label int64 0 1 | func1 stringlengths 173 53.1k | func2 stringlengths 173 53.1k | id int64 0 901k |
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1 | public void run() { LOG.debug(this); String[] parts = createCmdArray(getCommand()); Runtime runtime = Runtime.getRuntime(); try { Process process = runtime.exec(parts); if (isBlocking()) { process.waitFor(); StringWriter out = new StringWriter(); IOUtils.copy(process.getInputStream(), out); String stdout = out.toString().replaceFirst("\\s+$", ""); if (StringUtils.isNotBlank(stdout)) { LOG.info("Process stdout:\n" + stdout); } StringWriter err = new StringWriter(); IOUtils.copy(process.getErrorStream(), err); String stderr = err.toString().replaceFirst("\\s+$", ""); if (StringUtils.isNotBlank(stderr)) { LOG.error("Process stderr:\n" + stderr); } } } catch (IOException ioe) { LOG.error(String.format("Could not exec [%s]", getCommand()), ioe); } catch (InterruptedException ie) { LOG.error(String.format("Interrupted [%s]", getCommand()), ie); } } | public void run() { if (saveAsDialog == null) { saveAsDialog = new FileDialog(window.getShell(), SWT.SAVE); saveAsDialog.setFilterExtensions(saveAsTypes); } String outputFile = saveAsDialog.open(); if (outputFile != null) { Object inputFile = DataSourceSingleton.getInstance().getContainer().getWrapped(); InputStream in; try { if (inputFile instanceof URL) in = ((URL) inputFile).openStream(); else in = new FileInputStream((File) inputFile); OutputStream out = new FileOutputStream(outputFile); if (outputFile.endsWith("xml")) { int c; while ((c = in.read()) != -1) out.write(c); } else { PrintWriter pw = new PrintWriter(out); Element data = DataSourceSingleton.getInstance().getRawData(); writeTextFile(data, pw, -1); pw.close(); } in.close(); out.close(); } catch (MalformedURLException e1) { } catch (IOException e) { } } } | 12,400 |
1 | public void shouldAllowClosingInputStreamTwice() throws IOException { OutputStream outputStream = fileSystem.createOutputStream(_("hello"), OutputMode.OVERWRITE); outputStream.write(new byte[] { 1, 2, 3 }); outputStream.close(); InputStream inputStream = fileSystem.createInputStream(_("hello")); ByteArrayOutputStream buffer = new ByteArrayOutputStream(); IOUtils.copy(inputStream, buffer); inputStream.close(); inputStream.close(); } | private void copyFile(File sourcefile, File targetfile) { BufferedInputStream in = null; BufferedOutputStream out = null; try { in = new BufferedInputStream(new FileInputStream(sourcefile)); out = new BufferedOutputStream(new FileOutputStream(targetfile)); byte[] buffer = new byte[4096]; int bytesread = 0; while ((bytesread = in.read(buffer)) >= 0) { out.write(buffer, 0, bytesread); } } catch (IOException e) { e.printStackTrace(); } finally { try { if (in != null) { in.close(); } if (out != null) { out.close(); } } catch (IOException e) { e.printStackTrace(); } } } | 12,401 |
1 | public ActualTask(TEditor editor, TIGDataBase dataBase, String directoryPath, Vector images) { int i; lengthOfTask = images.size(); Element dataBaseXML = new Element("dataBase"); for (i = 0; ((i < images.size()) && !stop && !cancel); i++) { Vector imagen = new Vector(2); imagen = (Vector) images.elementAt(i); String element = (String) imagen.elementAt(0); current = i; String pathSrc = System.getProperty("user.dir") + File.separator + "images" + File.separator + element.substring(0, 1).toUpperCase() + File.separator + element; String name = pathSrc.substring(pathSrc.lastIndexOf(File.separator) + 1, pathSrc.length()); String pathDst = directoryPath + name; try { FileChannel srcChannel = new FileInputStream(pathSrc).getChannel(); FileChannel dstChannel = new FileOutputStream(pathDst).getChannel(); dstChannel.transferFrom(srcChannel, 0, srcChannel.size()); srcChannel.close(); dstChannel.close(); } catch (IOException exc) { System.out.println(exc.getMessage()); System.out.println(exc.toString()); } Vector<String> keyWords = new Vector<String>(); keyWords = TIGDataBase.asociatedConceptSearch(element); Element image = new Element("image"); image.setAttribute("name", name); if (keyWords.size() != 0) { for (int k = 0; k < keyWords.size(); k++) { Element category = new Element("category"); category.setText(keyWords.get(k).trim()); image.addContent(category); } } dataBaseXML.addContent(image); } Document doc = new Document(dataBaseXML); try { XMLOutputter out = new XMLOutputter(); FileOutputStream f = new FileOutputStream(directoryPath + "images.xml"); out.output(doc, f); f.flush(); f.close(); } catch (Exception e) { e.printStackTrace(); } current = lengthOfTask; } | public static final void copyFile(File source, File destination) throws IOException { FileChannel sourceChannel = new FileInputStream(source).getChannel(); FileChannel targetChannel = new FileOutputStream(destination).getChannel(); sourceChannel.transferTo(0, sourceChannel.size(), targetChannel); sourceChannel.close(); targetChannel.close(); } | 12,402 |
0 | protected void doBackupOrganizeRelation() throws Exception { Connection con = null; PreparedStatement ps = null; ResultSet result = null; String strSelQuery = "SELECT organize_id,organize_type_id,child_id,child_type_id,remark " + "FROM " + Common.ORGANIZE_RELATION_TABLE; String strInsQuery = "INSERT INTO " + Common.ORGANIZE_RELATION_B_TABLE + " " + "(version_no,organize_id,organize_type,child_id,child_type,remark) " + "VALUES (?,?,?,?,?,?)"; DBOperation dbo = factory.createDBOperation(POOL_NAME); try { try { con = dbo.getConnection(); con.setAutoCommit(false); ps = con.prepareStatement(strSelQuery); result = ps.executeQuery(); ps = con.prepareStatement(strInsQuery); while (result.next()) { ps.setInt(1, this.versionNO); ps.setString(2, result.getString("organize_id")); ps.setString(3, result.getString("organize_type_id")); ps.setString(4, result.getString("child_id")); ps.setString(5, result.getString("child_type_id")); ps.setString(6, result.getString("remark")); int resultCount = ps.executeUpdate(); if (resultCount != 1) { con.rollback(); throw new CesSystemException("Organize_backup.doBackupOrganizeRelation(): ERROR Inserting data " + "in T_SYS_ORGANIZE_RELATION_B INSERT !! resultCount = " + resultCount); } } con.commit(); } catch (SQLException se) { con.rollback(); throw new CesSystemException("Organize_backup.doBackupOrganizeRelation(): SQLException: " + se); } finally { con.setAutoCommit(true); close(dbo, ps, result); } } catch (SQLException se) { throw new CesSystemException("Organize_backup.doBackupOrganizeRelation(): SQLException while committing or rollback"); } } | protected static byte[] hashPassword(byte[] saltBytes, String plaintextPassword) throws AssertionError { MessageDigest digest; try { digest = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException ex) { throw (AssertionError) new AssertionError("No MD5 message digest supported.").initCause(ex); } digest.update(saltBytes); try { digest.update(plaintextPassword.getBytes("utf-8")); } catch (UnsupportedEncodingException ex) { throw (AssertionError) new AssertionError("No UTF-8 encoding supported.").initCause(ex); } byte[] passwordBytes = digest.digest(); return passwordBytes; } | 12,403 |
1 | public static String encryptPassword(String originalPassword) { if (!StringUtils.hasText(originalPassword)) { originalPassword = randomPassword(); } try { MessageDigest md5 = MessageDigest.getInstance(PASSWORD_ENCRYPTION_TYPE); md5.update(originalPassword.getBytes()); byte[] bytes = md5.digest(); int value; StringBuilder buf = new StringBuilder(); for (byte aByte : bytes) { value = aByte; if (value < 0) { value += 256; } if (value < 16) { buf.append("0"); } buf.append(Integer.toHexString(value)); } return buf.toString(); } catch (NoSuchAlgorithmException e) { log.debug("Do not encrypt password,use original password", e); return originalPassword; } } | public static String getDigest(String input) throws NoSuchAlgorithmException { MessageDigest md5 = MessageDigest.getInstance("MD5"); md5.update(input.getBytes()); byte[] outDigest = md5.digest(); StringBuffer outBuf = new StringBuffer(33); for (int i = 0; i < outDigest.length; i++) { byte b = outDigest[i]; int hi = (b >> 4) & 0x0f; outBuf.append(MD5Digest.hexTab[hi]); int lo = b & 0x0f; outBuf.append(MD5Digest.hexTab[lo]); } return outBuf.toString(); } | 12,404 |
1 | public static int my_rename(String source, String dest) { logger.debug("RENAME " + source + " to " + dest); if (source == null || dest == null) return -1; { logger.debug("\tMoving file across file systems."); FileChannel srcChannel = null; FileChannel dstChannel = null; FileLock lock = null; try { srcChannel = new FileInputStream(source).getChannel(); dstChannel = new FileOutputStream(dest).getChannel(); lock = dstChannel.lock(); dstChannel.transferFrom(srcChannel, 0, srcChannel.size()); dstChannel.force(true); } catch (IOException e) { logger.fatal("Error while copying file '" + source + "' to file '" + dest + "'. " + e.getMessage(), e); return common_h.ERROR; } finally { try { lock.release(); } catch (Throwable t) { logger.fatal("Error releasing file lock - " + dest); } try { srcChannel.close(); } catch (Throwable t) { } try { dstChannel.close(); } catch (Throwable t) { } } } return common_h.OK; } | public static File createTempFile(InputStream contentStream, String ext) throws IOException { ExceptionUtils.throwIfNull(contentStream, "contentStream"); File file = File.createTempFile("test", ext); FileOutputStream fos = new FileOutputStream(file); try { IOUtils.copy(contentStream, fos, false); } finally { fos.close(); } return file; } | 12,405 |
0 | public boolean saveTemplate(Template t) { try { conn.setAutoCommit(false); Statement stmt = conn.createStatement(); String query; ResultSet rset; if (Integer.parseInt(executeMySQLGet("SELECT COUNT(*) FROM templates WHERE name='" + escapeCharacters(t.getName()) + "'")) != 0) return false; query = "select * from templates where templateid = " + t.getID(); rset = stmt.executeQuery(query); if (rset.next()) { System.err.println("Updating already saved template is not supported!!!!!!"); return false; } else { query = "INSERT INTO templates (name, parentid) VALUES ('" + escapeCharacters(t.getName()) + "', " + t.getParentID() + ")"; try { stmt.executeUpdate(query); } catch (SQLException e) { conn.rollback(); conn.setAutoCommit(true); e.printStackTrace(); return false; } int templateid = Integer.parseInt(executeMySQLGet("SELECT LAST_INSERT_ID()")); t.setID(templateid); LinkedList<Field> fields = t.getFields(); ListIterator<Field> iter = fields.listIterator(); Field f = null; PreparedStatement pstmt = conn.prepareStatement("INSERT INTO templatefields(fieldtype, name, templateid, defaultvalue)" + "VALUES (?,?,?,?)"); try { while (iter.hasNext()) { f = iter.next(); if (f.getType() == Field.IMAGE) { System.out.println("field is an image."); byte data[] = ((FieldDataImage) f.getDefault()).getDataBytes(); pstmt.setBytes(4, data); } else { System.out.println("field is not an image"); String deflt = (f.getDefault()).getData(); pstmt.setString(4, deflt); } pstmt.setInt(1, f.getType()); pstmt.setString(2, f.getName()); pstmt.setInt(3, t.getID()); pstmt.execute(); f.setID(Integer.parseInt(executeMySQLGet("SELECT LAST_INSERT_ID()"))); } } catch (SQLException e) { conn.rollback(); conn.setAutoCommit(true); e.printStackTrace(); return false; } } conn.commit(); conn.setAutoCommit(true); } catch (SQLException ex) { System.err.println("Error saving the Template"); return false; } return true; } | public void _saveWebAsset(ActionRequest req, ActionResponse res, PortletConfig config, ActionForm form, User user, String subcmd) throws WebAssetException, Exception { long maxsize = 50; long maxwidth = 3000; long maxheight = 3000; long minheight = 10; ActionRequestImpl reqImpl = (ActionRequestImpl) req; HttpServletRequest httpReq = reqImpl.getHttpServletRequest(); try { UploadPortletRequest uploadReq = PortalUtil.getUploadPortletRequest(req); String parent = ParamUtil.getString(req, "parent"); int countFiles = ParamUtil.getInteger(req, "countFiles"); int fileCounter = 0; Folder folder = (Folder) InodeFactory.getInode(parent, Folder.class); _checkUserPermissions(folder, user, PERMISSION_WRITE); String userId = user.getUserId(); String customMessage = "Some file does not match the filters specified by the folder: "; boolean filterError = false; for (int k = 0; k < countFiles; k++) { File file = new File(); String title = ParamUtil.getString(req, "title" + k); String friendlyName = ParamUtil.getString(req, "friendlyName" + k); Date publishDate = new Date(); String fileName = ParamUtil.getString(req, "fileName" + k); fileName = checkMACFileName(fileName); if (!FolderFactory.matchFilter(folder, fileName)) { customMessage += fileName + ", "; filterError = true; continue; } if (fileName.length() > 0) { String mimeType = FileFactory.getMimeType(fileName); String URI = folder.getPath() + fileName; String suffix = UtilMethods.getFileExtension(fileName); file.setTitle(title); file.setFileName(fileName); file.setFriendlyName(friendlyName); file.setPublishDate(publishDate); file.setModUser(userId); InodeFactory.saveInode(file); String filePath = FileFactory.getRealAssetsRootPath(); new java.io.File(filePath).mkdir(); java.io.File uploadedFile = uploadReq.getFile("uploadedFile" + k); Logger.debug(this, "bytes" + uploadedFile.length()); file.setSize((int) uploadedFile.length() - 2); file.setMimeType(mimeType); Host host = HostFactory.getCurrentHost(httpReq); Identifier ident = IdentifierFactory.getIdentifierByURI(URI, host); String message = ""; if ((FileFactory.existsFileName(folder, fileName))) { InodeFactory.deleteInode(file); message = "The uploaded file " + fileName + " already exists in this folder"; SessionMessages.add(req, "custommessage", message); } else { String fileInodePath = String.valueOf(file.getInode()); if (fileInodePath.length() == 1) { fileInodePath = fileInodePath + "0"; } fileInodePath = fileInodePath.substring(0, 1) + java.io.File.separator + fileInodePath.substring(1, 2); new java.io.File(filePath + java.io.File.separator + fileInodePath.substring(0, 1)).mkdir(); new java.io.File(filePath + java.io.File.separator + fileInodePath).mkdir(); java.io.File f = new java.io.File(filePath + java.io.File.separator + fileInodePath + java.io.File.separator + file.getInode() + "." + suffix); java.io.FileOutputStream fout = new java.io.FileOutputStream(f); FileChannel outputChannel = fout.getChannel(); FileChannel inputChannel = new java.io.FileInputStream(uploadedFile).getChannel(); outputChannel.transferFrom(inputChannel, 0, inputChannel.size()); outputChannel.force(false); outputChannel.close(); inputChannel.close(); Logger.debug(this, "SaveFileAction New File in =" + filePath + java.io.File.separator + fileInodePath + java.io.File.separator + file.getInode() + "." + suffix); if (suffix.equals("jpg") || suffix.equals("gif")) { com.dotmarketing.util.Thumbnail.resizeImage(filePath + java.io.File.separator + fileInodePath + java.io.File.separator, String.valueOf(file.getInode()), suffix); int height = javax.imageio.ImageIO.read(f).getHeight(); file.setHeight(height); Logger.debug(this, "File height=" + height); int width = javax.imageio.ImageIO.read(f).getWidth(); file.setWidth(width); Logger.debug(this, "File width=" + width); long size = (f.length() / 1024); WebAssetFactory.createAsset(file, userId, folder); } else { WebAssetFactory.createAsset(file, userId, folder); } WorkingCache.addToWorkingAssetToCache(file); _setFilePermissions(folder, file, user); fileCounter += 1; if ((subcmd != null) && subcmd.equals(com.dotmarketing.util.Constants.PUBLISH)) { try { PublishFactory.publishAsset(file, httpReq); if (fileCounter > 1) { SessionMessages.add(req, "message", "message.file_asset.save"); } else { SessionMessages.add(req, "message", "message.fileupload.save"); } } catch (WebAssetException wax) { Logger.error(this, wax.getMessage(), wax); SessionMessages.add(req, "error", "message.webasset.published.failed"); } } } } } if (filterError) { customMessage = customMessage.substring(0, customMessage.lastIndexOf(",")); SessionMessages.add(req, "custommessage", customMessage); } } catch (IOException e) { Logger.error(this, "Exception saving file: " + e.getMessage()); throw new ActionException(e.getMessage()); } } | 12,406 |
1 | private static synchronized boolean doCopyFile(File srcFile, File destFile, boolean preserveFileDate) throws IOException { if (destFile.exists() && destFile.isDirectory()) { destFile = new File(destFile + FILE_SEPARATOR + srcFile.getName()); } FileInputStream input = new FileInputStream(srcFile); try { FileOutputStream output = new FileOutputStream(destFile); try { IOUtils.copy(input, output); } finally { IOUtils.closeQuietly(output); } } finally { IOUtils.closeQuietly(input); } if (srcFile.length() != destFile.length()) { throw new IOException("Failed to copy full contents from '" + srcFile + "' to '" + destFile + "'"); } if (preserveFileDate) { destFile.setLastModified(srcFile.lastModified()); } return destFile.exists(); } | public void convert(File src, File dest) throws IOException { InputStream in = new BufferedInputStream(new FileInputStream(src)); DcmParser p = pfact.newDcmParser(in); Dataset ds = fact.newDataset(); p.setDcmHandler(ds.getDcmHandler()); try { FileFormat format = p.detectFileFormat(); if (format != FileFormat.ACRNEMA_STREAM) { System.out.println("\n" + src + ": not an ACRNEMA stream!"); return; } p.parseDcmFile(format, Tags.PixelData); if (ds.contains(Tags.StudyInstanceUID) || ds.contains(Tags.SeriesInstanceUID) || ds.contains(Tags.SOPInstanceUID) || ds.contains(Tags.SOPClassUID)) { System.out.println("\n" + src + ": contains UIDs!" + " => probable already DICOM - do not convert"); return; } boolean hasPixelData = p.getReadTag() == Tags.PixelData; boolean inflate = hasPixelData && ds.getInt(Tags.BitsAllocated, 0) == 12; int pxlen = p.getReadLength(); if (hasPixelData) { if (inflate) { ds.putUS(Tags.BitsAllocated, 16); pxlen = pxlen * 4 / 3; } if (pxlen != (ds.getInt(Tags.BitsAllocated, 0) >>> 3) * ds.getInt(Tags.Rows, 0) * ds.getInt(Tags.Columns, 0) * ds.getInt(Tags.NumberOfFrames, 1) * ds.getInt(Tags.NumberOfSamples, 1)) { System.out.println("\n" + src + ": mismatch pixel data length!" + " => do not convert"); return; } } ds.putUI(Tags.StudyInstanceUID, uid(studyUID)); ds.putUI(Tags.SeriesInstanceUID, uid(seriesUID)); ds.putUI(Tags.SOPInstanceUID, uid(instUID)); ds.putUI(Tags.SOPClassUID, classUID); if (!ds.contains(Tags.NumberOfSamples)) { ds.putUS(Tags.NumberOfSamples, 1); } if (!ds.contains(Tags.PhotometricInterpretation)) { ds.putCS(Tags.PhotometricInterpretation, "MONOCHROME2"); } if (fmi) { ds.setFileMetaInfo(fact.newFileMetaInfo(ds, UIDs.ImplicitVRLittleEndian)); } OutputStream out = new BufferedOutputStream(new FileOutputStream(dest)); try { } finally { ds.writeFile(out, encodeParam()); if (hasPixelData) { if (!skipGroupLen) { out.write(PXDATA_GROUPLEN); int grlen = pxlen + 8; out.write((byte) grlen); out.write((byte) (grlen >> 8)); out.write((byte) (grlen >> 16)); out.write((byte) (grlen >> 24)); } out.write(PXDATA_TAG); out.write((byte) pxlen); out.write((byte) (pxlen >> 8)); out.write((byte) (pxlen >> 16)); out.write((byte) (pxlen >> 24)); } if (inflate) { int b2, b3; for (; pxlen > 0; pxlen -= 3) { out.write(in.read()); b2 = in.read(); b3 = in.read(); out.write(b2 & 0x0f); out.write(b2 >> 4 | ((b3 & 0x0f) << 4)); out.write(b3 >> 4); } } else { for (; pxlen > 0; --pxlen) { out.write(in.read()); } } out.close(); } System.out.print('.'); } finally { in.close(); } } | 12,407 |
0 | protected InputStream getInputStream(URL url) { InputStream is = null; if (url != null) { try { is = url.openStream(); } catch (Exception ex) { } } ClassLoader classLoader = Thread.currentThread().getContextClassLoader(); if (is == null) { try { is = classLoader.getResourceAsStream("osworkflow.xml"); } catch (Exception e) { } } if (is == null) { try { is = classLoader.getResourceAsStream("/osworkflow.xml"); } catch (Exception e) { } } if (is == null) { try { is = classLoader.getResourceAsStream("META-INF/osworkflow.xml"); } catch (Exception e) { } } if (is == null) { try { is = classLoader.getResourceAsStream("/META-INF/osworkflow.xml"); } catch (Exception e) { } } return is; } | public void createTableIfNotExisting(Connection conn) throws SQLException { String sql = "select * from " + tableName; PreparedStatement ps = null; try { ps = conn.prepareStatement(sql); ps.executeQuery(); } catch (SQLException sqle) { ps.close(); sql = "create table " + tableName + " ( tableName varchar(255) not null primary key, " + " lastId numeric(18) not null)"; ps = conn.prepareStatement(sql); ps.executeUpdate(); } finally { ps.close(); try { if (!conn.getAutoCommit()) conn.commit(); } catch (Exception e) { conn.rollback(); } } } | 12,408 |
1 | private static void readAndWriteFile(File source, File target) { try { FileInputStream in = new FileInputStream(source); FileOutputStream out = new FileOutputStream(target); int c; while ((c = in.read()) != -1) out.write(c); in.close(); out.close(); } catch (Exception e) { } } | public static void extractZip(Resource zip, FileObject outputDirectory) { ZipInputStream zis = null; try { zis = new ZipInputStream(zip.getResourceURL().openStream()); ZipEntry entry; while ((entry = zis.getNextEntry()) != null) { String[] pathElements = entry.getName().split("/"); FileObject extractDir = outputDirectory; for (int i = 0; i < pathElements.length - 1; i++) { String pathElementName = pathElements[i]; FileObject pathElementFile = extractDir.resolveFile(pathElementName); if (!pathElementFile.exists()) { pathElementFile.createFolder(); } extractDir = pathElementFile; } String fileName = entry.getName(); if (fileName.endsWith("/")) { fileName = fileName.substring(0, fileName.length() - 1); } if (fileName.contains("/")) { fileName = fileName.substring(fileName.lastIndexOf('/') + 1); } if (entry.isDirectory()) { extractDir.resolveFile(fileName).createFolder(); } else { FileObject file = extractDir.resolveFile(fileName); file.createFile(); int size = (int) entry.getSize(); byte[] unpackBuffer = new byte[size]; zis.read(unpackBuffer, 0, size); InputStream in = null; OutputStream out = null; try { in = new ByteArrayInputStream(unpackBuffer); out = file.getContent().getOutputStream(); IOUtils.copy(in, out); } finally { IOUtils.closeQuietly(in); IOUtils.closeQuietly(out); } } } } catch (IOException e2) { throw new RuntimeException(e2); } finally { IOUtils.closeQuietly(zis); } } | 12,409 |
0 | public static Image getImage(String urlChartString) throws IOException, JGoogleChartException { Image image = null; HttpURLConnection urlConn = null; URL url = new URL(urlChartString); urlConn = (HttpURLConnection) url.openConnection(); urlConn.setDoInput(true); urlConn.setDoOutput(true); urlConn.setUseCaches(false); urlConn.setRequestMethod("GET"); urlConn.setAllowUserInteraction(false); urlConn.setRequestProperty("HTTP-Version", "HTTP/1.1"); urlConn.setRequestProperty("Content-Type", "application/x-www-form-urlencoded"); int responseCode = urlConn.getResponseCode(); if (responseCode != 200) { throw new JGoogleChartException(JGoogleChartException.MSG_HTTP_ERROR_CODE + responseCode + " (" + urlConn.getResponseMessage()); } InputStream istream = urlConn.getInputStream(); image = ImageIO.read(istream); return image; } | private void regattaBackup() { SwingWorker sw = new SwingWorker() { Regatta lRegatta = fRegatta; public Object construct() { String fullName = lRegatta.getSaveDirectory() + lRegatta.getSaveName(); System.out.println(MessageFormat.format(res.getString("MainMessageBackingUp"), new Object[] { fullName + BAK })); try { FileInputStream fis = new FileInputStream(new File(fullName)); FileOutputStream fos = new FileOutputStream(new File(fullName + BAK)); int bufsize = 1024; byte[] buffer = new byte[bufsize]; int n = 0; while ((n = fis.read(buffer, 0, bufsize)) >= 0) fos.write(buffer, 0, n); fos.flush(); fos.close(); } catch (java.io.IOException ex) { Util.showError(ex, true); } return null; } }; sw.start(); } | 12,410 |
1 | @SmallTest public void testSha1() throws Exception { MessageDigest digest = MessageDigest.getInstance("SHA-1"); int numTests = mTestData.length; for (int i = 0; i < numTests; i++) { digest.update(mTestData[i].input.getBytes()); byte[] hash = digest.digest(); String encodedHash = encodeHex(hash); assertEquals(encodedHash, mTestData[i].result); } } | public String SHA1(String text) throws NoSuchAlgorithmException, UnsupportedEncodingException { MessageDigest md; md = MessageDigest.getInstance("SHA-1"); byte[] sha1hash = new byte[40]; md.update(text.getBytes("iso-8859-1"), 0, text.length()); sha1hash = md.digest(); return convertToHex(sha1hash); } | 12,411 |
1 | public String getClass(EmeraldjbBean eb) throws EmeraldjbException { Entity entity = (Entity) eb; StringBuffer sb = new StringBuffer(); String myPackage = getPackageName(eb); sb.append("package " + myPackage + ";\n"); sb.append("\n"); DaoValuesGenerator valgen = new DaoValuesGenerator(); String values_class_name = valgen.getClassName(entity); sb.append("\n"); List importList = new Vector(); importList.add("java.io.*;"); importList.add("java.sql.Date;"); importList.add("com.emeraldjb.runtime.patternXmlObj.*;"); importList.add("javax.xml.parsers.*;"); importList.add("java.text.ParseException;"); importList.add("org.xml.sax.*;"); importList.add("org.xml.sax.helpers.*;"); importList.add(valgen.getPackageName(eb) + "." + values_class_name + ";"); Iterator it = importList.iterator(); while (it.hasNext()) { String importName = (String) it.next(); sb.append("import " + importName + "\n"); } sb.append("\n"); String proto_version = entity.getPatternValue(GeneratorConst.PATTERN_STREAM_PROTO_VERSION, "1"); boolean short_version = entity.getPatternBooleanValue(GeneratorConst.PATTERN_STREAM_XML_SHORT, false); StringBuffer preface = new StringBuffer(); StringBuffer consts = new StringBuffer(); StringBuffer f_writer = new StringBuffer(); StringBuffer f_writer_short = new StringBuffer(); StringBuffer f_reader = new StringBuffer(); StringBuffer end_elems = new StringBuffer(); boolean end_elem_needs_catch = false; consts.append("\n public static final String EL_CLASS_TAG=\"" + values_class_name + "\";"); preface.append("\n xos.print(\"<!-- This format is optimised for space, below are the column mappings\");"); boolean has_times = false; boolean has_strings = false; it = entity.getMembers().iterator(); int col_num = 0; while (it.hasNext()) { col_num++; Member member = (Member) it.next(); String nm = member.getName(); preface.append("\n xos.print(\"c" + col_num + " = " + nm + "\");"); String elem_name = nm; String elem_name_short = "c" + col_num; String el_name = nm.toUpperCase(); if (member.getColLen() > 0 || !member.isNullAllowed()) { end_elem_needs_catch = true; } String element_const = "EL_" + el_name; String element_const_short = "EL_" + el_name + "_SHORT"; consts.append("\n public static final String " + element_const + "=\"" + elem_name + "\";" + "\n public static final String " + element_const_short + "=\"" + elem_name_short + "\";"); String getter = "obj." + methodGenerator.getMethodName(DaoGeneratorUtils.METHOD_GET, member); String setter = "values_." + methodGenerator.getMethodName(DaoGeneratorUtils.METHOD_SET, member); String pad = " "; JTypeBase gen_type = EmdFactory.getJTypeFactory().getJavaType(member.getType()); f_writer.append(gen_type.getToXmlCode(pad, element_const, getter + "()")); f_writer_short.append(gen_type.getToXmlCode(pad, element_const_short, getter + "()")); end_elems.append(gen_type.getFromXmlCode(pad, element_const, setter)); end_elems.append("\n //and also the short version"); end_elems.append(gen_type.getFromXmlCode(pad, element_const_short, setter)); } preface.append("\n xos.print(\"-->\");"); String body_part = f_writer.toString(); String body_part_short = preface.toString() + f_writer_short.toString(); String reader_vars = ""; String streamer_class_name = getClassName(entity); sb.append("public class " + streamer_class_name + " extends DefaultHandler implements TSParser\n"); sb.append("{" + consts + "\n public static final int PROTO_VERSION=" + proto_version + ";" + "\n private transient StringBuffer cdata_=new StringBuffer();" + "\n private transient String endElement_;" + "\n private transient TSParser parentParser_;" + "\n private transient XMLReader theReader_;\n" + "\n private " + values_class_name + " values_;"); sb.append("\n\n"); sb.append("\n /**" + "\n * This is really only here as an example. It is very rare to write a single" + "\n * object to a file - far more likely to have a collection or object graph. " + "\n * in which case you can write something similar - maybe using the writeXmlShort" + "\n * version instread." + "\n */" + "\n public static void writeToFile(String file_nm, " + values_class_name + " obj) throws IOException" + "\n {" + "\n if (file_nm==null || file_nm.length()==0) throw new IOException(\"Bad file name (null or zero length)\");" + "\n if (obj==null) throw new IOException(\"Bad value object parameter, cannot write null object to file\");" + "\n FileOutputStream fos = new FileOutputStream(file_nm);" + "\n XmlOutputFilter xos = new XmlOutputFilter(fos);" + "\n xos.openElement(\"FILE_\"+EL_CLASS_TAG);" + "\n writeXml(xos, obj);" + "\n xos.closeElement();" + "\n fos.close();" + "\n } // end of writeToFile" + "\n" + "\n public static void readFromFile(String file_nm, " + values_class_name + " obj) throws IOException, SAXException" + "\n {" + "\n if (file_nm==null || file_nm.length()==0) throw new IOException(\"Bad file name (null or zero length)\");" + "\n if (obj==null) throw new IOException(\"Bad value object parameter, cannot write null object to file\");" + "\n FileInputStream fis = new FileInputStream(file_nm);" + "\n DataInputStream dis = new DataInputStream(fis);" + "\n marshalFromXml(dis, obj);" + "\n fis.close();" + "\n } // end of readFromFile" + "\n" + "\n public static void writeXml(XmlOutputFilter xos, " + values_class_name + " obj) throws IOException" + "\n {" + "\n xos.openElement(EL_CLASS_TAG);" + body_part + "\n xos.closeElement();" + "\n } // end of writeXml" + "\n" + "\n public static void writeXmlShort(XmlOutputFilter xos, " + values_class_name + " obj) throws IOException" + "\n {" + "\n xos.openElement(EL_CLASS_TAG);" + body_part_short + "\n xos.closeElement();" + "\n } // end of writeXml" + "\n" + "\n public " + streamer_class_name + "(" + values_class_name + " obj) {" + "\n values_ = obj;" + "\n } // end of ctor" + "\n"); String xml_bit = addXmlFunctions(streamer_class_name, values_class_name, end_elem_needs_catch, end_elems, f_reader); String close = "\n" + "\n} // end of classs" + "\n\n" + "\n//**************" + "\n// End of file" + "\n//**************"; return sb.toString() + xml_bit + close; } | public void doPost(HttpServletRequest req, HttpServletResponse res) throws ServletException, IOException { PrintWriter out = null; ServletOutputStream outstream = null; try { String action = req.getParameter("nmrshiftdbaction"); String relativepath = ServletUtils.expandRelative(this.getServletConfig(), "/WEB-INF"); TurbineConfig tc = new TurbineConfig(relativepath + "..", relativepath + getServletConfig().getInitParameter("properties")); tc.init(); int spectrumId = -1; DBSpectrum spectrum = null; Export export = null; String format = req.getParameter("format"); if (action.equals("test")) { try { res.setContentType("text/plain"); out = res.getWriter(); List l = DBSpectrumPeer.executeQuery("select SPECTRUM_ID from SPECTRUM limit 1"); if (l.size() > 0) spectrumId = ((Record) l.get(0)).getValue(1).asInt(); out.write("success"); } catch (Exception ex) { out.write("failure"); } } else if (action.equals("rss")) { int numbertoexport = 10; out = res.getWriter(); if (req.getParameter("numbertoexport") != null) { try { numbertoexport = Integer.parseInt(req.getParameter("numbertoexport")); if (numbertoexport < 1 || numbertoexport > 20) throw new NumberFormatException("Number to small/large"); } catch (NumberFormatException ex) { out.println("The parameter <code>numbertoexport</code>must be an integer from 1 to 20"); } } res.setContentType("text/xml"); RssWriter rssWriter = new RssWriter(); rssWriter.setWriter(res.getWriter()); AtomContainerSet soac = new AtomContainerSet(); String query = "select distinct MOLECULE.MOLECULE_ID from MOLECULE, SPECTRUM where SPECTRUM.MOLECULE_ID = MOLECULE.MOLECULE_ID and SPECTRUM.REVIEW_FLAG =\"true\" order by MOLECULE.DATE desc;"; List l = NmrshiftdbUserPeer.executeQuery(query); for (int i = 0; i < numbertoexport; i++) { if (i == l.size()) break; DBMolecule mol = DBMoleculePeer.retrieveByPK(new NumberKey(((Record) l.get(i)).getValue(1).asInt())); IMolecule cdkmol = mol.getAsCDKMoleculeAsEntered(1); soac.addAtomContainer(cdkmol); rssWriter.getLinkmap().put(cdkmol, mol.getEasylink(req)); rssWriter.getDatemap().put(cdkmol, mol.getDate()); rssWriter.getTitlemap().put(cdkmol, mol.getChemicalNamesAsOneStringWithFallback()); rssWriter.getCreatormap().put(cdkmol, mol.getNmrshiftdbUser().getUserName()); rssWriter.setCreator(GeneralUtils.getAdminEmail(getServletConfig())); Vector v = mol.getDBCanonicalNames(); for (int k = 0; k < v.size(); k++) { DBCanonicalName canonName = (DBCanonicalName) v.get(k); if (canonName.getDBCanonicalNameType().getCanonicalNameType() == "INChI") { rssWriter.getInchimap().put(cdkmol, canonName.getName()); break; } } rssWriter.setTitle("NMRShiftDB"); rssWriter.setLink("http://www.nmrshiftdb.org"); rssWriter.setDescription("NMRShiftDB is an open-source, open-access, open-submission, open-content web database for chemical structures and their nuclear magnetic resonance data"); rssWriter.setPublisher("NMRShiftDB.org"); rssWriter.setImagelink("http://www.nmrshiftdb.org/images/nmrshift-logo.gif"); rssWriter.setAbout("http://www.nmrshiftdb.org/NmrshiftdbServlet?nmrshiftdbaction=rss"); Collection coll = new ArrayList(); Vector spectra = mol.selectSpectra(null); for (int k = 0; k < spectra.size(); k++) { Element el = ((DBSpectrum) spectra.get(k)).getCmlSpect(); Element el2 = el.getChildElements().get(0); el.removeChild(el2); coll.add(el2); } rssWriter.getMultiMap().put(cdkmol, coll); } rssWriter.write(soac); } else if (action.equals("getattachment")) { res.setContentType("application/zip"); outstream = res.getOutputStream(); DBSample sample = DBSamplePeer.retrieveByPK(new NumberKey(req.getParameter("sampleid"))); outstream.write(sample.getAttachment()); } else if (action.equals("createreport")) { res.setContentType("application/pdf"); outstream = res.getOutputStream(); boolean yearly = req.getParameter("style").equals("yearly"); int yearstart = Integer.parseInt(req.getParameter("yearstart")); int yearend = Integer.parseInt(req.getParameter("yearend")); int monthstart = 0; int monthend = 0; if (!yearly) { monthstart = Integer.parseInt(req.getParameter("monthstart")); monthend = Integer.parseInt(req.getParameter("monthend")); } int type = Integer.parseInt(req.getParameter("type")); JasperReport jasperReport = (JasperReport) JRLoader.loadObject(relativepath + "/reports/" + (yearly ? "yearly" : "monthly") + "_report_" + type + ".jasper"); Map parameters = new HashMap(); if (yearly) parameters.put("HEADER", "Report for years " + yearstart + " - " + yearend); else parameters.put("HEADER", "Report for " + monthstart + "/" + yearstart + " - " + monthend + "/" + yearend); DBConnection dbconn = TurbineDB.getConnection(); Connection conn = dbconn.getConnection(); Statement stmt = conn.createStatement(); ResultSet rs = null; if (type == 1) { rs = stmt.executeQuery("select YEAR(DATE) as YEAR, " + (yearly ? "" : " MONTH(DATE) as MONTH, ") + "AFFILIATION_1, AFFILIATION_2, MACHINE.NAME as NAME, count(*) as C, sum(WISHED_SPECTRUM like '%13C%' or WISHED_SPECTRUM like '%variable temperature%' or WISHED_SPECTRUM like '%ID sel. NOE%' or WISHED_SPECTRUM like '%solvent suppression%' or WISHED_SPECTRUM like '%standard spectrum%') as 1_D, sum(WISHED_SPECTRUM like '%H,H-COSY%' or WISHED_SPECTRUM like '%NOESY%' or WISHED_SPECTRUM like '%HMQC%' or WISHED_SPECTRUM like '%HMBC%') as 2_D, sum(OTHER_WISHED_SPECTRUM!='') as SPECIAL, sum(OTHER_NUCLEI!='') as HETERO, sum(PROCESS='self') as SELF, sum(PROCESS='robot') as ROBOT, sum(PROCESS='worker') as OPERATOR from (SAMPLE join TURBINE_USER using (USER_ID)) join MACHINE on MACHINE.MACHINE_ID=SAMPLE.MACHINE where YEAR(DATE)>=" + yearstart + " and YEAR(DATE)<=" + yearend + " and LOGIN_NAME<>'testuser' group by YEAR, " + (yearly ? "" : "MONTH, ") + "AFFILIATION_1, AFFILIATION_2, MACHINE.NAME"); } else if (type == 2) { rs = stmt.executeQuery("select YEAR(DATE) as YEAR, " + (yearly ? "" : " MONTH(DATE) as MONTH, ") + "MACHINE.NAME as NAME, count(*) as C, sum(WISHED_SPECTRUM like '%13C%' or WISHED_SPECTRUM like '%variable temperature%' or WISHED_SPECTRUM like '%ID sel. NOE%' or WISHED_SPECTRUM like '%solvent suppression%' or WISHED_SPECTRUM like '%standard spectrum%') as 1_D, sum(WISHED_SPECTRUM like '%H,H-COSY%' or WISHED_SPECTRUM like '%NOESY%' or WISHED_SPECTRUM like '%HMQC%' or WISHED_SPECTRUM like '%HMBC%') as 2_D, sum(OTHER_WISHED_SPECTRUM!='') as SPECIAL, sum(OTHER_NUCLEI!='') as HETERO, sum(PROCESS='self') as SELF, sum(PROCESS='robot') as ROBOT, sum(PROCESS='worker') as OPERATOR from (SAMPLE join TURBINE_USER using (USER_ID)) join MACHINE on MACHINE.MACHINE_ID=SAMPLE.MACHINE group by YEAR, " + (yearly ? "" : "MONTH, ") + "MACHINE.NAME"); } JasperPrint jasperPrint = JasperFillManager.fillReport(jasperReport, parameters, new JRResultSetDataSource(rs)); JasperExportManager.exportReportToPdfStream(jasperPrint, outstream); dbconn.close(); } else if (action.equals("exportcmlbyinchi")) { res.setContentType("text/xml"); out = res.getWriter(); String inchi = req.getParameter("inchi"); String spectrumtype = req.getParameter("spectrumtype"); Criteria crit = new Criteria(); crit.add(DBCanonicalNamePeer.NAME, inchi); crit.addJoin(DBCanonicalNamePeer.MOLECULE_ID, DBSpectrumPeer.MOLECULE_ID); crit.addJoin(DBSpectrumPeer.SPECTRUM_TYPE_ID, DBSpectrumTypePeer.SPECTRUM_TYPE_ID); crit.add(DBSpectrumTypePeer.NAME, spectrumtype); try { GeneralUtils.logToSql(crit.toString(), null); } catch (Exception ex) { } Vector spectra = DBSpectrumPeer.doSelect(crit); if (spectra.size() == 0) { out.write("No such molecule or spectrum"); } else { Element cmlElement = new Element("cml"); cmlElement.addAttribute(new Attribute("convention", "nmrshiftdb-convention")); cmlElement.setNamespaceURI("http://www.xml-cml.org/schema"); Element parent = ((DBSpectrum) spectra.get(0)).getDBMolecule().getCML(1); nu.xom.Node cmldoc = parent.getChild(0); ((Element) cmldoc).setNamespaceURI("http://www.xml-cml.org/schema"); parent.removeChildren(); cmlElement.appendChild(cmldoc); for (int k = 0; k < spectra.size(); k++) { Element parentspec = ((DBSpectrum) spectra.get(k)).getCmlSpect(); Node spectrumel = parentspec.getChild(0); parentspec.removeChildren(); cmlElement.appendChild(spectrumel); ((Element) spectrumel).setNamespaceURI("http://www.xml-cml.org/schema"); } out.write(cmlElement.toXML()); } } else if (action.equals("namelist")) { res.setContentType("application/zip"); outstream = res.getOutputStream(); ByteArrayOutputStream baos = new ByteArrayOutputStream(); ZipOutputStream zipout = new ZipOutputStream(baos); Criteria crit = new Criteria(); crit.addJoin(DBMoleculePeer.MOLECULE_ID, DBSpectrumPeer.MOLECULE_ID); crit.add(DBSpectrumPeer.REVIEW_FLAG, "true"); Vector v = DBMoleculePeer.doSelect(crit); for (int i = 0; i < v.size(); i++) { if (i % 500 == 0) { if (i != 0) { zipout.write(new String("<p>The list is continued <a href=\"nmrshiftdb.names." + i + ".html\">here</a></p></body></html>").getBytes()); zipout.closeEntry(); } zipout.putNextEntry(new ZipEntry("nmrshiftdb.names." + i + ".html")); zipout.write(new String("<html><body><h1>This is a list of strcutures in <a href=\"http://www.nmrshiftdb.org\">NMRShiftDB</a>, starting at " + i + ", Its main purpose is to be found by search engines</h1>").getBytes()); } DBMolecule mol = (DBMolecule) v.get(i); zipout.write(new String("<p><a href=\"" + mol.getEasylink(req) + "\">").getBytes()); Vector cannames = mol.getDBCanonicalNames(); for (int k = 0; k < cannames.size(); k++) { zipout.write(new String(((DBCanonicalName) cannames.get(k)).getName() + " ").getBytes()); } Vector chemnames = mol.getDBChemicalNames(); for (int k = 0; k < chemnames.size(); k++) { zipout.write(new String(((DBChemicalName) chemnames.get(k)).getName() + " ").getBytes()); } zipout.write(new String("</a>. Information we have got: NMR spectra").getBytes()); Vector spectra = mol.selectSpectra(); for (int k = 0; k < spectra.size(); k++) { zipout.write(new String(((DBSpectrum) spectra.get(k)).getDBSpectrumType().getName() + ", ").getBytes()); } if (mol.hasAny3d()) zipout.write(new String("3D coordinates, ").getBytes()); zipout.write(new String("File formats: CML, mol, png, jpeg").getBytes()); zipout.write(new String("</p>").getBytes()); } zipout.write(new String("</body></html>").getBytes()); zipout.closeEntry(); zipout.close(); InputStream is = new ByteArrayInputStream(baos.toByteArray()); byte[] buf = new byte[32 * 1024]; int nRead = 0; while ((nRead = is.read(buf)) != -1) { outstream.write(buf, 0, nRead); } } else if (action.equals("predictor")) { if (req.getParameter("symbol") == null) { res.setContentType("text/plain"); out = res.getWriter(); out.write("please give the symbol to create the predictor for in the request with symbol=X (e. g. symbol=C"); } res.setContentType("application/zip"); outstream = res.getOutputStream(); ByteArrayOutputStream baos = new ByteArrayOutputStream(); ZipOutputStream zipout = new ZipOutputStream(baos); String filename = "org/openscience/nmrshiftdb/PredictionTool.class"; zipout.putNextEntry(new ZipEntry(filename)); JarInputStream jip = new JarInputStream(new FileInputStream(ServletUtils.expandRelative(getServletConfig(), "/WEB-INF/lib/nmrshiftdb-lib.jar"))); JarEntry entry = jip.getNextJarEntry(); while (entry.getName().indexOf("PredictionTool.class") == -1) { entry = jip.getNextJarEntry(); } for (int i = 0; i < entry.getSize(); i++) { zipout.write(jip.read()); } zipout.closeEntry(); zipout.putNextEntry(new ZipEntry("nmrshiftdb.csv")); int i = 0; org.apache.turbine.util.db.pool.DBConnection conn = TurbineDB.getConnection(); HashMap mapsmap = new HashMap(); while (true) { Statement stmt = conn.createStatement(); ResultSet rs = stmt.executeQuery("select HOSE_CODE, VALUE, SYMBOL from HOSE_CODES where CONDITION_TYPE='m' and WITH_RINGS=0 and SYMBOL='" + req.getParameter("symbol") + "' limit " + (i * 1000) + ", 1000"); int m = 0; while (rs.next()) { String code = rs.getString(1); Double value = new Double(rs.getString(2)); String symbol = rs.getString(3); if (mapsmap.get(symbol) == null) { mapsmap.put(symbol, new HashMap()); } for (int spheres = 6; spheres > 0; spheres--) { StringBuffer hoseCodeBuffer = new StringBuffer(); StringTokenizer st = new StringTokenizer(code, "()/"); for (int k = 0; k < spheres; k++) { if (st.hasMoreTokens()) { String partcode = st.nextToken(); hoseCodeBuffer.append(partcode); } if (k == 0) { hoseCodeBuffer.append("("); } else if (k == 3) { hoseCodeBuffer.append(")"); } else { hoseCodeBuffer.append("/"); } } String hoseCode = hoseCodeBuffer.toString(); if (((HashMap) mapsmap.get(symbol)).get(hoseCode) == null) { ((HashMap) mapsmap.get(symbol)).put(hoseCode, new ArrayList()); } ((ArrayList) ((HashMap) mapsmap.get(symbol)).get(hoseCode)).add(value); } m++; } i++; stmt.close(); if (m == 0) break; } Set keySet = mapsmap.keySet(); Iterator it = keySet.iterator(); while (it.hasNext()) { String symbol = (String) it.next(); HashMap hosemap = ((HashMap) mapsmap.get(symbol)); Set keySet2 = hosemap.keySet(); Iterator it2 = keySet2.iterator(); while (it2.hasNext()) { String hoseCode = (String) it2.next(); ArrayList list = ((ArrayList) hosemap.get(hoseCode)); double[] values = new double[list.size()]; for (int k = 0; k < list.size(); k++) { values[k] = ((Double) list.get(k)).doubleValue(); } zipout.write(new String(symbol + "|" + hoseCode + "|" + Statistics.minimum(values) + "|" + Statistics.average(values) + "|" + Statistics.maximum(values) + "\r\n").getBytes()); } } zipout.closeEntry(); zipout.close(); InputStream is = new ByteArrayInputStream(baos.toByteArray()); byte[] buf = new byte[32 * 1024]; int nRead = 0; i = 0; while ((nRead = is.read(buf)) != -1) { outstream.write(buf, 0, nRead); } } else if (action.equals("exportspec") || action.equals("exportmol")) { if (spectrumId > -1) spectrum = DBSpectrumPeer.retrieveByPK(new NumberKey(spectrumId)); else spectrum = DBSpectrumPeer.retrieveByPK(new NumberKey(req.getParameter("spectrumid"))); export = new Export(spectrum); } else if (action.equals("exportmdl")) { res.setContentType("text/plain"); outstream = res.getOutputStream(); DBMolecule mol = DBMoleculePeer.retrieveByPK(new NumberKey(req.getParameter("moleculeid"))); outstream.write(mol.getStructureFile(Integer.parseInt(req.getParameter("coordsetid")), false).getBytes()); } else if (action.equals("exportlastinputs")) { format = action; } else if (action.equals("printpredict")) { res.setContentType("text/html"); out = res.getWriter(); HttpSession session = req.getSession(); VelocityContext context = PredictPortlet.getContext(session, true, true, new StringBuffer(), getServletConfig(), req, true); StringWriter w = new StringWriter(); Velocity.mergeTemplate("predictprint.vm", "ISO-8859-1", context, w); out.println(w.toString()); } else { res.setContentType("text/html"); out = res.getWriter(); out.println("No valid action"); } if (format == null) format = ""; if (format.equals("pdf") || format.equals("rtf")) { res.setContentType("application/" + format); out = res.getWriter(); } if (format.equals("docbook")) { res.setContentType("application/zip"); outstream = res.getOutputStream(); } if (format.equals("svg")) { res.setContentType("image/x-svg"); out = res.getWriter(); } if (format.equals("tiff")) { res.setContentType("image/tiff"); outstream = res.getOutputStream(); } if (format.equals("jpeg")) { res.setContentType("image/jpeg"); outstream = res.getOutputStream(); } if (format.equals("png")) { res.setContentType("image/png"); outstream = res.getOutputStream(); } if (format.equals("mdl") || format.equals("txt") || format.equals("cml") || format.equals("cmlboth") || format.indexOf("exsection") == 0) { res.setContentType("text/plain"); out = res.getWriter(); } if (format.equals("simplehtml") || format.equals("exportlastinputs")) { res.setContentType("text/html"); out = res.getWriter(); } if (action.equals("exportlastinputs")) { int numbertoexport = 4; if (req.getParameter("numbertoexport") != null) { try { numbertoexport = Integer.parseInt(req.getParameter("numbertoexport")); if (numbertoexport < 1 || numbertoexport > 20) throw new NumberFormatException("Number to small/large"); } catch (NumberFormatException ex) { out.println("The parameter <code>numbertoexport</code>must be an integer from 1 to 20"); } } NmrshiftdbUser user = null; try { user = NmrshiftdbUserPeer.getByName(req.getParameter("username")); } catch (NmrshiftdbException ex) { out.println("Seems <code>username</code> is not OK: " + ex.getMessage()); } if (user != null) { List l = NmrshiftdbUserPeer.executeQuery("SELECT LAST_DOWNLOAD_DATE FROM TURBINE_USER where LOGIN_NAME=\"" + user.getUserName() + "\";"); Date lastDownloadDate = ((Record) l.get(0)).getValue(1).asDate(); if (((new Date().getTime() - lastDownloadDate.getTime()) / 3600000) < 24) { out.println("Your last download was at " + lastDownloadDate + ". You may download your last inputs only once a day. Sorry for this, but we need to be carefull with resources. If you want to put your last inputs on your homepage best use some sort of cache (e. g. use wget for downlaod with crond and link to this static resource))!"); } else { NmrshiftdbUserPeer.executeStatement("UPDATE TURBINE_USER SET LAST_DOWNLOAD_DATE=NOW() where LOGIN_NAME=\"" + user.getUserName() + "\";"); Vector<String> parameters = new Vector<String>(); String query = "select distinct MOLECULE.MOLECULE_ID from MOLECULE, SPECTRUM where SPECTRUM.MOLECULE_ID = MOLECULE.MOLECULE_ID and SPECTRUM.REVIEW_FLAG =\"true\" and SPECTRUM.USER_ID=" + user.getUserId() + " order by MOLECULE.DATE desc;"; l = NmrshiftdbUserPeer.executeQuery(query); String url = javax.servlet.http.HttpUtils.getRequestURL(req).toString(); url = url.substring(0, url.length() - 17); for (int i = 0; i < numbertoexport; i++) { if (i == l.size()) break; DBMolecule mol = DBMoleculePeer.retrieveByPK(new NumberKey(((Record) l.get(i)).getValue(1).asInt())); parameters.add(new String("<a href=\"" + url + "/portal/pane0/Results?nmrshiftdbaction=showDetailsFromHome&molNumber=" + mol.getMoleculeId() + "\"><img src=\"" + javax.servlet.http.HttpUtils.getRequestURL(req).toString() + "?nmrshiftdbaction=exportmol&spectrumid=" + ((DBSpectrum) mol.getDBSpectrums().get(0)).getSpectrumId() + "&format=jpeg&size=150x150&backcolor=12632256\"></a>")); } VelocityContext context = new VelocityContext(); context.put("results", parameters); StringWriter w = new StringWriter(); Velocity.mergeTemplate("lateststructures.vm", "ISO-8859-1", context, w); out.println(w.toString()); } } } if (action.equals("exportspec")) { if (format.equals("txt")) { String lastsearchtype = req.getParameter("lastsearchtype"); if (lastsearchtype.equals(NmrshiftdbConstants.TOTALSPECTRUM) || lastsearchtype.equals(NmrshiftdbConstants.SUBSPECTRUM)) { List l = ParseUtils.parseSpectrumFromSpecFile(req.getParameter("lastsearchvalues")); spectrum.initSimilarity(l, lastsearchtype.equals(NmrshiftdbConstants.SUBSPECTRUM)); } Vector v = spectrum.getOptions(); DBMolecule mol = spectrum.getDBMolecule(); out.print(mol.getChemicalNamesAsOneString(false) + mol.getMolecularFormula(false) + "; " + mol.getMolecularWeight() + " Dalton\n\r"); out.print("\n\rAtom\t"); if (spectrum.getDBSpectrumType().getElementSymbol() == ("H")) out.print("Mult.\t"); out.print("Meas."); if (lastsearchtype.equals(NmrshiftdbConstants.TOTALSPECTRUM) || lastsearchtype.equals(NmrshiftdbConstants.SUBSPECTRUM)) { out.print("\tInput\tDiff"); } out.print("\n\r"); out.print("No.\t"); if (spectrum.getDBSpectrumType().getElementSymbol() == ("H")) out.print("\t"); out.print("Shift"); if (lastsearchtype.equals(NmrshiftdbConstants.TOTALSPECTRUM) || lastsearchtype.equals(NmrshiftdbConstants.SUBSPECTRUM)) { out.print("\tShift\tM-I"); } out.print("\n\r"); for (int i = 0; i < v.size(); i++) { out.print(((ValuesForVelocityBean) v.get(i)).getDisplayText() + "\t" + ((ValuesForVelocityBean) v.get(i)).getRange()); if (lastsearchtype.equals(NmrshiftdbConstants.TOTALSPECTRUM) || lastsearchtype.equals(NmrshiftdbConstants.SUBSPECTRUM)) { out.print("\t" + ((ValuesForVelocityBean) v.get(i)).getNameForElements() + "\t" + ((ValuesForVelocityBean) v.get(i)).getDelta()); } out.print("\n\r"); } } if (format.equals("simplehtml")) { String i1 = export.getImage(false, "jpeg", ServletUtils.expandRelative(this.getServletConfig(), "/nmrshiftdbhtml") + "/tmp/" + System.currentTimeMillis(), true); export.pictures[0] = new File(i1).getName(); String i2 = export.getImage(true, "jpeg", ServletUtils.expandRelative(this.getServletConfig(), "/nmrshiftdbhtml") + "/tmp/" + System.currentTimeMillis(), true); export.pictures[1] = new File(i2).getName(); String docbook = export.getHtml(); out.print(docbook); } if (format.equals("pdf") || format.equals("rtf")) { String svgSpec = export.getSpecSvg(400, 200); String svgspecfile = relativepath + "/tmp/" + System.currentTimeMillis() + "s.svg"; new FileOutputStream(svgspecfile).write(svgSpec.getBytes()); export.pictures[1] = svgspecfile; String molSvg = export.getMolSvg(true); String svgmolfile = relativepath + "/tmp/" + System.currentTimeMillis() + "m.svg"; new FileOutputStream(svgmolfile).write(molSvg.getBytes()); export.pictures[0] = svgmolfile; String docbook = export.getDocbook("pdf", "SVG"); TransformerFactory tFactory = TransformerFactory.newInstance(); Transformer transformer = tFactory.newTransformer(new StreamSource("file:" + GeneralUtils.getNmrshiftdbProperty("docbookxslpath", getServletConfig()) + "/fo/docbook.xsl")); ByteArrayOutputStream baos = new ByteArrayOutputStream(); transformer.transform(new StreamSource(new StringReader(docbook)), new StreamResult(baos)); FopFactory fopFactory = FopFactory.newInstance(); FOUserAgent foUserAgent = fopFactory.newFOUserAgent(); OutputStream out2 = new ByteArrayOutputStream(); Fop fop = fopFactory.newFop(format.equals("rtf") ? MimeConstants.MIME_RTF : MimeConstants.MIME_PDF, foUserAgent, out2); TransformerFactory factory = TransformerFactory.newInstance(); transformer = factory.newTransformer(); Source src = new StreamSource(new StringReader(baos.toString())); Result res2 = new SAXResult(fop.getDefaultHandler()); transformer.transform(src, res2); out.print(out2.toString()); } if (format.equals("docbook")) { String i1 = relativepath + "/tmp/" + System.currentTimeMillis() + ".svg"; new FileOutputStream(i1).write(export.getSpecSvg(300, 200).getBytes()); export.pictures[0] = new File(i1).getName(); String i2 = relativepath + "/tmp/" + System.currentTimeMillis() + ".svg"; new FileOutputStream(i2).write(export.getMolSvg(true).getBytes()); export.pictures[1] = new File(i2).getName(); String docbook = export.getDocbook("pdf", "SVG"); String docbookfile = relativepath + "/tmp/" + System.currentTimeMillis() + ".xml"; new FileOutputStream(docbookfile).write(docbook.getBytes()); ByteArrayOutputStream baos = export.makeZip(new String[] { docbookfile, i1, i2 }); outstream.write(baos.toByteArray()); } if (format.equals("svg")) { out.print(export.getSpecSvg(400, 200)); } if (format.equals("tiff") || format.equals("jpeg") || format.equals("png")) { InputStream is = new FileInputStream(export.getImage(false, format, relativepath + "/tmp/" + System.currentTimeMillis(), true)); byte[] buf = new byte[32 * 1024]; int nRead = 0; while ((nRead = is.read(buf)) != -1) { outstream.write(buf, 0, nRead); } } if (format.equals("cml")) { out.print(spectrum.getCmlSpect().toXML()); } if (format.equals("cmlboth")) { Element cmlElement = new Element("cml"); cmlElement.addAttribute(new Attribute("convention", "nmrshiftdb-convention")); cmlElement.setNamespaceURI("http://www.xml-cml.org/schema"); Element parent = spectrum.getDBMolecule().getCML(1, spectrum.getDBSpectrumType().getName().equals("1H")); nu.xom.Node cmldoc = parent.getChild(0); ((Element) cmldoc).setNamespaceURI("http://www.xml-cml.org/schema"); parent.removeChildren(); cmlElement.appendChild(cmldoc); Element parentspec = spectrum.getCmlSpect(); Node spectrumel = parentspec.getChild(0); parentspec.removeChildren(); cmlElement.appendChild(spectrumel); ((Element) spectrumel).setNamespaceURI("http://www.xml-cml.org/schema"); out.write(cmlElement.toXML()); } if (format.indexOf("exsection") == 0) { StringTokenizer st = new StringTokenizer(format, "-"); st.nextToken(); String template = st.nextToken(); Criteria crit = new Criteria(); crit.add(DBSpectrumPeer.USER_ID, spectrum.getUserId()); Vector v = spectrum.getDBMolecule().getDBSpectrums(crit); VelocityContext context = new VelocityContext(); context.put("spectra", v); context.put("molecule", spectrum.getDBMolecule()); StringWriter w = new StringWriter(); Velocity.mergeTemplate("exporttemplates/" + template, "ISO-8859-1", context, w); out.write(w.toString()); } } if (action.equals("exportmol")) { int width = -1; int height = -1; if (req.getParameter("size") != null) { StringTokenizer st = new StringTokenizer(req.getParameter("size"), "x"); width = Integer.parseInt(st.nextToken()); height = Integer.parseInt(st.nextToken()); } boolean shownumbers = true; if (req.getParameter("shownumbers") != null && req.getParameter("shownumbers").equals("false")) { shownumbers = false; } if (req.getParameter("backcolor") != null) { export.backColor = new Color(Integer.parseInt(req.getParameter("backcolor"))); } if (req.getParameter("markatom") != null) { export.selected = Integer.parseInt(req.getParameter("markatom")) - 1; } if (format.equals("svg")) { out.print(export.getMolSvg(true)); } if (format.equals("tiff") || format.equals("jpeg") || format.equals("png")) { InputStream is = new FileInputStream(export.getImage(true, format, relativepath + "/tmp/" + System.currentTimeMillis(), width, height, shownumbers, null)); byte[] buf = new byte[32 * 1024]; int nRead = 0; while ((nRead = is.read(buf)) != -1) { outstream.write(buf, 0, nRead); } } if (format.equals("mdl")) { out.println(spectrum.getDBMolecule().getStructureFile(1, false)); } if (format.equals("cml")) { out.println(spectrum.getDBMolecule().getCMLString(1)); } } if (out != null) out.flush(); else outstream.flush(); } catch (Exception ex) { ex.printStackTrace(); out.print(GeneralUtils.logError(ex, "NmrshiftdbServlet", null, true)); out.flush(); } } | 12,412 |
1 | public static final void parse(String infile, String outfile) throws IOException { BufferedReader reader = new BufferedReader(new FileReader(infile)); DataOutputStream output = new DataOutputStream(new FileOutputStream(outfile)); int w = Integer.parseInt(reader.readLine()); int h = Integer.parseInt(reader.readLine()); output.writeByte(w); output.writeByte(h); int lineCount = 2; try { do { for (int i = 0; i < h; i++) { lineCount++; String line = reader.readLine(); if (line == null) { throw new RuntimeException("Unexpected end of file at line " + lineCount); } for (int j = 0; j < w; j++) { char c = line.charAt(j); System.out.print(c); output.writeByte(c); } System.out.println(""); } lineCount++; output.writeShort(Short.parseShort(reader.readLine())); } while (reader.readLine() != null); } finally { reader.close(); output.close(); } } | @Test public void testCopy_readerToWriter_nullOut() throws Exception { InputStream in = new ByteArrayInputStream(inData); in = new YellOnCloseInputStreamTest(in); Reader reader = new InputStreamReader(in, "US-ASCII"); try { IOUtils.copy(reader, (Writer) null); fail(); } catch (NullPointerException ex) { } } | 12,413 |
1 | public String digest(String algorithm, String text) { MessageDigest digester = null; try { digester = MessageDigest.getInstance(algorithm); digester.update(text.getBytes(Digester.ENCODING)); } catch (NoSuchAlgorithmException nsae) { _log.error(nsae, nsae); } catch (UnsupportedEncodingException uee) { _log.error(uee, uee); } byte[] bytes = digester.digest(); if (_BASE_64) { return Base64.encode(bytes); } else { return new String(Hex.encodeHex(bytes)); } } | public synchronized String encrypt(String plaintext) { MessageDigest md = null; try { md = MessageDigest.getInstance("SHA"); md.update(plaintext.getBytes("UTF-8")); } catch (NoSuchAlgorithmException e) { log().error("failed to encrypt the password.", e); throw new RuntimeException("failed to encrypt the password.", e); } catch (UnsupportedEncodingException e) { log().error("failed to encrypt the password.", e); throw new RuntimeException("failed to encrypt the password.", e); } byte raw[] = md.digest(); String hash = (new BASE64Encoder()).encode(raw); return hash; } | 12,414 |
1 | private void deleteProject(String uid, String home, HttpServletRequest request, HttpServletResponse response) throws Exception { String project = request.getParameter("project"); String line; response.setContentType("text/html"); PrintWriter out = response.getWriter(); htmlHeader(out, "Project Status", ""); try { synchronized (Class.forName("com.sun.gep.SunTCP")) { Vector list = new Vector(); String directory = home; Runtime.getRuntime().exec("/usr/bin/rm -rf " + directory + project); FilePermission perm = new FilePermission(directory + SUNTCP_LIST, "read,write,execute"); File listfile = new File(directory + SUNTCP_LIST); BufferedReader read = new BufferedReader(new FileReader(listfile)); while ((line = read.readLine()) != null) { if (!((new StringTokenizer(line, "\t")).nextToken().equals(project))) { list.addElement(line); } } read.close(); if (list.size() > 0) { PrintWriter write = new PrintWriter(new BufferedWriter(new FileWriter(listfile))); for (int i = 0; i < list.size(); i++) { write.println((String) list.get(i)); } write.close(); } else { listfile.delete(); } out.println("The project was successfully deleted."); } } catch (Exception e) { out.println("Error accessing this project."); } out.println("<center><form><input type=button value=Continue onClick=\"opener.location.reload(); window.close()\"></form></center>"); htmlFooter(out); } | public static File unGzip(File infile, boolean deleteGzipfileOnSuccess) throws IOException { GZIPInputStream gin = new GZIPInputStream(new FileInputStream(infile)); File outFile = new File(infile.getParent(), infile.getName().replaceAll("\\.gz$", "")); FileOutputStream fos = new FileOutputStream(outFile); byte[] buf = new byte[100000]; int len; while ((len = gin.read(buf)) > 0) fos.write(buf, 0, len); gin.close(); fos.close(); if (deleteGzipfileOnSuccess) infile.delete(); return outFile; } | 12,415 |
0 | private String unJar(String jarPath, String jarEntry) { String path; if (jarPath.lastIndexOf("lib/") >= 0) path = jarPath.substring(0, jarPath.lastIndexOf("lib/")); else path = jarPath.substring(0, jarPath.lastIndexOf("/")); String relPath = jarEntry.substring(0, jarEntry.lastIndexOf("/")); try { new File(path + "/" + relPath).mkdirs(); JarFile jar = new JarFile(jarPath); ZipEntry ze = jar.getEntry(jarEntry); File bin = new File(path + "/" + jarEntry); IOUtils.copy(jar.getInputStream(ze), new FileOutputStream(bin)); } catch (Exception e) { e.printStackTrace(); } return path + "/" + jarEntry; } | public void addUrl(URL url) throws IOException, SAXException { InputStream inStream = url.openStream(); String path = url.getPath(); int slashInx = path.lastIndexOf('/'); String name = path.substring(slashInx + 1); Document doc = docBuild.parse(inStream); Element root = doc.getDocumentElement(); String rootTag = root.getTagName(); if (rootTag.equals("graphml")) { NodeList graphNodes = root.getElementsByTagName("graph"); for (int i = 0; i < graphNodes.getLength(); i++) { Element elem = (Element) graphNodes.item(i); String graphName = elem.getAttribute("id"); if (graphName == null) { graphName = name; } addStructure(new GraphSpec(graphName)); urlRefs.put(graphName, url); } } else if (rootTag.equals("tree")) { addStructure(new TreeSpec(name)); urlRefs.put(name, url); } else { throw new IllegalArgumentException("Format of " + url + " not understood."); } inStream.close(); } | 12,416 |
1 | public static void doVersionCheck(View view) { view.showWaitCursor(); try { URL url = new URL(jEdit.getProperty("version-check.url")); InputStream in = url.openStream(); BufferedReader bin = new BufferedReader(new InputStreamReader(in)); String line; String version = null; String build = null; while ((line = bin.readLine()) != null) { if (line.startsWith(".version")) version = line.substring(8).trim(); else if (line.startsWith(".build")) build = line.substring(6).trim(); } bin.close(); if (version != null && build != null) { if (jEdit.getBuild().compareTo(build) < 0) newVersionAvailable(view, version, url); else { GUIUtilities.message(view, "version-check" + ".up-to-date", new String[0]); } } } catch (IOException e) { String[] args = { jEdit.getProperty("version-check.url"), e.toString() }; GUIUtilities.error(view, "read-error", args); } view.hideWaitCursor(); } | public static int UsePassword(String username, String password, String new_password) { try { URL url = new URL("http://eiffel.itba.edu.ar/hci/service/Security.groovy?method=ChangePassword&username=" + username + "&password=" + password + "&new_password=" + new_password); URLConnection urlc = url.openConnection(); urlc.setDoOutput(false); urlc.setAllowUserInteraction(false); BufferedReader br = new BufferedReader(new InputStreamReader(urlc.getInputStream())); String str; StringBuffer sb = new StringBuffer(); while ((str = br.readLine()) != null) { sb.append(str); sb.append("\n"); } br.close(); String response = sb.toString(); if (response == null) { return -1; } DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance(); DocumentBuilder db = dbf.newDocumentBuilder(); InputSource is = new InputSource(); is.setCharacterStream(new StringReader(response)); Document dom = db.parse(is); NodeList nl = dom.getElementsByTagName("response"); String status = ((Element) nl.item(0)).getAttributes().item(0).getTextContent(); if (status.toString().equals("fail")) { return -1; } return 0; } catch (Exception e) { e.printStackTrace(); } return -1; } | 12,417 |
1 | public void copy(File aSource, File aDestDir) throws IOException { FileInputStream myInFile = new FileInputStream(aSource); FileOutputStream myOutFile = new FileOutputStream(new File(aDestDir, aSource.getName())); FileChannel myIn = myInFile.getChannel(); FileChannel myOut = myOutFile.getChannel(); boolean end = false; while (true) { int myBytes = myIn.read(theBuffer); if (myBytes != -1) { theBuffer.flip(); myOut.write(theBuffer); theBuffer.clear(); } else break; } myIn.close(); myOut.close(); myInFile.close(); myOutFile.close(); long myEnd = System.currentTimeMillis(); } | public void sendResponse(DjdocRequest req, HttpServletResponse res) throws IOException { File file = (File) req.getResult(); InputStream in = null; try { in = new FileInputStream(file); IOUtils.copy(in, res.getOutputStream()); } finally { if (in != null) { in.close(); } } } | 12,418 |
1 | public void resumereceive(HttpServletRequest req, HttpServletResponse resp, SessionCommand command) { setHeader(resp); try { logger.debug("ResRec: Resume a 'receive' session with session id " + command.getSession() + " this client already received " + command.getLen() + " bytes"); File tempFile = new File(this.getSyncWorkDirectory(req), command.getSession() + ".smodif"); if (!tempFile.exists()) { logger.debug("ResRec: the file doesn't exist, so we created it by serializing the entities"); try { OutputStream fos = new FileOutputStream(tempFile); syncServer.getServerModifications(command.getSession(), fos); fos.close(); } catch (ImogSerializationException mse) { logger.error(mse.getMessage(), mse); } } InputStream fis = new FileInputStream(tempFile); fis.skip(command.getLen()); resp.setContentLength(fis.available()); while (fis.available() > 0) { resp.getOutputStream().write(fis.read()); } resp.getOutputStream().flush(); resp.flushBuffer(); fis.close(); } catch (IOException ioe) { logger.error(ioe.getMessage()); } } | public void copyFile(File sourceFile, File destFile) throws IOException { if (!destFile.exists()) { destFile.createNewFile(); } FileChannel source = null; FileChannel destination = null; Closer c = new Closer(); try { source = c.register(new FileInputStream(sourceFile).getChannel()); destination = c.register(new FileOutputStream(destFile).getChannel()); destination.transferFrom(source, 0, source.size()); } catch (IOException e) { c.doNotThrow(); throw e; } finally { c.closeAll(); } } | 12,419 |
1 | public static void main(String[] args) throws IOException { System.out.println("Start filtering zgps..."); final Config config = ConfigUtils.loadConfig(args[0]); final String CONFIG_MODULE = "GPSFilterZGPS"; File sourceFileSelectedStages = new File(config.findParam(CONFIG_MODULE, "sourceFileSelectedStages")); File sourceFileZGPS = new File(config.findParam(CONFIG_MODULE, "sourceFileZGPS")); File targetFile = new File(config.findParam(CONFIG_MODULE, "targetFile")); System.out.println("Start reading selected stages..."); FilterZGPSSelectedStages selectedStages = new FilterZGPSSelectedStages(); selectedStages.createSelectedStages(sourceFileSelectedStages); System.out.println("Done. " + selectedStages.getSelectedStages().size() + " stages were stored"); System.out.println("Start reading and writing zgps..."); try { BufferedReader in = new BufferedReader(new InputStreamReader(new FileInputStream(sourceFileZGPS))); BufferedWriter out = new BufferedWriter(new FileWriter(targetFile)); out.write(in.readLine()); out.newLine(); String lineFromInputFile; while ((lineFromInputFile = in.readLine()) != null) { String[] entries = lineFromInputFile.split("\t"); if (selectedStages.containsStage(Integer.parseInt(entries[0]), Integer.parseInt(entries[1]), Integer.parseInt(entries[2]))) { out.write(lineFromInputFile); out.newLine(); out.flush(); } } in.close(); out.close(); } catch (FileNotFoundException e) { System.out.println("Could not find source file for selected stages."); e.printStackTrace(); } catch (IOException e) { System.out.println("IO Exception while reading or writing zgps."); e.printStackTrace(); } System.out.println("Done."); } | @Override protected void doGet(HttpServletRequest req, HttpServletResponse resp) throws ServletException, IOException { resp.addHeader("Cache-Control", "max-age=" + Constants.HTTP_CACHE_SECONDS); String uuid = req.getRequestURI().substring(req.getRequestURI().indexOf(Constants.SERVLET_FULL_PREFIX) + Constants.SERVLET_FULL_PREFIX.length() + 1); boolean notScale = ClientUtils.toBoolean(req.getParameter(Constants.URL_PARAM_NOT_SCALE)); ServletOutputStream os = resp.getOutputStream(); if (uuid != null && !"".equals(uuid)) { try { String mimetype = fedoraAccess.getMimeTypeForStream(uuid, FedoraUtils.IMG_FULL_STREAM); if (mimetype == null) { mimetype = "image/jpeg"; } ImageMimeType loadFromMimeType = ImageMimeType.loadFromMimeType(mimetype); if (loadFromMimeType == ImageMimeType.JPEG || loadFromMimeType == ImageMimeType.PNG) { StringBuffer sb = new StringBuffer(); sb.append(config.getFedoraHost()).append("/objects/").append(uuid).append("/datastreams/IMG_FULL/content"); InputStream is = RESTHelper.get(sb.toString(), config.getFedoraLogin(), config.getFedoraPassword(), false); if (is == null) { return; } try { IOUtils.copyStreams(is, os); } catch (IOException e) { resp.setStatus(HttpURLConnection.HTTP_NOT_FOUND); LOGGER.error("Unable to open full image.", e); } finally { os.flush(); if (is != null) { try { is.close(); } catch (IOException e) { resp.setStatus(HttpURLConnection.HTTP_NOT_FOUND); LOGGER.error("Unable to close stream.", e); } finally { is = null; } } } } else { Image rawImg = KrameriusImageSupport.readImage(uuid, FedoraUtils.IMG_FULL_STREAM, this.fedoraAccess, 0, loadFromMimeType); BufferedImage scaled = null; if (!notScale) { scaled = KrameriusImageSupport.getSmallerImage(rawImg, 1250, 1000); } else { scaled = KrameriusImageSupport.getSmallerImage(rawImg, 2500, 2000); } KrameriusImageSupport.writeImageToStream(scaled, "JPG", os); resp.setContentType(ImageMimeType.JPEG.getValue()); resp.setStatus(HttpURLConnection.HTTP_OK); } } catch (IOException e) { resp.setStatus(HttpURLConnection.HTTP_NOT_FOUND); LOGGER.error("Unable to open full image.", e); } catch (XPathExpressionException e) { resp.setStatus(HttpURLConnection.HTTP_NOT_FOUND); LOGGER.error("Unable to create XPath expression.", e); } finally { os.flush(); } } } | 12,420 |
1 | public static boolean encodeFileToFile(String infile, String outfile) { boolean success = false; java.io.InputStream in = null; java.io.OutputStream out = null; try { in = new Base64.InputStream(new java.io.BufferedInputStream(new java.io.FileInputStream(infile)), Base64.ENCODE); out = new java.io.BufferedOutputStream(new java.io.FileOutputStream(outfile)); byte[] buffer = new byte[65536]; int read = -1; while ((read = in.read(buffer)) >= 0) { out.write(buffer, 0, read); } success = true; } catch (java.io.IOException exc) { exc.printStackTrace(); } finally { try { in.close(); } catch (Exception exc) { } try { out.close(); } catch (Exception exc) { } } return success; } | public static void copyFile(File src, File dest) throws IOException { FileInputStream fis = new FileInputStream(src); FileOutputStream fos = new FileOutputStream(dest); java.nio.channels.FileChannel channelSrc = fis.getChannel(); java.nio.channels.FileChannel channelDest = fos.getChannel(); channelSrc.transferTo(0, channelSrc.size(), channelDest); fis.close(); fos.close(); } | 12,421 |
0 | public boolean authenticate(String plaintext) throws NoSuchAlgorithmException { String[] passwordParts = this.password.split("\\$"); md = MessageDigest.getInstance("SHA-1"); md.update(passwordParts[1].getBytes()); isAuthenticated = toHex(md.digest(plaintext.getBytes())).equalsIgnoreCase(passwordParts[2]); return isAuthenticated; } | public static String sendGetRequest(String endpoint, String requestParameters) { String result = null; if (endpoint.startsWith("http://")) { try { StringBuffer data = new StringBuffer(); String urlStr = endpoint; if (requestParameters != null && requestParameters.length() > 0) { urlStr += "?" + requestParameters; } URL url = new URL(urlStr); URLConnection conn = url.openConnection(); BufferedReader rd = new BufferedReader(new InputStreamReader(conn.getInputStream())); StringBuffer sb = new StringBuffer(); String line; while ((line = rd.readLine()) != null) { sb.append(line + "\n"); } rd.close(); result = sb.toString(); } catch (Exception e) { } } return result; } | 12,422 |
1 | public void write(OutputStream out, String className, InputStream classDefStream) throws IOException { ByteArrayOutputStream a = new ByteArrayOutputStream(); IOUtils.copy(classDefStream, a); a.close(); DataOutputStream da = new DataOutputStream(out); da.writeUTF(className); da.writeUTF(new String(base64.cipher(a.toByteArray()))); } | public static Checksum checksum(File file, Checksum checksum) throws IOException { if (file.isDirectory()) { throw new IllegalArgumentException("Checksums can't be computed on directories"); } InputStream in = null; try { in = new CheckedInputStream(new FileInputStream(file), checksum); IOUtils.copy(in, new NullOutputStream()); } finally { IOUtils.closeQuietly(in); } return checksum; } | 12,423 |
0 | private static void readAndRewrite(File inFile, File outFile) throws IOException { ImageInputStream iis = ImageIO.createImageInputStream(new BufferedInputStream(new FileInputStream(inFile))); DcmParser dcmParser = DcmParserFactory.getInstance().newDcmParser(iis); Dataset ds = DcmObjectFactory.getInstance().newDataset(); dcmParser.setDcmHandler(ds.getDcmHandler()); dcmParser.parseDcmFile(null, Tags.PixelData); PixelDataReader pdReader = pdFact.newReader(ds, iis, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); System.out.println("reading " + inFile + "..."); pdReader.readPixelData(false); ImageOutputStream out = ImageIO.createImageOutputStream(new BufferedOutputStream(new FileOutputStream(outFile))); DcmEncodeParam dcmEncParam = DcmEncodeParam.IVR_LE; ds.writeDataset(out, dcmEncParam); ds.writeHeader(out, dcmEncParam, Tags.PixelData, dcmParser.getReadVR(), dcmParser.getReadLength()); System.out.println("writing " + outFile + "..."); PixelDataWriter pdWriter = pdFact.newWriter(pdReader.getPixelDataArray(), false, ds, out, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); pdWriter.writePixelData(); out.flush(); out.close(); System.out.println("done!"); } | public static IProject createEMFProject(IPath javaSource, URI projectLocationURI, List<IProject> referencedProjects, Monitor monitor, int style, List<?> pluginVariables) { IProgressMonitor progressMonitor = BasicMonitor.toIProgressMonitor(monitor); String projectName = javaSource.segment(0); IProject project = null; try { List<IClasspathEntry> classpathEntries = new UniqueEList<IClasspathEntry>(); progressMonitor.beginTask("", 10); progressMonitor.subTask(CodeGenEcorePlugin.INSTANCE.getString("_UI_CreatingEMFProject_message", new Object[] { projectName, projectLocationURI != null ? projectLocationURI.toString() : projectName })); IWorkspace workspace = ResourcesPlugin.getWorkspace(); project = workspace.getRoot().getProject(projectName); if (!project.exists()) { URI location = projectLocationURI; if (location == null) { location = URI.createFileURI(workspace.getRoot().getLocation().append(projectName).toOSString()); } location = location.appendSegment(".project"); File projectFile = new File(location.toString()); if (projectFile.exists()) { projectFile.renameTo(new File(location.toString() + ".old")); } } IJavaProject javaProject = JavaCore.create(project); IProjectDescription projectDescription = null; if (!project.exists()) { projectDescription = ResourcesPlugin.getWorkspace().newProjectDescription(projectName); if (projectLocationURI != null) { projectDescription.setLocationURI(new java.net.URI(projectLocationURI.toString())); } project.create(projectDescription, new SubProgressMonitor(progressMonitor, 1)); project.open(new SubProgressMonitor(progressMonitor, 1)); } else { projectDescription = project.getDescription(); project.open(new SubProgressMonitor(progressMonitor, 1)); if (project.hasNature(JavaCore.NATURE_ID)) { classpathEntries.addAll(Arrays.asList(javaProject.getRawClasspath())); } } boolean isInitiallyEmpty = classpathEntries.isEmpty(); { if (referencedProjects.size() != 0 && (style & (EMF_PLUGIN_PROJECT_STYLE | EMF_EMPTY_PROJECT_STYLE)) == 0) { projectDescription.setReferencedProjects(referencedProjects.toArray(new IProject[referencedProjects.size()])); for (IProject referencedProject : referencedProjects) { IClasspathEntry referencedProjectClasspathEntry = JavaCore.newProjectEntry(referencedProject.getFullPath()); classpathEntries.add(referencedProjectClasspathEntry); } } String[] natureIds = projectDescription.getNatureIds(); if (natureIds == null) { natureIds = new String[] { JavaCore.NATURE_ID, "org.eclipse.pde.PluginNature" }; } else { if (!project.hasNature(JavaCore.NATURE_ID)) { String[] oldNatureIds = natureIds; natureIds = new String[oldNatureIds.length + 1]; System.arraycopy(oldNatureIds, 0, natureIds, 0, oldNatureIds.length); natureIds[oldNatureIds.length] = JavaCore.NATURE_ID; } if (!project.hasNature("org.eclipse.pde.PluginNature")) { String[] oldNatureIds = natureIds; natureIds = new String[oldNatureIds.length + 1]; System.arraycopy(oldNatureIds, 0, natureIds, 0, oldNatureIds.length); natureIds[oldNatureIds.length] = "org.eclipse.pde.PluginNature"; } } projectDescription.setNatureIds(natureIds); ICommand[] builders = projectDescription.getBuildSpec(); if (builders == null) { builders = new ICommand[0]; } boolean hasManifestBuilder = false; boolean hasSchemaBuilder = false; for (int i = 0; i < builders.length; ++i) { if ("org.eclipse.pde.ManifestBuilder".equals(builders[i].getBuilderName())) { hasManifestBuilder = true; } if ("org.eclipse.pde.SchemaBuilder".equals(builders[i].getBuilderName())) { hasSchemaBuilder = true; } } if (!hasManifestBuilder) { ICommand[] oldBuilders = builders; builders = new ICommand[oldBuilders.length + 1]; System.arraycopy(oldBuilders, 0, builders, 0, oldBuilders.length); builders[oldBuilders.length] = projectDescription.newCommand(); builders[oldBuilders.length].setBuilderName("org.eclipse.pde.ManifestBuilder"); } if (!hasSchemaBuilder) { ICommand[] oldBuilders = builders; builders = new ICommand[oldBuilders.length + 1]; System.arraycopy(oldBuilders, 0, builders, 0, oldBuilders.length); builders[oldBuilders.length] = projectDescription.newCommand(); builders[oldBuilders.length].setBuilderName("org.eclipse.pde.SchemaBuilder"); } projectDescription.setBuildSpec(builders); project.setDescription(projectDescription, new SubProgressMonitor(progressMonitor, 1)); IContainer sourceContainer = project; if (javaSource.segmentCount() > 1) { IPath sourceContainerPath = javaSource.removeFirstSegments(1).makeAbsolute(); sourceContainer = project.getFolder(sourceContainerPath); if (!sourceContainer.exists()) { for (int i = sourceContainerPath.segmentCount() - 1; i >= 0; i--) { sourceContainer = project.getFolder(sourceContainerPath.removeLastSegments(i)); if (!sourceContainer.exists()) { ((IFolder) sourceContainer).create(false, true, new SubProgressMonitor(progressMonitor, 1)); } } } IClasspathEntry sourceClasspathEntry = JavaCore.newSourceEntry(javaSource); for (Iterator<IClasspathEntry> i = classpathEntries.iterator(); i.hasNext(); ) { IClasspathEntry classpathEntry = i.next(); if (classpathEntry.getPath().isPrefixOf(javaSource)) { i.remove(); } } classpathEntries.add(0, sourceClasspathEntry); } if (isInitiallyEmpty) { IClasspathEntry jreClasspathEntry = JavaCore.newVariableEntry(new Path(JavaRuntime.JRELIB_VARIABLE), new Path(JavaRuntime.JRESRC_VARIABLE), new Path(JavaRuntime.JRESRCROOT_VARIABLE)); for (Iterator<IClasspathEntry> i = classpathEntries.iterator(); i.hasNext(); ) { IClasspathEntry classpathEntry = i.next(); if (classpathEntry.getPath().isPrefixOf(jreClasspathEntry.getPath())) { i.remove(); } } String jreContainer = JavaRuntime.JRE_CONTAINER; String complianceLevel = CodeGenUtil.EclipseUtil.getJavaComplianceLevel(project); if ("1.5".equals(complianceLevel)) { jreContainer += "/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/J2SE-1.5"; } else if ("1.6".equals(complianceLevel)) { jreContainer += "/org.eclipse.jdt.internal.debug.ui.launcher.StandardVMType/JavaSE-1.6"; } classpathEntries.add(JavaCore.newContainerEntry(new Path(jreContainer))); } if ((style & EMF_EMPTY_PROJECT_STYLE) == 0) { if ((style & EMF_PLUGIN_PROJECT_STYLE) != 0) { classpathEntries.add(JavaCore.newContainerEntry(new Path("org.eclipse.pde.core.requiredPlugins"))); for (Iterator<IClasspathEntry> i = classpathEntries.iterator(); i.hasNext(); ) { IClasspathEntry classpathEntry = i.next(); if (classpathEntry.getEntryKind() == IClasspathEntry.CPE_VARIABLE && !JavaRuntime.JRELIB_VARIABLE.equals(classpathEntry.getPath().toString()) || classpathEntry.getEntryKind() == IClasspathEntry.CPE_PROJECT) { i.remove(); } } } else { CodeGenUtil.EclipseUtil.addClasspathEntries(classpathEntries, "ECLIPSE_CORE_RUNTIME", "org.eclipse.core.runtime"); CodeGenUtil.EclipseUtil.addClasspathEntries(classpathEntries, "ECLIPSE_CORE_RESOURCES", "org.eclipse.core.resources"); CodeGenUtil.EclipseUtil.addClasspathEntries(classpathEntries, "EMF_COMMON", "org.eclipse.emf.common"); CodeGenUtil.EclipseUtil.addClasspathEntries(classpathEntries, "EMF_ECORE", "org.eclipse.emf.ecore"); if ((style & EMF_XML_PROJECT_STYLE) != 0) { CodeGenUtil.EclipseUtil.addClasspathEntries(classpathEntries, "EMF_ECORE_XMI", "org.eclipse.emf.ecore.xmi"); } if ((style & EMF_MODEL_PROJECT_STYLE) == 0) { CodeGenUtil.EclipseUtil.addClasspathEntries(classpathEntries, "EMF_EDIT", "org.eclipse.emf.edit"); if ((style & EMF_EDIT_PROJECT_STYLE) == 0) { CodeGenUtil.EclipseUtil.addClasspathEntries(classpathEntries, "ECLIPSE_SWT", "org.eclipse.swt"); CodeGenUtil.EclipseUtil.addClasspathEntries(classpathEntries, "ECLIPSE_JFACE", "org.eclipse.jface"); CodeGenUtil.EclipseUtil.addClasspathEntries(classpathEntries, "ECLIPSE_UI_VIEWS", "org.eclipse.ui.views"); CodeGenUtil.EclipseUtil.addClasspathEntries(classpathEntries, "ECLIPSE_UI_EDITORS", "org.eclipse.ui.editors"); CodeGenUtil.EclipseUtil.addClasspathEntries(classpathEntries, "ECLIPSE_UI_IDE", "org.eclipse.ui.ide"); CodeGenUtil.EclipseUtil.addClasspathEntries(classpathEntries, "ECLIPSE_UI_WORKBENCH", "org.eclipse.ui.workbench"); CodeGenUtil.EclipseUtil.addClasspathEntries(classpathEntries, "EMF_COMMON_UI", "org.eclipse.emf.common.ui"); CodeGenUtil.EclipseUtil.addClasspathEntries(classpathEntries, "EMF_EDIT_UI", "org.eclipse.emf.edit.ui"); if ((style & EMF_XML_PROJECT_STYLE) == 0) { CodeGenUtil.EclipseUtil.addClasspathEntries(classpathEntries, "EMF_ECORE_XMI", "org.eclipse.emf.ecore.xmi"); } } } if ((style & EMF_TESTS_PROJECT_STYLE) != 0) { CodeGenUtil.EclipseUtil.addClasspathEntries(classpathEntries, "JUNIT", "org.junit"); } if (pluginVariables != null) { for (Iterator<?> i = pluginVariables.iterator(); i.hasNext(); ) { Object variable = i.next(); if (variable instanceof IClasspathEntry) { classpathEntries.add((IClasspathEntry) variable); } else if (variable instanceof String) { String pluginVariable = (String) variable; String name; String id; int index = pluginVariable.indexOf("="); if (index == -1) { name = pluginVariable.replace('.', '_').toUpperCase(); id = pluginVariable; } else { name = pluginVariable.substring(0, index); id = pluginVariable.substring(index + 1); } CodeGenUtil.EclipseUtil.addClasspathEntries(classpathEntries, name, id); } } } } } javaProject.setRawClasspath(classpathEntries.toArray(new IClasspathEntry[classpathEntries.size()]), new SubProgressMonitor(progressMonitor, 1)); } if (isInitiallyEmpty) { javaProject.setOutputLocation(new Path("/" + javaSource.segment(0) + "/bin"), new SubProgressMonitor(progressMonitor, 1)); } } catch (Exception exception) { exception.printStackTrace(); CodeGenEcorePlugin.INSTANCE.log(exception); } finally { progressMonitor.done(); } return project; } | 12,424 |
1 | public static void copyFile(final File sourceFile, final File destFile) throws IOException { if (!destFile.exists()) { destFile.createNewFile(); } FileInputStream inStream = null; FileOutputStream outStream = null; FileChannel source = null; FileChannel destination = null; try { source = (inStream = new FileInputStream(sourceFile)).getChannel(); destination = (outStream = new FileOutputStream(destFile)).getChannel(); destination.transferFrom(source, 0, source.size()); } finally { closeIO(source); closeIO(inStream); closeIO(destination); closeIO(outStream); } } | public static boolean copyFile(String fileIn, String fileOut) { FileChannel in = null; FileChannel out = null; boolean retour = false; try { in = new FileInputStream(fileIn).getChannel(); out = new FileOutputStream(fileOut).getChannel(); in.transferTo(0, in.size(), out); in.close(); out.close(); retour = true; } catch (IOException e) { System.err.println("File : " + fileIn); e.printStackTrace(); } return retour; } | 12,425 |
1 | public void copyJarContent(File jarPath, File targetDir) throws IOException { log.info("Copying natives from " + jarPath.getName()); JarFile jar = new JarFile(jarPath); Enumeration<JarEntry> entries = jar.entries(); while (entries.hasMoreElements()) { JarEntry file = entries.nextElement(); File f = new File(targetDir, file.getName()); log.info("Copying native - " + file.getName()); File parentFile = f.getParentFile(); parentFile.mkdirs(); if (file.isDirectory()) { f.mkdir(); continue; } InputStream is = null; FileOutputStream fos = null; try { is = jar.getInputStream(file); fos = new FileOutputStream(f); IOUtils.copy(is, fos); } finally { if (fos != null) fos.close(); if (is != null) is.close(); } } } | public final void saveAsCopy(String current_image, String destination) { BufferedInputStream from = null; BufferedOutputStream to = null; String source = temp_dir + key + current_image; try { from = new BufferedInputStream(new FileInputStream(source)); to = new BufferedOutputStream(new FileOutputStream(destination)); byte[] buffer = new byte[65535]; int bytes_read; while ((bytes_read = from.read(buffer)) != -1) to.write(buffer, 0, bytes_read); } catch (Exception e) { LogWriter.writeLog("Exception " + e + " copying file"); } try { to.close(); from.close(); } catch (Exception e) { LogWriter.writeLog("Exception " + e + " closing files"); } } | 12,426 |
1 | public boolean authenticate(String user, String pass) throws IOException { MessageDigest hash = null; try { MessageDigest.getInstance("BrokenMD4"); } catch (NoSuchAlgorithmException x) { throw new Error(x); } hash.update(new byte[4], 0, 4); try { hash.update(pass.getBytes("US-ASCII"), 0, pass.length()); hash.update(challenge.getBytes("US-ASCII"), 0, challenge.length()); } catch (java.io.UnsupportedEncodingException shouldNeverHappen) { } String response = Util.base64(hash.digest()); Util.writeASCII(out, user + " " + response + '\n'); String reply = Util.readLine(in); if (reply.startsWith(RSYNCD_OK)) { authReqd = false; return true; } connected = false; error = reply; return false; } | public static String toPWD(String pwd) { MessageDigest messageDigest = null; try { messageDigest = MessageDigest.getInstance("MD5"); messageDigest.reset(); messageDigest.update(pwd.getBytes("UTF-8")); } catch (NoSuchAlgorithmException e) { System.out.println("NoSuchAlgorithmException caught!"); System.exit(-1); } catch (UnsupportedEncodingException e) { e.printStackTrace(); } byte[] byteArray = messageDigest.digest(); StringBuffer md5StrBuff = new StringBuffer(); for (int i = 0; i < byteArray.length; i++) { if (Integer.toHexString(0xFF & byteArray[i]).length() == 1) md5StrBuff.append("0").append(Integer.toHexString(0xFF & byteArray[i])); else md5StrBuff.append(Integer.toHexString(0xFF & byteArray[i])); } return md5StrBuff.toString(); } | 12,427 |
0 | public void convert(File src, File dest) throws IOException { InputStream in = new BufferedInputStream(new FileInputStream(src)); DcmParser p = pfact.newDcmParser(in); Dataset ds = fact.newDataset(); p.setDcmHandler(ds.getDcmHandler()); try { FileFormat format = p.detectFileFormat(); if (format != FileFormat.ACRNEMA_STREAM) { System.out.println("\n" + src + ": not an ACRNEMA stream!"); return; } p.parseDcmFile(format, Tags.PixelData); if (ds.contains(Tags.StudyInstanceUID) || ds.contains(Tags.SeriesInstanceUID) || ds.contains(Tags.SOPInstanceUID) || ds.contains(Tags.SOPClassUID)) { System.out.println("\n" + src + ": contains UIDs!" + " => probable already DICOM - do not convert"); return; } boolean hasPixelData = p.getReadTag() == Tags.PixelData; boolean inflate = hasPixelData && ds.getInt(Tags.BitsAllocated, 0) == 12; int pxlen = p.getReadLength(); if (hasPixelData) { if (inflate) { ds.putUS(Tags.BitsAllocated, 16); pxlen = pxlen * 4 / 3; } if (pxlen != (ds.getInt(Tags.BitsAllocated, 0) >>> 3) * ds.getInt(Tags.Rows, 0) * ds.getInt(Tags.Columns, 0) * ds.getInt(Tags.NumberOfFrames, 1) * ds.getInt(Tags.NumberOfSamples, 1)) { System.out.println("\n" + src + ": mismatch pixel data length!" + " => do not convert"); return; } } ds.putUI(Tags.StudyInstanceUID, uid(studyUID)); ds.putUI(Tags.SeriesInstanceUID, uid(seriesUID)); ds.putUI(Tags.SOPInstanceUID, uid(instUID)); ds.putUI(Tags.SOPClassUID, classUID); if (!ds.contains(Tags.NumberOfSamples)) { ds.putUS(Tags.NumberOfSamples, 1); } if (!ds.contains(Tags.PhotometricInterpretation)) { ds.putCS(Tags.PhotometricInterpretation, "MONOCHROME2"); } if (fmi) { ds.setFileMetaInfo(fact.newFileMetaInfo(ds, UIDs.ImplicitVRLittleEndian)); } OutputStream out = new BufferedOutputStream(new FileOutputStream(dest)); try { } finally { ds.writeFile(out, encodeParam()); if (hasPixelData) { if (!skipGroupLen) { out.write(PXDATA_GROUPLEN); int grlen = pxlen + 8; out.write((byte) grlen); out.write((byte) (grlen >> 8)); out.write((byte) (grlen >> 16)); out.write((byte) (grlen >> 24)); } out.write(PXDATA_TAG); out.write((byte) pxlen); out.write((byte) (pxlen >> 8)); out.write((byte) (pxlen >> 16)); out.write((byte) (pxlen >> 24)); } if (inflate) { int b2, b3; for (; pxlen > 0; pxlen -= 3) { out.write(in.read()); b2 = in.read(); b3 = in.read(); out.write(b2 & 0x0f); out.write(b2 >> 4 | ((b3 & 0x0f) << 4)); out.write(b3 >> 4); } } else { for (; pxlen > 0; --pxlen) { out.write(in.read()); } } out.close(); } System.out.print('.'); } finally { in.close(); } } | public ScoreModel(URL url) throws IOException { BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream())); String line; list = new ArrayList<ScoreModelItem>(); map = new HashMap<String, ScoreModelItem>(); line = in.readLine(); int n = 1; String[] rowAttrib; ScoreModelItem item; while ((line = in.readLine()) != null) { rowAttrib = line.split(";"); item = new ScoreModelItem(n, Double.valueOf(rowAttrib[3]), Double.valueOf(rowAttrib[4]), Double.valueOf(rowAttrib[2]), Double.valueOf(rowAttrib[5]), rowAttrib[1]); list.add(item); map.put(item.getHash(), item); n++; } in.close(); } | 12,428 |
1 | public static void copyFiles(String strPath, String dstPath) throws IOException { File src = new File(strPath); File dest = new File(dstPath); if (src.isDirectory()) { dest.mkdirs(); String list[] = src.list(); for (int i = 0; i < list.length; i++) { String dest1 = dest.getAbsolutePath() + File.separatorChar + list[i]; String src1 = src.getAbsolutePath() + File.separatorChar + list[i]; copyFiles(src1, dest1); } } else { FileInputStream fin = new FileInputStream(src); FileOutputStream fout = new FileOutputStream(dest); int c; while ((c = fin.read()) >= 0) fout.write(c); fin.close(); fout.close(); } } | public static void main(String[] args) { if (args.length != 2) throw new IllegalArgumentException(); String inFileName = args[0]; String outFileName = args[1]; File fInput = new File(inFileName); Scanner in = null; try { in = new Scanner(fInput); } catch (FileNotFoundException e) { e.printStackTrace(); } PrintWriter out = null; try { out = new PrintWriter(outFileName); } catch (FileNotFoundException e) { e.printStackTrace(); } while (in.hasNextLine()) { out.println(in.nextLine()); } in.close(); out.close(); } | 12,429 |
1 | private void createPolicy(String policyName) throws SPLException { URL url = getClass().getResource(policyName + ".spl"); StringBuffer contents = new StringBuffer(); try { BufferedReader input = new BufferedReader(new InputStreamReader(url.openStream())); String line = null; while ((line = input.readLine()) != null) { contents.append(line); contents.append(System.getProperty("line.separator")); } input.close(); System.out.println(policyName); System.out.println(contents.toString()); boolean createReturn = jspl.createPolicy(policyName, contents.toString()); System.out.println("Policy Created : " + policyName + " - " + createReturn); System.out.println(""); } catch (IOException ex) { ex.printStackTrace(); } } | public IntactOntology parseOboFile(URL url, boolean keepTemporaryFile) throws PsiLoaderException { if (url == null) { throw new IllegalArgumentException("Please give a non null URL."); } StringBuffer buffer = new StringBuffer(1024 * 8); try { System.out.println("Loading URL: " + url); BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream()), 1024); String line; int lineCount = 0; while ((line = in.readLine()) != null) { lineCount++; buffer.append(line).append(NEW_LINE); if ((lineCount % 20) == 0) { System.out.print("."); System.out.flush(); if ((lineCount % 500) == 0) { System.out.println(" " + lineCount); } } } in.close(); File tempDirectory = new File(System.getProperty("java.io.tmpdir", "tmp")); if (!tempDirectory.exists()) { if (!tempDirectory.mkdirs()) { throw new IOException("Cannot create temp directory: " + tempDirectory.getAbsolutePath()); } } System.out.println("Using temp directory: " + tempDirectory.getAbsolutePath()); File tempFile = File.createTempFile("psimi.v25.", ".obo", tempDirectory); tempFile.deleteOnExit(); tempFile.deleteOnExit(); System.out.println("The OBO file is temporary store as: " + tempFile.getAbsolutePath()); BufferedWriter out = new BufferedWriter(new FileWriter(tempFile), 1024); out.write(buffer.toString()); out.flush(); out.close(); return parseOboFile(tempFile); } catch (IOException e) { throw new PsiLoaderException("Error while loading URL (" + url + ")", e); } } | 12,430 |
1 | @Override public String execute() throws Exception { SystemContext sc = getSystemContext(); if (sc.getExpireTime() == -1) { return LOGIN; } else if (upload != null) { try { Enterprise e = LicenceUtils.get(upload); sc.setEnterpriseName(e.getEnterpriseName()); sc.setExpireTime(e.getExpireTime()); String webPath = ServletActionContext.getServletContext().getRealPath("/"); File desFile = new File(webPath, LicenceUtils.LICENCE_FILE_NAME); FileChannel sourceChannel = new FileInputStream(upload).getChannel(); FileChannel destinationChannel = new FileOutputStream(desFile).getChannel(); sourceChannel.transferTo(0, sourceChannel.size(), destinationChannel); sourceChannel.close(); destinationChannel.close(); return LOGIN; } catch (Exception e) { } } return "license"; } | private static void readAndRewrite(File inFile, File outFile) throws IOException { ImageInputStream iis = ImageIO.createImageInputStream(new BufferedInputStream(new FileInputStream(inFile))); DcmParser dcmParser = DcmParserFactory.getInstance().newDcmParser(iis); Dataset ds = DcmObjectFactory.getInstance().newDataset(); dcmParser.setDcmHandler(ds.getDcmHandler()); dcmParser.parseDcmFile(null, Tags.PixelData); PixelDataReader pdReader = pdFact.newReader(ds, iis, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); System.out.println("reading " + inFile + "..."); pdReader.readPixelData(false); ImageOutputStream out = ImageIO.createImageOutputStream(new BufferedOutputStream(new FileOutputStream(outFile))); DcmEncodeParam dcmEncParam = DcmEncodeParam.IVR_LE; ds.writeDataset(out, dcmEncParam); ds.writeHeader(out, dcmEncParam, Tags.PixelData, dcmParser.getReadVR(), dcmParser.getReadLength()); System.out.println("writing " + outFile + "..."); PixelDataWriter pdWriter = pdFact.newWriter(pdReader.getPixelDataArray(), false, ds, out, dcmParser.getDcmDecodeParam().byteOrder, dcmParser.getReadVR()); pdWriter.writePixelData(); out.flush(); out.close(); System.out.println("done!"); } | 12,431 |
1 | private void copyFile(File sourceFile, File destFile) throws IOException { if (log.isDebugEnabled()) { log.debug("CopyFile : Source[" + sourceFile.getAbsolutePath() + "] Dest[" + destFile.getAbsolutePath() + "]"); } if (!destFile.exists()) { destFile.createNewFile(); } FileChannel source = null; FileChannel destination = null; try { source = new FileInputStream(sourceFile).getChannel(); destination = new FileOutputStream(destFile).getChannel(); destination.transferFrom(source, 0, source.size()); } finally { if (source != null) { source.close(); } if (destination != null) { destination.close(); } } } | public void end() throws Exception { handle.waitFor(); Calendar endTime = Calendar.getInstance(); File resultsDir = new File(runDir, "results"); if (!resultsDir.isDirectory()) throw new Exception("The results directory not found!"); String resHtml = null; String resTxt = null; String[] resultFiles = resultsDir.list(); for (String resultFile : resultFiles) { if (resultFile.indexOf("html") >= 0) resHtml = resultFile; else if (resultFile.indexOf("txt") >= 0) resTxt = resultFile; } if (resHtml == null) throw new IOException("SPECweb2005 output (html) file not found"); if (resTxt == null) throw new IOException("SPECweb2005 output (txt) file not found"); File resultHtml = new File(resultsDir, resHtml); copyFile(resultHtml.getAbsolutePath(), runDir + "SPECWeb-result.html", false); BufferedReader reader = new BufferedReader(new FileReader(new File(resultsDir, resTxt))); logger.fine("Text file: " + resultsDir + resTxt); Writer writer = new FileWriter(runDir + "summary.xml"); SummaryParser parser = new SummaryParser(getRunId(), startTime, endTime, logger); parser.convert(reader, writer); writer.close(); reader.close(); } | 12,432 |
0 | protected InputStream openInputStream(String filename) throws FileNotFoundException { InputStream in = null; try { URL url = new URL(filename); in = url.openConnection().getInputStream(); logger.info("Opening file " + filename); } catch (FileNotFoundException e) { logger.error("Resource file not found: " + filename); throw e; } catch (IOException e) { logger.error("Resource file can not be readed: " + filename); throw new FileNotFoundException("Resource file can not be readed: " + filename); } if (in == null) { logger.error("Resource file not found: " + filename); throw new FileNotFoundException(filename); } return in; } | public static final void copy(String source, String destination) { BufferedInputStream from = null; BufferedOutputStream to = null; try { from = new BufferedInputStream(new FileInputStream(source)); to = new BufferedOutputStream(new FileOutputStream(destination)); byte[] buffer = new byte[65535]; int bytes_read; while ((bytes_read = from.read(buffer)) != -1) to.write(buffer, 0, bytes_read); } catch (Exception e) { LogWriter.writeLog("Exception " + e + " copying file"); } try { to.close(); from.close(); } catch (Exception e) { LogWriter.writeLog("Exception " + e + " closing files"); } } | 12,433 |
1 | public static void copyFile(File in, File out) throws IOException { FileChannel inChannel = new FileInputStream(in).getChannel(); FileChannel outChannel = new FileOutputStream(out).getChannel(); try { inChannel.transferTo(0, inChannel.size(), outChannel); } catch (IOException e) { throw e; } finally { if (inChannel != null) { inChannel.close(); } if (outChannel != null) { outChannel.close(); } } } | public static final void copyFile(String srcFilename, String dstFilename) throws IOException { FileInputStream fis = null; FileOutputStream fos = null; FileChannel ifc = null; FileChannel ofc = null; Util.copyBuffer.clear(); try { fis = new FileInputStream(srcFilename); ifc = fis.getChannel(); fos = new FileOutputStream(dstFilename); ofc = fos.getChannel(); int sz = (int) ifc.size(); int n = 0; while (n < sz) { if (ifc.read(Util.copyBuffer) < 0) { break; } Util.copyBuffer.flip(); n += ofc.write(Util.copyBuffer); Util.copyBuffer.compact(); } } finally { try { if (ifc != null) { ifc.close(); } else if (fis != null) { fis.close(); } } catch (IOException exc) { } try { if (ofc != null) { ofc.close(); } else if (fos != null) { fos.close(); } } catch (IOException exc) { } } } | 12,434 |
1 | private void copy(File sourceFile, File destinationFile) { try { FileChannel in = new FileInputStream(sourceFile).getChannel(); FileChannel out = new FileOutputStream(destinationFile).getChannel(); try { in.transferTo(0, in.size(), out); in.close(); out.close(); } catch (IOException e) { GTLogger.getInstance().error(e); } } catch (FileNotFoundException e) { GTLogger.getInstance().error(e); } } | protected List<Datastream> getDatastreams(final DepositCollection pDeposit) throws IOException, SWORDException { LOG.debug("copying file"); String tTempFileName = this.getTempDir() + "uploaded-file.tmp"; IOUtils.copy(pDeposit.getFile(), new FileOutputStream(tTempFileName)); Datastream tDatastream = new LocalDatastream(this.getGenericFileName(pDeposit), this.getContentType(), tTempFileName); List<Datastream> tDatastreams = new ArrayList<Datastream>(); tDatastreams.add(tDatastream); return tDatastreams; } | 12,435 |
1 | public void readPersistentProperties() { try { String file = System.getProperty("user.home") + System.getProperty("file.separator") + ".das2rc"; File f = new File(file); if (f.canRead()) { try { InputStream in = new FileInputStream(f); load(in); in.close(); } catch (IOException e) { e.printStackTrace(); org.das2.util.DasExceptionHandler.handle(e); } } else { if (!f.exists() && f.canWrite()) { try { OutputStream out = new FileOutputStream(f); store(out, ""); out.close(); } catch (IOException e) { e.printStackTrace(); org.das2.util.DasExceptionHandler.handle(e); } } else { System.err.println("Unable to read or write " + file + ". Using defaults."); } } } catch (SecurityException ex) { ex.printStackTrace(); } } | private static Collection<String> createTopLevelFiles(Configuration configuration, Collections collections, Sets sets) throws FlickrException, SAXException, IOException, JDOMException, TransformerException { Collection<String> createdFiles = new HashSet<String>(); File toplevelXmlFilename = getToplevelXmlFilename(configuration.photosBaseDirectory); Logger.getLogger(FlickrDownload.class).info("Creating XML file " + toplevelXmlFilename.getAbsolutePath()); MediaIndexer indexer = new XmlMediaIndexer(configuration); Element toplevel = new Element("flickr").addContent(XmlUtils.createApplicationXml()).addContent(XmlUtils.createUserXml(configuration)).addContent(collections.createTopLevelXml()).addContent(sets.createTopLevelXml()).addContent(new Stats(sets).createStatsXml(indexer)); createdFiles.addAll(indexer.writeIndex()); XmlUtils.outputXmlFile(toplevelXmlFilename, toplevel); createdFiles.add(toplevelXmlFilename.getName()); Logger.getLogger(FlickrDownload.class).info("Copying support files and performing XSLT transformations"); IOUtils.copyToFileAndCloseStreams(XmlUtils.class.getResourceAsStream("xslt/" + PHOTOS_CSS_FILENAME), new File(configuration.photosBaseDirectory, PHOTOS_CSS_FILENAME)); createdFiles.add(PHOTOS_CSS_FILENAME); IOUtils.copyToFileAndCloseStreams(XmlUtils.class.getResourceAsStream("xslt/" + PLAY_ICON_FILENAME), new File(configuration.photosBaseDirectory, PLAY_ICON_FILENAME)); createdFiles.add(PLAY_ICON_FILENAME); XmlUtils.performXsltTransformation(configuration, "all_sets.xsl", toplevelXmlFilename, new File(configuration.photosBaseDirectory, ALL_SETS_HTML_FILENAME)); createdFiles.add(ALL_SETS_HTML_FILENAME); XmlUtils.performXsltTransformation(configuration, "all_collections.xsl", toplevelXmlFilename, new File(configuration.photosBaseDirectory, ALL_COLLECTIONS_HTML_FILENAME)); createdFiles.add(ALL_COLLECTIONS_HTML_FILENAME); createdFiles.add(Collections.COLLECTIONS_ICON_DIRECTORY); XmlUtils.performXsltTransformation(configuration, "stats.xsl", toplevelXmlFilename, new File(configuration.photosBaseDirectory, STATS_HTML_FILENAME)); createdFiles.add(STATS_HTML_FILENAME); sets.performXsltTransformation(); for (AbstractSet set : sets.getSets()) { createdFiles.add(set.getSetId()); } return createdFiles; } | 12,436 |
0 | public String hasheMotDePasse(String mdp) { MessageDigest sha = null; try { sha = MessageDigest.getInstance("SHA-1"); } catch (NoSuchAlgorithmException ex) { } sha.reset(); sha.update(mdp.getBytes()); byte[] digest = sha.digest(); String pass = new String(Base64.encode(digest)); pass = "{SHA}" + pass; return pass; } | private InputStream loadSource(String url) throws ClientProtocolException, IOException { HttpClient httpclient = new DefaultHttpClient(); httpclient.getParams().setParameter(HTTP.USER_AGENT, "Mozilla/4.0 (compatible; MSIE 7.0b; Windows NT 6.0)"); HttpGet httpget = new HttpGet(url); HttpResponse response = httpclient.execute(httpget); HttpEntity entity = response.getEntity(); return entity.getContent(); } | 12,437 |
0 | @Override public ArrayList<String> cacheAgeingProcess(int numberOfDays) throws DatabaseException { IMAGE_LIFETIME = numberOfDays; PreparedStatement statement = null; ArrayList<String> ret = new ArrayList<String>(); try { statement = getConnection().prepareStatement(SELECT_ITEMS_FOR_DELETION_STATEMENT); ResultSet rs = statement.executeQuery(); int i = 0; int rowsAffected = 0; while (rs.next()) { ret.add(rs.getString("imageFile")); i++; } if (i > 0) { statement = getConnection().prepareStatement(DELETE_ITEMS_STATEMENT); rowsAffected = statement.executeUpdate(); } if (rowsAffected == i) { getConnection().commit(); LOGGER.debug("DB has been updated."); LOGGER.debug(i + " images are going to be removed."); } else { getConnection().rollback(); LOGGER.error("DB has not been updated -> rollback!"); } } catch (SQLException e) { LOGGER.error(e); } finally { closeConnection(); } return ret; } | private void nioBuild() { try { final ByteBuffer buffer = ByteBuffer.allocateDirect(1024 * 4); final FileChannel out = new FileOutputStream(dest).getChannel(); for (File part : parts) { setState(part.getName(), BUILDING); FileChannel in = new FileInputStream(part).getChannel(); while (in.read(buffer) > 0) { buffer.flip(); written += out.write(buffer); buffer.clear(); } in.close(); } out.close(); } catch (Exception e) { e.printStackTrace(); } } | 12,438 |
0 | public static int gunzipFile(File file_input, File dir_output) { GZIPInputStream gzip_in_stream; try { FileInputStream in = new FileInputStream(file_input); BufferedInputStream source = new BufferedInputStream(in); gzip_in_stream = new GZIPInputStream(source); } catch (IOException e) { return STATUS_IN_FAIL; } String file_input_name = file_input.getName(); String file_output_name = file_input_name.substring(0, file_input_name.length() - 3); File output_file = new File(dir_output, file_output_name); byte[] input_buffer = new byte[BUF_SIZE]; int len = 0; try { FileOutputStream out = new FileOutputStream(output_file); BufferedOutputStream destination = new BufferedOutputStream(out, BUF_SIZE); while ((len = gzip_in_stream.read(input_buffer, 0, BUF_SIZE)) != -1) destination.write(input_buffer, 0, len); destination.flush(); out.close(); } catch (IOException e) { return STATUS_GUNZIP_FAIL; } try { gzip_in_stream.close(); } catch (IOException e) { } return STATUS_OK; } | public TestReport runImpl() throws Exception { DocumentFactory df = new SAXDocumentFactory(GenericDOMImplementation.getDOMImplementation(), parserClassName); File f = (new File(testFileName)); URL url = f.toURL(); Document doc = df.createDocument(null, rootTag, url.toString(), url.openStream()); File ser1 = File.createTempFile("doc1", "ser"); File ser2 = File.createTempFile("doc2", "ser"); try { ObjectOutputStream oos; oos = new ObjectOutputStream(new FileOutputStream(ser1)); oos.writeObject(doc); oos.close(); ObjectInputStream ois; ois = new ObjectInputStream(new FileInputStream(ser1)); doc = (Document) ois.readObject(); ois.close(); oos = new ObjectOutputStream(new FileOutputStream(ser2)); oos.writeObject(doc); oos.close(); } catch (IOException e) { DefaultTestReport report = new DefaultTestReport(this); report.setErrorCode("io.error"); report.addDescriptionEntry("message", e.getClass().getName() + ": " + e.getMessage()); report.addDescriptionEntry("file.name", testFileName); report.setPassed(false); return report; } InputStream is1 = new FileInputStream(ser1); InputStream is2 = new FileInputStream(ser2); for (; ; ) { int i1 = is1.read(); int i2 = is2.read(); if (i1 == -1 && i2 == -1) { return reportSuccess(); } if (i1 != i2) { DefaultTestReport report = new DefaultTestReport(this); report.setErrorCode("difference.found"); report.addDescriptionEntry("file.name", testFileName); report.setPassed(false); return report; } } } | 12,439 |
0 | private void invokeTest(String queryfile, String target) { try { String query = IOUtils.toString(XPathMarkBenchmarkTest.class.getResourceAsStream(queryfile)).trim(); String args = EXEC_CMD + " \"" + query + "\" \"" + target + '"'; System.out.println("Invoke command: \n " + args); Process proc = Runtime.getRuntime().exec(args, null, benchmarkDir); InputStream is = proc.getInputStream(); File outFile = new File(outDir, queryfile + ".result"); IOUtils.copy(is, new FileOutputStream(outFile)); is.close(); int ret = proc.waitFor(); if (ret != 0) { System.out.println("process exited with value : " + ret); } } catch (IOException ioe) { throw new IllegalStateException(ioe); } catch (InterruptedException irre) { throw new IllegalStateException(irre); } } | public static CMLUnitList createUnitList(URL url) throws IOException, CMLException { Document dictDoc = null; InputStream in = null; try { in = url.openStream(); dictDoc = new CMLBuilder().build(in); } catch (NullPointerException e) { e.printStackTrace(); throw new CMLException("NULL " + e.getMessage() + S_SLASH + e.getCause() + " in " + url); } catch (ValidityException e) { throw new CMLException(S_EMPTY + e.getMessage() + S_SLASH + e.getCause() + " in " + url); } catch (ParsingException e) { e.printStackTrace(); throw new CMLException(e, " in " + url); } finally { if (in != null) { try { in.close(); } catch (IOException e) { e.printStackTrace(); } } } CMLUnitList dt = null; if (dictDoc != null) { Element root = dictDoc.getRootElement(); if (root instanceof CMLUnitList) { dt = new CMLUnitList((CMLUnitList) root); } else { } } if (dt != null) { dt.indexEntries(); } return dt; } | 12,440 |
1 | @Override public DownloadingItem download(Playlist playlist, String title, File folder, StopDownloadCondition condition, String uuid) throws IOException, StoreStateException { boolean firstIteration = true; Iterator<PlaylistEntry> entries = playlist.getEntries().iterator(); DownloadingItem prevItem = null; File[] previousDownloadedFiles = new File[0]; while (entries.hasNext()) { PlaylistEntry entry = entries.next(); DownloadingItem item = null; LOGGER.info("Downloading from '" + entry.getTitle() + "'"); InputStream is = RESTHelper.inputStream(entry.getUrl()); boolean stopped = false; File nfile = null; try { nfile = createFileStream(folder, entry); item = new DownloadingItem(nfile, uuid.toString(), title, entry, new Date(), getPID(), condition); if (previousDownloadedFiles.length > 0) { item.setPreviousFiles(previousDownloadedFiles); } addItem(item); if (prevItem != null) deletePrevItem(prevItem); prevItem = item; stopped = IOUtils.copyStreams(is, new FileOutputStream(nfile), condition); } catch (IOException e) { LOGGER.log(Level.SEVERE, e.getMessage(), e); radioScheduler.fireException(e); if (!condition.isStopped()) { File[] nfiles = new File[previousDownloadedFiles.length + 1]; System.arraycopy(previousDownloadedFiles, 0, nfiles, 0, previousDownloadedFiles.length); nfiles[nfiles.length - 1] = item.getFile(); previousDownloadedFiles = nfiles; if ((!entries.hasNext()) && (firstIteration)) { firstIteration = false; entries = playlist.getEntries().iterator(); } continue; } } if (stopped) { item.setState(ProcessStates.STOPPED); this.radioScheduler.fireStopDownloading(item); return item; } } return null; } | private static void main(String[] args) { try { File f = new File("test.txt"); if (f.exists()) { throw new IOException(f + " already exists. I don't want to overwrite it."); } StraightStreamReader in; char[] cbuf = new char[0x1000]; int read; int totRead; FileOutputStream out = new FileOutputStream(f); for (int i = 0x00; i < 0x100; i++) { out.write(i); } out.close(); in = new StraightStreamReader(new FileInputStream(f)); for (int i = 0x00; i < 0x100; i++) { read = in.read(); if (read != i) { System.err.println("Error: " + i + " read as " + read); } } in.close(); in = new StraightStreamReader(new FileInputStream(f)); totRead = in.read(cbuf); if (totRead != 0x100) { System.err.println("Simple buffered read did not read the full amount: 0x" + Integer.toHexString(totRead)); } for (int i = 0x00; i < totRead; i++) { if (cbuf[i] != i) { System.err.println("Error: 0x" + i + " read as 0x" + cbuf[i]); } } in.close(); in = new StraightStreamReader(new FileInputStream(f)); totRead = 0; while (totRead <= 0x100 && (read = in.read(cbuf, totRead, 0x100 - totRead)) > 0) { totRead += read; } if (totRead != 0x100) { System.err.println("Not enough read. Bytes read: " + Integer.toHexString(totRead)); } for (int i = 0x00; i < totRead; i++) { if (cbuf[i] != i) { System.err.println("Error: 0x" + i + " read as 0x" + cbuf[i]); } } in.close(); in = new StraightStreamReader(new FileInputStream(f)); totRead = 0; while (totRead <= 0x100 && (read = in.read(cbuf, totRead + 0x123, 0x100 - totRead)) > 0) { totRead += read; } if (totRead != 0x100) { System.err.println("Not enough read. Bytes read: " + Integer.toHexString(totRead)); } for (int i = 0x00; i < totRead; i++) { if (cbuf[i + 0x123] != i) { System.err.println("Error: 0x" + i + " read as 0x" + cbuf[i + 0x123]); } } in.close(); in = new StraightStreamReader(new FileInputStream(f)); totRead = 0; while (totRead <= 0x100 && (read = in.read(cbuf, totRead + 0x123, 7)) > 0) { totRead += read; } if (totRead != 0x100) { System.err.println("Not enough read. Bytes read: " + Integer.toHexString(totRead)); } for (int i = 0x00; i < totRead; i++) { if (cbuf[i + 0x123] != i) { System.err.println("Error: 0x" + i + " read as 0x" + cbuf[i + 0x123]); } } in.close(); f.delete(); } catch (IOException x) { System.err.println(x.getMessage()); } } | 12,441 |
0 | public String hash(String plainTextPassword) { try { MessageDigest digest = MessageDigest.getInstance(digestAlgorithm); digest.update(plainTextPassword.getBytes(charset)); byte[] rawHash = digest.digest(); return new String(Hex.encodeHex(rawHash)); } catch (Exception ex) { throw new RuntimeException(ex); } } | public void readData() throws IOException { i = 0; j = 0; URL url = getClass().getResource("resources/tuneGridMaster.dat"); InputStream is = url.openStream(); InputStreamReader isr = new InputStreamReader(is); BufferedReader br = new BufferedReader(isr); s = br.readLine(); StringTokenizer st = new StringTokenizer(s); tune_x[i][j] = Double.parseDouble(st.nextToken()); gridmin = tune_x[i][j]; temp_prev = tune_x[i][j]; tune_y[i][j] = Double.parseDouble(st.nextToken()); kd[i][j] = Double.parseDouble(st.nextToken()); kfs[i][j] = Double.parseDouble(st.nextToken()); kfl[i][j] = Double.parseDouble(st.nextToken()); kdee[i][j] = Double.parseDouble(st.nextToken()); kdc[i][j] = Double.parseDouble(st.nextToken()); kfc[i][j] = Double.parseDouble(st.nextToken()); j++; int k = 0; while ((s = br.readLine()) != null) { st = new StringTokenizer(s); temp_new = Double.parseDouble(st.nextToken()); if (temp_new != temp_prev) { temp_prev = temp_new; i++; j = 0; } tune_x[i][j] = temp_new; tune_y[i][j] = Double.parseDouble(st.nextToken()); kd[i][j] = Double.parseDouble(st.nextToken()); kfs[i][j] = Double.parseDouble(st.nextToken()); kfl[i][j] = Double.parseDouble(st.nextToken()); kdee[i][j] = Double.parseDouble(st.nextToken()); kdc[i][j] = Double.parseDouble(st.nextToken()); kfc[i][j] = Double.parseDouble(st.nextToken()); imax = i; jmax = j; j++; k++; } gridmax = tune_x[i][j - 1]; } | 12,442 |
0 | public static void main(String[] args) { LogFrame.getInstance(); for (int i = 0; i < args.length; i++) { String arg = args[i]; if (arg.trim().startsWith(DEBUG_PARAMETER_NAME + "=")) { properties.put(DEBUG_PARAMETER_NAME, arg.trim().substring(DEBUG_PARAMETER_NAME.length() + 1).trim()); if (properties.getProperty(DEBUG_PARAMETER_NAME).toLowerCase().equals(DEBUG_TRUE)) { DEBUG = true; } } else if (arg.trim().startsWith(MODE_PARAMETER_NAME + "=")) { properties.put(MODE_PARAMETER_NAME, arg.trim().substring(MODE_PARAMETER_NAME.length() + 1).trim()); } else if (arg.trim().startsWith(AUTOCONNECT_PARAMETER_NAME + "=")) { properties.put(AUTOCONNECT_PARAMETER_NAME, arg.trim().substring(AUTOCONNECT_PARAMETER_NAME.length() + 1).trim()); } else if (arg.trim().startsWith(SITE_CONFIG_URL_PARAMETER_NAME + "=")) { properties.put(SITE_CONFIG_URL_PARAMETER_NAME, arg.trim().substring(SITE_CONFIG_URL_PARAMETER_NAME.length() + 1).trim()); } else if (arg.trim().startsWith(LOAD_PLUGINS_PARAMETER_NAME + "=")) { properties.put(LOAD_PLUGINS_PARAMETER_NAME, arg.trim().substring(LOAD_PLUGINS_PARAMETER_NAME.length() + 1).trim()); } else if (arg.trim().startsWith(ONTOLOGY_URL_PARAMETER_NAME + "=")) { properties.put(ONTOLOGY_URL_PARAMETER_NAME, arg.trim().substring(ONTOLOGY_URL_PARAMETER_NAME.length() + 1).trim()); } else if (arg.trim().startsWith(REPOSITORY_PARAMETER_NAME + "=")) { properties.put(REPOSITORY_PARAMETER_NAME, arg.trim().substring(REPOSITORY_PARAMETER_NAME.length() + 1).trim()); } else if (arg.trim().startsWith(ONTOLOGY_TYPE_PARAMETER_NAME + "=")) { properties.put(ONTOLOGY_TYPE_PARAMETER_NAME, arg.trim().substring(ONTOLOGY_TYPE_PARAMETER_NAME.length() + 1).trim()); if (!(properties.getProperty(ONTOLOGY_TYPE_PARAMETER_NAME).equals(ONTOLOGY_TYPE_RDFXML) || properties.getProperty(ONTOLOGY_TYPE_PARAMETER_NAME).equals(ONTOLOGY_TYPE_TURTLE) || properties.getProperty(ONTOLOGY_TYPE_PARAMETER_NAME).equals(ONTOLOGY_TYPE_NTRIPPLES))) System.out.println("WARNING! Unknown ontology type: '" + properties.getProperty(ONTOLOGY_TYPE_PARAMETER_NAME) + "' (Known types are: '" + ONTOLOGY_TYPE_RDFXML + "', '" + ONTOLOGY_TYPE_TURTLE + "', '" + ONTOLOGY_TYPE_NTRIPPLES + "')"); } else if (arg.trim().startsWith(OWLIMSERVICE_URL_PARAMETER_NAME + "=")) { properties.put(OWLIMSERVICE_URL_PARAMETER_NAME, arg.trim().substring(OWLIMSERVICE_URL_PARAMETER_NAME.length() + 1).trim()); } else if (arg.trim().startsWith(DOCSERVICE_URL_PARAMETER_NAME + "=")) { properties.put(DOCSERVICE_URL_PARAMETER_NAME, arg.trim().substring(DOCSERVICE_URL_PARAMETER_NAME.length() + 1).trim()); } else if (arg.trim().startsWith(DOC_ID_PARAMETER_NAME + "=")) { properties.put(DOC_ID_PARAMETER_NAME, arg.trim().substring(DOC_ID_PARAMETER_NAME.length() + 1).trim()); } else if (arg.trim().startsWith(ANNSET_NAME_PARAMETER_NAME + "=")) { properties.put(ANNSET_NAME_PARAMETER_NAME, arg.trim().substring(ANNSET_NAME_PARAMETER_NAME.length() + 1).trim()); } else if (arg.trim().startsWith(EXECUTIVE_SERVICE_URL_PARAMETER_NAME + "=")) { properties.put(EXECUTIVE_SERVICE_URL_PARAMETER_NAME, arg.trim().substring(EXECUTIVE_SERVICE_URL_PARAMETER_NAME.length() + 1).trim()); } else if (arg.trim().startsWith(USER_ID_PARAMETER_NAME + "=")) { properties.put(USER_ID_PARAMETER_NAME, arg.trim().substring(USER_ID_PARAMETER_NAME.length() + 1).trim()); } else if (arg.trim().startsWith(USER_PASSWORD_PARAMETER_NAME + "=")) { properties.put(USER_PASSWORD_PARAMETER_NAME, arg.trim().substring(USER_PASSWORD_PARAMETER_NAME.length() + 1).trim()); } else if (arg.trim().startsWith(EXECUTIVE_PROXY_FACTORY_PARAMETER_NAME + "=")) { properties.put(EXECUTIVE_PROXY_FACTORY_PARAMETER_NAME, arg.trim().substring(EXECUTIVE_PROXY_FACTORY_PARAMETER_NAME.length() + 1).trim()); } else if (arg.trim().startsWith(DOCSERVICE_PROXY_FACTORY_PARAMETER_NAME + "=")) { properties.put(DOCSERVICE_PROXY_FACTORY_PARAMETER_NAME, arg.trim().substring(DOCSERVICE_PROXY_FACTORY_PARAMETER_NAME.length() + 1).trim()); RichUIUtils.setDocServiceProxyFactoryClassname(properties.getProperty(DOCSERVICE_PROXY_FACTORY_PARAMETER_NAME)); } else if (arg.trim().startsWith(LOAD_ANN_SCHEMAS_NAME + "=")) { properties.put(LOAD_ANN_SCHEMAS_NAME, arg.trim().substring(LOAD_ANN_SCHEMAS_NAME.length() + 1).trim()); } else if (arg.trim().startsWith(SELECT_AS_PARAMETER_NAME + "=")) { properties.put(SELECT_AS_PARAMETER_NAME, arg.trim().substring(SELECT_AS_PARAMETER_NAME.length() + 1).trim()); } else if (arg.trim().startsWith(SELECT_ANN_TYPES_PARAMETER_NAME + "=")) { properties.put(SELECT_ANN_TYPES_PARAMETER_NAME, arg.trim().substring(SELECT_ANN_TYPES_PARAMETER_NAME.length() + 1).trim()); } else if (arg.trim().startsWith(ENABLE_ONTOLOGY_EDITOR_PARAMETER_NAME + "=")) { properties.put(ENABLE_ONTOLOGY_EDITOR_PARAMETER_NAME, arg.trim().substring(ENABLE_ONTOLOGY_EDITOR_PARAMETER_NAME.length() + 1).trim()); } else if (arg.trim().startsWith(CLASSES_TO_HIDE_PARAMETER_NAME + "=")) { properties.put(CLASSES_TO_HIDE_PARAMETER_NAME, arg.trim().substring(CLASSES_TO_HIDE_PARAMETER_NAME.length() + 1).trim()); } else if (arg.trim().startsWith(CLASSES_TO_SHOW_PARAMETER_NAME + "=")) { properties.put(CLASSES_TO_SHOW_PARAMETER_NAME, arg.trim().substring(CLASSES_TO_SHOW_PARAMETER_NAME.length() + 1).trim()); } else if (arg.trim().startsWith(ENABLE_APPLICATION_LOG_PARAMETER_NAME + "=")) { properties.put(ENABLE_APPLICATION_LOG_PARAMETER_NAME, arg.trim().substring(ENABLE_APPLICATION_LOG_PARAMETER_NAME.length() + 1).trim()); } else { System.out.println("WARNING! Unknown or undefined parameter: '" + arg.trim() + "'"); } } System.out.println(startupParamsToString()); if (properties.getProperty(MODE_PARAMETER_NAME) == null || (!(properties.getProperty(MODE_PARAMETER_NAME).toLowerCase().equals(POOL_MODE)) && !(properties.getProperty(MODE_PARAMETER_NAME).toLowerCase().equals(DIRECT_MODE)))) { String err = "Mandatory parameter '" + MODE_PARAMETER_NAME + "' must be defined and must have a value either '" + POOL_MODE + "' or '" + DIRECT_MODE + "'.\n\nApplication will exit."; System.out.println(err); JOptionPane.showMessageDialog(new JFrame(), err, "Error!", JOptionPane.ERROR_MESSAGE); System.exit(-1); } if (properties.getProperty(SITE_CONFIG_URL_PARAMETER_NAME) == null || properties.getProperty(SITE_CONFIG_URL_PARAMETER_NAME).length() == 0) { String err = "Mandatory parameter '" + SITE_CONFIG_URL_PARAMETER_NAME + "' is missing.\n\nApplication will exit."; System.out.println(err); JOptionPane.showMessageDialog(new JFrame(), err, "Error!", JOptionPane.ERROR_MESSAGE); System.exit(-1); } try { String context = System.getProperty(CONTEXT); if (context == null || "".equals(context)) { context = DEFAULT_CONTEXT; } String s = System.getProperty(GateConstants.GATE_HOME_PROPERTY_NAME); if (s == null || s.length() == 0) { File f = File.createTempFile("foo", ""); String gateHome = f.getParent().toString() + context; f.delete(); System.setProperty(GateConstants.GATE_HOME_PROPERTY_NAME, gateHome); f = new File(System.getProperty(GateConstants.GATE_HOME_PROPERTY_NAME)); if (!f.exists()) { f.mkdirs(); } } s = System.getProperty(GateConstants.PLUGINS_HOME_PROPERTY_NAME); if (s == null || s.length() == 0) { System.setProperty(GateConstants.PLUGINS_HOME_PROPERTY_NAME, System.getProperty(GateConstants.GATE_HOME_PROPERTY_NAME) + "/plugins"); File f = new File(System.getProperty(GateConstants.PLUGINS_HOME_PROPERTY_NAME)); if (!f.exists()) { f.mkdirs(); } } s = System.getProperty(GateConstants.GATE_SITE_CONFIG_PROPERTY_NAME); if (s == null || s.length() == 0) { System.setProperty(GateConstants.GATE_SITE_CONFIG_PROPERTY_NAME, System.getProperty(GateConstants.GATE_HOME_PROPERTY_NAME) + "/gate.xml"); } if (properties.getProperty(SITE_CONFIG_URL_PARAMETER_NAME) != null && properties.getProperty(SITE_CONFIG_URL_PARAMETER_NAME).length() > 0) { File f = new File(System.getProperty(GateConstants.GATE_SITE_CONFIG_PROPERTY_NAME)); if (f.exists()) { f.delete(); } f.getParentFile().mkdirs(); f.createNewFile(); URL url = new URL(properties.getProperty(SITE_CONFIG_URL_PARAMETER_NAME)); InputStream is = url.openStream(); FileOutputStream fos = new FileOutputStream(f); int i = is.read(); while (i != -1) { fos.write(i); i = is.read(); } fos.close(); is.close(); } try { Gate.init(); gate.Main.applyUserPreferences(); } catch (Exception e) { e.printStackTrace(); } s = BASE_PLUGIN_NAME + "," + properties.getProperty(LOAD_PLUGINS_PARAMETER_NAME); System.out.println("Loading plugins: " + s); loadPlugins(s, true); loadAnnotationSchemas(properties.getProperty(LOAD_ANN_SCHEMAS_NAME), true); } catch (Throwable e) { e.printStackTrace(); } MainFrame.getInstance().setVisible(true); MainFrame.getInstance().pack(); if (properties.getProperty(MODE_PARAMETER_NAME).toLowerCase().equals(DIRECT_MODE)) { if (properties.getProperty(AUTOCONNECT_PARAMETER_NAME, "").toLowerCase().equals(AUTOCONNECT_TRUE)) { if (properties.getProperty(DOC_ID_PARAMETER_NAME) == null || properties.getProperty(DOC_ID_PARAMETER_NAME).length() == 0) { String err = "Can't autoconnect. A parameter '" + DOC_ID_PARAMETER_NAME + "' is missing."; System.out.println(err); JOptionPane.showMessageDialog(MainFrame.getInstance(), err, "Error!", JOptionPane.ERROR_MESSAGE); ActionShowDocserviceConnectDialog.getInstance().actionPerformed(null); } else { ActionConnectToDocservice.getInstance().actionPerformed(null); } } else { ActionShowDocserviceConnectDialog.getInstance().actionPerformed(null); } } else { if (properties.getProperty(AUTOCONNECT_PARAMETER_NAME, "").toLowerCase().equals(AUTOCONNECT_TRUE)) { if (properties.getProperty(USER_ID_PARAMETER_NAME) == null || properties.getProperty(USER_ID_PARAMETER_NAME).length() == 0) { String err = "Can't autoconnect. A parameter '" + USER_ID_PARAMETER_NAME + "' is missing."; System.out.println(err); JOptionPane.showMessageDialog(MainFrame.getInstance(), err, "Error!", JOptionPane.ERROR_MESSAGE); ActionShowExecutiveConnectDialog.getInstance().actionPerformed(null); } else { ActionConnectToExecutive.getInstance().actionPerformed(null); } } else { ActionShowExecutiveConnectDialog.getInstance().actionPerformed(null); } } } | protected IStatus run(IProgressMonitor monitor) { try { updateRunning = true; distributor = getFromFile("[SERVER]", "csz", getAppPath() + "/server.ini"); MAC = getFromFile("[SPECIFICINFO]", "MAC", getAppPath() + "/register.ini"); serial = getFromFile("[SPECIFICINFO]", "serial", getAppPath() + "/register.ini"); if (MAC.equals("not_found") || serial.equals("not_found") || !serial.startsWith(distributor)) { try { MAC = getFromFile("[SPECIFICINFO]", "MAC", getAppPath() + "/register.ini"); serial = getFromFile("[SPECIFICINFO]", "serial", getAppPath() + "/register.ini"); } catch (Exception e) { System.out.println(e); } } else { try { url = new URL("http://" + getFromFile("[SERVER]", "url", getAppPath() + "/server.ini")); } catch (MalformedURLException e) { System.out.println(e); } download = "/download2.php?distributor=" + distributor + "&&mac=" + MAC + "&&serial=" + serial; readXML(); if (htmlMessage.contains("error")) { try { PrintWriter pw = new PrintWriter(getAppPath() + "/register.ini"); pw.write(""); pw.close(); } catch (IOException e) { System.out.println(e); } setProperty(IProgressConstants.ICON_PROPERTY, IconImg.liveUpIco); if (isModal(this)) { showResults2(); } else { setProperty(IProgressConstants.KEEP_PROPERTY, Boolean.TRUE); setProperty(IProgressConstants.ACTION_PROPERTY, getUpdateCompletedAction2()); } } else { if (!getDBVersion().equals(latestVersion)) { try { OutputStream out = null; HttpURLConnection conn = null; InputStream in = null; int size; try { URL url = new URL(fileLoc); String outFile = getAppPath() + "/temp/" + getFileName(url); File oFile = new File(outFile); oFile.delete(); out = new BufferedOutputStream(new FileOutputStream(outFile)); monitor.beginTask("Connecting to NWD Server", 100); conn = (HttpURLConnection) url.openConnection(); conn.setConnectTimeout(20000); conn.connect(); if (conn.getResponseCode() / 100 != 2) { System.out.println("Error: " + conn.getResponseCode()); return null; } monitor.worked(100); monitor.done(); size = conn.getContentLength(); monitor.beginTask("Download Worm Definition", size); in = conn.getInputStream(); byte[] buffer; String downloadedSize; long numWritten = 0; boolean status = true; while (status) { if (size - numWritten > 1024) { buffer = new byte[1024]; } else { buffer = new byte[(int) (size - numWritten)]; } int read = in.read(buffer); if (read == -1) { break; } out.write(buffer, 0, read); numWritten += read; downloadedSize = Long.toString(numWritten / 1024) + " KB"; monitor.worked(read); monitor.subTask(downloadedSize + " of " + Integer.toString(size / 1024) + " KB"); if (size == numWritten) { status = false; } if (monitor.isCanceled()) return Status.CANCEL_STATUS; } if (in != null) { in.close(); } if (out != null) { out.close(); } try { ZipFile zFile = new ZipFile(outFile); Enumeration all = zFile.entries(); while (all.hasMoreElements()) { ZipEntry zEntry = (ZipEntry) all.nextElement(); long zSize = zEntry.getSize(); if (zSize > 0) { if (zEntry.getName().endsWith("script")) { InputStream instream = zFile.getInputStream(zEntry); FileOutputStream fos = new FileOutputStream(oldLoc[0]); int ch; while ((ch = instream.read()) != -1) { fos.write(ch); } instream.close(); fos.close(); } else if (zEntry.getName().endsWith("data")) { InputStream instream = zFile.getInputStream(zEntry); FileOutputStream fos = new FileOutputStream(oldLoc[1]); int ch; while ((ch = instream.read()) != -1) { fos.write(ch); } instream.close(); fos.close(); } } } File xFile = new File(outFile); xFile.deleteOnExit(); } catch (Exception e) { e.printStackTrace(); } try { monitor.done(); monitor.beginTask("Install Worm Definition", 10000); monitor.worked(2500); CorePlugin.getDefault().getRawPacketHandler().removeRawPacketListener(p); p = null; if (!wormDB.getConn().isClosed()) { shutdownDB(); } System.out.println(wormDB.getConn().isClosed()); for (int i = 0; i < 2; i++) { try { Process pid = Runtime.getRuntime().exec("cmd /c copy \"" + oldLoc[i].replace("/", "\\") + "\" \"" + newLoc[i].replace("/", "\\") + "\"/y"); } catch (Exception e) { e.printStackTrace(); } new File(oldLoc[i]).deleteOnExit(); } monitor.worked(2500); initialArray(); p = new PacketPrinter(); CorePlugin.getDefault().getRawPacketHandler().addRawPacketListener(p); monitor.worked(2500); monitor.done(); setProperty(IProgressConstants.ICON_PROPERTY, IconImg.liveUpIco); if (isModal(this)) { showResults(); } else { setProperty(IProgressConstants.KEEP_PROPERTY, Boolean.TRUE); setProperty(IProgressConstants.ACTION_PROPERTY, getUpdateCompletedAction()); } } catch (Exception e) { setProperty(IProgressConstants.ICON_PROPERTY, IconImg.liveUpIco); if (isModal(this)) { showResults2(); } else { setProperty(IProgressConstants.KEEP_PROPERTY, Boolean.TRUE); setProperty(IProgressConstants.ACTION_PROPERTY, getUpdateCompletedAction2()); } System.out.println(e); } finally { } } catch (Exception e) { e.printStackTrace(); } } catch (Exception e) { setProperty(IProgressConstants.ICON_PROPERTY, IconImg.liveUpIco); if (isModal(this)) { showResults2(); } else { setProperty(IProgressConstants.KEEP_PROPERTY, Boolean.TRUE); setProperty(IProgressConstants.ACTION_PROPERTY, getUpdateCompletedAction2()); } e.printStackTrace(); } } else { cancel(); setProperty(IProgressConstants.ICON_PROPERTY, IconImg.liveUpIco); if (isModal(this)) { showResults1(); } else { setProperty(IProgressConstants.KEEP_PROPERTY, Boolean.TRUE); setProperty(IProgressConstants.ACTION_PROPERTY, getUpdateCompletedAction1()); } } } } return Status.OK_STATUS; } catch (Exception e) { showResults2(); return Status.OK_STATUS; } finally { lock.release(); updateRunning = false; if (getValue("AUTO_UPDATE")) schedule(10800000); } } | 12,443 |
0 | public static File copyFile(File srcFile, File destFolder, FileCopyListener copyListener) { File dest = new File(destFolder, srcFile.getName()); try { FileInputStream in = new FileInputStream(srcFile); FileOutputStream out = new FileOutputStream(dest); byte[] readBuf = new byte[1024 * 512]; int readLength; long totalCopiedSize = 0; long totalSize = srcFile.length(); boolean canceled = false; if (copyListener == null) { while ((readLength = in.read(readBuf)) != -1) { out.write(readBuf, 0, readLength); } } else { while ((readLength = in.read(readBuf)) != -1) { out.write(readBuf, 0, readLength); if (!copyListener.updateCheck(readLength, totalSize)) { canceled = true; break; } } } in.close(); out.close(); if (canceled) { dest.delete(); } } catch (FileNotFoundException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } return dest; } | public static String encrypt(String algorithm, String[] input) { try { MessageDigest md = MessageDigest.getInstance(algorithm); md.reset(); for (int i = 0; i < input.length; i++) { if (input[i] != null) md.update(input[i].getBytes("UTF-8")); } byte[] messageDigest = md.digest(); StringBuffer hexString = new StringBuffer(); for (int i = 0; i < messageDigest.length; i++) { hexString.append(Integer.toHexString((0xf0 & messageDigest[i]) >> 4)); hexString.append(Integer.toHexString(0x0f & messageDigest[i])); } return hexString.toString(); } catch (NoSuchAlgorithmException e) { throw new RuntimeException(e); } catch (UnsupportedEncodingException e) { throw new RuntimeException(e); } catch (NullPointerException e) { return new StringBuffer().toString(); } } | 12,444 |
0 | public void write(URL output, String model, String mainResourceClass) throws InfoUnitIOException { InfoUnitXMLData iur = new InfoUnitXMLData(STRUCTURE_RDF); rdf = iur.load("rdf"); rdfResource = rdf.ft("resource"); rdfParseType = rdf.ft("parse type"); try { PrintWriter outw = new PrintWriter(new OutputStreamWriter(new FileOutputStream(output.getFile()), "UTF-8")); URL urlModel = new URL(model); BufferedReader inr = new BufferedReader(new InputStreamReader(urlModel.openStream())); String finalTag = "</" + rdf.ft("main") + ">"; String line = inr.readLine(); while (line != null && !line.equalsIgnoreCase(finalTag)) { outw.println(line); line = inr.readLine(); } inr.close(); InfoNode nodeType = infoRoot.path(rdf.ft("constraint")); String type = null; if (nodeType != null) { type = nodeType.getValue().toString(); try { infoRoot.removeChildNode(nodeType); } catch (InvalidChildInfoNode error) { } } else if (mainResourceClass != null) type = mainResourceClass; else type = rdf.ft("description"); outw.println(" <" + type + " " + rdf.ft("about") + "=\"" + ((infoNamespaces == null) ? infoRoot.getLabel() : infoNamespaces.convertEntity(infoRoot.getLabel().toString())) + "\">"); Set<InfoNode> nl = infoRoot.getChildren(); writeNodeList(nl, outw, 5); outw.println(" </" + type + ">"); if (line != null) outw.println(finalTag); outw.close(); } catch (IOException error) { throw new InfoUnitIOException(error.getMessage()); } } | @Override public String encryptPassword(String password) throws JetspeedSecurityException { if (securePasswords == false) { return password; } if (password == null) { return null; } try { if ("SHA-512".equals(passwordsAlgorithm)) { password = password + JetspeedResources.getString("aipo.encrypt_key"); MessageDigest md = MessageDigest.getInstance(passwordsAlgorithm); md.reset(); md.update(password.getBytes()); byte[] hash = md.digest(); StringBuffer sb = new StringBuffer(); for (int i = 0; i < hash.length; i++) { sb.append(Integer.toHexString((hash[i] >> 4) & 0x0F)); sb.append(Integer.toHexString(hash[i] & 0x0F)); } return sb.toString(); } else { MessageDigest md = MessageDigest.getInstance(passwordsAlgorithm); byte[] digest = md.digest(password.getBytes(ALEipConstants.DEF_CONTENT_ENCODING)); ByteArrayOutputStream bas = new ByteArrayOutputStream(digest.length + digest.length / 3 + 1); OutputStream encodedStream = MimeUtility.encode(bas, "base64"); encodedStream.write(digest); encodedStream.flush(); encodedStream.close(); return bas.toString(); } } catch (Exception e) { logger.error("Unable to encrypt password." + e.getMessage(), e); return null; } } | 12,445 |
0 | public void setRemoteConfig(String s) { try { HashMap<String, String> map = new HashMap<String, String>(); URL url = new URL(s); BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream())); String line = null; while ((line = in.readLine()) != null) { if (line.startsWith("#")) continue; String[] split = line.split("="); if (split.length >= 2) { map.put(split[0], split[1]); } } MethodAndFieldSetter.setMethodsAndFields(this, map); } catch (Exception e) { e.printStackTrace(); } } | private void addPlugin(URL url) throws IOException { logger.debug("Adding plugin with URL {}", url); InputStream in = url.openStream(); try { Properties properties = new Properties(); properties.load(in); plugins.add(new WtfPlugin(properties)); } finally { in.close(); } } | 12,446 |
0 | public void go() throws FBConnectionException, FBErrorException, IOException { clearError(); results = new LoginResults(); URL url = new URL(getHost() + getPath()); HttpURLConnection conn = (HttpURLConnection) url.openConnection(); conn.setRequestProperty("X-FB-User", getUser()); conn.setRequestProperty("X-FB-Auth", makeResponse()); conn.setRequestProperty("X-FB-Mode", "Login"); conn.setRequestProperty("X-FB-Login.ClientVersion", agent); conn.connect(); Element fbresponse; try { fbresponse = readXML(conn); } catch (FBConnectionException fbce) { throw fbce; } catch (FBErrorException fbee) { throw fbee; } catch (Exception e) { FBConnectionException fbce = new FBConnectionException("XML parsing failed"); fbce.attachSubException(e); throw fbce; } NodeList nl = fbresponse.getElementsByTagName("LoginResponse"); for (int i = 0; i < nl.getLength(); i++) { if (nl.item(i) instanceof Element && hasError((Element) nl.item(i))) { error = true; FBErrorException e = new FBErrorException(); e.setErrorCode(errorcode); e.setErrorText(errortext); throw e; } } results.setMessage(DOMUtil.getAllElementText(fbresponse, "Message")); results.setServerTime(DOMUtil.getAllElementText(fbresponse, "ServerTime")); NodeList quotas = fbresponse.getElementsByTagName("Quota"); for (int i = 0; i < quotas.getLength(); i++) { if (quotas.item(i) instanceof Node) { NodeList children = quotas.item(i).getChildNodes(); for (int j = 0; j < children.getLength(); j++) { if (children.item(j) instanceof Element) { Element working = (Element) children.item(j); if (working.getNodeName().equals("Remaining")) { try { results.setQuotaRemaining(Long.parseLong(DOMUtil.getSimpleElementText(working))); } catch (Exception e) { } } if (working.getNodeName().equals("Used")) { try { results.setQuotaUsed(Long.parseLong(DOMUtil.getSimpleElementText(working))); } catch (Exception e) { } } if (working.getNodeName().equals("Total")) { try { results.setQuotaTotal(Long.parseLong(DOMUtil.getSimpleElementText(working))); } catch (Exception e) { } } } } } } results.setRawXML(getLastRawXML()); return; } | private String generateUniqueIdMD5(String workgroupIdString, String runIdString) { String passwordUnhashed = workgroupIdString + "-" + runIdString; MessageDigest m = null; try { m = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException e) { e.printStackTrace(); } m.update(passwordUnhashed.getBytes(), 0, passwordUnhashed.length()); String uniqueIdMD5 = new BigInteger(1, m.digest()).toString(16); return uniqueIdMD5; } | 12,447 |
0 | @Override public void doMove(File from, File to) throws IOException { int res = showConfirmation("File will be moved in p4, are you sure to move ", from.getAbsolutePath()); if (res == JOptionPane.NO_OPTION) { return; } Status status = fileStatusProvider.getFileStatusForce(from); if (status == null) { return; } if (status.isLocal()) { logWarning(this, from.getName() + " is not revisioned. Should not be deleted by p4nb"); return; } to.getParentFile().mkdirs(); BufferedInputStream in = new BufferedInputStream(new FileInputStream(from)); BufferedOutputStream out = new BufferedOutputStream(new FileOutputStream(to)); byte[] buffer = new byte[8192]; int read = 0; while ((read = in.read(buffer)) >= 0) { out.write(buffer, 0, read); } in.close(); out.flush(); out.close(); if (status != Status.NONE) { revert(from); } if (status != Status.ADD) { delete(from); } else { from.delete(); } add(to); } | private void readFromStorableInput(String filename) { try { URL url = new URL(getCodeBase(), filename); InputStream stream = url.openStream(); StorableInput input = new StorableInput(stream); fDrawing.release(); fDrawing = (Drawing) input.readStorable(); view().setDrawing(fDrawing); } catch (IOException e) { initDrawing(); showStatus("Error:" + e); } } | 12,448 |
1 | public static String md5Encode16(String s) { try { MessageDigest md = MessageDigest.getInstance("MD5"); md.update(s.getBytes("utf-8")); byte b[] = md.digest(); int i; StringBuilder buf = new StringBuilder(""); for (int offset = 0; offset < b.length; offset++) { i = b[offset]; if (i < 0) i += 256; if (i < 16) buf.append("0"); buf.append(Integer.toHexString(i)); } return buf.toString().substring(8, 24); } catch (NoSuchAlgorithmException e) { throw new IllegalArgumentException(e); } catch (UnsupportedEncodingException e) { throw new IllegalArgumentException(e); } } | public String getDigest(String algorithm, String data) throws IOException, NoSuchAlgorithmException { MessageDigest md = java.security.MessageDigest.getInstance(algorithm); md.reset(); md.update(data.getBytes()); return md.digest().toString(); } | 12,449 |
1 | public Boolean compress(String sSourceDir, ArrayList<String> aFiles, String sDestinationFilename) { logger.debug("compress(%s, %s, %s)", sSourceDir, aFiles, sDestinationFilename); BufferedInputStream oOrigin = null; FileOutputStream oDestination; ZipOutputStream oOutput = null; Iterator<String> oIterator; byte[] aData; try { oDestination = new FileOutputStream(sDestinationFilename); oOutput = new ZipOutputStream(new BufferedOutputStream(oDestination)); aData = new byte[BUFFER_SIZE]; oIterator = aFiles.iterator(); while (oIterator.hasNext()) { try { String sFilename = (String) oIterator.next(); FileInputStream fisInput = new FileInputStream(sSourceDir + File.separator + sFilename); oOrigin = new BufferedInputStream(fisInput, BUFFER_SIZE); ZipEntry oEntry = new ZipEntry(sFilename.replace('\\', '/')); oOutput.putNextEntry(oEntry); int iCount; while ((iCount = oOrigin.read(aData, 0, BUFFER_SIZE)) != -1) oOutput.write(aData, 0, iCount); } finally { StreamHelper.close(oOrigin); } } } catch (Exception oException) { logger.error(oException.getMessage(), oException); return false; } finally { StreamHelper.close(oOutput); } return true; } | public static void copy(String from_name, String to_name) throws IOException { File from_file = new File(from_name); File to_file = new File(to_name); if (!from_file.exists()) abort("FileCopy: no such source file: " + from_name); if (!from_file.isFile()) abort("FileCopy: can't copy directory: " + from_name); if (!from_file.canRead()) abort("FileCopy: source file is unreadable: " + from_name); if (to_file.isDirectory()) to_file = new File(to_file, from_file.getName()); if (to_file.exists()) { if (!to_file.canWrite()) abort("FileCopy: destination file is unwriteable: " + to_name); System.out.print("Overwrite existing file " + to_name + "? (Y/N): "); System.out.flush(); BufferedReader in = new BufferedReader(new InputStreamReader(System.in)); String response = in.readLine(); if (!response.equals("Y") && !response.equals("y")) abort("FileCopy: existing file was not overwritten."); } else { String parent = to_file.getParent(); if (parent == null) parent = System.getProperty("user.dir"); File dir = new File(parent); if (!dir.exists()) abort("FileCopy: destination directory doesn't exist: " + parent); if (dir.isFile()) abort("FileCopy: destination is not a directory: " + parent); if (!dir.canWrite()) abort("FileCopy: destination directory is unwriteable: " + parent); } FileInputStream from = null; FileOutputStream to = null; try { from = new FileInputStream(from_file); to = new FileOutputStream(to_file); byte[] buffer = new byte[4096]; int bytes_read; while ((bytes_read = from.read(buffer)) != -1) to.write(buffer, 0, bytes_read); } finally { if (from != null) try { from.close(); } catch (IOException e) { ; } if (to != null) try { to.close(); } catch (IOException e) { ; } } } | 12,450 |
0 | static String MD5(String text) throws NoSuchAlgorithmException, UnsupportedEncodingException { MessageDigest md; md = MessageDigest.getInstance("MD5"); byte[] md5hash = new byte[32]; md.update(text.getBytes("iso-8859-1"), 0, text.length()); md5hash = md.digest(); return convertToHex(md5hash); } | public void convert(File src, File dest) throws IOException { InputStream in = new BufferedInputStream(new FileInputStream(src)); DcmParser p = pfact.newDcmParser(in); Dataset ds = fact.newDataset(); p.setDcmHandler(ds.getDcmHandler()); try { FileFormat format = p.detectFileFormat(); if (format != FileFormat.ACRNEMA_STREAM) { System.out.println("\n" + src + ": not an ACRNEMA stream!"); return; } p.parseDcmFile(format, Tags.PixelData); if (ds.contains(Tags.StudyInstanceUID) || ds.contains(Tags.SeriesInstanceUID) || ds.contains(Tags.SOPInstanceUID) || ds.contains(Tags.SOPClassUID)) { System.out.println("\n" + src + ": contains UIDs!" + " => probable already DICOM - do not convert"); return; } boolean hasPixelData = p.getReadTag() == Tags.PixelData; boolean inflate = hasPixelData && ds.getInt(Tags.BitsAllocated, 0) == 12; int pxlen = p.getReadLength(); if (hasPixelData) { if (inflate) { ds.putUS(Tags.BitsAllocated, 16); pxlen = pxlen * 4 / 3; } if (pxlen != (ds.getInt(Tags.BitsAllocated, 0) >>> 3) * ds.getInt(Tags.Rows, 0) * ds.getInt(Tags.Columns, 0) * ds.getInt(Tags.NumberOfFrames, 1) * ds.getInt(Tags.NumberOfSamples, 1)) { System.out.println("\n" + src + ": mismatch pixel data length!" + " => do not convert"); return; } } ds.putUI(Tags.StudyInstanceUID, uid(studyUID)); ds.putUI(Tags.SeriesInstanceUID, uid(seriesUID)); ds.putUI(Tags.SOPInstanceUID, uid(instUID)); ds.putUI(Tags.SOPClassUID, classUID); if (!ds.contains(Tags.NumberOfSamples)) { ds.putUS(Tags.NumberOfSamples, 1); } if (!ds.contains(Tags.PhotometricInterpretation)) { ds.putCS(Tags.PhotometricInterpretation, "MONOCHROME2"); } if (fmi) { ds.setFileMetaInfo(fact.newFileMetaInfo(ds, UIDs.ImplicitVRLittleEndian)); } OutputStream out = new BufferedOutputStream(new FileOutputStream(dest)); try { } finally { ds.writeFile(out, encodeParam()); if (hasPixelData) { if (!skipGroupLen) { out.write(PXDATA_GROUPLEN); int grlen = pxlen + 8; out.write((byte) grlen); out.write((byte) (grlen >> 8)); out.write((byte) (grlen >> 16)); out.write((byte) (grlen >> 24)); } out.write(PXDATA_TAG); out.write((byte) pxlen); out.write((byte) (pxlen >> 8)); out.write((byte) (pxlen >> 16)); out.write((byte) (pxlen >> 24)); } if (inflate) { int b2, b3; for (; pxlen > 0; pxlen -= 3) { out.write(in.read()); b2 = in.read(); b3 = in.read(); out.write(b2 & 0x0f); out.write(b2 >> 4 | ((b3 & 0x0f) << 4)); out.write(b3 >> 4); } } else { for (; pxlen > 0; --pxlen) { out.write(in.read()); } } out.close(); } System.out.print('.'); } finally { in.close(); } } | 12,451 |
1 | public static String digestString(String data, String algorithm) { String result = null; if (data != null) { try { MessageDigest _md = MessageDigest.getInstance(algorithm); _md.update(data.getBytes()); byte[] _digest = _md.digest(); String _ds; _ds = toHexString(_digest, 0, _digest.length); result = _ds; } catch (NoSuchAlgorithmException e) { result = null; } } return result; } | public void test(TestHarness harness) { harness.checkPoint("TestOfMD4"); try { Security.addProvider(new JarsyncProvider()); algorithm = MessageDigest.getInstance("BrokenMD4", "JARSYNC"); } catch (Exception x) { harness.debug(x); harness.fail("TestOfMD4.provider"); throw new Error(x); } try { for (int i = 0; i < 64; i++) algorithm.update((byte) 'a'); byte[] md = algorithm.digest(); String exp = "755cd64425f260e356f5303ee82a2d5f"; harness.check(exp.equals(Util.toHexString(md)), "testSixtyFourA"); } catch (Exception x) { harness.debug(x); harness.fail("TestOfMD4.provider"); } try { harness.verbose("NOTE: This test may take a while."); for (int i = 0; i < 536870913; i++) algorithm.update((byte) 'a'); byte[] md = algorithm.digest(); String exp = "b6cea9f528a85963f7529a9e3a2153db"; harness.check(exp.equals(Util.toHexString(md)), "test536870913A"); } catch (Exception x) { harness.debug(x); harness.fail("TestOfMD4.provider"); } try { byte[] md = algorithm.digest("a".getBytes()); String exp = "bde52cb31de33e46245e05fbdbd6fb24"; harness.check(exp.equals(Util.toHexString(md)), "testA"); } catch (Exception x) { harness.debug(x); harness.fail("TestOfMD4.testA"); } try { byte[] md = algorithm.digest("abc".getBytes()); String exp = "a448017aaf21d8525fc10ae87aa6729d"; harness.check(exp.equals(Util.toHexString(md)), "testABC"); } catch (Exception x) { harness.debug(x); harness.fail("TestOfMD4.testABC"); } try { byte[] md = algorithm.digest("message digest".getBytes()); String exp = "d9130a8164549fe818874806e1c7014b"; harness.check(exp.equals(Util.toHexString(md)), "testMessageDigest"); } catch (Exception x) { harness.debug(x); harness.fail("TestOfMD4.testMessageDigest"); } try { byte[] md = algorithm.digest("abcdefghijklmnopqrstuvwxyz".getBytes()); String exp = "d79e1c308aa5bbcdeea8ed63df412da9"; harness.check(exp.equals(Util.toHexString(md)), "testAlphabet"); } catch (Exception x) { harness.debug(x); harness.fail("TestOfMD4.testAlphabet"); } try { byte[] md = algorithm.digest("ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789".getBytes()); String exp = "043f8582f241db351ce627e153e7f0e4"; harness.check(exp.equals(Util.toHexString(md)), "testAsciiSubset"); } catch (Exception x) { harness.debug(x); harness.fail("TestOfMD4.testAsciiSubset"); } try { byte[] md = algorithm.digest("12345678901234567890123456789012345678901234567890123456789012345678901234567890".getBytes()); String exp = "e33b4ddc9c38f2199c3e7b164fcc0536"; harness.check(exp.equals(Util.toHexString(md)), "testEightyNumerics"); } catch (Exception x) { harness.debug(x); harness.fail("TestOfMD4.testEightyNumerics"); } try { algorithm.update("a".getBytes(), 0, 1); clone = (MessageDigest) algorithm.clone(); byte[] md = algorithm.digest(); String exp = "bde52cb31de33e46245e05fbdbd6fb24"; harness.check(exp.equals(Util.toHexString(md)), "testCloning #1"); clone.update("bc".getBytes(), 0, 2); md = clone.digest(); exp = "a448017aaf21d8525fc10ae87aa6729d"; harness.check(exp.equals(Util.toHexString(md)), "testCloning #2"); } catch (Exception x) { harness.debug(x); harness.fail("TestOfMD4.testCloning"); } } | 12,452 |
1 | @Override public Collection<IAuthor> doImport() throws Exception { progress.initialize(2, "Ściągam autorów amerykańskich"); String url = "http://pl.wikipedia.org/wiki/Kategoria:Ameryka%C5%84scy_autorzy_fantastyki"; UrlResource resource = new UrlResource(url); InputStream urlInputStream = resource.getInputStream(); StringWriter writer = new StringWriter(); IOUtils.copy(urlInputStream, writer); progress.advance("Parsuję autorów amerykańskich"); DocumentBuilderFactory factory = DocumentBuilderFactory.newInstance(); DocumentBuilder builder = factory.newDocumentBuilder(); String httpDoc = writer.toString(); httpDoc = httpDoc.replaceFirst("(?s)<!DOCTYPE.+?>\\n", ""); httpDoc = httpDoc.replaceAll("(?s)<script.+?</script>", ""); httpDoc = "<?xml version=\"1.0\" encoding=\"UTF-8\" standalone=\"no\" ?>\n" + httpDoc; ByteArrayInputStream byteInputStream = new ByteArrayInputStream(httpDoc.getBytes("UTF-8")); Document doc = builder.parse(byteInputStream); ArrayList<String> authorNames = new ArrayList<String>(); ArrayList<IAuthor> authors = new ArrayList<IAuthor>(); XPathFactory xpathFactory = XPathFactory.newInstance(); XPath xpath = xpathFactory.newXPath(); NodeList list = (NodeList) xpath.evaluate("//ul/li/div/div/a", doc, XPathConstants.NODESET); for (int i = 0; i < list.getLength(); i++) { String name = list.item(i).getTextContent(); if (StringUtils.isNotBlank(name)) { authorNames.add(name); } } list = (NodeList) xpath.evaluate("//td/ul/li/a", doc, XPathConstants.NODESET); for (int i = 0; i < list.getLength(); i++) { String name = list.item(i).getTextContent(); if (StringUtils.isNotBlank(name)) { authorNames.add(name); } } for (String name : authorNames) { int idx = name.lastIndexOf(' '); String fname = name.substring(0, idx).trim(); String lname = name.substring(idx + 1).trim(); authors.add(new Author(fname, lname)); } progress.advance("Wykonano"); return authors; } | public static void main(String[] args) throws Exception { long start = System.currentTimeMillis(); XSLTBuddy buddy = new XSLTBuddy(); buddy.parseArgs(args); XSLTransformer transformer = new XSLTransformer(); if (buddy.templateDir != null) { transformer.setTemplateDir(buddy.templateDir); } FileReader xslReader = new FileReader(buddy.xsl); Templates xslTemplate = transformer.getXSLTemplate(buddy.xsl, xslReader); for (Enumeration e = buddy.params.keys(); e.hasMoreElements(); ) { String key = (String) e.nextElement(); transformer.addParam(key, buddy.params.get(key)); } Reader reader = null; if (buddy.src == null) { reader = new StringReader(XSLTBuddy.BLANK_XML); } else { reader = new FileReader(buddy.src); } if (buddy.out == null) { String result = transformer.doTransform(reader, xslTemplate, buddy.xsl); buddy.getLogger().info("\n\nXSLT Result:\n\n" + result + "\n"); } else { File file = new File(buddy.out); File dir = file.getParentFile(); if (dir != null) { dir.mkdirs(); } FileWriter writer = new FileWriter(buddy.out); transformer.doTransform(reader, xslTemplate, buddy.xsl, writer); writer.flush(); writer.close(); } buddy.getLogger().info("Transform done successfully in " + (System.currentTimeMillis() - start) + " milliseconds"); } | 12,453 |
0 | public void run() { try { if (useStream || inputStream != null) { InputStream inputStream = null; if (LoadDocumentOperation.this.inputStream != null) inputStream = LoadDocumentOperation.this.inputStream; else inputStream = url.openStream(); if (frame != null) document = officeApplication.getDocumentService().loadDocument(frame, inputStream, documentDescriptor); else document = officeApplication.getDocumentService().loadDocument(inputStream, documentDescriptor); try { inputStream.close(); } catch (Throwable throwable) { } } else { if (frame != null) document = officeApplication.getDocumentService().loadDocument(frame, url.toString(), documentDescriptor); else document = officeApplication.getDocumentService().loadDocument(url.toString(), documentDescriptor); } done = true; } catch (Exception exception) { this.exception = exception; } catch (ThreadDeath threadDeath) { } } | public void addGames(List<Game> games) throws StadiumException, SQLException { Connection conn = ConnectionManager.getManager().getConnection(); conn.setAutoCommit(false); PreparedStatement stm = null; ResultSet rs = null; try { for (Game game : games) { stm = conn.prepareStatement(Statements.SELECT_STADIUM); stm.setString(1, game.getStadiumName()); stm.setString(2, game.getStadiumCity()); rs = stm.executeQuery(); int stadiumId = -1; while (rs.next()) { stadiumId = rs.getInt("stadiumID"); } if (stadiumId == -1) throw new StadiumException("No such stadium"); stm = conn.prepareStatement(Statements.INSERT_GAME); stm.setInt(1, stadiumId); stm.setDate(2, game.getGameDate()); stm.setTime(3, game.getGameTime()); stm.setString(4, game.getTeamA()); stm.setString(5, game.getTeamB()); stm.executeUpdate(); int gameId = getMaxId(); List<SectorPrice> sectorPrices = game.getSectorPrices(); for (SectorPrice price : sectorPrices) { stm = conn.prepareStatement(Statements.INSERT_TICKET_PRICE); stm.setInt(1, gameId); stm.setInt(2, price.getSectorId()); stm.setInt(3, price.getPrice()); stm.executeUpdate(); } } } catch (SQLException e) { conn.rollback(); throw e; } finally { rs.close(); stm.close(); } conn.commit(); conn.setAutoCommit(true); } | 12,454 |
0 | public String setEncryptedPassword(String rawPassword) { String out = null; try { MessageDigest md = MessageDigest.getInstance("MD5"); md.reset(); md.update(rawPassword.getBytes()); byte raw[] = md.digest(); out = new String(); for (int x = 0; x < raw.length; x++) { String hex2 = Integer.toHexString((int) raw[x] & 0xFF); if (1 == hex2.length()) { hex2 = "0" + hex2; } out += hex2; int a = 1; } } catch (NoSuchAlgorithmException e) { e.printStackTrace(); } return out; } | private void loadProperties() { if (properties == null) { properties = new Properties(); try { URL url = getClass().getResource(propsFile); properties.load(url.openStream()); } catch (IOException ioe) { ioe.printStackTrace(); } } } | 12,455 |
1 | public static void copyFolderStucture(String strPath, String dstPath) throws IOException { Constants.iLog.LogInfoLine("copying " + strPath); File src = new File(strPath); File dest = new File(dstPath); if (src.isDirectory()) { dest.mkdirs(); String list[] = src.list(); for (int i = 0; i < list.length; i++) { String dest1 = dest.getAbsolutePath() + "\\" + list[i]; String src1 = src.getAbsolutePath() + "\\" + list[i]; copyFolderStucture(src1, dest1); } } else { FileInputStream fin = new FileInputStream(src); FileOutputStream fout = new FileOutputStream(dest); int c; while ((c = fin.read()) >= 0) fout.write(c); fin.close(); fout.close(); } } | protected int doWork() { SAMFileReader reader = new SAMFileReader(IoUtil.openFileForReading(INPUT)); reader.getFileHeader().setSortOrder(SORT_ORDER); SAMFileWriter writer = new SAMFileWriterFactory().makeSAMOrBAMWriter(reader.getFileHeader(), false, OUTPUT); Iterator<SAMRecord> iterator = reader.iterator(); while (iterator.hasNext()) writer.addAlignment(iterator.next()); reader.close(); writer.close(); return 0; } | 12,456 |
1 | private void writeMessage(ChannelBuffer buffer, File dst) throws IOException { ChannelBufferInputStream is = new ChannelBufferInputStream(buffer); OutputStream os = null; try { os = new FileOutputStream(dst); IOUtils.copyLarge(is, os); } finally { IOUtils.closeQuietly(os); } } | private static void doCopyFile(File srcFile, File destFile, boolean preserveFileDate) throws IOException { if (destFile.exists() && destFile.isDirectory()) { throw new IOException("Destination '" + destFile + "' exists but is a directory"); } FileInputStream input = new FileInputStream(srcFile); try { FileOutputStream output = new FileOutputStream(destFile); try { IOUtils.copy(input, output); } finally { IOUtils.closeQuietly(output); } } finally { IOUtils.closeQuietly(input); } if (srcFile.length() != destFile.length()) { throw new IOException("Failed to copy full contents from '" + srcFile + "' to '" + destFile + "'"); } if (preserveFileDate) { destFile.setLastModified(srcFile.lastModified()); } } | 12,457 |
0 | protected static String encodePassword(String password) { try { MessageDigest md = MessageDigest.getInstance("SHA"); md.update(password.getBytes()); return HexString.bufferToHex(md.digest()); } catch (NoSuchAlgorithmException e) { throw new RuntimeException(e); } } | private int addPollToDB(DataSource database) { int pollid = -2; Connection con = null; try { con = database.getConnection(); con.setAutoCommit(false); String add = "insert into polls" + " values( ?, ?, ?, ?)"; PreparedStatement prepStatement = con.prepareStatement(add); prepStatement.setString(1, selectedCourse.getAdmin()); prepStatement.setString(2, selectedCourse.getCourseId()); prepStatement.setString(3, getTitle()); prepStatement.setInt(4, 0); prepStatement.executeUpdate(); String findNewID = "select max(pollid) from polls"; prepStatement = con.prepareStatement(findNewID); ResultSet newID = prepStatement.executeQuery(); pollid = -2; while (newID.next()) { pollid = newID.getInt(1); } if (pollid == -2) { this.sqlError = true; throw new Exception(); } String[] options = getAllOptions(); for (int i = 0; i < 4; i++) { String insertOption = "insert into polloptions values ( ?, ?, ? )"; prepStatement = con.prepareStatement(insertOption); prepStatement.setString(1, options[i]); prepStatement.setInt(2, 0); prepStatement.setInt(3, pollid); prepStatement.executeUpdate(); } prepStatement.close(); con.commit(); } catch (Exception e) { sqlError = true; e.printStackTrace(); if (con != null) try { con.rollback(); } catch (Exception logOrIgnore) { } try { throw e; } catch (Exception e1) { e1.printStackTrace(); } } finally { if (con != null) try { con.close(); } catch (Exception logOrIgnore) { } } return pollid; } | 12,458 |
0 | public String generateKey(String className, String methodName, String text, String meaning) { if (text == null) { return null; } MessageDigest md5; try { md5 = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException e) { throw new RuntimeException("Error initializing MD5", e); } try { md5.update(text.getBytes("UTF-8")); if (meaning != null) { md5.update(meaning.getBytes("UTF-8")); } } catch (UnsupportedEncodingException e) { throw new RuntimeException("UTF-8 unsupported", e); } return StringUtils.toHexString(md5.digest()); } | private static final BufferedInputStream createInputStreamFromRemoteUrl(String uri, ClientConnectionManager connectionManager) { InputStream contentInput = null; if (connectionManager == null) { try { URL url = new URI(uri).toURL(); URLConnection conn = url.openConnection(); conn.connect(); contentInput = conn.getInputStream(); } catch (Exception e) { Log.w(TAG, "Request failed: " + uri); e.printStackTrace(); return null; } } else { final DefaultHttpClient mHttpClient = new DefaultHttpClient(connectionManager, HTTP_PARAMS); HttpUriRequest request = new HttpGet(uri); HttpResponse httpResponse = null; try { httpResponse = mHttpClient.execute(request); HttpEntity entity = httpResponse.getEntity(); if (entity != null) { contentInput = entity.getContent(); } } catch (Exception e) { Log.w(TAG, "Request failed: " + request.getURI()); return null; } } if (contentInput != null) { return new BufferedInputStream(contentInput, 4096); } else { return null; } } | 12,459 |
1 | public static void copyFile(File sourceFile, File targetFile) throws IOException { if (sourceFile == null || targetFile == null) { throw new NullPointerException("Source file and target file must not be null"); } File directory = targetFile.getParentFile(); if (!directory.exists() && !directory.mkdirs()) { throw new IOException("Could not create directory '" + directory + "'"); } InputStream inputStream = null; OutputStream outputStream = null; try { inputStream = new BufferedInputStream(new FileInputStream(sourceFile)); outputStream = new BufferedOutputStream(new FileOutputStream(targetFile)); try { byte[] buffer = new byte[32768]; for (int readBytes = inputStream.read(buffer); readBytes > 0; readBytes = inputStream.read(buffer)) { outputStream.write(buffer, 0, readBytes); } } catch (IOException ex) { targetFile.delete(); throw ex; } } finally { if (inputStream != null) { try { inputStream.close(); } catch (IOException ex) { } } if (outputStream != null) { try { outputStream.close(); } catch (IOException ex) { } } } } | public static void copy(FileInputStream source, FileOutputStream dest) throws IOException { FileChannel in = null, out = null; try { in = source.getChannel(); out = dest.getChannel(); long size = in.size(); MappedByteBuffer buf = in.map(FileChannel.MapMode.READ_ONLY, 0, size); out.write(buf); } finally { if (in != null) in.close(); if (out != null) out.close(); } } | 12,460 |
1 | public static void copyFile(File sourceFile, File destFile, boolean overwrite) throws IOException, DirNotFoundException, FileNotFoundException, FileExistsAlreadyException { File destDir = new File(destFile.getParent()); if (!destDir.exists()) { throw new DirNotFoundException(destDir.getAbsolutePath()); } if (!sourceFile.exists()) { throw new FileNotFoundException(sourceFile.getAbsolutePath()); } if (!overwrite && destFile.exists()) { throw new FileExistsAlreadyException(destFile.getAbsolutePath()); } FileInputStream in = new FileInputStream(sourceFile); FileOutputStream out = new FileOutputStream(destFile); byte[] buffer = new byte[8 * 1024]; int count = 0; do { out.write(buffer, 0, count); count = in.read(buffer, 0, buffer.length); } while (count != -1); in.close(); out.close(); } | public void convert(File src, File dest) throws IOException { InputStream in = new BufferedInputStream(new FileInputStream(src)); DcmParser p = pfact.newDcmParser(in); Dataset ds = fact.newDataset(); p.setDcmHandler(ds.getDcmHandler()); try { FileFormat format = p.detectFileFormat(); if (format != FileFormat.ACRNEMA_STREAM) { System.out.println("\n" + src + ": not an ACRNEMA stream!"); return; } p.parseDcmFile(format, Tags.PixelData); if (ds.contains(Tags.StudyInstanceUID) || ds.contains(Tags.SeriesInstanceUID) || ds.contains(Tags.SOPInstanceUID) || ds.contains(Tags.SOPClassUID)) { System.out.println("\n" + src + ": contains UIDs!" + " => probable already DICOM - do not convert"); return; } boolean hasPixelData = p.getReadTag() == Tags.PixelData; boolean inflate = hasPixelData && ds.getInt(Tags.BitsAllocated, 0) == 12; int pxlen = p.getReadLength(); if (hasPixelData) { if (inflate) { ds.putUS(Tags.BitsAllocated, 16); pxlen = pxlen * 4 / 3; } if (pxlen != (ds.getInt(Tags.BitsAllocated, 0) >>> 3) * ds.getInt(Tags.Rows, 0) * ds.getInt(Tags.Columns, 0) * ds.getInt(Tags.NumberOfFrames, 1) * ds.getInt(Tags.NumberOfSamples, 1)) { System.out.println("\n" + src + ": mismatch pixel data length!" + " => do not convert"); return; } } ds.putUI(Tags.StudyInstanceUID, uid(studyUID)); ds.putUI(Tags.SeriesInstanceUID, uid(seriesUID)); ds.putUI(Tags.SOPInstanceUID, uid(instUID)); ds.putUI(Tags.SOPClassUID, classUID); if (!ds.contains(Tags.NumberOfSamples)) { ds.putUS(Tags.NumberOfSamples, 1); } if (!ds.contains(Tags.PhotometricInterpretation)) { ds.putCS(Tags.PhotometricInterpretation, "MONOCHROME2"); } if (fmi) { ds.setFileMetaInfo(fact.newFileMetaInfo(ds, UIDs.ImplicitVRLittleEndian)); } OutputStream out = new BufferedOutputStream(new FileOutputStream(dest)); try { } finally { ds.writeFile(out, encodeParam()); if (hasPixelData) { if (!skipGroupLen) { out.write(PXDATA_GROUPLEN); int grlen = pxlen + 8; out.write((byte) grlen); out.write((byte) (grlen >> 8)); out.write((byte) (grlen >> 16)); out.write((byte) (grlen >> 24)); } out.write(PXDATA_TAG); out.write((byte) pxlen); out.write((byte) (pxlen >> 8)); out.write((byte) (pxlen >> 16)); out.write((byte) (pxlen >> 24)); } if (inflate) { int b2, b3; for (; pxlen > 0; pxlen -= 3) { out.write(in.read()); b2 = in.read(); b3 = in.read(); out.write(b2 & 0x0f); out.write(b2 >> 4 | ((b3 & 0x0f) << 4)); out.write(b3 >> 4); } } else { for (; pxlen > 0; --pxlen) { out.write(in.read()); } } out.close(); } System.out.print('.'); } finally { in.close(); } } | 12,461 |
0 | public static void doVersionCheck(View view) { view.showWaitCursor(); try { URL url = new URL(jEdit.getProperty("version-check.url")); InputStream in = url.openStream(); BufferedReader bin = new BufferedReader(new InputStreamReader(in)); String line; String version = null; String build = null; while ((line = bin.readLine()) != null) { if (line.startsWith(".version")) version = line.substring(8).trim(); else if (line.startsWith(".build")) build = line.substring(6).trim(); } bin.close(); if (version != null && build != null) { if (jEdit.getBuild().compareTo(build) < 0) newVersionAvailable(view, version, url); else { GUIUtilities.message(view, "version-check" + ".up-to-date", new String[0]); } } } catch (IOException e) { String[] args = { jEdit.getProperty("version-check.url"), e.toString() }; GUIUtilities.error(view, "read-error", args); } view.hideWaitCursor(); } | public static byte[] hash(final byte[] saltBefore, final String content, final byte[] saltAfter, final int repeatedHashingCount) throws NoSuchAlgorithmException, UnsupportedEncodingException { if (content == null) return null; final MessageDigest digest = MessageDigest.getInstance(DIGEST); if (digestLength == -1) digestLength = digest.getDigestLength(); for (int i = 0; i < repeatedHashingCount; i++) { if (i > 0) digest.update(digest.digest()); digest.update(saltBefore); digest.update(content.getBytes(WebCastellumParameter.DEFAULT_CHARACTER_ENCODING.getValue())); digest.update(saltAfter); } return digest.digest(); } | 12,462 |
0 | public void fetchFile(String ID) { String url = "http://www.nal.usda.gov/cgi-bin/agricola-ind?bib=" + ID + "&conf=010000++++++++++++++&screen=MA"; System.out.println(url); try { PrintWriter pw = new PrintWriter(new FileWriter("MARC" + ID + ".txt")); if (!id.contains("MARC" + ID + ".txt")) { id.add("MARC" + ID + ".txt"); } in = new BufferedReader(new InputStreamReader((new URL(url)).openStream())); in.readLine(); String inputLine, stx = ""; StringBuffer sb = new StringBuffer(); while ((inputLine = in.readLine()) != null) { if (inputLine.startsWith("<TR><TD><B>")) { String sts = (inputLine.substring(inputLine.indexOf("B>") + 2, inputLine.indexOf("</"))); int i = 0; try { i = Integer.parseInt(sts); } catch (NumberFormatException nfe) { } if (i > 0) { stx = stx + "\n" + sts + " - "; } else { stx += sts; } } if (!(inputLine.startsWith("<") || inputLine.startsWith(" <") || inputLine.startsWith(">"))) { String tx = inputLine.trim(); stx += tx; } } pw.println(stx); pw.close(); } catch (Exception e) { System.out.println("Couldn't open stream"); System.out.println(e); } } | @Override public void run(ProcedureRunner runner) throws Exception { if (url == null) { throw BuiltinExceptionFactory.createAttributeMissing(this, "url"); } if (inputPath == null) { throw BuiltinExceptionFactory.createAttributeMissing(this, "inputPath"); } CompositeMap context = runner.getContext(); Object inputObject = context.getObject(inputPath); if (inputObject == null) throw BuiltinExceptionFactory.createDataFromXPathIsNull(this, inputPath); if (!(inputObject instanceof CompositeMap)) throw BuiltinExceptionFactory.createInstanceTypeWrongException(inputPath, CompositeMap.class, inputObject.getClass()); URI uri = new URI(url); URL url = uri.toURL(); PrintWriter out = null; BufferedReader br = null; CompositeMap soapBody = createSOAPBody(); soapBody.addChild((CompositeMap) inputObject); String content = XMLOutputter.defaultInstance().toXML(soapBody.getRoot(), true); LoggingContext.getLogger(context, this.getClass().getCanonicalName()).config("request:\r\n" + content); HttpURLConnection httpUrlConnection = null; try { httpUrlConnection = (HttpURLConnection) url.openConnection(); httpUrlConnection.setDoInput(true); httpUrlConnection.setDoOutput(true); httpUrlConnection.setRequestMethod("POST"); httpUrlConnection.setRequestProperty("SOAPAction", "urn:anonOutInOp"); httpUrlConnection.setRequestProperty("Content-Type", "text/xml; charset=UTF-8"); httpUrlConnection.connect(); OutputStream os = httpUrlConnection.getOutputStream(); out = new PrintWriter(os); out.println("<?xml version='1.0' encoding='UTF-8'?>"); out.println(new String(content.getBytes("UTF-8"))); out.flush(); out.close(); String soapResponse = null; CompositeMap soap = null; CompositeLoader cl = new CompositeLoader(); if (HttpURLConnection.HTTP_OK == httpUrlConnection.getResponseCode()) { soap = cl.loadFromStream(httpUrlConnection.getInputStream()); soapResponse = soap.toXML(); LoggingContext.getLogger(context, this.getClass().getCanonicalName()).config("correct response:" + soapResponse); } else { soap = cl.loadFromStream(httpUrlConnection.getErrorStream()); soapResponse = soap.toXML(); LoggingContext.getLogger(context, this.getClass().getCanonicalName()).config("error response:" + soapResponse); if (raiseExceptionOnError) { throw new ConfigurationFileException(WS_INVOKER_ERROR_CODE, new Object[] { url, soapResponse }, this); } } httpUrlConnection.disconnect(); CompositeMap result = (CompositeMap) soap.getChild(SOAPServiceInterpreter.BODY.getLocalName()).getChilds().get(0); if (returnPath != null) runner.getContext().putObject(returnPath, result, true); } catch (Exception e) { LoggingContext.getLogger(context, this.getClass().getCanonicalName()).log(Level.SEVERE, "", e); throw new RuntimeException(e); } finally { if (out != null) { out.close(); } if (br != null) { br.close(); } if (httpUrlConnection != null) { httpUrlConnection.disconnect(); } } } | 12,463 |
1 | public void format(File source, File target) { if (!source.exists()) { throw new IllegalArgumentException("Source '" + source + " doesn't exist"); } if (!source.isFile()) { throw new IllegalArgumentException("Source '" + source + " is not a file"); } target.mkdirs(); String fileExtension = source.getName().substring(source.getName().lastIndexOf(".") + 1); String _target = source.getName().replace(fileExtension, "html"); target = new File(target.getPath() + "/" + _target); try { Reader reader = new FileReader(source); Writer writer = new FileWriter(target); this.format(reader, writer); } catch (Exception e) { e.printStackTrace(); } } | public void writeTo(OutputStream out) throws IOException, MessagingException { InputStream in = getInputStream(); Base64OutputStream base64Out = new Base64OutputStream(out); IOUtils.copy(in, base64Out); base64Out.close(); mFile.delete(); } | 12,464 |
0 | public String getHash(String type, String text, String salt) throws NoSuchAlgorithmException, UnsupportedEncodingException { MessageDigest md; md = MessageDigest.getInstance(type); byte[] hash = new byte[md.getDigestLength()]; if (!salt.isEmpty()) { md.update(salt.getBytes("iso-8859-1"), 0, salt.length()); } md.update(text.getBytes("iso-8859-1"), 0, text.length()); hash = md.digest(); return convertToHex(hash); } | private static String completeGet(String encodedURLStr) throws IOException { URL url = new URL(encodedURLStr); HttpURLConnection connection = initConnection(url); String result = getReply(url.openStream()); connection.disconnect(); return result; } | 12,465 |
0 | public static void downloadFile(String url, String filePath) throws IOException { BufferedInputStream inputStream = new BufferedInputStream(new URL(url).openStream()); BufferedOutputStream bos = new BufferedOutputStream(new FileOutputStream(filePath)); try { int i = 0; while ((i = inputStream.read()) != -1) { bos.write(i); } } finally { if (inputStream != null) { inputStream.close(); } if (bos != null) { bos.close(); } } } | public static void get_PK_data() { try { FileWriter file_writer = new FileWriter("xml_data/PK_data_dump.xml"); BufferedWriter file_buffered_writer = new BufferedWriter(file_writer); URL fdt = new URL("http://opendata.5t.torino.it/get_pk"); URLConnection url_connection = fdt.openConnection(); BufferedReader in = new BufferedReader(new InputStreamReader(url_connection.getInputStream())); String input_line; int num_lines = 0; while ((input_line = in.readLine()) != null) { file_buffered_writer.write(input_line + "\n"); num_lines++; } System.out.println("Parking :: Writed " + num_lines + " lines."); in.close(); } catch (Exception e) { System.err.println("Error: " + e.getMessage()); } } | 12,466 |
0 | public static String makeMD5(String pin) { try { MessageDigest digest = java.security.MessageDigest.getInstance("MD5"); digest.update(pin.getBytes()); byte[] hash = digest.digest(); StringBuffer hexString = new StringBuffer(); for (int i = 0; i < hash.length; i++) { hexString.append(Integer.toHexString(0xFF & hash[i])); } return hexString.toString(); } catch (Exception e) { return null; } } | public static boolean encodeFileToFile(String infile, String outfile) { boolean success = false; java.io.InputStream in = null; java.io.OutputStream out = null; try { in = new Base64.InputStream(new java.io.BufferedInputStream(new java.io.FileInputStream(infile)), Base64.ENCODE); out = new java.io.BufferedOutputStream(new java.io.FileOutputStream(outfile)); byte[] buffer = new byte[65536]; int read = -1; while ((read = in.read(buffer)) >= 0) { out.write(buffer, 0, read); } success = true; } catch (java.io.IOException exc) { exc.printStackTrace(); } finally { try { in.close(); } catch (Exception exc) { } try { out.close(); } catch (Exception exc) { } } return success; } | 12,467 |
1 | @Override public void copyTo(ManagedFile other) throws ManagedIOException { try { if (other.getType() == ManagedFileType.FILE) { IOUtils.copy(this.getContent().getInputStream(), other.getContent().getOutputStream()); } else { ManagedFile newFile = other.retrive(this.getPath()); newFile.createFile(); IOUtils.copy(this.getContent().getInputStream(), newFile.getContent().getOutputStream()); } } catch (IOException ioe) { throw ManagedIOException.manage(ioe); } } | public void convert(File src, File dest) throws IOException { InputStream in = new BufferedInputStream(new FileInputStream(src)); DcmParser p = pfact.newDcmParser(in); Dataset ds = fact.newDataset(); p.setDcmHandler(ds.getDcmHandler()); try { FileFormat format = p.detectFileFormat(); if (format != FileFormat.ACRNEMA_STREAM) { System.out.println("\n" + src + ": not an ACRNEMA stream!"); return; } p.parseDcmFile(format, Tags.PixelData); if (ds.contains(Tags.StudyInstanceUID) || ds.contains(Tags.SeriesInstanceUID) || ds.contains(Tags.SOPInstanceUID) || ds.contains(Tags.SOPClassUID)) { System.out.println("\n" + src + ": contains UIDs!" + " => probable already DICOM - do not convert"); return; } boolean hasPixelData = p.getReadTag() == Tags.PixelData; boolean inflate = hasPixelData && ds.getInt(Tags.BitsAllocated, 0) == 12; int pxlen = p.getReadLength(); if (hasPixelData) { if (inflate) { ds.putUS(Tags.BitsAllocated, 16); pxlen = pxlen * 4 / 3; } if (pxlen != (ds.getInt(Tags.BitsAllocated, 0) >>> 3) * ds.getInt(Tags.Rows, 0) * ds.getInt(Tags.Columns, 0) * ds.getInt(Tags.NumberOfFrames, 1) * ds.getInt(Tags.NumberOfSamples, 1)) { System.out.println("\n" + src + ": mismatch pixel data length!" + " => do not convert"); return; } } ds.putUI(Tags.StudyInstanceUID, uid(studyUID)); ds.putUI(Tags.SeriesInstanceUID, uid(seriesUID)); ds.putUI(Tags.SOPInstanceUID, uid(instUID)); ds.putUI(Tags.SOPClassUID, classUID); if (!ds.contains(Tags.NumberOfSamples)) { ds.putUS(Tags.NumberOfSamples, 1); } if (!ds.contains(Tags.PhotometricInterpretation)) { ds.putCS(Tags.PhotometricInterpretation, "MONOCHROME2"); } if (fmi) { ds.setFileMetaInfo(fact.newFileMetaInfo(ds, UIDs.ImplicitVRLittleEndian)); } OutputStream out = new BufferedOutputStream(new FileOutputStream(dest)); try { } finally { ds.writeFile(out, encodeParam()); if (hasPixelData) { if (!skipGroupLen) { out.write(PXDATA_GROUPLEN); int grlen = pxlen + 8; out.write((byte) grlen); out.write((byte) (grlen >> 8)); out.write((byte) (grlen >> 16)); out.write((byte) (grlen >> 24)); } out.write(PXDATA_TAG); out.write((byte) pxlen); out.write((byte) (pxlen >> 8)); out.write((byte) (pxlen >> 16)); out.write((byte) (pxlen >> 24)); } if (inflate) { int b2, b3; for (; pxlen > 0; pxlen -= 3) { out.write(in.read()); b2 = in.read(); b3 = in.read(); out.write(b2 & 0x0f); out.write(b2 >> 4 | ((b3 & 0x0f) << 4)); out.write(b3 >> 4); } } else { for (; pxlen > 0; --pxlen) { out.write(in.read()); } } out.close(); } System.out.print('.'); } finally { in.close(); } } | 12,468 |
1 | public static String stringOfUrl(String addr) throws IOException { ByteArrayOutputStream output = new ByteArrayOutputStream(); URL url = new URL(addr); IOUtils.copy(url.openStream(), output); return output.toString(); } | public static void copyClassPathResource(String classPathResourceName, String fileSystemDirectoryName) { InputStream resourceInputStream = null; OutputStream fileOutputStream = null; try { resourceInputStream = FileUtils.class.getResourceAsStream(classPathResourceName); String fileName = StringUtils.substringAfterLast(classPathResourceName, "/"); File fileSystemDirectory = new File(fileSystemDirectoryName); fileSystemDirectory.mkdirs(); fileOutputStream = new FileOutputStream(fileSystemDirectoryName + "/" + fileName); IOUtils.copy(resourceInputStream, fileOutputStream); } catch (IOException e) { throw new UnitilsException(e); } finally { closeQuietly(resourceInputStream); closeQuietly(fileOutputStream); } } | 12,469 |
0 | private String[] readFile(String filename) { final Vector<String> buf = new Vector<String>(); try { final URL url = new URL(getCodeBase(), filename); final InputStream in = url.openStream(); BufferedReader dis = new BufferedReader(new InputStreamReader(in)); String line; while ((line = dis.readLine()) != null) { buf.add(line); } in.close(); } catch (IOException e) { System.out.println("catch: " + e); return null; } return buf.toArray(new String[0]); } | public static byte[] SHA1byte(String text) throws NoSuchAlgorithmException, UnsupportedEncodingException { MessageDigest md; md = MessageDigest.getInstance("SHA-1"); byte[] sha1hash = new byte[40]; md.update(text.getBytes("iso-8859-1"), 0, text.length()); sha1hash = md.digest(); return sha1hash; } | 12,470 |
0 | static List<String> readZipFilesOftypeToFolder(String zipFileLocation, String outputDir, String fileType) { List<String> list = new ArrayList<String>(); ZipFile zipFile = readZipFile(zipFileLocation); FileOutputStream output = null; InputStream inputStream = null; Enumeration<ZipEntry> entries = (Enumeration<ZipEntry>) zipFile.entries(); try { while (entries.hasMoreElements()) { java.util.zip.ZipEntry entry = entries.nextElement(); String entryName = entry.getName(); if (entryName != null && entryName.toLowerCase().endsWith(fileType)) { inputStream = zipFile.getInputStream(entry); String fileName = outputDir + entryName.substring(entryName.lastIndexOf("/")); File file = new File(fileName); output = new FileOutputStream(file); IOUtils.copy(inputStream, output); list.add(fileName); } } } catch (Exception e) { throw new RuntimeException(e); } finally { try { if (output != null) output.close(); if (inputStream != null) inputStream.close(); if (zipFile != null) zipFile.close(); } catch (IOException e) { throw new RuntimeException(e); } } return list; } | private void setup() { env = new EnvAdvanced(); try { URL url = Sysutil.getURL("world.env"); BufferedReader br = new BufferedReader(new InputStreamReader(url.openStream())); String line; while ((line = br.readLine()) != null) { String[] fields = line.split(","); if (fields[0].equalsIgnoreCase("skybox")) { env.setRoom(new EnvSkyRoom(fields[1])); } else if (fields[0].equalsIgnoreCase("camera")) { env.setCameraXYZ(Double.parseDouble(fields[1]), Double.parseDouble(fields[2]), Double.parseDouble(fields[3])); env.setCameraYaw(Double.parseDouble(fields[4])); env.setCameraPitch(Double.parseDouble(fields[5])); } else if (fields[0].equalsIgnoreCase("terrain")) { terrain = new EnvTerrain(fields[1]); terrain.setTexture(fields[2]); env.addObject(terrain); } else if (fields[0].equalsIgnoreCase("object")) { GameObject n = (GameObject) Class.forName(fields[10]).newInstance(); n.setX(Double.parseDouble(fields[1])); n.setY(Double.parseDouble(fields[2])); n.setZ(Double.parseDouble(fields[3])); n.setScale(Double.parseDouble(fields[4])); n.setRotateX(Double.parseDouble(fields[5])); n.setRotateY(Double.parseDouble(fields[6])); n.setRotateZ(Double.parseDouble(fields[7])); n.setTexture(fields[9]); n.setModel(fields[8]); n.setEnv(env); env.addObject(n); } } } catch (Exception e) { e.printStackTrace(); } } | 12,471 |
1 | public void convert(File src, File dest) throws IOException { InputStream in = new BufferedInputStream(new FileInputStream(src)); DcmParser p = pfact.newDcmParser(in); Dataset ds = fact.newDataset(); p.setDcmHandler(ds.getDcmHandler()); try { FileFormat format = p.detectFileFormat(); if (format != FileFormat.ACRNEMA_STREAM) { System.out.println("\n" + src + ": not an ACRNEMA stream!"); return; } p.parseDcmFile(format, Tags.PixelData); if (ds.contains(Tags.StudyInstanceUID) || ds.contains(Tags.SeriesInstanceUID) || ds.contains(Tags.SOPInstanceUID) || ds.contains(Tags.SOPClassUID)) { System.out.println("\n" + src + ": contains UIDs!" + " => probable already DICOM - do not convert"); return; } boolean hasPixelData = p.getReadTag() == Tags.PixelData; boolean inflate = hasPixelData && ds.getInt(Tags.BitsAllocated, 0) == 12; int pxlen = p.getReadLength(); if (hasPixelData) { if (inflate) { ds.putUS(Tags.BitsAllocated, 16); pxlen = pxlen * 4 / 3; } if (pxlen != (ds.getInt(Tags.BitsAllocated, 0) >>> 3) * ds.getInt(Tags.Rows, 0) * ds.getInt(Tags.Columns, 0) * ds.getInt(Tags.NumberOfFrames, 1) * ds.getInt(Tags.NumberOfSamples, 1)) { System.out.println("\n" + src + ": mismatch pixel data length!" + " => do not convert"); return; } } ds.putUI(Tags.StudyInstanceUID, uid(studyUID)); ds.putUI(Tags.SeriesInstanceUID, uid(seriesUID)); ds.putUI(Tags.SOPInstanceUID, uid(instUID)); ds.putUI(Tags.SOPClassUID, classUID); if (!ds.contains(Tags.NumberOfSamples)) { ds.putUS(Tags.NumberOfSamples, 1); } if (!ds.contains(Tags.PhotometricInterpretation)) { ds.putCS(Tags.PhotometricInterpretation, "MONOCHROME2"); } if (fmi) { ds.setFileMetaInfo(fact.newFileMetaInfo(ds, UIDs.ImplicitVRLittleEndian)); } OutputStream out = new BufferedOutputStream(new FileOutputStream(dest)); try { } finally { ds.writeFile(out, encodeParam()); if (hasPixelData) { if (!skipGroupLen) { out.write(PXDATA_GROUPLEN); int grlen = pxlen + 8; out.write((byte) grlen); out.write((byte) (grlen >> 8)); out.write((byte) (grlen >> 16)); out.write((byte) (grlen >> 24)); } out.write(PXDATA_TAG); out.write((byte) pxlen); out.write((byte) (pxlen >> 8)); out.write((byte) (pxlen >> 16)); out.write((byte) (pxlen >> 24)); } if (inflate) { int b2, b3; for (; pxlen > 0; pxlen -= 3) { out.write(in.read()); b2 = in.read(); b3 = in.read(); out.write(b2 & 0x0f); out.write(b2 >> 4 | ((b3 & 0x0f) << 4)); out.write(b3 >> 4); } } else { for (; pxlen > 0; --pxlen) { out.write(in.read()); } } out.close(); } System.out.print('.'); } finally { in.close(); } } | public static PortalConfig install(File xml, File dir) throws IOException, ConfigurationException { if (!dir.exists()) { log.info("Creating directory {}", dir); dir.mkdirs(); } if (!xml.exists()) { log.info("Installing default configuration to {}", xml); OutputStream output = new FileOutputStream(xml); try { InputStream input = ResourceLoader.open("res://" + PORTAL_CONFIG_XML); try { IOUtils.copy(input, output); } finally { input.close(); } } finally { output.close(); } } return create(xml, dir); } | 12,472 |
1 | public void encryptPassword() { MessageDigest digest = null; try { digest = MessageDigest.getInstance("SHA"); } catch (NoSuchAlgorithmException e) { System.out.print(e); } try { digest.update(passwordIn.getBytes("UTF-8")); } catch (UnsupportedEncodingException e) { System.out.println("cannot find char set for getBytes"); } byte digestBytes[] = digest.digest(); passwordHash = (new BASE64Encoder()).encode(digestBytes); } | private String md5Digest(String plain) throws Exception { MessageDigest digest = MessageDigest.getInstance("MD5"); digest.update(plain.trim().getBytes()); byte pwdDigest[] = digest.digest(); StringBuilder md5buffer = new StringBuilder(); for (int i = 0; i < pwdDigest.length; i++) { int number = 0xFF & pwdDigest[i]; if (number <= 0xF) { md5buffer.append('0'); } md5buffer.append(Integer.toHexString(number)); } return md5buffer.toString(); } | 12,473 |
1 | @Test public void testCopy_inputStreamToOutputStream_IO84() throws Exception { long size = (long) Integer.MAX_VALUE + (long) 1; InputStream in = new NullInputStreamTest(size); OutputStream out = new OutputStream() { @Override public void write(int b) throws IOException { } @Override public void write(byte[] b) throws IOException { } @Override public void write(byte[] b, int off, int len) throws IOException { } }; assertEquals(-1, IOUtils.copy(in, out)); in.close(); assertEquals("copyLarge()", size, IOUtils.copyLarge(in, out)); } | public static void zipDirectory(String dir, String zipfile) throws IOException, IllegalArgumentException { File d = new File(dir); if (!d.isDirectory()) throw new IllegalArgumentException("Not a directory: " + dir); String[] entries = d.list(); byte[] buffer = new byte[4096]; int bytesRead; ZipOutputStream out = new ZipOutputStream(new FileOutputStream(zipfile)); for (int i = 0; i < entries.length; i++) { File f = new File(d, entries[i]); if (f.isDirectory()) continue; FileInputStream in = new FileInputStream(f); ZipEntry entry = new ZipEntry(f.getPath()); out.putNextEntry(entry); while ((bytesRead = in.read(buffer)) != -1) out.write(buffer, 0, bytesRead); in.close(); } out.close(); } | 12,474 |
0 | public void test2() throws Exception { SpreadsheetDocument document = new SpreadsheetDocument(); Sheet sheet = new Sheet("Planilha 1"); sheet.setLandscape(true); Row row = new Row(); row.setHeight(20); sheet.getMerges().add(new IntegerCellMerge(0, 0, 0, 5)); sheet.getImages().add(new Image(new FileInputStream("D:/image001.jpg"), 0, 0, ImageType.JPEG, 80, 60)); for (int i = 0; i < 10; i++) { Cell cell = new Cell(); cell.setValue("Celula " + i); cell.setBackgroundColor(new Color(192, 192, 192)); cell.setUnderline(true); cell.setBold(true); cell.setItalic(true); cell.setFont("Times New Roman"); cell.setFontSize(10); cell.setFontColor(new Color(255, 0, 0)); Border border = new Border(); border.setWidth(1); border.setColor(new Color(0, 0, 0)); cell.setLeftBorder(border); cell.setTopBorder(border); cell.setRightBorder(border); cell.setBottomBorder(border); row.getCells().add(cell); sheet.getColumnsWith().put(new Integer(i), new Integer(25)); } sheet.getRows().add(row); document.getSheets().add(sheet); FileOutputStream fos = new FileOutputStream("D:/teste2.xls"); SpreadsheetDocumentWriter writer = HSSFSpreadsheetDocumentWriter.getInstance(); writer.write(document, fos); fos.close(); } | private Collection<Class<? extends Plugin>> loadFromResource(ClassLoader classLoader, String resource) throws IOException { Collection<Class<? extends Plugin>> pluginClasses = new HashSet<Class<? extends Plugin>>(); Enumeration providerFiles = classLoader.getResources(resource); if (!providerFiles.hasMoreElements()) { logger.warning("Can't find the resource: " + resource); return pluginClasses; } do { URL url = (URL) providerFiles.nextElement(); InputStream stream = url.openStream(); BufferedReader reader; try { reader = new BufferedReader(new InputStreamReader(stream, "UTF-8")); } catch (IOException e) { continue; } String line; while ((line = reader.readLine()) != null) { int index = line.indexOf('#'); if (index != -1) { line = line.substring(0, index); } line = line.trim(); if (line.length() > 0) { Class pluginClass; try { pluginClass = classLoader.loadClass(line); } catch (ClassNotFoundException e) { logger.log(Level.WARNING, "Can't use the Pluginclass with the name " + line + ".", e); continue; } if (Plugin.class.isAssignableFrom(pluginClass)) { pluginClasses.add((Class<? extends Plugin>) pluginClass); } else { logger.warning("The Pluginclass with the name " + line + " isn't a subclass of Plugin."); } } } reader.close(); stream.close(); } while (providerFiles.hasMoreElements()); return pluginClasses; } | 12,475 |
0 | private void loginImageShack() throws Exception { loginsuccessful = false; HttpParams params = new BasicHttpParams(); params.setParameter("http.useragent", "Mozilla/5.0 (Windows; U; Windows NT 6.1; en-GB; rv:1.9.2) Gecko/20100115 Firefox/3.6"); DefaultHttpClient httpclient = new DefaultHttpClient(params); NULogger.getLogger().info("Trying to log in to imageshack.us"); HttpPost httppost = new HttpPost("http://imageshack.us/auth.php"); httppost.setHeader("Referer", "http://www.uploading.com/"); httppost.setHeader("Accept", "application/xml,application/xhtml+xml,text/html;q=0.9,text/plain;q=0.8,image/png,*/*;q=0.5"); httppost.setHeader("Cookie", newcookie + ";" + phpsessioncookie + ";" + imgshckcookie + ";" + uncookie + ";" + latestcookie + ";" + langcookie); List<NameValuePair> formparams = new ArrayList<NameValuePair>(); formparams.add(new BasicNameValuePair("username", getUsername())); formparams.add(new BasicNameValuePair("password", getPassword())); formparams.add(new BasicNameValuePair("stay_logged_in", "")); formparams.add(new BasicNameValuePair("format", "json")); UrlEncodedFormEntity entity = new UrlEncodedFormEntity(formparams, "UTF-8"); httppost.setEntity(entity); HttpResponse httpresponse = httpclient.execute(httppost); HttpEntity en = httpresponse.getEntity(); uploadresponse = EntityUtils.toString(en); NULogger.getLogger().log(Level.INFO, "Upload response : {0}", uploadresponse); NULogger.getLogger().info("Getting cookies........"); Iterator<Cookie> it = httpclient.getCookieStore().getCookies().iterator(); Cookie escookie = null; while (it.hasNext()) { escookie = it.next(); if (escookie.getName().equalsIgnoreCase("myid")) { myidcookie = escookie.getValue(); NULogger.getLogger().info(myidcookie); loginsuccessful = true; } if (escookie.getName().equalsIgnoreCase("myimages")) { myimagescookie = escookie.getValue(); NULogger.getLogger().info(myimagescookie); } if (escookie.getName().equalsIgnoreCase("isUSER")) { usercookie = escookie.getValue(); NULogger.getLogger().info(usercookie); } } if (loginsuccessful) { NULogger.getLogger().info("ImageShack Login Success"); loginsuccessful = true; username = getUsername(); password = getPassword(); } else { NULogger.getLogger().info("ImageShack Login failed"); loginsuccessful = false; username = ""; password = ""; JOptionPane.showMessageDialog(NeembuuUploader.getInstance(), "<html><b>" + HOSTNAME + "</b> " + TranslationProvider.get("neembuuuploader.accounts.loginerror") + "</html>", HOSTNAME, JOptionPane.WARNING_MESSAGE); AccountsManager.getInstance().setVisible(true); } } | public static void sort(float norm_abst[]) { float temp; for (int i = 0; i < 7; i++) { for (int j = 0; j < 7; j++) { if (norm_abst[j] > norm_abst[j + 1]) { temp = norm_abst[j]; norm_abst[j] = norm_abst[j + 1]; norm_abst[j + 1] = temp; } } } printFixed(norm_abst[0]); print(" "); printFixed(norm_abst[1]); print(" "); printFixed(norm_abst[2]); print(" "); printFixed(norm_abst[3]); print(" "); printFixed(norm_abst[4]); print(" "); printFixed(norm_abst[5]); print(" "); printFixed(norm_abst[6]); print(" "); printFixed(norm_abst[7]); print("\n"); } | 12,476 |
1 | private String readJsonString() { StringBuilder builder = new StringBuilder(); HttpClient client = new DefaultHttpClient(); HttpGet httpGet = new HttpGet(SERVER_URL); try { HttpResponse response = client.execute(httpGet); StatusLine statusLine = response.getStatusLine(); int statusCode = statusLine.getStatusCode(); if (statusCode == 200) { HttpEntity entity = response.getEntity(); InputStream content = entity.getContent(); BufferedReader reader = new BufferedReader(new InputStreamReader(content)); String line; while ((line = reader.readLine()) != null) { builder.append(line); } } else { Log.e(TAG, "Failed to download file"); } } catch (ClientProtocolException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } return builder.toString(); } | private static void loadEmoticons() { emoticons = new Hashtable(); URL url = ChatPanel.class.getResource("/resources/text/emoticon.properties"); BufferedReader br = null; try { br = new BufferedReader(new InputStreamReader(url.openStream())); String line = null; while ((line = br.readLine()) != null) { if (line.trim().length() == 0 || line.charAt(0) == '#') continue; int i0 = line.indexOf('='); if (i0 != -1) { String key = line.substring(0, i0).trim(); String value = line.substring(i0 + 1).trim(); value = StringUtil.replaceString(value, "\\n", "\n"); URL eUrl = ChatPanel.class.getResource("/resources/emoticon/" + value); if (eUrl != null) emoticons.put(key, new ImageIcon(eUrl)); } } } catch (Exception e) { e.printStackTrace(); } finally { if (br != null) { try { br.close(); } catch (Exception e) { } } } } | 12,477 |
1 | public void copyFilesIntoProject(HashMap<String, String> files) { Set<String> filenames = files.keySet(); for (String key : filenames) { String realPath = files.get(key); if (key.equals("fw4ex.xml")) { try { FileReader in = new FileReader(new File(realPath)); FileWriter out = new FileWriter(new File(project.getLocation() + "/" + bundle.getString("Stem") + STEM_FILE_EXETENSION)); int c; while ((c = in.read()) != -1) out.write(c); in.close(); out.close(); } catch (FileNotFoundException e) { Activator.getDefault().showMessage("File " + key + " not found... Error while moving files to the new project."); } catch (IOException ie) { Activator.getDefault().showMessage("Error while moving " + key + " to the new project."); } } else { try { FileReader in = new FileReader(new File(realPath)); FileWriter out = new FileWriter(new File(project.getLocation() + "/" + key)); int c; while ((c = in.read()) != -1) out.write(c); in.close(); out.close(); } catch (FileNotFoundException e) { Activator.getDefault().showMessage("File " + key + " not found... Error while moving files to the new project."); } catch (IOException ie) { Activator.getDefault().showMessage("Error while moving " + key + " to the new project."); } } } } | public void unzip(String zipFileName, String outputDirectory) throws Exception { ZipInputStream in = new ZipInputStream(new FileInputStream(zipFileName)); ZipEntry z; while ((z = in.getNextEntry()) != null) { System.out.println("unziping " + z.getName()); if (z.isDirectory()) { String name = z.getName(); name = name.substring(0, name.length() - 1); File f = new File(outputDirectory + File.separator + name); f.mkdir(); System.out.println("mkdir " + outputDirectory + File.separator + name); } else { File f = new File(outputDirectory + File.separator + z.getName()); f.createNewFile(); FileOutputStream out = new FileOutputStream(f); int b; while ((b = in.read()) != -1) out.write(b); out.close(); } } in.close(); } | 12,478 |
0 | public static Image getPluginImage(Object plugin, String name) { try { try { URL url = getPluginImageURL(plugin, name); if (m_URLImageMap.containsKey(url)) return m_URLImageMap.get(url); InputStream is = url.openStream(); Image image; try { image = getImage(is); m_URLImageMap.put(url, image); } finally { is.close(); } return image; } catch (Throwable e) { } } catch (Throwable e) { } return null; } | public TVRageShowInfo(String xmlShowName) { String[] tmp, tmp2; String line = ""; this.usrShowName = xmlShowName; try { URL url = new URL("http://www.tvrage.com/quickinfo.php?show=" + xmlShowName.replaceAll(" ", "%20")); BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream())); while ((line = in.readLine()) != null) { tmp = line.split("@"); if (tmp[0].equals("Show Name")) showName = tmp[1]; if (tmp[0].equals("Show URL")) showURL = tmp[1]; if (tmp[0].equals("Latest Episode")) { StringTokenizer st = new StringTokenizer(tmp[1], "^"); for (int i = 0; st.hasMoreTokens(); i++) { if (i == 0) { tmp2 = st.nextToken().split("x"); latestSeasonNum = tmp2[0]; latestEpisodeNum = tmp2[1]; if (latestSeasonNum.charAt(0) == '0') latestSeasonNum = latestSeasonNum.substring(1); } else if (i == 1) latestTitle = st.nextToken().replaceAll("&", "and"); else latestAirDate = st.nextToken(); } } if (tmp[0].equals("Next Episode")) { StringTokenizer st = new StringTokenizer(tmp[1], "^"); for (int i = 0; st.hasMoreTokens(); i++) { if (i == 0) { tmp2 = st.nextToken().split("x"); nextSeasonNum = tmp2[0]; nextEpisodeNum = tmp2[1]; if (nextSeasonNum.charAt(0) == '0') nextSeasonNum = nextSeasonNum.substring(1); } else if (i == 1) nextTitle = st.nextToken().replaceAll("&", "and"); else nextAirDate = st.nextToken(); } } if (tmp[0].equals("Status")) status = tmp[1]; if (tmp[0].equals("Airtime")) airTime = tmp[1]; } in.close(); url = new URL(showURL); in = new BufferedReader(new InputStreamReader(url.openStream())); while ((line = in.readLine()) != null) { if (line.indexOf("<b>Latest Episode: </b>") > -1) { tmp = line.split("'>"); if (tmp[2].indexOf(':') > -1) { tmp = tmp[2].split(":"); latestSeriesNum = tmp[0]; } } else if (line.indexOf("<b>Next Episode: </b>") > -1) { tmp = line.split("'>"); if (tmp[2].indexOf(':') > -1) { tmp = tmp[2].split(":"); nextSeriesNum = tmp[0]; } } } in.close(); } catch (MalformedURLException e) { } catch (IOException e) { } } | 12,479 |
1 | public static String downloadWebpage2(String address) throws MalformedURLException, IOException { URL url = new URL(address); HttpURLConnection conn = (HttpURLConnection) url.openConnection(); HttpURLConnection.setFollowRedirects(true); String encoding = conn.getContentEncoding(); InputStream is = null; if(encoding != null && encoding.equalsIgnoreCase("gzip")) { is = new GZIPInputStream(conn.getInputStream()); } else if (encoding != null && encoding.equalsIgnoreCase("deflate")) { is = new InflaterInputStream(conn.getInputStream()); } else { is = conn.getInputStream(); } BufferedReader br = new BufferedReader(new InputStreamReader(is)); String line; String page = ""; while((line = br.readLine()) != null) { page += line + "\n"; } br.close(); return page; } | @Override public String baiDuHotNews() { HttpClient client = new DefaultHttpClient(); HttpGet httpGet = new HttpGet("http://news.baidu.com/z/wise_topic_processor/wise_hotwords_list.php?bd_page_type=1&tn=wapnews_hotwords_list&type=1&index=1&pfr=3-11-bdindex-top-3--"); String hostNews = ""; try { HttpResponse response = client.execute(httpGet); HttpEntity httpEntity = response.getEntity(); BufferedReader buffer = new BufferedReader(new InputStreamReader(httpEntity.getContent())); String line = ""; boolean todayNewsExist = false, firstNewExist = false; int newsCount = -1; while ((line = buffer.readLine()) != null) { if (todayNewsExist || line.contains("<div class=\"news_title\">")) todayNewsExist = true; else continue; if (firstNewExist || line.contains("<div class=\"list-item\">")) { firstNewExist = true; newsCount++; } else continue; if (todayNewsExist && firstNewExist && (newsCount == 1)) { Pattern hrefPattern = Pattern.compile("<a.*>(.+?)</a>.*"); Matcher matcher = hrefPattern.matcher(line); if (matcher.find()) { hostNews = matcher.group(1); break; } else newsCount--; } } } catch (ClientProtocolException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } return hostNews; } | 12,480 |
1 | public static void zip(File srcDir, File destFile, FileFilter filter) throws IOException { ZipOutputStream out = null; try { out = new ZipOutputStream(new FileOutputStream(destFile)); Collection<File> files = FileUtils.listFiles(srcDir, TrueFileFilter.TRUE, TrueFileFilter.TRUE); for (File f : files) { if (filter == null || filter.accept(f)) { FileInputStream in = FileUtils.openInputStream(f); out.putNextEntry(new ZipEntry(Util.relativePath(srcDir, f).replace('\\', '/'))); IOUtils.copyLarge(in, out); out.closeEntry(); IOUtils.closeQuietly(in); } } IOUtils.closeQuietly(out); } catch (Throwable t) { throw new IOException("Failed to create zip file", t); } finally { if (out != null) { out.flush(); IOUtils.closeQuietly(out); } } } | public static void copyFileStreams(File fromFile, File toFile) throws IOException { if (!fromFile.exists()) { return; } FileInputStream fis = new FileInputStream(fromFile); FileOutputStream fos = new FileOutputStream(toFile); int read = 0; byte[] buf = new byte[1024]; while (-1 != read) { read = fis.read(buf); if (read >= 0) { fos.write(buf, 0, read); } } fos.close(); fis.close(); } | 12,481 |
1 | @SuppressWarnings("unchecked") protected void processTransformAction(HttpServletRequest request, HttpServletResponse response, String action) throws Exception { File transformationFile = null; String tr = request.getParameter(Definitions.REQUEST_PARAMNAME_XSLT); if (StringUtils.isNotBlank(tr)) { transformationFile = new File(xslBase, tr); if (!transformationFile.isFile()) { response.sendError(HttpServletResponse.SC_BAD_REQUEST, "Parameter \"" + Definitions.REQUEST_PARAMNAME_XSLT + "\" " + "with value \"" + tr + "\" refers to non existing file"); return; } } StreamResult result; ByteArrayOutputStream baos = null; if (isDevelopmentMode) { baos = new ByteArrayOutputStream(); if (StringUtils.equals(action, "get")) { result = new StreamResult(new Base64.OutputStream(baos, Base64.DECODE)); } else { result = new StreamResult(baos); } } else { if (StringUtils.equals(action, "get")) { result = new StreamResult(new Base64.OutputStream(response.getOutputStream(), Base64.DECODE)); } else { result = new StreamResult(response.getOutputStream()); } } HashMap<String, Object> params = new HashMap<String, Object>(); params.putAll(request.getParameterMap()); params.put("{" + Definitions.CONFIGURATION_NAMESPACE + "}configuration", configuration); params.put("{" + Definitions.REQUEST_NAMESPACE + "}request", request); params.put("{" + Definitions.RESPONSE_NAMESPACE + "}response", response); params.put("{" + Definitions.SESSION_NAMESPACE + "}session", request.getSession()); params.put("{" + Definitions.INFOFUZE_NAMESPACE + "}development-mode", new Boolean(Config.getInstance().isDevelopmentMode())); Transformer transformer = new Transformer(); transformer.setTransformationFile(transformationFile); transformer.setParams(params); transformer.setTransformMode(TransformMode.NORMAL); transformer.setConfiguration(configuration); transformer.setErrorListener(new TransformationErrorListener(response)); transformer.setLogInfo(false); String method = transformer.getOutputProperties().getProperty(OutputKeys.METHOD, "xml"); String contentType; if (method.endsWith("html")) { contentType = Definitions.MIMETYPE_HTML; } else if (method.equals("xml")) { contentType = Definitions.MIMETYPE_XML; } else { contentType = Definitions.MIMETYPE_TEXTPLAIN; } String encoding = transformer.getOutputProperties().getProperty(OutputKeys.ENCODING, "UTF-8"); response.setContentType(contentType + ";charset=" + encoding); DataSourceIf dataSource = new NullSource(); transformer.transform((Source) dataSource, result); if (isDevelopmentMode) { IOUtils.copy(new ByteArrayInputStream(baos.toByteArray()), response.getOutputStream()); } } | private static URL downloadFile(URL url, File destFile) throws Exception { try { URLConnection urlConnection = url.openConnection(); File tmpFile = null; try { tmpFile = File.createTempFile("remoteLib_", null); InputStream in = null; FileOutputStream out = null; try { in = urlConnection.getInputStream(); out = new FileOutputStream(tmpFile); IOUtils.copy(in, out); } finally { if (out != null) { out.close(); } if (in != null) { in.close(); } } FileUtils.copyFile(tmpFile, destFile); } finally { if (tmpFile != null) { tmpFile.delete(); } } URL localURL = destFile.toURI().toURL(); return localURL; } catch (Exception ex) { throw new RuntimeException("Could not download URL: " + url, ex); } } | 12,482 |
1 | public static String encriptar(String string) throws Exception { MessageDigest md = null; try { md = MessageDigest.getInstance("MD5"); } catch (NoSuchAlgorithmException e) { e.printStackTrace(); throw new Exception("Algoritmo de Criptografia não encontrado."); } md.update(string.getBytes()); BigInteger hash = new BigInteger(1, md.digest()); String retorno = hash.toString(16); return retorno; } | private byte[] digestPassword(byte[] salt, String password) throws AuthenticationException { try { MessageDigest md = MessageDigest.getInstance("MD5"); md.update(salt); md.update(password.getBytes("UTF8")); return md.digest(); } catch (Exception e) { throw new AuthenticationException(MESSAGE_CONFIGURATION_ERROR_KEY, e); } } | 12,483 |
0 | protected void migrateOnDemand() { try { if (fso.fileExists(prefix + ".fat") && !fso.fileExists(prefix + EXTENSIONS[UBM_FILE])) { RandomAccessFile ubm, meta, ctr, rbm; InputStream inputStream; OutputStream outputStream; fso.renameFile(prefix + ".fat", prefix + EXTENSIONS[UBM_FILE]); ubm = fso.openFile(prefix + EXTENSIONS[UBM_FILE], "rw"); meta = fso.openFile(prefix + EXTENSIONS[MTD_FILE], "rw"); ctr = fso.openFile(prefix + EXTENSIONS[CTR_FILE], "rw"); ubm.seek(ubm.length() - 16); meta.writeInt(blockSize = ubm.readInt()); meta.writeInt(size = ubm.readInt()); ctr.setLength(ubm.readLong() + blockSize); ctr.close(); meta.close(); ubm.setLength(ubm.length() - 16); ubm.seek(0); rbm = fso.openFile(prefix + EXTENSIONS[UBM_FILE], "rw"); inputStream = new BufferedInputStream(new RandomAccessFileInputStream(ubm)); outputStream = new BufferedOutputStream(new RandomAccessFileOutputStream(rbm)); for (int b; (b = inputStream.read()) != -1; ) outputStream.write(b); outputStream.close(); inputStream.close(); rbm.close(); ubm.close(); } } catch (IOException ie) { throw new WrappingRuntimeException(ie); } } | public void testPreparedStatement0009() throws Exception { Connection cx = getConnection(); dropTable("#t0009"); Statement stmt = cx.createStatement(); stmt.executeUpdate("create table #t0009 " + " (i integer not null, " + " s char(10) not null) "); cx.setAutoCommit(false); PreparedStatement pStmt = cx.prepareStatement("insert into #t0009 values (?, ?)"); int rowsToAdd = 8; final String theString = "abcdefghijklmnopqrstuvwxyz"; int count = 0; for (int i = 1; i <= rowsToAdd; i++) { pStmt.setInt(1, i); pStmt.setString(2, theString.substring(0, i)); count += pStmt.executeUpdate(); } assertTrue(count == rowsToAdd); cx.rollback(); stmt = cx.createStatement(); ResultSet rs = stmt.executeQuery("select s, i from #t0009"); assertNotNull(rs); count = 0; while (rs.next()) { count++; assertTrue(rs.getString(1).trim().length() == rs.getInt(2)); } assertTrue(count == 0); cx.commit(); rowsToAdd = 6; count = 0; for (int i = 1; i <= rowsToAdd; i++) { pStmt.setInt(1, i); pStmt.setString(2, theString.substring(0, i)); count += pStmt.executeUpdate(); } assertTrue(count == rowsToAdd); cx.commit(); rs = stmt.executeQuery("select s, i from #t0009"); count = 0; while (rs.next()) { count++; assertTrue(rs.getString(1).trim().length() == rs.getInt(2)); } assertTrue(count == rowsToAdd); cx.commit(); cx.setAutoCommit(true); } | 12,484 |
1 | public BufferedWriter createOutputStream(String inFile, String outFile) throws IOException { int k_blockSize = 1024; int byteCount; char[] buf = new char[k_blockSize]; File ofp = new File(outFile); ZipOutputStream zos = new ZipOutputStream(new FileOutputStream(ofp)); zos.setMethod(ZipOutputStream.DEFLATED); OutputStreamWriter osw = new OutputStreamWriter(zos, "ISO-8859-1"); BufferedWriter bw = new BufferedWriter(osw); ZipEntry zot = null; File ifp = new File(inFile); ZipInputStream zis = new ZipInputStream(new FileInputStream(ifp)); InputStreamReader isr = new InputStreamReader(zis, "ISO-8859-1"); BufferedReader br = new BufferedReader(isr); ZipEntry zit = null; while ((zit = zis.getNextEntry()) != null) { if (zit.getName().equals("content.xml")) { continue; } zot = new ZipEntry(zit.getName()); zos.putNextEntry(zot); while ((byteCount = br.read(buf, 0, k_blockSize)) >= 0) bw.write(buf, 0, byteCount); bw.flush(); zos.closeEntry(); } zos.putNextEntry(new ZipEntry("content.xml")); bw.flush(); osw = new OutputStreamWriter(zos, "UTF8"); bw = new BufferedWriter(osw); return bw; } | public Writer createWriter(File outfile, String encoding) throws UnsupportedEncodingException, IOException { int k_blockSize = 1024; int byteCount; char[] buf = new char[k_blockSize]; ZipOutputStream zos = new ZipOutputStream(new FileOutputStream(outfile)); zos.setMethod(ZipOutputStream.DEFLATED); OutputStreamWriter osw = new OutputStreamWriter(zos, "ISO-8859-1"); BufferedWriter bw = new BufferedWriter(osw); ZipEntry zot; ZipInputStream zis = new ZipInputStream(new FileInputStream(infile)); InputStreamReader isr = new InputStreamReader(zis, "ISO-8859-1"); BufferedReader br = new BufferedReader(isr); ZipEntry zit; while ((zit = zis.getNextEntry()) != null) { if (zit.getName().equals("content.xml")) { continue; } zot = new ZipEntry(zit.getName()); zos.putNextEntry(zot); while ((byteCount = br.read(buf, 0, k_blockSize)) >= 0) bw.write(buf, 0, byteCount); bw.flush(); zos.closeEntry(); } zos.putNextEntry(new ZipEntry("content.xml")); bw.flush(); return new OutputStreamWriter(zos, "UTF-8"); } | 12,485 |
0 | public File getFile(String file) { DirProperties dp; List files = new ArrayList(); for (int i = 0; i < locs.size(); i++) { dp = (DirProperties) locs.get(i); if (dp.isReadable()) { File g = new File(dp.getLocation() + slash() + file); if (g.exists()) files.add(g); } } if (files.size() == 0) { throw new UnsupportedOperationException("at least one DirProperty should get 'read=true'"); } else if (files.size() == 1) { return (File) files.get(0); } else { File fromFile = (File) files.get(files.size() - 2); File toFile = (File) files.get(files.size() - 1); byte reading[] = new byte[2024]; try { FileInputStream stream = new FileInputStream(fromFile); FileOutputStream outStr = new FileOutputStream(toFile); while (stream.read(reading) != -1) { outStr.write(reading); } } catch (FileNotFoundException ex) { getLogger().severe("FileNotFound: while copying from " + fromFile + " to " + toFile); } catch (IOException ex) { getLogger().severe("IOException: while copying from " + fromFile + " to " + toFile); } return toFile; } } | public static String getFurigana(String sentence) throws Exception { Log.d("--VOA--", "getFurigana START"); sbFurigana = new StringBuffer(); String urlStr = getYahooApiURL(); urlStr = addSentence(urlStr, sentence); URL url = new URL(urlStr); URLConnection uc = url.openConnection(); DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance(); dbf.setNamespaceAware(true); DocumentBuilder db = dbf.newDocumentBuilder(); Log.d("--VOA--", uc.getURL().toString()); InputStream is = uc.getInputStream(); doc = db.parse(is); walkThrough(); Log.d("--VOA--", "getFurigana END"); return sbFurigana.toString(); } | 12,486 |
0 | public static void copy(File source, File destination) throws IOException { InputStream in = new FileInputStream(source); OutputStream out = new FileOutputStream(destination); byte[] buffer = new byte[1024]; int len; while ((len = in.read(buffer)) > 0) out.write(buffer, 0, len); in.close(); out.close(); } | public void download(String target) { try { if (url == null) return; conn = (HttpURLConnection) url.openConnection(); conn.setRequestProperty("User-Agent", "Internet Explorer"); conn.setReadTimeout(10000); conn.connect(); httpReader = new BufferedReader(new InputStreamReader(conn.getInputStream())); java.io.BufferedWriter out = new BufferedWriter(new FileWriter(target, false)); String str = httpReader.readLine(); while (str != null) { out.write(str); str = httpReader.readLine(); } out.close(); System.out.println("file download successfully: " + url.getHost() + url.getPath()); System.out.println("saved to: " + target); } catch (Exception e) { System.out.println("file download failed: " + url.getHost() + url.getPath()); e.printStackTrace(); } } | 12,487 |
0 | private Document saveFile(Document document, File file) throws Exception { List<Preference> preferences = prefService.findAll(); if (preferences != null && !preferences.isEmpty()) { preference = preferences.get(0); } SimpleDateFormat sdf = new SimpleDateFormat(Constants.DATEFORMAT_YYYYMMDD); String repo = preference.getRepository(); Calendar calendar = Calendar.getInstance(); StringBuffer sbRepo = new StringBuffer(repo); sbRepo.append(File.separator); StringBuffer sbFolder = new StringBuffer(sdf.format(calendar.getTime())); sbFolder.append(File.separator).append(calendar.get(Calendar.HOUR_OF_DAY)); File folder = new File(sbRepo.append(sbFolder).toString()); if (!folder.exists()) { folder.mkdirs(); } FileChannel fcSource = null, fcDest = null; try { StringBuffer sbFile = new StringBuffer(folder.getAbsolutePath()); StringBuffer fname = new StringBuffer(document.getId().toString()); fname.append(".").append(document.getExt()); sbFile.append(File.separator).append(fname); fcSource = new FileInputStream(file).getChannel(); fcDest = new FileOutputStream(sbFile.toString()).getChannel(); fcDest.transferFrom(fcSource, 0, fcSource.size()); document.setLocation(sbFolder.toString()); documentService.save(document); } catch (FileNotFoundException notFoundEx) { log.error("saveFile file not found: " + document.getName(), notFoundEx); } catch (IOException ioEx) { log.error("saveFile IOException: " + document.getName(), ioEx); } finally { try { if (fcSource != null) { fcSource.close(); } if (fcDest != null) { fcDest.close(); } } catch (Exception e) { log.error(e.getMessage(), e); } } return document; } | private static String doHash(String frase, String algorithm) { try { String ret; MessageDigest md = MessageDigest.getInstance(algorithm); md.update(frase.getBytes()); BigInteger bigInt = new BigInteger(1, md.digest()); ret = bigInt.toString(16); return ret; } catch (NoSuchAlgorithmException e) { return null; } } | 12,488 |
1 | public static void main(String[] args) { String url = "jdbc:mysql://localhost/test"; String user = "root"; String password = "password"; String imageLocation = "C:\\Documents and Settings\\EddyM\\Desktop\\Nick\\01100002.tif"; String imageLocation2 = "C:\\Documents and Settings\\EddyM\\Desktop\\Nick\\011000022.tif"; try { Class.forName("com.mysql.jdbc.Driver"); } catch (ClassNotFoundException ex) { ex.printStackTrace(); } try { File f = new File(imageLocation); InputStream fis = new FileInputStream(f); Connection c = DriverManager.getConnection(url, user, password); ResultSet rs = c.createStatement().executeQuery("SELECT Image FROM ImageTable WHERE ImageID=12345678"); new File(imageLocation2).createNewFile(); rs.first(); System.out.println("GotFirst"); InputStream is = rs.getAsciiStream("Image"); System.out.println("gotStream"); FileOutputStream fos = new FileOutputStream(new File(imageLocation2)); int readInt; int i = 0; while (true) { readInt = is.read(); if (readInt == -1) { System.out.println("ReadInt == -1"); break; } i++; if (i % 1000000 == 0) System.out.println(i + " / " + is.available()); fos.write(readInt); } c.close(); } catch (SQLException ex) { ex.printStackTrace(); } catch (IOException ex) { ex.printStackTrace(); } } | public void launchJob(final String workingDir, final AppConfigType appConfig) throws FaultType { logger.info("called for job: " + jobID); MessageContext mc = MessageContext.getCurrentContext(); HttpServletRequest req = (HttpServletRequest) mc.getProperty(HTTPConstants.MC_HTTP_SERVLETREQUEST); String clientDN = (String) req.getAttribute(GSIConstants.GSI_USER_DN); if (clientDN != null) { logger.info("Client's DN: " + clientDN); } else { clientDN = "Unknown client"; } String remoteIP = req.getRemoteAddr(); SOAPService service = mc.getService(); String serviceName = service.getName(); if (serviceName == null) { serviceName = "Unknown service"; } if (appConfig.isParallel()) { if (AppServiceImpl.drmaaInUse) { if (AppServiceImpl.drmaaPE == null) { logger.error("drmaa.pe property must be specified in opal.properties " + "for parallel execution using DRMAA"); throw new FaultType("drmaa.pe property must be specified in opal.properties " + "for parallel execution using DRMAA"); } if (AppServiceImpl.mpiRun == null) { logger.error("mpi.run property must be specified in opal.properties " + "for parallel execution using DRMAA"); throw new FaultType("mpi.run property must be specified in " + "opal.properties for parallel execution " + "using DRMAA"); } } else if (!AppServiceImpl.globusInUse) { if (AppServiceImpl.mpiRun == null) { logger.error("mpi.run property must be specified in opal.properties " + "for parallel execution without using Globus"); throw new FaultType("mpi.run property must be specified in " + "opal.properties for parallel execution " + "without using Globus"); } } if (jobIn.getNumProcs() == null) { logger.error("Number of processes unspecified for parallel job"); throw new FaultType("Number of processes unspecified for parallel job"); } else if (jobIn.getNumProcs().intValue() > AppServiceImpl.numProcs) { logger.error("Processors required - " + jobIn.getNumProcs() + ", available - " + AppServiceImpl.numProcs); throw new FaultType("Processors required - " + jobIn.getNumProcs() + ", available - " + AppServiceImpl.numProcs); } } try { status.setCode(GramJob.STATUS_PENDING); status.setMessage("Launching executable"); status.setBaseURL(new URI(AppServiceImpl.tomcatURL + jobID)); } catch (MalformedURIException mue) { logger.error("Cannot convert base_url string to URI - " + mue.getMessage()); throw new FaultType("Cannot convert base_url string to URI - " + mue.getMessage()); } if (!AppServiceImpl.dbInUse) { AppServiceImpl.statusTable.put(jobID, status); } else { Connection conn = null; try { conn = DriverManager.getConnection(AppServiceImpl.dbUrl, AppServiceImpl.dbUser, AppServiceImpl.dbPasswd); } catch (SQLException e) { logger.error("Cannot connect to database - " + e.getMessage()); throw new FaultType("Cannot connect to database - " + e.getMessage()); } String time = new SimpleDateFormat("MMM d, yyyy h:mm:ss a", Locale.US).format(new Date()); String sqlStmt = "insert into job_status(job_id, code, message, base_url, " + "client_dn, client_ip, service_name, start_time, last_update) " + "values ('" + jobID + "', " + status.getCode() + ", " + "'" + status.getMessage() + "', " + "'" + status.getBaseURL() + "', " + "'" + clientDN + "', " + "'" + remoteIP + "', " + "'" + serviceName + "', " + "'" + time + "', " + "'" + time + "');"; try { Statement stmt = conn.createStatement(); stmt.executeUpdate(sqlStmt); conn.close(); } catch (SQLException e) { logger.error("Cannot insert job status into database - " + e.getMessage()); throw new FaultType("Cannot insert job status into database - " + e.getMessage()); } } String args = appConfig.getDefaultArgs(); if (args == null) { args = jobIn.getArgList(); } else { String userArgs = jobIn.getArgList(); if (userArgs != null) args += " " + userArgs; } if (args != null) { args = args.trim(); } logger.debug("Argument list: " + args); if (AppServiceImpl.drmaaInUse) { String cmd = null; String[] argsArray = null; if (appConfig.isParallel()) { cmd = "/bin/sh"; String newArgs = AppServiceImpl.mpiRun + " -machinefile $TMPDIR/machines" + " -np " + jobIn.getNumProcs() + " " + appConfig.getBinaryLocation(); if (args != null) { args = newArgs + " " + args; } else { args = newArgs; } logger.debug("CMD: " + args); argsArray = new String[] { "-c", args }; } else { cmd = appConfig.getBinaryLocation(); if (args == null) args = ""; logger.debug("CMD: " + cmd + " " + args); argsArray = args.split(" "); } try { logger.debug("Working directory: " + workingDir); JobTemplate jt = session.createJobTemplate(); if (appConfig.isParallel()) jt.setNativeSpecification("-pe " + AppServiceImpl.drmaaPE + " " + jobIn.getNumProcs()); jt.setRemoteCommand(cmd); jt.setArgs(argsArray); jt.setJobName(jobID); jt.setWorkingDirectory(workingDir); jt.setErrorPath(":" + workingDir + "/stderr.txt"); jt.setOutputPath(":" + workingDir + "/stdout.txt"); drmaaJobID = session.runJob(jt); logger.info("DRMAA job has been submitted with id " + drmaaJobID); session.deleteJobTemplate(jt); } catch (Exception ex) { logger.error(ex); status.setCode(GramJob.STATUS_FAILED); status.setMessage("Error while running executable via DRMAA - " + ex.getMessage()); if (AppServiceImpl.dbInUse) { try { updateStatusInDatabase(jobID, status); } catch (SQLException e) { logger.error(e); throw new FaultType("Cannot update status into database - " + e.getMessage()); } } return; } status.setCode(GramJob.STATUS_ACTIVE); status.setMessage("Execution in progress"); if (AppServiceImpl.dbInUse) { try { updateStatusInDatabase(jobID, status); } catch (SQLException e) { logger.error(e); throw new FaultType("Cannot update status into database - " + e.getMessage()); } } } else if (AppServiceImpl.globusInUse) { String rsl = null; if (appConfig.isParallel()) { rsl = "&(directory=" + workingDir + ")" + "(executable=" + appConfig.getBinaryLocation() + ")" + "(count=" + jobIn.getNumProcs() + ")" + "(jobtype=mpi)" + "(stdout=stdout.txt)" + "(stderr=stderr.txt)"; } else { rsl = "&(directory=" + workingDir + ")" + "(executable=" + appConfig.getBinaryLocation() + ")" + "(stdout=stdout.txt)" + "(stderr=stderr.txt)"; } if (args != null) { args = "\"" + args + "\""; args = args.replaceAll("[\\s]+", "\" \""); rsl += "(arguments=" + args + ")"; } logger.debug("RSL: " + rsl); try { job = new GramJob(rsl); GlobusCredential globusCred = new GlobusCredential(AppServiceImpl.serviceCertPath, AppServiceImpl.serviceKeyPath); GSSCredential gssCred = new GlobusGSSCredentialImpl(globusCred, GSSCredential.INITIATE_AND_ACCEPT); job.setCredentials(gssCred); job.addListener(this); job.request(AppServiceImpl.gatekeeperContact); } catch (Exception ge) { logger.error(ge); status.setCode(GramJob.STATUS_FAILED); status.setMessage("Error while running executable via Globus - " + ge.getMessage()); if (AppServiceImpl.dbInUse) { try { updateStatusInDatabase(jobID, status); } catch (SQLException e) { logger.error(e); throw new FaultType("Cannot update status into database - " + e.getMessage()); } } return; } } else { String cmd = null; if (appConfig.isParallel()) { cmd = new String(AppServiceImpl.mpiRun + " " + "-np " + jobIn.getNumProcs() + " " + appConfig.getBinaryLocation()); } else { cmd = new String(appConfig.getBinaryLocation()); } if (args != null) { cmd += " " + args; } logger.debug("CMD: " + cmd); try { logger.debug("Working directory: " + workingDir); proc = Runtime.getRuntime().exec(cmd, null, new File(workingDir)); stdoutThread = writeStdOut(proc, workingDir); stderrThread = writeStdErr(proc, workingDir); } catch (IOException ioe) { logger.error(ioe); status.setCode(GramJob.STATUS_FAILED); status.setMessage("Error while running executable via fork - " + ioe.getMessage()); if (AppServiceImpl.dbInUse) { try { updateStatusInDatabase(jobID, status); } catch (SQLException e) { logger.error(e); throw new FaultType("Cannot update status into database - " + e.getMessage()); } } return; } status.setCode(GramJob.STATUS_ACTIVE); status.setMessage("Execution in progress"); if (AppServiceImpl.dbInUse) { try { updateStatusInDatabase(jobID, status); } catch (SQLException e) { logger.error(e); throw new FaultType("Cannot update status into database - " + e.getMessage()); } } } new Thread() { public void run() { try { waitForCompletion(); } catch (FaultType f) { logger.error(f); synchronized (status) { status.notifyAll(); } return; } if (AppServiceImpl.drmaaInUse || !AppServiceImpl.globusInUse) { done = true; status.setCode(GramJob.STATUS_STAGE_OUT); status.setMessage("Writing output metadata"); if (AppServiceImpl.dbInUse) { try { updateStatusInDatabase(jobID, status); } catch (SQLException e) { status.setCode(GramJob.STATUS_FAILED); status.setMessage("Cannot update status database after finish - " + e.getMessage()); logger.error(e); synchronized (status) { status.notifyAll(); } return; } } } try { if (!AppServiceImpl.drmaaInUse && !AppServiceImpl.globusInUse) { try { logger.debug("Waiting for all outputs to be written out"); stdoutThread.join(); stderrThread.join(); logger.debug("All outputs successfully written out"); } catch (InterruptedException ignore) { } } File stdOutFile = new File(workingDir + File.separator + "stdout.txt"); if (!stdOutFile.exists()) { throw new IOException("Standard output missing for execution"); } File stdErrFile = new File(workingDir + File.separator + "stderr.txt"); if (!stdErrFile.exists()) { throw new IOException("Standard error missing for execution"); } if (AppServiceImpl.archiveData) { logger.debug("Archiving output files"); File f = new File(workingDir); File[] outputFiles = f.listFiles(); ZipOutputStream out = new ZipOutputStream(new FileOutputStream(workingDir + File.separator + jobID + ".zip")); byte[] buf = new byte[1024]; try { for (int i = 0; i < outputFiles.length; i++) { FileInputStream in = new FileInputStream(outputFiles[i]); out.putNextEntry(new ZipEntry(outputFiles[i].getName())); int len; while ((len = in.read(buf)) > 0) { out.write(buf, 0, len); } out.closeEntry(); in.close(); } out.close(); } catch (IOException e) { logger.error(e); logger.error("Error not fatal - moving on"); } } File f = new File(workingDir); File[] outputFiles = f.listFiles(); OutputFileType[] outputFileObj = new OutputFileType[outputFiles.length - 2]; int j = 0; for (int i = 0; i < outputFiles.length; i++) { if (outputFiles[i].getName().equals("stdout.txt")) { outputs.setStdOut(new URI(AppServiceImpl.tomcatURL + jobID + "/stdout.txt")); } else if (outputFiles[i].getName().equals("stderr.txt")) { outputs.setStdErr(new URI(AppServiceImpl.tomcatURL + jobID + "/stderr.txt")); } else { OutputFileType next = new OutputFileType(); next.setName(outputFiles[i].getName()); next.setUrl(new URI(AppServiceImpl.tomcatURL + jobID + "/" + outputFiles[i].getName())); outputFileObj[j++] = next; } } outputs.setOutputFile(outputFileObj); } catch (IOException e) { status.setCode(GramJob.STATUS_FAILED); status.setMessage("Cannot retrieve outputs after finish - " + e.getMessage()); logger.error(e); if (AppServiceImpl.dbInUse) { try { updateStatusInDatabase(jobID, status); } catch (SQLException se) { logger.error(se); } } synchronized (status) { status.notifyAll(); } return; } if (!AppServiceImpl.dbInUse) { AppServiceImpl.outputTable.put(jobID, outputs); } else { Connection conn = null; try { conn = DriverManager.getConnection(AppServiceImpl.dbUrl, AppServiceImpl.dbUser, AppServiceImpl.dbPasswd); } catch (SQLException e) { status.setCode(GramJob.STATUS_FAILED); status.setMessage("Cannot connect to database after finish - " + e.getMessage()); logger.error(e); synchronized (status) { status.notifyAll(); } return; } String sqlStmt = "insert into job_output(job_id, std_out, std_err) " + "values ('" + jobID + "', " + "'" + outputs.getStdOut().toString() + "', " + "'" + outputs.getStdErr().toString() + "');"; Statement stmt = null; try { stmt = conn.createStatement(); stmt.executeUpdate(sqlStmt); } catch (SQLException e) { status.setCode(GramJob.STATUS_FAILED); status.setMessage("Cannot update job output database after finish - " + e.getMessage()); logger.error(e); try { updateStatusInDatabase(jobID, status); } catch (SQLException se) { logger.error(se); } synchronized (status) { status.notifyAll(); } return; } OutputFileType[] outputFile = outputs.getOutputFile(); for (int i = 0; i < outputFile.length; i++) { sqlStmt = "insert into output_file(job_id, name, url) " + "values ('" + jobID + "', " + "'" + outputFile[i].getName() + "', " + "'" + outputFile[i].getUrl().toString() + "');"; try { stmt = conn.createStatement(); stmt.executeUpdate(sqlStmt); } catch (SQLException e) { status.setCode(GramJob.STATUS_FAILED); status.setMessage("Cannot update output_file DB after finish - " + e.getMessage()); logger.error(e); try { updateStatusInDatabase(jobID, status); } catch (SQLException se) { logger.error(se); } synchronized (status) { status.notifyAll(); } return; } } } if (terminatedOK()) { status.setCode(GramJob.STATUS_DONE); status.setMessage("Execution complete - " + "check outputs to verify successful execution"); } else { status.setCode(GramJob.STATUS_FAILED); status.setMessage("Execution failed"); } if (AppServiceImpl.dbInUse) { try { updateStatusInDatabase(jobID, status); } catch (SQLException e) { status.setCode(GramJob.STATUS_FAILED); status.setMessage("Cannot update status database after finish - " + e.getMessage()); logger.error(e); synchronized (status) { status.notifyAll(); } return; } } AppServiceImpl.jobTable.remove(jobID); synchronized (status) { status.notifyAll(); } logger.info("Execution complete for job: " + jobID); } }.start(); } | 12,489 |
0 | public ServiceAdapterIfc deploy(String session, String name, byte jarBytes[], String jarName, String serviceClass, String serviceInterface) throws RemoteException, MalformedURLException, StartServiceException, SessionException { try { File jarFile = new File(jarName); jarName = jarFile.getName(); String jarName2 = jarName; jarFile = new File(jarName2); int n = 0; while (jarFile.exists()) { jarName2 = jarName + n++; jarFile = new File(jarName2); } FileOutputStream fos = new FileOutputStream(jarName2); IOUtils.copy(new ByteArrayInputStream(jarBytes), fos); SCClassLoader cl = new SCClassLoader(new URL[] { new URL("file://" + jarFile.getAbsolutePath()) }, getMasterNode().getSCClassLoaderCounter()); return startService(session, name, serviceClass, serviceInterface, cl); } catch (SessionException e) { throw e; } catch (Exception e) { throw new StartServiceException("Could not deploy service: " + e.getMessage(), e); } } | public static XMLShowInfo NzbSearch(TVRageShowInfo tvrage, XMLShowInfo xmldata, int latestOrNext) { String newzbin_query = "", csvData = "", hellaQueueDir = "", newzbinUsr = "", newzbinPass = ""; String[] tmp; DateFormat tvRageDateFormat = new SimpleDateFormat("MMM/dd/yyyy"); DateFormat tvRageDateFormatFix = new SimpleDateFormat("yyyy-MM-dd"); newzbin_query = "?q=" + xmldata.showName + "+"; if (latestOrNext == 0) { if (xmldata.searchBy.equals("ShowName Season x Episode")) newzbin_query += tvrage.latestSeasonNum + "x" + tvrage.latestEpisodeNum; else if (xmldata.searchBy.equals("Showname SeriesNum")) newzbin_query += tvrage.latestSeriesNum; else if (xmldata.searchBy.equals("Showname YYYY-MM-DD")) { try { Date airTime = tvRageDateFormat.parse(tvrage.latestAirDate); newzbin_query += tvRageDateFormatFix.format(airTime); } catch (ParseException e) { e.printStackTrace(); } } else if (xmldata.searchBy.equals("Showname EpisodeTitle")) newzbin_query += tvrage.latestTitle; } else { if (xmldata.searchBy.equals("ShowName Season x Episode")) newzbin_query += tvrage.nextSeasonNum + "x" + tvrage.nextEpisodeNum; else if (xmldata.searchBy.equals("Showname SeriesNum")) newzbin_query += tvrage.nextSeriesNum; else if (xmldata.searchBy.equals("Showname YYYY-MM-DD")) { try { Date airTime = tvRageDateFormat.parse(tvrage.nextAirDate); newzbin_query += tvRageDateFormatFix.format(airTime); } catch (ParseException e) { e.printStackTrace(); } } else if (xmldata.searchBy.equals("Showname EpisodeTitle")) newzbin_query += tvrage.nextTitle; } newzbin_query += "&searchaction=Search"; newzbin_query += "&fpn=p"; newzbin_query += "&category=8category=11"; newzbin_query += "&area=-1"; newzbin_query += "&u_nfo_posts_only=0"; newzbin_query += "&u_url_posts_only=0"; newzbin_query += "&u_comment_posts_only=0"; newzbin_query += "&u_v3_retention=1209600"; newzbin_query += "&ps_rb_language=" + xmldata.language; newzbin_query += "&sort=ps_edit_date"; newzbin_query += "&order=desc"; newzbin_query += "&areadone=-1"; newzbin_query += "&feed=csv"; newzbin_query += "&ps_rb_video_format=" + xmldata.format; newzbin_query = newzbin_query.replaceAll(" ", "%20"); System.out.println("http://v3.newzbin.com/search/" + newzbin_query); try { URL url = new URL("http://v3.newzbin.com/search/" + newzbin_query); BufferedReader in = new BufferedReader(new InputStreamReader(url.openStream())); csvData = in.readLine(); if (csvData != null) { JavaNZB.searchCount++; if (searchCount == 6) { searchCount = 0; System.out.println("Sleeping for 60 seconds"); try { Thread.sleep(60000); } catch (InterruptedException e) { e.printStackTrace(); } } tmp = csvData.split(","); tmp[2] = tmp[2].substring(1, tmp[2].length() - 1); tmp[3] = tmp[3].substring(1, tmp[3].length() - 1); Pattern p = Pattern.compile("[\\\\</:>?\\[|\\]\"]"); Matcher matcher = p.matcher(tmp[3]); tmp[3] = matcher.replaceAll(" "); tmp[3] = tmp[3].replaceAll("&", "and"); URLConnection urlConn; DataOutputStream printout; url = new URL("http://v3.newzbin.com/api/dnzb/"); urlConn = url.openConnection(); urlConn.setDoInput(true); urlConn.setDoOutput(true); urlConn.setUseCaches(false); urlConn.setRequestProperty("Content-Type", "application/x-www-form-urlencoded"); printout = new DataOutputStream(urlConn.getOutputStream()); String content = "username=" + JavaNZB.newzbinUsr + "&password=" + JavaNZB.newzbinPass + "&reportid=" + tmp[2]; printout.writeBytes(content); printout.flush(); printout.close(); BufferedReader nzbInput = new BufferedReader(new InputStreamReader(urlConn.getInputStream())); File f = new File(JavaNZB.hellaQueueDir, tmp[3] + ".nzb"); BufferedWriter out = new BufferedWriter(new FileWriter(f)); String str; System.out.println("--Downloading " + tmp[3] + ".nzb" + " to queue directory--"); while (null != ((str = nzbInput.readLine()))) out.write(str); nzbInput.close(); out.close(); if (latestOrNext == 0) { xmldata.episode = tvrage.latestEpisodeNum; xmldata.season = tvrage.latestSeasonNum; } else { xmldata.episode = tvrage.nextEpisodeNum; xmldata.season = tvrage.nextSeasonNum; } } else System.out.println("No new episode posted"); System.out.println(); } catch (MalformedURLException e) { } catch (IOException e) { System.out.println("IO Exception from NzbSearch"); } return xmldata; } | 12,490 |
1 | public void sendFile(File file, String filename, String contentType) throws SearchLibException { response.setContentType(contentType); response.addHeader("Content-Disposition", "attachment; filename=" + filename); FileInputStream inputStream = null; try { inputStream = new FileInputStream(file); ServletOutputStream outputStream = getOutputStream(); IOUtils.copy(inputStream, outputStream); outputStream.close(); } catch (FileNotFoundException e) { throw new SearchLibException(e); } catch (IOException e) { throw new SearchLibException(e); } finally { if (inputStream != null) IOUtils.closeQuietly(inputStream); } } | private void copyIntoFile(String resource, File output) throws IOException { FileOutputStream out = null; InputStream in = null; try { out = FileUtils.openOutputStream(output); in = GroovyInstanceTest.class.getResourceAsStream(resource); IOUtils.copy(in, out); } finally { IOUtils.closeQuietly(out); IOUtils.closeQuietly(in); } } | 12,491 |
1 | public void copy(File source, File dest) throws IOException { System.out.println("copy " + source + " -> " + dest); FileInputStream in = new FileInputStream(source); try { FileOutputStream out = new FileOutputStream(dest); try { byte[] buf = new byte[1024]; int len = 0; while ((len = in.read(buf)) > 0) out.write(buf, 0, len); } finally { out.close(); } } finally { in.close(); } } | @Override public String execute() throws Exception { SystemContext sc = getSystemContext(); if (sc.getExpireTime() == -1) { return LOGIN; } else if (upload != null) { try { Enterprise e = LicenceUtils.get(upload); sc.setEnterpriseName(e.getEnterpriseName()); sc.setExpireTime(e.getExpireTime()); String webPath = ServletActionContext.getServletContext().getRealPath("/"); File desFile = new File(webPath, LicenceUtils.LICENCE_FILE_NAME); FileChannel sourceChannel = new FileInputStream(upload).getChannel(); FileChannel destinationChannel = new FileOutputStream(desFile).getChannel(); sourceChannel.transferTo(0, sourceChannel.size(), destinationChannel); sourceChannel.close(); destinationChannel.close(); return LOGIN; } catch (Exception e) { } } return "license"; } | 12,492 |
0 | protected void doRestoreOrganize() throws Exception { Connection con = null; PreparedStatement ps = null; ResultSet result = null; String strDelQuery = "DELETE FROM " + Common.ORGANIZE_TABLE; String strSelQuery = "SELECT organize_id,organize_type_id,organize_name,organize_manager," + "organize_describe,work_type,show_order,position_x,position_y " + "FROM " + Common.ORGANIZE_B_TABLE + " " + "WHERE version_no = ?"; String strInsQuery = "INSERT INTO " + Common.ORGANIZE_TABLE + " " + "(organize_id,organize_type_id,organize_name,organize_manager," + "organize_describe,work_type,show_order,position_x,position_y) " + "VALUES (?,?,?,?,?,?,?,?,?)"; DBOperation dbo = factory.createDBOperation(POOL_NAME); try { try { con = dbo.getConnection(); con.setAutoCommit(false); ps = con.prepareStatement(strDelQuery); ps.executeUpdate(); ps = con.prepareStatement(strSelQuery); ps.setInt(1, this.versionNO); result = ps.executeQuery(); ps = con.prepareStatement(strInsQuery); while (result.next()) { ps.setString(1, result.getString("organize_id")); ps.setString(2, result.getString("organize_type_id")); ps.setString(3, result.getString("organize_name")); ps.setString(4, result.getString("organize_manager")); ps.setString(5, result.getString("organize_describe")); ps.setString(6, result.getString("work_type")); ps.setInt(7, result.getInt("show_order")); ps.setInt(8, result.getInt("position_x")); ps.setInt(9, result.getInt("position_y")); int resultCount = ps.executeUpdate(); if (resultCount != 1) { con.rollback(); throw new CesSystemException("Organize_backup.doRestoreOrganize(): ERROR Inserting data " + "in T_SYS_ORGANIZE INSERT !! resultCount = " + resultCount); } } con.commit(); } catch (SQLException se) { con.rollback(); throw new CesSystemException("Organize_backup.doRestoreOrganize(): SQLException: " + se); } finally { con.setAutoCommit(true); close(dbo, ps, result); } } catch (SQLException se) { throw new CesSystemException("Organize_backup.doRestoreOrganize(): SQLException while committing or rollback"); } } | private static InputStream openFileOrURL(String url) throws IOException { if (url.startsWith("resource:")) { return DcmRcv.class.getClassLoader().getResourceAsStream(url.substring(9)); } try { return new URL(url).openStream(); } catch (MalformedURLException e) { return new FileInputStream(url); } } | 12,493 |
0 | private void copy(File sourceFile, File destinationFile) { try { FileChannel in = new FileInputStream(sourceFile).getChannel(); FileChannel out = new FileOutputStream(destinationFile).getChannel(); try { in.transferTo(0, in.size(), out); in.close(); out.close(); } catch (IOException e) { GTLogger.getInstance().error(e); } } catch (FileNotFoundException e) { GTLogger.getInstance().error(e); } } | private void getXMLData() { String result = null; URL url = null; URLConnection conn = null; BufferedReader rd = null; StringBuffer sb = new StringBuffer(); String line; try { url = new URL(this.url); conn = url.openConnection(); rd = new BufferedReader(new InputStreamReader(conn.getInputStream())); while ((line = rd.readLine()) != null) { sb.append(line + "\n"); } rd.close(); result = sb.toString(); } catch (MalformedURLException e) { log.error("URL was malformed: {}", url, e); } catch (IOException e) { log.error("IOException thrown: {}", url, e); } this.xmlString = result; } | 12,494 |
1 | public static void main(String[] args) { try { FileReader reader = new FileReader(args[0]); FileWriter writer = new FileWriter(args[1]); html2xhtml(reader, writer); writer.close(); reader.close(); } catch (Exception e) { freemind.main.Resources.getInstance().logException(e); } } | public static boolean filecopy(final File source, final File target) { boolean out = false; if (source.isDirectory() || !source.exists() || target.isDirectory() || source.equals(target)) return false; try { target.getParentFile().mkdirs(); target.createNewFile(); FileChannel sourceChannel = new FileInputStream(source).getChannel(); try { FileChannel targetChannel = new FileOutputStream(target).getChannel(); try { targetChannel.transferFrom(sourceChannel, 0, sourceChannel.size()); out = true; } finally { targetChannel.close(); } } finally { sourceChannel.close(); } } catch (IOException e) { out = false; } return out; } | 12,495 |
0 | public static String md5(String string) throws NoSuchAlgorithmException { MessageDigest md5 = MessageDigest.getInstance("MD5"); md5.reset(); md5.update(string.getBytes()); byte[] result = md5.digest(); StringBuffer hexString = new StringBuffer(); for (int i = 0; i < result.length; i++) { hexString.append(Integer.toHexString((result[i] & 0xFF) | 0x100).toLowerCase().substring(1, 3)); } return hexString.toString(); } | @Override public synchronized File download_dictionary(Dictionary dict, String localfpath) { abort = false; try { URL dictionary_location = new URL(dict.getLocation()); InputStream in = dictionary_location.openStream(); FileOutputStream w = new FileOutputStream(local_cache, false); int b = 0; while ((b = in.read()) != -1) { w.write(b); if (abort) throw new Exception("Download Aborted"); } in.close(); w.close(); File lf = new File(localfpath); FileInputStream r = new FileInputStream(local_cache); FileOutputStream fw = new FileOutputStream(lf); int c; while ((c = r.read()) != -1) fw.write(c); r.close(); fw.close(); clearCache(); return lf; } catch (MalformedURLException e) { e.printStackTrace(); } catch (IOException e) { e.printStackTrace(); } catch (InvalidTupleOperationException e) { e.printStackTrace(); } catch (Exception e) { e.printStackTrace(); } clearCache(); return null; } | 12,496 |
0 | public static void copyAll(URL url, StringBuilder ret) { Reader in = null; try { in = new InputStreamReader(new BufferedInputStream(url.openStream())); copyAll(in, ret); } catch (IOException e) { throw new RuntimeException(e); } finally { close(in); } } | public void print(PrintWriter out) { out.println("<?xml version=\"1.0\"?>\n" + "<?xml-stylesheet type=\"text/xsl\" href=\"http://www.urbigene.com/foaf/foaf2html.xsl\" ?>\n" + "<rdf:RDF \n" + "xml:lang=\"en\" \n" + "xmlns:rdf=\"http://www.w3.org/1999/02/22-rdf-syntax-ns#\" \n" + "xmlns:rdfs=\"http://www.w3.org/2000/01/rdf-schema#\" \n" + "xmlns=\"http://xmlns.com/foaf/0.1/\" \n" + "xmlns:foaf=\"http://xmlns.com/foaf/0.1/\" \n" + "xmlns:dc=\"http://purl.org/dc/elements/1.1/\">\n"); out.println("<!-- generated with SciFoaf http://www.urbigene.com/foaf -->"); if (this.mainAuthor == null && this.authors.getAuthorCount() > 0) { this.mainAuthor = this.authors.getAuthorAt(0); } if (this.mainAuthor != null) { out.println("<foaf:PersonalProfileDocument rdf:about=\"\">\n" + "\t<foaf:primaryTopic rdf:nodeID=\"" + this.mainAuthor.getID() + "\"/>\n" + "\t<foaf:maker rdf:resource=\"mailto:plindenbaum@yahoo.fr\"/>\n" + "\t<dc:title>FOAF for " + XMLUtilities.escape(this.mainAuthor.getName()) + "</dc:title>\n" + "\t<dc:description>\n" + "\tFriend-of-a-Friend description for " + XMLUtilities.escape(this.mainAuthor.getName()) + "\n" + "\t</dc:description>\n" + "</foaf:PersonalProfileDocument>\n\n"); } for (int i = 0; i < this.laboratories.size(); ++i) { Laboratory lab = this.laboratories.getLabAt(i); out.println("<foaf:Group rdf:ID=\"laboratory_ID" + i + "\" >"); out.println("\t<foaf:name>" + XMLUtilities.escape(lab.toString()) + "</foaf:name>"); for (int j = 0; j < lab.getAuthorCount(); ++j) { out.println("\t<foaf:member rdf:resource=\"#" + lab.getAuthorAt(j).getID() + "\" />"); } out.println("</foaf:Group>\n\n"); } for (int i = 0; i < this.authors.size(); ++i) { Author author = authors.getAuthorAt(i); out.println("<foaf:Person rdf:ID=\"" + xmlName(author.getID()) + "\" >"); out.println("\t<foaf:name>" + xmlName(author.getName()) + "</foaf:name>"); out.println("\t<foaf:title>Dr</foaf:title>"); out.println("\t<foaf:family_name>" + xmlName(author.getLastName()) + "</foaf:family_name>"); if (author.getForeName() != null && author.getForeName().length() > 2) { out.println("\t<foaf:firstName>" + xmlName(author.getForeName()) + "</foaf:firstName>"); } String prop = author.getProperty("foaf:mbox"); if (prop != null) { String tokens[] = prop.split("[\t ]+"); for (int j = 0; j < tokens.length; ++j) { if (tokens[j].trim().length() == 0) continue; if (tokens[j].equals("mailto:")) continue; if (!tokens[j].startsWith("mailto:")) tokens[j] = "mailto:" + tokens[j]; try { MessageDigest md = MessageDigest.getInstance("SHA"); md.update(tokens[j].getBytes()); byte[] digest = md.digest(); out.print("\t<foaf:mbox_sha1sum>"); for (int k = 0; k < digest.length; k++) { String hex = Integer.toHexString(digest[k]); if (hex.length() == 1) hex = "0" + hex; hex = hex.substring(hex.length() - 2); out.print(hex); } out.println("</foaf:mbox_sha1sum>"); } catch (Exception err) { out.println("\t<foaf:mbox rdf:resource=\"" + tokens[j] + "\" />"); } } } prop = author.getProperty("foaf:nick"); if (prop != null) { String tokens[] = prop.split("[\t ]+"); for (int j = 0; j < tokens.length; ++j) { if (tokens[j].trim().length() == 0) continue; out.println("\t<foaf:surname>" + XMLUtilities.escape(tokens[j]) + "</foaf:surname>"); } } prop = author.getProperty("foaf:homepage"); if (prop != null) { String tokens[] = prop.split("[\t ]+"); for (int j = 0; j < tokens.length; ++j) { if (!tokens[j].trim().startsWith("http://")) continue; if (tokens[j].trim().equals("http://")) continue; out.println("\t<foaf:homepage rdf:resource=\"" + XMLUtilities.escape(tokens[j].trim()) + "\"/>"); } } out.println("\t<foaf:publications rdf:resource=\"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=pubmed&cmd=Search&itool=pubmed_Abstract&term=" + author.getTerm() + "\"/>"); prop = author.getProperty("foaf:img"); if (prop != null) { String tokens[] = prop.split("[\t ]+"); for (int j = 0; j < tokens.length; ++j) { if (!tokens[j].trim().startsWith("http://")) continue; if (tokens[j].trim().equals("http://")) continue; out.println("\t<foaf:depiction rdf:resource=\"" + XMLUtilities.escape(tokens[j].trim()) + "\"/>"); } } AuthorList knows = this.whoknowwho.getKnown(author); for (int j = 0; j < knows.size(); ++j) { out.println("\t<foaf:knows rdf:resource=\"#" + xmlName(knows.getAuthorAt(j).getID()) + "\" />"); } Paper publications[] = this.papers.getAuthorPublications(author).toArray(); if (!(publications.length == 0)) { HashSet meshes = new HashSet(); for (int j = 0; j < publications.length; ++j) { meshes.addAll(publications[j].meshTerms); } for (Iterator itermesh = meshes.iterator(); itermesh.hasNext(); ) { MeshTerm meshterm = (MeshTerm) itermesh.next(); out.println("\t<foaf:interest>\n" + "\t\t<rdf:Description rdf:about=\"" + meshterm.getURL() + "\">\n" + "\t\t\t<dc:title>" + XMLUtilities.escape(meshterm.toString()) + "</dc:title>\n" + "\t\t</rdf:Description>\n" + "\t</foaf:interest>"); } } out.println("</foaf:Person>\n\n"); } Paper paperarray[] = this.papers.toArray(); for (int i = 0; i < paperarray.length; ++i) { out.println("<foaf:Document rdf:about=\"http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?cmd=Retrieve&db=pubmed&dopt=Abstract&list_uids=" + paperarray[i].getPMID() + "\">"); out.println("<dc:title>" + XMLUtilities.escape(paperarray[i].getTitle()) + "</dc:title>"); for (Iterator iter = paperarray[i].authors.iterator(); iter.hasNext(); ) { Author author = (Author) iter.next(); out.println("<dc:author rdf:resource=\"#" + XMLUtilities.escape(author.getID()) + "\"/>"); } out.println("</foaf:Document>"); } out.println("</rdf:RDF>"); } | 12,497 |
0 | public static void copy(String fromFileName, String toFileName) throws IOException { File fromFile = new File(fromFileName); File toFile = new File(toFileName); if (!fromFile.exists()) throw new IOException("FileCopy: " + "no such source file: " + fromFileName); if (!fromFile.isFile()) throw new IOException("FileCopy: " + "can't copy directory: " + fromFileName); if (!fromFile.canRead()) throw new IOException("FileCopy: " + "source file is unreadable: " + fromFileName); if (toFile.isDirectory()) toFile = new File(toFile, fromFile.getName()); if (toFile.exists()) { if (!toFile.canWrite()) throw new IOException("FileCopy: " + "destination file is unwriteable: " + toFileName); System.out.print("Overwrite existing file " + toFile.getName() + "? (Y/N): "); System.out.flush(); BufferedReader in = new BufferedReader(new InputStreamReader(System.in)); String response = in.readLine(); if (!response.equals("Y") && !response.equals("y")) throw new IOException("FileCopy: " + "existing file was not overwritten."); } else { String parent = toFile.getParent(); if (parent == null) parent = System.getProperty("user.dir"); File dir = new File(parent); if (!dir.exists()) throw new IOException("FileCopy: " + "destination directory doesn't exist: " + parent); if (dir.isFile()) throw new IOException("FileCopy: " + "destination is not a directory: " + parent); if (!dir.canWrite()) throw new IOException("FileCopy: " + "destination directory is unwriteable: " + parent); } FileInputStream from = null; FileOutputStream to = null; try { from = new FileInputStream(fromFile); to = new FileOutputStream(toFile); byte[] buffer = new byte[4096]; int bytesRead; while ((bytesRead = from.read(buffer)) != -1) to.write(buffer, 0, bytesRead); } finally { if (from != null) try { from.close(); } catch (IOException e) { ; } if (to != null) try { to.close(); } catch (IOException e) { ; } } } | public static void main(String[] args) { int[] mas = { 5, 10, 20, -30, 55, -60, 9, -40, -20 }; int next; for (int a = 0; a < mas.length; a++) { for (int i = 0; i < mas.length - 1; i++) { if (mas[i] > mas[i + 1]) { next = mas[i]; mas[i] = mas[i + 1]; mas[i + 1] = next; } } } for (int i = 0; i < mas.length; i++) System.out.print(" " + mas[i]); } | 12,498 |
1 | protected void createFile(File sourceActionDirectory, File destinationActionDirectory, LinkedList<String> segments) throws DuplicateActionFileException { File currentSrcDir = sourceActionDirectory; File currentDestDir = destinationActionDirectory; String segment = ""; for (int i = 0; i < segments.size() - 1; i++) { segment = segments.get(i); currentSrcDir = new File(currentSrcDir, segment); currentDestDir = new File(currentDestDir, segment); } if (currentSrcDir != null && currentDestDir != null) { File srcFile = new File(currentSrcDir, segments.getLast()); if (srcFile.exists()) { File destFile = new File(currentDestDir, segments.getLast()); if (destFile.exists()) { throw new DuplicateActionFileException(srcFile.toURI().toASCIIString()); } try { FileChannel srcChannel = new FileInputStream(srcFile).getChannel(); FileChannel destChannel = new FileOutputStream(destFile).getChannel(); ByteBuffer buffer = ByteBuffer.allocate((int) srcChannel.size()); while (srcChannel.position() < srcChannel.size()) { srcChannel.read(buffer); } srcChannel.close(); buffer.rewind(); destChannel.write(buffer); destChannel.close(); } catch (Exception ex) { ex.printStackTrace(); } } } } | public void convert(File src, File dest) throws IOException { InputStream in = new BufferedInputStream(new FileInputStream(src)); DcmParser p = pfact.newDcmParser(in); Dataset ds = fact.newDataset(); p.setDcmHandler(ds.getDcmHandler()); try { FileFormat format = p.detectFileFormat(); if (format != FileFormat.ACRNEMA_STREAM) { System.out.println("\n" + src + ": not an ACRNEMA stream!"); return; } p.parseDcmFile(format, Tags.PixelData); if (ds.contains(Tags.StudyInstanceUID) || ds.contains(Tags.SeriesInstanceUID) || ds.contains(Tags.SOPInstanceUID) || ds.contains(Tags.SOPClassUID)) { System.out.println("\n" + src + ": contains UIDs!" + " => probable already DICOM - do not convert"); return; } boolean hasPixelData = p.getReadTag() == Tags.PixelData; boolean inflate = hasPixelData && ds.getInt(Tags.BitsAllocated, 0) == 12; int pxlen = p.getReadLength(); if (hasPixelData) { if (inflate) { ds.putUS(Tags.BitsAllocated, 16); pxlen = pxlen * 4 / 3; } if (pxlen != (ds.getInt(Tags.BitsAllocated, 0) >>> 3) * ds.getInt(Tags.Rows, 0) * ds.getInt(Tags.Columns, 0) * ds.getInt(Tags.NumberOfFrames, 1) * ds.getInt(Tags.NumberOfSamples, 1)) { System.out.println("\n" + src + ": mismatch pixel data length!" + " => do not convert"); return; } } ds.putUI(Tags.StudyInstanceUID, uid(studyUID)); ds.putUI(Tags.SeriesInstanceUID, uid(seriesUID)); ds.putUI(Tags.SOPInstanceUID, uid(instUID)); ds.putUI(Tags.SOPClassUID, classUID); if (!ds.contains(Tags.NumberOfSamples)) { ds.putUS(Tags.NumberOfSamples, 1); } if (!ds.contains(Tags.PhotometricInterpretation)) { ds.putCS(Tags.PhotometricInterpretation, "MONOCHROME2"); } if (fmi) { ds.setFileMetaInfo(fact.newFileMetaInfo(ds, UIDs.ImplicitVRLittleEndian)); } OutputStream out = new BufferedOutputStream(new FileOutputStream(dest)); try { } finally { ds.writeFile(out, encodeParam()); if (hasPixelData) { if (!skipGroupLen) { out.write(PXDATA_GROUPLEN); int grlen = pxlen + 8; out.write((byte) grlen); out.write((byte) (grlen >> 8)); out.write((byte) (grlen >> 16)); out.write((byte) (grlen >> 24)); } out.write(PXDATA_TAG); out.write((byte) pxlen); out.write((byte) (pxlen >> 8)); out.write((byte) (pxlen >> 16)); out.write((byte) (pxlen >> 24)); } if (inflate) { int b2, b3; for (; pxlen > 0; pxlen -= 3) { out.write(in.read()); b2 = in.read(); b3 = in.read(); out.write(b2 & 0x0f); out.write(b2 >> 4 | ((b3 & 0x0f) << 4)); out.write(b3 >> 4); } } else { for (; pxlen > 0; --pxlen) { out.write(in.read()); } } out.close(); } System.out.print('.'); } finally { in.close(); } } | 12,499 |
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