem.setTitle(mediaSettings.getTitle());
if (mediaSettings.isMusic())
mediaMenuItem.getSubMenu().findItem(R.id.media_music).setChecked(true);
else if (mediaSettings.isLiveTv())
mediaMenuItem.getSubMenu().findItem(R.id.media_tv).setChecked(true);
else if (mediaSettings.isMovies())
mediaMenuItem.getSubMenu().findItem(R.id.media_movies).setChecked(true);
else if (mediaSettings.isTvSeries())
mediaMenuItem.getSubMenu().findItem(R.id.media_tv_series).setChecked(true);
else if (mediaSettings.isVideos())
mediaMenuItem.getSubMenu().findItem(R.id.media_videos).setChecked(true);
else
mediaMenuItem.getSubMenu().findItem(R.id.media_recordings).setChecked(true);
moviesMenuItem = mediaMenuItem.getSubMenu().findItem(R.id.media_movies);
showMoviesMenuItem(supportsMovies());
tvSeriesMenuItem = mediaMenuItem.getSubMenu().findItem(R.id.media_tv_series);
showTvSeriesMenuItem(supportsTvSeries());
musicMenuItem = mediaMenuItem.getSubMenu().findItem(R.id.media_music);
showMusicMenuItem(supportsMusic());
}
searchMenuItem = menu.findItem(R.id.menu_search);
showSearchMenu(supportsSearch());
sortMenuItem = menu.findItem(R.id.menu_sort);
showSortMenu(supportsSort());
viewMenuItem = menu.findItem(R.id.menu_view);
showViewMenu(supportsViewMenu());
mythwebMenuItem = menu.findItem(R.id.menu_mythweb);
showMythwebMenu(supportsMythwebMenu());
return super.onPrepareOptionsMenu(menu);
}
protected void showSearchMenu(boolean show)
{
if (searchMenuItem != null)
{
searchMenuItem.setEnabled(show);
searchMenuItem.setVisible(show);
}
}
protected void showMoviesMenuItem(boolean show)
{
if (moviesMenuItem != null)
{
moviesMenuItem.setEnabled(show);
moviesMenuItem.setVisible(show);
}
}
protected void showTvSeriesMenuItem(boolean show)
{
if (tvSeriesMenuItem != null)
{
tvSeriesMenuItem.setEnabled(show);
tvSeriesMenuItem.setVisible(show);
}
}
protected void showMusicMenuItem(boolean show)
{
if (musicMenuItem != null)
{
musicMenuItem.setEnabled(show);
musicMenuItem.setVisible(show);
}
}
protected void showViewMenu(boolean show)
{
if (viewMenuItem != null)
{
MediaSettings mediaSettings = appSettings.getMediaSettings();
if (show)
{
viewMenuItem.setTitle("");
viewMenuItem.setIcon(mediaSettings.getViewIcon());
if (mediaSettings.getViewType() == ViewType.detail)
viewMenuItem.getSubMenu().findItem(R.id.view_detail).setChecked(true);
else
viewMenuItem.getSubMenu().findItem(R.id.view_list).setChecked(true);
}
else
{
mediaSettings.setViewType(ViewType.list);
}
viewMenuItem.setEnabled(show);
viewMenuItem.setVisible(show);
}
}
protected void showMythwebMenu(boolean show)
{
if (mythwebMenuItem != null)
{
mythwebMenuItem.setEnabled(show);
mythwebMenuItem.setVisible(show);
}
}
protected void showSortMenu(boolean show)
{
if (sortMenuItem != null)
{
if (show)
{
MediaSettings mediaSettings = appSettings.getMediaSettings();
sortMenuItem.setTitle(mediaSettings.getSortTypeTitle());
if (mediaSettings.getSortType() == SortType.byDate)
sortMenuItem.getSubMenu().findItem(R.id.sort_byDate).setChecked(true);
else if (mediaSettings.getSortType() == SortType.byRating)
sortMenuItem.getSubMenu().findItem(R.id.sort_byRating).setChecked(true);
else
sortMenuItem.getSubMenu().findItem(R.id.sort_byTitle).setChecked(true);
}
sortMenuItem.setEnabled(show);
sortMenuItem.setVisible(show);
}
}
protected boolean supportsSearch()
{
return getAppSettings().isMythlingMediaServices();
}
protected boolean supportsSort()
{
return mediaList != null && mediaList.supportsSort();
}
protected boolean supportsViewMenu()
{
return mediaList != null && mediaList.canHaveArtwork();
}
protected boolean supportsMovies()
{
return getAppSettings().isVideosCategorization();
}
protected boolean supportsTvSeries()
{
return getAppSettings().isVideosCategorization();
}
protected boolean supportsMusic()
{
return getAppSettings().isMythlingMediaServices();
}
protected boolean supportsMythwebMenu()
{
return getAppSettings().isMythWebAccessEnabled();
}
protected boolean isListView()
{
return !isDetailView();
}
protected boolean isDetailView()
{
return false;
}
@Override
public boolean onCreateOptionsMenu(Menu menu)
{
getMenuInflater().inflate(R.menu.main, menu);
return true;
}
@Override
public boolean onOptionsItemSelected(MenuItem item)
{
if (item.getItemId() == android.R.id.home)
{
NavUtils.navigateUpFromSameTask(this);
return true;
}
try
{
if (sortMenuItem != null)
sortMenuItem.setTitle(appSettings.getMediaSettings().getSortTypeTitle());
if (viewMenuItem != null)
viewMenuItem.setIcon(appSettings.getMediaSettings().getViewIcon());
if (item.getItemId() == R.id.media_music)
{
appSettings.setMediaType(MediaType.music);
item.setChecked(true);
mediaMenuItem.setTitle(MediaSettings.getMediaTitle(MediaType.music));
showViewMenu(supportsViewMenu());
showSortMenu(supportsSort());
refresh();
return true;
}
else if (item.getItemId() == R.id.media_videos)
{
appSettings.setMediaType(MediaType.videos);
item.setChecked(true);
mediaMenuItem.setTitle(MediaSettings.getMediaTitle(MediaType.videos));
showViewMenu(supportsViewMenu());
showSortMenu(supportsSort());
refresh();
return true;
}
else if (item.getItemId() == R.id.media_recordings)
{
appSettings.setMediaType(MediaType.recordings);
item.setChecked(true);
mediaMenuItem.setTitle(MediaSettings.getMediaTitle(MediaType.recordings));
showViewMenu(supportsViewMenu());
showSortMenu(supportsSort());
refresh();
return true;
}
else if (item.getItemId() == R.id.media_tv)
{
appSettings.setMediaType(MediaType.liveTv);
item.setChecked(true);
mediaMenuItem.setTitle(MediaSettings.getMediaTitle(MediaType.liveTv));
showViewMenu(supportsViewMenu());
showSortMenu(supportsSort());
refresh();
return true;
}
else if (item.getItemId() == R.id.media_movies)
{
appSettings.setMediaType(MediaType.movies);
item.setChecked(true);
mediaMenuItem.setTitle(MediaSettings.getMediaTitle(MediaType.movies));
showViewMenu(supportsViewMenu());
showSortMenu(supportsSort());
refresh();
return true;
}
else if (item.getItemId() == R.id.media_tv_series)
{
appSettings.setMediaType(MediaType.tvSeries);
item.setChecked(true);
mediaMenuItem.setTitle(MediaSettings.getMediaTitle(MediaType.tvSeries));
showViewMenu(supportsViewMenu());
showSortMenu(supportsSort());
refresh();
return true;
}
else if (item.getItemId() == R.id.sort_byTitle)
{
appSettings.setSortType(SortType.byTitle);
item.setChecked(true);
sortMenuItem.setTitle(R.string.menu_byTitle);
sort();
return true;
}
else if (item.getItemId() == R.id.sort_byDate)
{
appSettings.setSortType(SortType.byDate);
item.setChecked(true);
sortMenuItem.setTitle(R.string.menu_byDate);
sort();
return true;
}
else if (item.getItemId() == R.id.sort_byRating)
{
appSettings.setSortType(SortType.byRating);
item.setChecked(true);
sortMenuItem.setTitle(R.string.menu_byRating);
sort();
return true;
}
else if (item.getItemId() == R.id.view_list)
{
appSettings.setViewType(ViewType.list);
item.setChecked(true);
viewMenuItem.setIcon(R.drawable.ic_menu_list);
goListView();
return true;
}
else if (item.getItemId() == R.id.view_detail)
{
appSettings.setViewType(ViewType.detail);
item.setChecked(true);
viewMenuItem.setIcon(R.drawable.ic_menu_detail);
goDetailView();
return true;
}
else if (item.getItemId() == R.id.menu_refresh)
{
refresh();
return true;
}
else if (item.getItemId() == R.id.menu_settings)
{
startActivity(new Intent(this, PrefsActivity.class));
return true;
}
else if (item.getItemId() == R.id.menu_search)
{
return onSearchRequested();
}
else if (item.getItemId() == R.id.menu_mythweb)
{
startActivity(new Intent(Intent.ACTION_VIEW, Uri.parse(appSettings.getMythWebUrl())));
return true;
}
else if (item.getItemId() == R.id.menu_help)
{
String url = getResources().getString(R.string.url_help);
startActivity(new Intent(Intent.ACTION_VIEW, Uri.parse(url), getApplicationContext(), WebViewActivity.class));
return true;
}
}
catch (BadSettingsException ex)
{
stopProgress();
Toast.makeText(getApplicationContext(), "Bad or missing setting:\n" + ex.getMessage(), Toast.LENGTH_LONG).show();
}
catch (Exception ex)
{
if (BuildConfig.DEBUG)
Log.e(TAG, ex.getMessage(), ex);
stopProgress();
Toast.makeText(getApplicationContext(), "Error: " + ex.toString(), Toast.LENGTH_LONG).show();
}
return super.onOptionsItemSelected(item);
}
protected void playItem(final Item item)
{
try
{
AppSettings appSettings = getAppSettings();
if (appSettings.isDevicePlayback())
{
if (getListView() != null) // TODO what about pager activity?
{
String msg = (item.isMusic() ? "Playing: '" : "Loading: '") + item.getTitle() + "'";
ArrayAdapter<String> adapter = new ArrayAdapter<String>(this, android.R.layout.simple_list_item_1, android.R.id.text1, new String[]{msg});
getListView().setAdapter(adapter);
}
startProgress();
stopMediaPlayer(); // music
if (item.isMusic())
{
if (mediaPlayer == null)
{
mediaPlayer = new MediaPlayer();
mediaPlayer.setOnCompletionListener(new OnCompletionListener()
{
public void onCompletion(MediaPlayer mp)
{
mediaPlayer.reset();
onResume();
}
});
}
String musicUrl = appSettings.getMythTvServicesBaseUrlWithCredentials() + "/Content/GetMusic?Id=" + item.getId();
mediaPlayer.setDataSource(appSettings.getAppContext(), Uri.parse(musicUrl));
// TODO async?
mediaPlayer.prepare();
mediaPlayer.start();
stopProgress();
}
else
{
if (item.isLiveTv() || item.isMovie())
{
if (item.isLiveTv() && ((TvShow)item).getEndTime().compareTo(Calendar.getInstance(TimeZone.getTimeZone("UTC")).getTime()) < 0)
{
new AlertDialog.Builder(this)
.setIcon(android.R.drawable.ic_dialog_alert)
.setTitle("Live TV")
.setMessage("Show has already ended: " + ((TvShow)item).getShowInfo())
.setPositiveButton("OK", null)
.show();
stopProgress();
onResume();
return;
}
String msg = null;
if (item.isLiveTv())
msg = ((TvShow)item).getShowInfo() + "\n\nRecording will be scheduled if necessary.";
else
msg = ((Movie)item).getShowInfo();
new AlertDialog.Builder(this)
.setIcon(android.R.drawable.ic_dialog_info)
.setTitle(item.getTitle())
.setMessage(msg)
.setPositiveButton("Watch", new DialogInterface.OnClickListener()
{
public void onClick(DialogInterface dialog, int which)
{
try
{
if (item.isLiveTv())
new StreamTvTask((TvShow)item).execute(getAppSettings().getMythTvServicesBaseUrl());
else
new StreamVideoTask(item).execute(getAppSettings().getMythTvServicesBaseUrl());
}
catch (MalformedURLException ex)
{
stopProgress();
if (BuildConfig.DEBUG)
Log.e(TAG, ex.getMessage(), ex);
Toast.makeText(getApplicationContext(), "Error: " + ex.toString(), Toast.LENGTH_LONG).show();
}
}
})
.setNegativeButton("Cancel", new DialogInterface.OnClickListener()
{
public void onClick(DialogInterface dialog, int which)
{
stopProgress();
onResume();
}
})
.show();
}
else
{
new StreamVideoTask(item).execute(appSettings.getMythTvServicesBaseUrl());
}
}
}
else // frontend playback
{
final FrontendPlayer player;
if (item.isMusic() || mediaList.getStorageGroup() == null) // frontend services require storage groups
player = new SocketFrontendPlayer(appSettings, mediaList.getBasePath(), item, getCharSet());
else
player = new ServiceFrontendPlayer(appSettings, item);
if (player.checkIsPlaying())
{
new AlertDialog.Builder(this)
.setIcon(android.R.drawable.ic_dialog_alert)
.setTitle("Interrupt")
.setMessage("Stop current playback?")
.setPositiveButton("Yes", new DialogInterface.OnClickListener()
{
public void onClick(DialogInterface dialog, int which)
{
player.stop();
startPlayback(item, player);
}
})
.setNegativeButton("No", null)
.show();
}
else
{
startPlayback(item, player);
}
}
}
catch (Exception ex)
{
if (BuildConfig.DEBUG)
Log.e(TAG, ex.getMessage(), ex);
Toast.makeText(getApplicationContext(), "Error: " + ex.toString(), Toast.LENGTH_LONG).show();
}
}
private void stopMediaPlayer()
{
if (mediaPlayer != null)
{
if (mediaPlayer.isPlaying())
{
mediaPlayer.stop();
mediaPlayer.release();
}
mediaPlayer.reset();
}
}
protected void goDetailView()
{
// default does nothing
}
protected void goListView()
{
// default does nothing
}
public void sort() throws IOException, JSONException, ParseException
{
startProgress();
refreshMediaList();
}
private void startPlayback(Item item, final FrontendPlayer player)
{
if (item.isLiveTv())
{
new AlertDialog.Builder(this)
.setIcon(android.R.drawable.ic_dialog_alert)
.setTitle(item.getTitle())
.setMessage("TODO: Frontend Live TV playback not yet supported.")
.setPositiveButton("OK", null)
.show();
}
else if (item.isRecording())
{
new AlertDialog.Builder(this)
.setIcon(android.R.drawable.ic_dialog_alert)
.setTitle(item.getTitle())
.setMessage(((Recording)item).getShowInfo())
.setPositiveButton("Play", new DialogInterface.OnClickListener()
{
public void onClick(DialogInterface dialog, int which)
{
player.play();
}
})
.setNegativeButton("Cancel", null)
.show();
}
else
{
try
{
player.play();
// reset progress
count = 0;
// prepare for a progress bar dialog
countdownDialog = new ProgressDialog(this);
countdownDialog.setCancelable(true);
countdownDialog.setMessage("Playing " + MediaSettings.getMediaLabel(item.getType()) + ": " + item.getLabel());
countdownDialog.setProgressStyle(ProgressDialog.STYLE_HORIZONTAL);
countdownDialog.setProgressPercentFormat(null);
countdownDialog.setProgressNumberFormat(null);
countdownDialog.setMax(10);
countdownDialog.setCancelable(true);
countdownDialog.setButton(Dialog.BUTTON_POSITIVE, "OK", new DialogInterface.OnClickListener()
{
public void onClick(DialogInterface dialog, int which)
{
dialog.dismiss();
stopTimer();
}
});
countdownDialog.setButton(Dialog.BUTTON_NEGATIVE, "Stop", new DialogInterface.OnClickListener()
{
public void onClick(DialogInterface dialog, int which)
{
player.stop();
dialog.dismiss();
stopTimer();
}
});
countdownDialog.setCanceledOnTouchOutside(true);
countdownDialog.show();
countdownDialog.setProgress(10);
tick();
}
catch (Exception ex)
{
if (BuildConfig.DEBUG)
Log.e(TAG, ex.getMessage(), ex);
stopTimer();
}
}
}
@Override
protected void onStop()
{
if (countdownDialog != null && countdownDialog.isShowing())
countdownDialog.dismiss();
stopTimer();
super.onStop();
}
private void stopTimer()
{
if (timer != null)
timer.cancel();
count = 0;
}
private void tick()
{
if (timer != null)
timer.cancel();
timer = new Timer();
timer.schedule(new TimerTask()
{
public void run()
{
countdownDialog.setProgress(10 - count);
if (count == 10)
{
countdownDialog.dismiss();
stopTimer();
}
else
{
count++;
tick();
}
}
}, 1000);
}
protected void refreshMediaList()
{
try
{
getAppSettings().clearMediaSettings(); // in case prefs changed
if (getAppSettings().getMediaSettings().getType() == MediaType.movies && !supportsMovies())
getAppSettings().setMediaType(MediaType.valueOf(AppSettings.DEFAULT_MEDIA_TYPE));
if (getAppSettings().getMediaSettings().getType() == MediaType.tvSeries && !supportsTvSeries())
getAppSettings().setMediaType(MediaType.valueOf(AppSettings.DEFAULT_MEDIA_TYPE));
if (getAppSettings().getMediaSettings().getType() == MediaType.music && !supportsMusic())
getAppSettings().setMediaType(MediaType.valueOf(AppSettings.DEFAULT_MEDIA_TYPE));
new RefreshTask().execute(getAppSettings().getUrls(getAppSettings().getMediaListUrl()));
}
catch (Exception ex)
{
throw new RuntimeException(ex.getMessage(), ex);
}
}
protected void populate() throws IOException, JSONException, ParseException, BadSettingsException
{
// default does nothing
}
protected Transcoder getTranscoder(Item item)
{
if (mediaList.getStorageGroup() == null)
return new Transcoder(getAppSettings(), mediaList.getBasePath());
else
return new Transcoder(getAppSettings(), mediaList.getStorageGroup());
}
/**
* must be run in background thread
*/
protected Map<String,StorageGroup> retrieveStorageGroups() throws IOException, JSONException
{
URL baseUrl = getAppSettings().getMythTvServicesBaseUrl();
HttpHelper downloader = getAppSettings().getMediaListDownloader(getAppSettings().getUrls(new URL(baseUrl + "/Myth/GetStorageGroupDirs")));
String sgJson = new String(downloader.get());
return new MythTvParser(sgJson, getAppSettings()).parseStorageGroups();
}
private class RefreshTask extends AsyncTask<URL,Integer,Long>
{
private String mediaListJson;
private Exception ex;
protected Long doInBackground(URL... urls)
{
try
{
MediaSettings mediaSettings = getAppSettings().getMediaSettings();
HttpHelper downloader = getAppSettings().getMediaListDownloader(urls);
byte[] bytes = downloader.get();
mediaListJson = new String(bytes, downloader.getCharSet());
if (mediaListJson.startsWith("<"))
{
// just display html
ex = new IOException(mediaListJson);
return -1L;
}
MediaListParser mediaListParser = getAppSettings().getMediaListParser(mediaListJson);
if (getAppSettings().isMythlingMediaServices())
{
mediaList = mediaListParser.parseMediaList(mediaSettings.getType());
if (mediaList.getBasePath() == null) // otherwise can avoid retrieving storage groups at least until MythTV 0.28
{
mediaList.setStorageGroup(retrieveStorageGroups().get(getAppSettings().getStorageGroup()));
}
}
else
{
Map<String,StorageGroup> storageGroups = retrieveStorageGroups();
StorageGroup mediaStorageGroup = storageGroups.get(getAppSettings().getStorageGroup());
if (mediaStorageGroup != null)
{
mediaList = ((MythTvParser)mediaListParser).parseMediaList(mediaSettings.getType(), mediaStorageGroup, null, null);
}
else
{
// no storage group for media type
URL baseUrl = getAppSettings().getMythTvServicesBaseUrl();
String basePath = null;
if (mediaSettings.getType() == MediaType.videos || mediaSettings.getType() == MediaType.movies || mediaSettings.getType() == MediaType.tvSeries)
{
// handle videos by getting the base path setting
downloader = getAppSettings().getMediaListDownloader(getAppSettings().getUrls(new URL(baseUrl + "/Myth/GetHostName")));
String hostName = new MythTvParser(new String(downloader.get()), getAppSettings()).parseString();
String key = "VideoStartupDir";
downloader = getAppSettings().getMediaListDownloader(getAppSettings().getUrls(new URL(baseUrl + "/Myth/GetSetting?Key=" + key + "&HostName=" + hostName)));
basePath = new MythTvParser(new String(downloader.get()), getAppSettings()).parseMythTvSetting(key);
if (basePath == null)
{
// try without host name
downloader = getAppSettings().getMediaListDownloader(getAppSettings().getUrls(new URL(baseUrl + "/Myth/GetSetting?Key=" + key)));
basePath = new MythTvParser(new String(downloader.get()), getAppSettings()).parseMythTvSetting(key);
}
}
StorageGroup artworkStorageGroup = storageGroups.get(getAppSettings().getArtworkStorageGroup());
mediaList = ((MythTvParser)mediaListParser).parseMediaList(mediaSettings.getType(), null, basePath, artworkStorageGroup);
}
}
mediaList.setArtworkStorageGroup(getAppSettings().getArtworkStorageGroup(mediaSettings.getType()));
mediaList.setCharSet(downloader.getCharSet());
getAppSettings().clearPagerCurrentPosition(mediaList.getMediaType(), "");
return 0L;
}
catch (Exception ex)
{
this.ex = ex;
if (BuildConfig.DEBUG)
Log.e(TAG, ex.getMessage(), ex);
return -1L;
}
}
protected void onPostExecute(Long result)
{
if (result != 0L)
{
stopProgress();
if (ex != null)
Toast.makeText(getApplicationContext(), ex.toString(), Toast.LENGTH_LONG).show();
}
else
{
AppData appData = new AppData(getApplicationContext());
appData.setMediaList(mediaList);
setAppData(appData);
setMediaType(appData.getMediaList().getMediaType());
getAppSettings().setLastLoad(System.currentTimeMillis());
try
{
appData.writeMediaList(mediaListJson);
ViewType viewType = getAppSettings().getMediaSettings().getViewType();
if (viewType == ViewType.list && isDetailView())
{
goListView();
}
else if (viewType == ViewType.detail && isListView())
{
goDetailView();
}
else
{
stopProgress();
populate();
}
}
catch (Exception ex)
{
stopProgress();
if (BuildConfig.DEBUG)
Log.e(TAG, ex.getMessage(), ex);
}
}
}
}
private class StreamVideoTask extends AsyncTask<URL,Integer,Long>
{
private Item item;
private LiveStreamInfo streamInfo;
private Exception ex;
public StreamVideoTask(Item item)
{
this.item = item;
}
protected Long doInBackground(URL... urls)
{
try
{
Transcoder transcoder = getTranscoder(item);
// TODO: do this retry for tv playback
int ct = 0;
int maxTries = 3;
// empty relative url i think means myth has not started transcoding
while ((streamInfo == null || streamInfo.getRelativeUrl().isEmpty()) && ct < maxTries )
{
transcoder.beginTranscode(item);
streamInfo = transcoder.getStreamInfo();
ct++;
Thread.sleep(1000);
}
if (streamInfo == null || streamInfo.getRelativeUrl().isEmpty())
throw new IOException("Transcoding does not seem to have started");
transcoder.waitAvailable();
return 0L;
}
catch (Exception ex)
{
this.ex = ex;
if (BuildConfig.DEBUG)
Log.e(TAG, ex.getMessage(), ex);
return -1L;
}
}
protected void onPostExecute(Long result)
{
if (result != 0L)
{
stopProgress();
if (ex != null)
Toast.makeText(getApplicationContext(), ex.toString(), Toast.LENGTH_LONG).show();
onResume();
}
else
{
try
{
playLiveStream(streamInfo);
}
catch (Exception ex)
{
if (BuildConfig.DEBUG)
Log.e(TAG, ex.getMessage(), ex);
Toast.makeText(getApplicationContext(), ex.toString(), Toast.LENGTH_LONG).show();
}
}
}
}
protected class TranscodeVideoTask extends AsyncTask<URL,Integer,Long>
{
private Item item;
private Exception ex;
public TranscodeVideoTask(Item item)
{
this.item = item;
}
protected Long doInBackground(URL... urls)
{
try
{
Transcoder transcoder = getTranscoder(item);
transcoder.beginTranscode(item);
return 0L;
}
catch (Exception ex)
{
this.ex = ex;
if (BuildConfig.DEBUG)
Log.e(TAG, ex.getMessage(), ex);
return -1L;
}
}
protected void onPostExecute(Long result)
{
stopProgress();
if (result != 0L)
{
if (ex != null)
Toast.makeText(getApplicationContext(), ex.toString(), Toast.LENGTH_LONG).show();
onResume();
}
}
}
protected class StreamTvTask extends AsyncTask<URL,Integer,Long>
{
private TvShow tvShow;
private Recording recordingToDelete;
private LiveStreamInfo streamInfo;
private Exception ex;
public StreamTvTask(TvShow tvShow)
{
this.tvShow = tvShow;
}
public StreamTvTask(TvShow tvShow, Recording recordingToDelete)
{
this.tvShow = tvShow;
this.recordingToDelete = recordingToDelete;
}
protected Long doInBackground(URL... urls)
{
try
{
Recorder recorder = new Recorder(getAppSettings());
if (recordingToDelete != null)
recorder.deleteRecording(recordingToDelete);
boolean recordAvail = recorder.scheduleRecording(tvShow);
if (!recordAvail)
recorder.waitAvailable();
Transcoder transcoder = getTranscoder(tvShow);
boolean streamAvail = transcoder.beginTranscode(recorder.getRecording());
streamInfo = transcoder.getStreamInfo();
if (!streamAvail)
transcoder.waitAvailable();
return 0L;
}
catch (Exception ex)
{
this.ex = ex;
if (BuildConfig.DEBUG)
Log.e(TAG, ex.getMessage(), ex);
return -1L;
}
}
protected void onPostExecute(Long result)
{
stopProgress();
if (result != 0L)
{
if (ex instanceof TunerInUseException)
{
new AlertDialog.Builder(MediaActivity.this)
.setIcon(android.R.drawable.ic_dialog_info)
.setTitle("Recording Conflict")
.setMessage("Tuner already in use recording:\n" + ex.getMessage() + "\nDelete this recording and proceed?")
.setPositiveButton("Delete", new DialogInterface.OnClickListener()
{
public void onClick(DialogInterface dialog, int which)
{
final Recording inProgressRecording = ((TunerInUseException)ex).getRecording();
new AlertDialog.Builder(MediaActivity.this)
.setIcon(android.R.drawable.ic_dialog_alert)
.setTitle("Confirm Delete")
.setMessage("Delete in-progress recording?\n" + inProgressRecording)
.setPositiveButton("Yes", new DialogInterface.OnClickListener()
{
public void onClick(DialogInterface dialog, int which)
{
try
{
startProgress();
new StreamTvTask(tvShow, inProgressRecording).execute(getAppSettings().getMythTvServicesBaseUrl());
}
catch (MalformedURLException ex)
{
stopProgress();
if (BuildConfig.DEBUG)
Log.e(TAG, ex.getMessage(), ex);
Toast.makeText(getApplicationContext(), "Error: " + ex.toString(), Toast.LENGTH_LONG).show();
}
}
})
.setNegativeButton("No", new DialogInterface.OnClickListener()
{
public void onClick(DialogInterface dialog, int which)
{
stopProgress();
onResume();
}
})
.show();
}
})
.setNegativeButton("Cancel", new DialogInterface.OnClickListener()
{
public void onClick(DialogInterface dialog, int which)
{
stopProgress();
onResume();
}
})
.show();
}
else
{
if (ex != null)
Toast.makeText(getApplicationContext(), ex.toString(), Toast.LENGTH_LONG).show();
onResume();
}
}
else
{
try
{
playLiveStream(streamInfo);
}
catch (Exception ex)
{
if (BuildConfig.DEBUG)
Log.e(TAG, ex.getMessage(), ex);
Toast.makeText(getApplicationContext(), ex.toString(), Toast.LENGTH_LONG).show();
}
}
}
}
protected void playLiveStream(LiveStreamInfo streamInfo) throws IOException
{
String streamUrl = appSettings.getMythTvServicesBaseUrlWithCredentials() + streamInfo.getRelativeUrl();
// avoid retrieving unnecessary audio-only streams
int lastDot = streamUrl.lastIndexOf('.');
streamUrl = streamUrl.substring(0, lastDot) + ".av" + streamUrl.substring(lastDot);
stopProgress();
if (appSettings.isExternalPlayer())
{
Intent toStart = new Intent(Intent.ACTION_VIEW);
|
package edu.chalmers.sankoss.desktop;
import edu.chalmers.sankoss.core.core.Coordinate;
import edu.chalmers.sankoss.core.core.Ship;
import edu.chalmers.sankoss.desktop.mvc.placement.PlacementModel;
import org.junit.Test;
import static org.junit.Assert.assertFalse;
import static org.junit.Assert.assertTrue;
/**
* Description of class.
* More detailed description.
*
* @author Mikael Malmqvist
* @modified Fredrik Thune
*/
public class PlacementModelTest {
@Test
public void testAddShip() throws Exception {
PlacementModel testModel = new PlacementModel();
Ship myShip = new Ship(new Coordinate(2,2), new Coordinate(2,5));
testModel.addShip(myShip);
assertTrue(testModel.getFleet().getShip(0).equals(myShip));
assertFalse(testModel.addShip(new Ship(new Coordinate(2,2), new Coordinate(2,5))));
assertFalse(testModel.addShip(new Ship(new Coordinate(2,2), new Coordinate(5,2))));
assertFalse(testModel.addShip(new Ship(new Coordinate(-1,2), new Coordinate(2,2))));
assertFalse(testModel.addShip(new Ship(new Coordinate(2,-1), new Coordinate(2,5))));
assertFalse(testModel.addShip(new Ship(new Coordinate(12,2), new Coordinate(2,2))));
assertFalse(testModel.addShip(new Ship(new Coordinate(2,12), new Coordinate(2,5))));
assertFalse(testModel.addShip(new Ship(new Coordinate(2,2), new Coordinate(-1,2))));
assertFalse(testModel.addShip(new Ship(new Coordinate(2,2), new Coordinate(2,-1))));
assertFalse(testModel.addShip(new Ship(new Coordinate(2,2), new Coordinate(12,2))));
assertFalse(testModel.addShip(new Ship(new Coordinate(2,2), new Coordinate(2,12))));
}
@Test
public void testValidate() throws Exception {
// TODO: Test stuff
}
@Test
public void testUpdateNationality() throws Exception {
// This could not be tested due to network coding.
// There is no instance of SankossClient..
assertTrue(true);
}
}
|
package org.springsource.ide.eclipse.commons.quicksearch.util;
import org.eclipse.jdt.internal.ui.wizards.dialogfields.ListDialogField.ColumnsDescription;
import org.eclipse.jface.viewers.TableViewer;
import org.eclipse.swt.events.ControlEvent;
import org.eclipse.swt.events.ControlListener;
import org.eclipse.swt.graphics.Rectangle;
import org.eclipse.swt.widgets.Composite;
import org.eclipse.swt.widgets.Table;
import org.eclipse.swt.widgets.TableColumn;
/**
* Resizes table columns such that columns fit the table width. The table is
* initially resized when the resize is enabled, and its columns continue being
* resized automatically as the user resizes the table.
*
*/
public class TableResizeHelper {
private final TableViewer tableViewer;
public TableResizeHelper(TableViewer tableViewer) {
this.tableViewer = tableViewer;
}
public void enableResizing() {
ControlListener resizeListener = new ControlListener() {
public void controlResized(ControlEvent e) {
resizeTable();
}
public void controlMoved(ControlEvent e) {
}
};
tableViewer.getTable().addControlListener(resizeListener);
TableColumn[] cols = tableViewer.getTable().getColumns();
if (cols!=null) {
for (int i = 0; i < cols.length-1; i++) {
cols[i].addControlListener(resizeListener);
}
}
// Initial resize of the columns
resizeTable();
}
protected void resizeTable() {
Composite tableComposite = tableViewer.getTable();//.getParent();
Rectangle tableCompositeArea = tableComposite.getClientArea();
int width = tableCompositeArea.width;
// ScrollBar sb = tableViewer.getTable().getVerticalBar();
// if (sb!=null && sb.isVisible()) {
// width = width - sb.getSize().x;
resizeTableColumns(width, tableViewer.getTable());
}
protected void resizeTableColumns(int tableWidth, Table table) {
TableColumn[] tableColumns = table.getColumns();
if (tableColumns.length == 0) {
return;
}
int total = 0;
for (TableColumn column : tableColumns) {
total += column.getWidth();
}
TableColumn lastColumn = tableColumns[tableColumns.length - 1];
int newWidth = (tableWidth - total) + lastColumn.getWidth();
if (newWidth>0) {
lastColumn.setWidth(newWidth);
}
}
}
|
package fr.openwide.core.commons.util.functional;
import java.io.Serializable;
import java.util.ArrayList;
import java.util.Comparator;
import java.util.HashMap;
import java.util.HashSet;
import java.util.LinkedHashMap;
import java.util.LinkedHashSet;
import java.util.LinkedList;
import java.util.List;
import java.util.Map;
import java.util.Set;
import java.util.SortedMap;
import java.util.SortedSet;
import java.util.TreeMap;
import java.util.TreeSet;
import com.google.common.base.Supplier;
import com.google.common.base.Suppliers;
import com.google.common.collect.Lists;
import com.google.common.collect.Maps;
import com.google.common.collect.Sets;
/**
* More useful suppliers.
*
* <p>All methods return serializable suppliers as long as they're given
* serializable parameters.
*
* <p>Methods named xAsY ({@link #linkedListAsList()}, {@link #treeSetAsSet(Comparator)}, and so on) are just here to
* make your like easy when you want to use the diamond operator on a method that receives your supplier as a parameter.
* For instance:
* <code><pre>
* public MyType<T, C extends Collection<T>> {
* public MyType(Supplier<C> supplier) {
* // ...
* }
* }
*
* // With the original method
* ... = new MyType<>((Supplier<? extends List<T>>)Suppliers2.<T>arrayList());
*
* // With xAsY
* ... = new MyType<>(Suppliers2.<T>arrayListAsList());
* // ... which is a tad shorter
* </pre></code>
*
* @see Suppliers
*
*/
public final class Suppliers2 {
private Suppliers2() { }
public static <T> Supplier<T> constant(T value) {
return new ConstantSupplier<T>(value);
}
private static class ConstantSupplier<T> implements Supplier<T>, Serializable {
private static final long serialVersionUID = 6476238745119640079L;
private final T value;
public ConstantSupplier(T value) {
super();
this.value = value;
}
@Override
public T get() {
return value;
}
}
@SuppressWarnings({ "unchecked", "rawtypes" }) // LinkedListSupplier works for any T
public static <T> Supplier<LinkedList<T>> linkedList() {
return (Supplier) LinkedListSupplier.INSTANCE;
}
public static <T> Supplier<? extends List<T>> linkedListAsList() {
return linkedList();
}
private static enum LinkedListSupplier implements Supplier<LinkedList<?>> {
INSTANCE;
@Override
public LinkedList<?> get() {
return Lists.newLinkedList();
}
}
@SuppressWarnings({ "unchecked", "rawtypes" }) // ArrayListSupplier works for any T
public static <T> Supplier<ArrayList<T>> arrayList() {
return (Supplier) ArrayListSupplier.INSTANCE;
}
public static <T> Supplier<? extends List<T>> arrayListAsList() {
return arrayList();
}
private static enum ArrayListSupplier implements Supplier<ArrayList<?>> {
INSTANCE;
@Override
public ArrayList<?> get() {
return Lists.newArrayList();
}
}
@SuppressWarnings({ "unchecked", "rawtypes" }) // HashSetSupplier works for any T
public static <T> Supplier<HashSet<T>> hashSet() {
return (Supplier) HashSetSupplier.INSTANCE;
}
public static <T> Supplier<? extends Set<T>> hashSetAsSet() {
return hashSet();
}
private static enum HashSetSupplier implements Supplier<HashSet<?>> {
INSTANCE;
@Override
public HashSet<?> get() {
return Sets.newHashSet();
}
}
@SuppressWarnings({ "unchecked", "rawtypes" }) // HashSetSupplier works for any T
public static <T> Supplier<LinkedHashSet<T>> linkedHashSet() {
return (Supplier) LinkedHashSetSupplier.INSTANCE;
}
public static <T> Supplier<? extends Set<T>> linkedHashSetAsSet() {
return linkedHashSet();
}
private static enum LinkedHashSetSupplier implements Supplier<LinkedHashSet<?>> {
INSTANCE;
@Override
public LinkedHashSet<?> get() {
return Sets.newLinkedHashSet();
}
}
@SuppressWarnings({ "unchecked", "rawtypes" }) // NaturalOrderTreeSetSupplier works for any T
public static <T extends Comparable> Supplier<TreeSet<T>> treeSet() {
return (Supplier) NaturalOrderTreeSetSupplier.INSTANCE;
}
@SuppressWarnings("rawtypes")
public static <T extends Comparable> Supplier<? extends Set<T>> treeSetAsSet() {
return treeSet();
}
@SuppressWarnings("rawtypes")
public static <T extends Comparable> Supplier<? extends SortedSet<T>> treeSetAsSortedSet() {
return treeSet();
}
private static enum NaturalOrderTreeSetSupplier implements Supplier<TreeSet<?>> {
INSTANCE;
@Override
@SuppressWarnings("rawtypes")
public TreeSet<?> get() {
return (TreeSet) Sets.newTreeSet();
}
}
public static <T> Supplier<TreeSet<T>> treeSet(Comparator<? super T> comparator) {
return new ComparatorTreeSetSupplier<T>(comparator);
}
public static <T> Supplier<? extends Set<T>> treeSetAsSet(Comparator<? super T> comparator) {
return treeSet(comparator);
}
public static <T> Supplier<? extends SortedSet<T>> treeSetAsSortedSet(Comparator<? super T> comparator) {
return treeSet(comparator);
}
private static class ComparatorTreeSetSupplier<T> implements Supplier<TreeSet<T>>, Serializable {
private static final long serialVersionUID = 6476238745119640079L;
private final Comparator<? super T> comparator;
public ComparatorTreeSetSupplier(Comparator<? super T> comparator) {
super();
this.comparator = comparator;
}
@Override
public TreeSet<T> get() {
return Sets.newTreeSet(comparator);
}
}
@SuppressWarnings({ "unchecked", "rawtypes" }) // HashMapSupplier works for any K and V
public static <K, V> Supplier<HashMap<K, V>> hashMap() {
return (Supplier) HashMapSupplier.INSTANCE;
}
public static <K, V> Supplier<? extends Map<K, V>> hashMapAsMap() {
return hashMap();
}
private static enum HashMapSupplier implements Supplier<HashMap<?, ?>> {
INSTANCE;
@Override
public HashMap<?, ?> get() {
return Maps.newHashMap();
}
}
@SuppressWarnings({ "unchecked", "rawtypes" }) // HashMapSupplier works any K and V
public static <K, V> Supplier<LinkedHashMap<K, V>> linkedHashMap() {
return (Supplier) LinkedHashMapSupplier.INSTANCE;
}
public static <K, V> Supplier<? extends Map<K, V>> linkedHashMapAsMap() {
return linkedHashMap();
}
private static enum LinkedHashMapSupplier implements Supplier<LinkedHashMap<?, ?>> {
INSTANCE;
@Override
public LinkedHashMap<?, ?> get() {
return Maps.newLinkedHashMap();
}
}
@SuppressWarnings({ "unchecked", "rawtypes" }) // NaturalOrderTreeMapSupplier works for any K and V
public static <K extends Comparable, V> Supplier<TreeMap<K, V>> treeMap() {
return (Supplier) NaturalOrderTreeMapSupplier.INSTANCE;
}
@SuppressWarnings("rawtypes")
public static <K extends Comparable, V> Supplier<? extends Map<K, V>> treeMapAsMap() {
return treeMap();
}
@SuppressWarnings("rawtypes")
public static <K extends Comparable, V> Supplier<? extends SortedMap<K, V>> treeMapAsSortedMap() {
return treeMap();
}
private static enum NaturalOrderTreeMapSupplier implements Supplier<TreeMap<?, ?>> {
INSTANCE;
@Override
@SuppressWarnings("rawtypes")
public TreeMap<?, ?> get() {
return (TreeMap) Maps.newTreeMap();
}
}
public static <K, V> Supplier<TreeMap<K, V>> treeMap(Comparator<? super K> comparator) {
return new ComparatorTreeMapSupplier<K, V>(comparator);
}
public static <K, V> Supplier<? extends Map<K, V>> treeMapAsMap(Comparator<? super K> comparator) {
return treeMap(comparator);
}
public static <K, V> Supplier<? extends SortedMap<K, V>> treeMapAsSortedMap(Comparator<? super K> comparator) {
return treeMap(comparator);
}
private static class ComparatorTreeMapSupplier<K, V> implements Supplier<TreeMap<K, V>>, Serializable {
private static final long serialVersionUID = 6476238745119640079L;
private final Comparator<? super K> comparator;
public ComparatorTreeMapSupplier(Comparator<? super K> comparator) {
super();
this.comparator = comparator;
}
@Override
public TreeMap<K, V> get() {
return Maps.newTreeMap(comparator);
}
}
}
|
package nl.tudelft.ewi.dea.dao;
import static com.google.common.base.Preconditions.checkArgument;
import static com.google.common.base.Preconditions.checkNotNull;
import static org.apache.commons.lang3.StringUtils.isNotEmpty;
import java.util.List;
import javax.persistence.EntityManager;
import javax.persistence.NoResultException;
import javax.persistence.TypedQuery;
import javax.persistence.criteria.CriteriaBuilder;
import javax.persistence.criteria.CriteriaQuery;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import com.google.inject.persist.Transactional;
public abstract class AbstractDaoBase<T> implements Dao<T> {
private static final Logger LOG = LoggerFactory.getLogger(AbstractDaoBase.class);
private final EntityManager em;
private final Class<T> entityClass;
private final String entityName;
protected AbstractDaoBase(final EntityManager em, final Class<T> clazz) {
this.em = em;
entityClass = clazz;
entityName = entityClass.getSimpleName();
}
@Override
@Transactional
public final List<T> findAll() {
LOG.trace("{}: Find all...", getEntityName());
final TypedQuery<T> query = createQuery("FROM " + getEntityName());
return query.getResultList();
}
@Override
@Transactional
public final T findById(final long id) {
LOG.trace("{}: Find by id: {}", getEntityName(), id);
final T result = em.find(entityClass, id);
if (result == null) {
throw new NoResultException("No result found for id: " + id);
}
return result;
}
@Override
@Transactional
public final void persist(final T object) {
LOG.trace("{}: Persist: {}", getEntityName(), object);
checkNotNull(object, "object must be non-null");
em.persist(object);
LOG.trace("{}: Persisted: {}", getEntityName(), object);
}
@Override
@Transactional
public final void persist(final Object... objects) {
LOG.trace("{}: Persist: {}", getEntityName(), objects);
checkNotNull(objects, "objects must be non-null");
for (final Object object : objects) {
em.persist(object);
}
}
@Override
@Transactional
public void detach(final T entity) {
checkNotNull(entity, "entity must be non-null");
em.detach(entity);
}
@Override
@Transactional
public final T merge(final T entity) {
checkNotNull(entity, "entity must be non-null");
return em.merge(entity);
}
@Override
@Transactional
public final void remove(final T object) {
LOG.trace("{}: Remove: {}", getEntityName(), object);
checkNotNull(object, "object must be non-null");
em.remove(object);
}
@Override
@Transactional
public final void remove(final Object... objects) {
LOG.trace("{}: Remove: {}", getEntityName(), objects);
checkNotNull(objects, "objects must be non-null");
for (final Object object : objects) {
em.remove(object);
}
}
@Transactional
protected final CriteriaBuilder getCriteriaBuilder() {
return em.getCriteriaBuilder();
}
@Transactional
protected final TypedQuery<T> createQuery(final String query) {
checkArgument(isNotEmpty(query), "query must be non-empty");
return em.createQuery(query, entityClass);
}
@Transactional
protected final TypedQuery<T> createQuery(CriteriaQuery<T> criteria) {
checkNotNull(criteria, "query must be non-empty");
return em.createQuery(criteria);
}
public String getEntityName() {
return entityName;
}
}
|
package com.redhat.ceylon.common;
import java.io.BufferedReader;
import java.io.IOException;
import java.io.InputStream;
import java.io.InputStreamReader;
import java.io.LineNumberReader;
import java.io.PushbackReader;
import java.io.Reader;
import java.nio.CharBuffer;
import java.nio.charset.Charset;
import java.util.InvalidPropertiesFormatException;
public class ConfigReader {
private ConfigReaderListener listener;
private InputStream in;
private LineNumberReader counterdr;
private MemoPushbackReader reader;
private String section;
private enum Token { section, option, assign, comment, eol, error, eof };
public ConfigReader(InputStream in, ConfigReaderListener listener) {
this.in = in;
this.listener = listener;
}
public void process() throws IOException {
section = null;
try {
counterdr = new LineNumberReader(new BufferedReader(new InputStreamReader(in, Charset.forName("UTF-8"))));
reader = new MemoPushbackReader(counterdr);
Token tok;
skipWhitespace(true);
flushWhitespace();
while ((tok = peekToken()) != Token.eof) {
switch (tok) {
case section:
handleSection();
break;
case option:
if (section != null) {
handleOption();
} else {
throw new InvalidPropertiesFormatException("Option without section in configuration file at line " + (counterdr.getLineNumber() + 1));
}
break;
case comment:
skipToNextLine();
listener.onComment(reader.getAndClearMemo());
break;
case eol:
skipToNextLine();
listener.onWhitespace(reader.getAndClearMemo());
break;
default:
throw new InvalidPropertiesFormatException("Unexpected token in configuration file at line " + (counterdr.getLineNumber() + 1));
}
skipWhitespace(true);
flushWhitespace();
}
} finally {
if (reader != null) {
reader.close();
}
}
}
private void handleSection() throws IOException {
expect('[');
section = readName(true).toLowerCase();
if (!section.matches("[\\p{L}\\p{Nd}]+(\\.[\\p{L}\\p{Nd}]+)*")) {
throw new InvalidPropertiesFormatException("Invalid section name in configuration file at line " + (counterdr.getLineNumber() + 1));
}
skipWhitespace(false);
if (reader.peek() == '\"') {
String subSection = readString();
expect('"');
section += "." + subSection;
skipWhitespace(false);
}
expect(']');
listener.onSection(section, reader.getAndClearMemo());
}
private void handleOption() throws IOException {
String option = readName(false);
String optName = section + "." + option;
String value;
skipWhitespace(false);
Token tok = peekToken();
if (tok == Token.assign) {
expect('=');
value = readValue();
} else if (tok == Token.error) {
throw new InvalidPropertiesFormatException("Unexpected token in configuration file at line " + (counterdr.getLineNumber() + 1));
} else {
value = "true";
}
listener.onOption(optName, value, reader.getAndClearMemo());
}
private String readName(boolean forSection) throws IOException {
StringBuilder str = new StringBuilder();
int c;
while ((c = reader.read()) != -1) {
if ((!forSection && isOptionNameChar(c)) || (forSection && isSectionNameChar(c))) {
str.append((char)c);
} else {
reader.unread(c);
break;
}
}
return str.toString();
}
private String readString() throws IOException {
StringBuilder str = new StringBuilder();
gobble('\"');
int c;
while ((c = reader.read()) != -1) {
if (c == '"') {
reader.unread(c);
break;
} else if (c == '\\') {
int c2 = reader.read();
if (c2 == '\\') {
// Do nothing
} else if (c2 == '\"') {
c = c2;
} else {
throw new InvalidPropertiesFormatException("Illegal escape character in configuration file at line " + (counterdr.getLineNumber() + 1));
}
}
str.append((char)c);
}
return str.toString();
}
private String readValue() throws IOException {
StringBuilder str = new StringBuilder();
skipWhitespace(false);
boolean hasQuote = gobble('\"');
int c;
while ((c = reader.read()) != -1) {
if (c == '"') {
reader.unread(c);
break;
} else if (isNewLineChar(c)) {
reader.unread(c);
break;
} else if (isCommentChar(c) && !hasQuote) {
break;
} else if (c == '\\') {
int c2 = reader.read();
if (c2 == '\\') {
// Do nothing
} else if (c2 == '\"') {
c = c2;
} else if (c2 == 't') {
c = '\t';
} else if (c2 == 'n') {
c = '\n';
} else if (isNewLineChar(c2)) {
skipNewLine(c2);
c = '\n';
} else {
throw new InvalidPropertiesFormatException("Illegal escape character in configuration file at line " + (counterdr.getLineNumber() + 1));
}
}
str.append((char)c);
}
if (hasQuote) {
expect('\"');
return str.toString();
} else {
return str.toString().trim();
}
}
private void expect(int expected) throws IOException {
int c;
if ((c = reader.read()) != expected) {
throw new InvalidPropertiesFormatException("Unexpected token in configuration file at line " + (counterdr.getLineNumber() + 1) + ", expected '" + Character.valueOf((char)expected) + "' but got '" + Character.valueOf((char)c) + "'");
}
}
private void skipWhitespace(boolean multiline) throws IOException {
int c;
while ((c = reader.read()) != -1) {
if (!Character.isWhitespace(c) || (!multiline && isNewLineChar(c))) {
reader.unread(c);
break;
}
}
}
private void skipToNextLine() throws IOException {
int c;
while ((c = reader.read()) != -1) {
if (isNewLineChar(c)) {
skipNewLine(c);
break;
}
}
}
private Token peekToken() throws IOException {
int c = reader.peek();
if (isCommentChar(c)) {
return Token.comment;
} else if (c == '[') {
return Token.section;
} else if (c == '=') {
return Token.assign;
} else if (isNewLineChar(c)) {
return Token.eol;
} else if (isOptionNameChar(c)) {
return Token.option;
} else if (c == -1) {
return Token.eof;
} else {
return Token.error;
}
}
private boolean gobble(int chr) throws IOException {
int c = reader.read();
if (c != chr) {
reader.unread(c);
return false;
}
return true;
}
private void skipNewLine(int c) throws IOException {
if (c == '\r') {
c = reader.read();
if (c != '\n') {
reader.unread(c);
}
}
}
private void flushWhitespace() {
String ws = reader.getAndClearMemo();
if (!ws.isEmpty()) {
listener.onWhitespace(ws);
}
}
private boolean isOptionNameChar(int c) {
return Character.isLetterOrDigit(c) || c == '-';
}
private boolean isSectionNameChar(int c) {
return isOptionNameChar(c) || c == '.';
}
private boolean isCommentChar(int c) {
return c == ';' || c == '
}
private boolean isNewLineChar(int c) {
return c == '\n' || c == '\r';
}
}
class MemoPushbackReader extends PushbackReader {
private StringBuilder memo;
public MemoPushbackReader(Reader in) {
super(in);
memo = new StringBuilder(1024);
}
@Override
public int read() throws IOException {
int c = super.read();
if (c != -1) {
memo.append((char)c);
}
return c;
}
@Override
public void unread(int c) throws IOException {
super.unread(c);
memo.setLength(memo.length() - 1);
}
public int peek() throws IOException {
int c = super.read();
if (c != -1) {
super.unread(c);
}
return c;
}
@Override
public void reset() throws IOException {
super.reset();
memo.setLength(0);
}
public String getAndClearMemo() {
String result = memo.toString();
memo.setLength(0);
return result;
}
// All the following methods we don't really need so they aren't implemented
// to prevent anybody from accidentally using them they throw an error
@Override
public int read(char[] cbuf, int off, int len) throws IOException {
throw new UnsupportedOperationException();
}
@Override
public long skip(long n) throws IOException {
throw new UnsupportedOperationException();
}
@Override
public void unread(char[] cbuf, int off, int len) throws IOException {
throw new UnsupportedOperationException();
}
@Override
public void unread(char[] cbuf) throws IOException {
throw new UnsupportedOperationException();
}
@Override
public int read(char[] cbuf) throws IOException {
throw new UnsupportedOperationException();
}
@Override
public int read(CharBuffer target) throws IOException {
throw new UnsupportedOperationException();
}
}
|
package fr.openwide.core.jpa.business.generic.dao;
import java.util.Arrays;
import java.util.List;
import java.util.ListIterator;
import javax.persistence.EntityManager;
import javax.persistence.NoResultException;
import javax.persistence.PersistenceContext;
import javax.persistence.PersistenceException;
import javax.persistence.TypedQuery;
import javax.persistence.criteria.CriteriaBuilder;
import javax.persistence.criteria.CriteriaQuery;
import javax.persistence.criteria.Expression;
import javax.persistence.criteria.Order;
import javax.persistence.criteria.Predicate;
import javax.persistence.criteria.Root;
import javax.persistence.metamodel.SingularAttribute;
import org.hibernate.Session;
public class JpaDaoSupport {
@PersistenceContext
private EntityManager entityManager;
protected <T> TypedQuery<T> buildTypedQuery(CriteriaQuery<T> criteria, Integer limit, Integer offset) {
TypedQuery<T> query = getEntityManager().createQuery(criteria);
if (offset != null) {
query.setFirstResult(offset);
}
if (limit != null) {
query.setMaxResults(limit);
}
return query;
}
protected void filterCriteriaQuery(CriteriaQuery<?> criteria, Expression<Boolean> filter) {
if (filter != null) {
Predicate currentFilter = criteria.getRestriction();
if (currentFilter != null) {
filter = getEntityManager().getCriteriaBuilder().and(currentFilter, filter);
}
criteria.where(filter);
}
}
protected <T> Root<T> rootCriteriaQuery(CriteriaBuilder builder, CriteriaQuery<?> criteria, Class<T> objectClass) {
return criteria.from(objectClass);
}
public <T, K> T getEntity(Class<T> clazz, K id) {
return getEntityManager().find(clazz, id);
}
@SuppressWarnings("unchecked")
public <T> T getEntityByNaturalId(Class<T> clazz, String naturalId) {
if (naturalId == null) {
throw new IllegalArgumentException("Natural id may not be null");
}
Session session = getEntityManager().unwrap(Session.class);
return (T) session.bySimpleNaturalId(clazz).load(naturalId);
}
public <T, V> T getEntityByField(Class<T> clazz, SingularAttribute<? super T, V> attribute, V fieldValue) {
CriteriaBuilder builder = getEntityManager().getCriteriaBuilder();
CriteriaQuery<T> criteria = builder.createQuery(clazz);
Root<T> root = criteria.from(clazz);
criteria.where(builder.equal(root.get(attribute), fieldValue));
try {
return buildTypedQuery(criteria, null, null).getSingleResult();
} catch (NoResultException e) {
return null;
}
}
public <T> T getEntityByFieldIgnoreCase(Class<T> clazz, SingularAttribute<? super T, String> attribute, String fieldValue) {
CriteriaBuilder builder = getEntityManager().getCriteriaBuilder();
CriteriaQuery<T> criteria = builder.createQuery(clazz);
Root<T> root = criteria.from(clazz);
criteria.where(builder.equal(
builder.lower(root.get(attribute)),
builder.lower(builder.literal(fieldValue))
));
try {
return buildTypedQuery(criteria, null, null).getSingleResult();
} catch (NoResultException e) {
return null;
}
}
protected <T> void update(T entity) {
if (!getEntityManager().contains(entity)) {
throw new PersistenceException("Updated entity must be attached");
}
}
protected <T> void save(T entity) {
getEntityManager().persist(entity);
}
protected <T> void delete(T entity) {
getEntityManager().remove(entity);
}
protected <T> T refresh(T entity) {
getEntityManager().refresh(entity);
return entity;
}
public void flush() {
getEntityManager().flush();
}
public void clear() {
getEntityManager().clear();
}
protected <T> List<T> listEntity(Class<T> objectClass, Expression<Boolean> filter, Integer limit, Integer offset, Order... orders) {
CriteriaBuilder builder = getEntityManager().getCriteriaBuilder();
CriteriaQuery<T> criteria = builder.createQuery(objectClass);
rootCriteriaQuery(builder, criteria, objectClass);
if (filter != null) {
filterCriteriaQuery(criteria, filter);
}
if (orders != null && orders.length > 0) {
criteria.orderBy(orders);
}
TypedQuery<T> query = buildTypedQuery(criteria, limit, offset);
List<T> entities = query.getResultList();
if (orders == null || orders.length == 0) {
sort(entities);
}
return entities;
}
protected <T> List<T> listEntity(Class<T> objectClass) {
return listEntity(objectClass, null, null, null);
}
protected <T> List<T> listEntity(Class<T> objectClass, Expression<Boolean> filter) {
return listEntity(objectClass, filter, null, null);
}
protected <T, V> List<T> listEntityByField(Class<T> objectClass, SingularAttribute<? super T, V> attribute, V fieldValue) {
CriteriaBuilder builder = getEntityManager().getCriteriaBuilder();
CriteriaQuery<T> criteria = builder.createQuery(objectClass);
Root<T> root = rootCriteriaQuery(builder, criteria, objectClass);
criteria.where(builder.equal(root.get(attribute), fieldValue));
List<T> entities = buildTypedQuery(criteria, null, null).getResultList();
sort(entities);
return entities;
}
protected <T> Long countEntity(Class<T> clazz) {
CriteriaBuilder builder = getEntityManager().getCriteriaBuilder();
CriteriaQuery<Long> criteria = builder.createQuery(Long.class);
Root<T> root = rootCriteriaQuery(builder, criteria, clazz);
criteria.select(builder.count(root));
return buildTypedQuery(criteria, null, null).getSingleResult();
}
protected <T, V> Long countEntityByField(Class<T> clazz, SingularAttribute<? super T, V> attribute, V fieldValue) {
CriteriaBuilder builder = getEntityManager().getCriteriaBuilder();
CriteriaQuery<Long> criteria = builder.createQuery(Long.class);
Root<T> root = rootCriteriaQuery(builder, criteria, clazz);
criteria.select(builder.count(root));
Expression<Boolean> filter = builder.equal(root.get(attribute), fieldValue);
filterCriteriaQuery(criteria, filter);
return buildTypedQuery(criteria, null, null).getSingleResult();
}
protected <T> Long countEntity(Class<T> clazz, Expression<Boolean> filter) {
CriteriaBuilder builder = getEntityManager().getCriteriaBuilder();
CriteriaQuery<Long> criteria = builder.createQuery(Long.class);
Root<T> root = rootCriteriaQuery(builder, criteria, clazz);
criteria.select(builder.count(root));
filterCriteriaQuery(criteria, filter);
return buildTypedQuery(criteria, null, null).getSingleResult();
}
protected <E> E getSingleResultOrNull(CriteriaQuery<E> cq) {
try {
return getEntityManager().createQuery(cq).getSingleResult();
} catch (NoResultException e) {
return null;
}
}
protected <E> E getSingleResultOrNull(TypedQuery<E> tq) {
try {
return tq.getSingleResult();
} catch (NoResultException e) {
return null;
}
}
protected EntityManager getEntityManager() {
return entityManager;
}
@SuppressWarnings("unchecked")
protected <T> void sort(List<T> entities) {
Object[] a = entities.toArray();
Arrays.sort(a);
ListIterator<T> i = entities.listIterator();
for (int j = 0; j < a.length; j++) {
i.next();
i.set((T) a[j]);
}
}
}
|
package com.robrua.orianna.type.dto.team;
import java.util.HashSet;
import java.util.List;
import java.util.Set;
import javax.persistence.CascadeType;
import javax.persistence.Entity;
import javax.persistence.Id;
import javax.persistence.OneToMany;
import javax.persistence.OneToOne;
import javax.persistence.Table;
import com.robrua.orianna.type.dto.OriannaDto;
@Entity(name = "team.Team")
@Table(name = "team")
public class Team extends OriannaDto {
private static final long serialVersionUID = 7937264447395600368L;
private Long createDate, lastGameDate, lastJoinDate, lastJoinedRankedTeamQueueDate, modifyDate, secondLastJoinDate, thirdLastJoinDate;
@Id
private String fullId;
@OneToMany(cascade = CascadeType.ALL)
private List<MatchHistorySummary> matchHistory;
private String name, status, tag;
@OneToOne(cascade = CascadeType.ALL)
private Roster roster;
@OneToMany(cascade = CascadeType.ALL)
private List<TeamStatDetail> teamStatDetails;
/*
* (non-Javadoc)
* @see java.lang.Object#equals(java.lang.Object)
*/
@Override
public boolean equals(final Object obj) {
if(this == obj) {
return true;
}
if(obj == null) {
return false;
}
if(!(obj instanceof Team)) {
return false;
}
final Team other = (Team)obj;
if(fullId == null) {
if(other.fullId != null) {
return false;
}
}
else if(!fullId.equals(other.fullId)) {
return false;
}
return true;
}
/**
* @return the createDate
*/
public Long getCreateDate() {
return createDate;
}
@Override
public String getDataStoreIndexField(final Class<?> keyType) {
if(keyType.equals(String.class)) {
return "fullId";
}
return null;
}
/**
* @return the fullId
*/
public String getFullId() {
return fullId;
}
/**
* @return the lastGameDate
*/
public Long getLastGameDate() {
return lastGameDate;
}
/**
* @return the lastJoinDate
*/
public Long getLastJoinDate() {
return lastJoinDate;
}
/**
* @return the lastJoinedRankedTeamQueueDate
*/
public Long getLastJoinedRankedTeamQueueDate() {
return lastJoinedRankedTeamQueueDate;
}
/**
* @return the matchHistory
*/
public List<MatchHistorySummary> getMatchHistory() {
return matchHistory;
}
/**
* @return the modifyDate
*/
public Long getModifyDate() {
return modifyDate;
}
/**
* @return the name
*/
public String getName() {
return name;
}
/**
* @return the roster
*/
public Roster getRoster() {
return roster;
}
/**
* @return the secondLastJoinDate
*/
public Long getSecondLastJoinDate() {
return secondLastJoinDate;
}
/**
* @return the status
*/
public String getStatus() {
return status;
}
/**
* Gets all stored summoner IDs for batch lookup
*
* @return the summoner IDs
*/
public Set<Long> getSummonerIDs() {
final Set<Long> set = new HashSet<>();
set.add(roster.getOwnerId());
if(roster.getMemberList() != null) {
for(final TeamMemberInfo member : roster.getMemberList()) {
set.add(member.getPlayerId());
}
}
return set;
}
/**
* @return the tag
*/
public String getTag() {
return tag;
}
/**
* @return the teamStatDetails
*/
public List<TeamStatDetail> getTeamStatDetails() {
return teamStatDetails;
}
/**
* @return the thirdLastJoinDate
*/
public Long getThirdLastJoinDate() {
return thirdLastJoinDate;
}
/*
* (non-Javadoc)
* @see java.lang.Object#hashCode()
*/
@Override
public int hashCode() {
final int prime = 31;
int result = 1;
result = prime * result + (fullId == null ? 0 : fullId.hashCode());
return result;
}
/**
* @param createDate
* the createDate to set
*/
public void setCreateDate(final Long createDate) {
this.createDate = createDate;
}
/**
* @param fullId
* the fullId to set
*/
public void setFullId(final String fullId) {
this.fullId = fullId;
}
/**
* @param lastGameDate
* the lastGameDate to set
*/
public void setLastGameDate(final Long lastGameDate) {
this.lastGameDate = lastGameDate;
}
/**
* @param lastJoinDate
* the lastJoinDate to set
*/
public void setLastJoinDate(final Long lastJoinDate) {
this.lastJoinDate = lastJoinDate;
}
/**
* @param lastJoinedRankedTeamQueueDate
* the lastJoinedRankedTeamQueueDate to set
*/
public void setLastJoinedRankedTeamQueueDate(final Long lastJoinedRankedTeamQueueDate) {
this.lastJoinedRankedTeamQueueDate = lastJoinedRankedTeamQueueDate;
}
/**
* @param matchHistory
* the matchHistory to set
*/
public void setMatchHistory(final List<MatchHistorySummary> matchHistory) {
this.matchHistory = matchHistory;
}
/**
* @param modifyDate
* the modifyDate to set
*/
public void setModifyDate(final Long modifyDate) {
this.modifyDate = modifyDate;
}
/**
* @param name
* the name to set
*/
public void setName(final String name) {
this.name = name;
}
/**
* @param roster
* the roster to set
*/
public void setRoster(final Roster roster) {
this.roster = roster;
}
/**
* @param secondLastJoinDate
* the secondLastJoinDate to set
*/
public void setSecondLastJoinDate(final Long secondLastJoinDate) {
this.secondLastJoinDate = secondLastJoinDate;
}
/**
* @param status
* the status to set
*/
public void setStatus(final String status) {
this.status = status;
}
/**
* @param tag
* the tag to set
*/
public void setTag(final String tag) {
this.tag = tag;
}
/**
* @param teamStatDetails
* the teamStatDetails to set
*/
public void setTeamStatDetails(final List<TeamStatDetail> teamStatDetails) {
this.teamStatDetails = teamStatDetails;
}
/**
* @param thirdLastJoinDate
* the thirdLastJoinDate to set
*/
public void setThirdLastJoinDate(final Long thirdLastJoinDate) {
this.thirdLastJoinDate = thirdLastJoinDate;
}
/*
* (non-Javadoc)
* @see java.lang.Object#toString()
*/
@Override
public String toString() {
return "Team [createDate=" + createDate + ", lastGameDate=" + lastGameDate + ", lastJoinDate=" + lastJoinDate + ", lastJoinedRankedTeamQueueDate="
+ lastJoinedRankedTeamQueueDate + ", modifyDate=" + modifyDate + ", secondLastJoinDate=" + secondLastJoinDate + ", thirdLastJoinDate="
+ thirdLastJoinDate + ", fullId=" + fullId + ", name=" + name + ", status=" + status + ", tag=" + tag + ", matchHistory=" + matchHistory
+ ", roster=" + roster + ", teamStatDetails=" + teamStatDetails + "]";
}
}
|
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