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MemoEntry._ID + " = ?", new String[]{String.valueOf(memoId)}); } public long updateMemoContent(long memoId, String memoContent) { ContentValues values = new ContentValues(); <BUG>values.put(MemoEntry.COLUMN_CONTENT, memoContent); return db.update(</BUG> MemoEntry.TABLE_NAME, values, MemoEntry._ID + " = ?",
return db.update(
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import android.widget.RelativeLayout; import android.widget.TextView; import com.kiminonawa.mydiary.R; import com.kiminonawa.mydiary.db.DBManager; import com.kiminonawa.mydiary.shared.EditMode; <BUG>import com.kiminonawa.mydiary.shared.ThemeManager; import java.util.List; public class MemoAdapter extends RecyclerView.A...
import com.marshalchen.ultimaterecyclerview.dragsortadapter.DragSortAdapter; public class MemoAdapter extends DragSortAdapter<DragSortAdapter.ViewHolder> implements EditMode {
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private DBManager dbManager; private boolean isEditMode = false; private EditMemoDialogFragment.MemoCallback callback; private static final int TYPE_HEADER = 0; private static final int TYPE_ITEM = 1; <BUG>public MemoAdapter(FragmentActivity activity, long topicId, List<MemoEntity> memoList, DBManager dbManager, EditMe...
public MemoAdapter(FragmentActivity activity, long topicId, List<MemoEntity> memoList, DBManager dbManager, EditMemoDialogFragment.MemoCallback callback, RecyclerView recyclerView) { super(recyclerView); this.mActivity = activity;
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this.memoList = memoList; this.dbManager = dbManager; this.callback = callback; } @Override <BUG>public RecyclerView.ViewHolder onCreateViewHolder(ViewGroup parent, int viewType) { </BUG> View view; if (isEditMode) { if (viewType == TYPE_HEADER) {
public DragSortAdapter.ViewHolder onCreateViewHolder(ViewGroup parent, int viewType) {
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editMemoDialogFragment.show(mActivity.getSupportFragmentManager(), "editMemoDialogFragment"); } }); } } <BUG>protected class MemoViewHolder extends RecyclerView.ViewHolder implements View.OnClickListener { private View rootView; private TextView TV_memo_item_content;</BUG> private ImageView IV_memo_item_delete;
protected class MemoViewHolder extends DragSortAdapter.ViewHolder implements View.OnClickListener, View.OnLongClickListener { private ImageView IV_memo_item_dot; private TextView TV_memo_item_content;
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import java.net.URI; import java.util.Calendar; import java.util.Date; import java.util.Formatter; import java.util.List; <BUG>import javax.ws.rs.core.UriBuilder; import org.apache.commons.httpclient.URIException; import org.apache.commons.httpclient.util.URIUtil;</BUG> import org.suigeneris.jrcs.rcs.Version; import or...
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if (home != null) { space.setHome(home.getPrefixedFullName()); space.setXwikiRelativeUrl(home.getURL("view")); space.setXwikiAbsoluteUrl(home.getExternalURL("view")); } <BUG>String pagesUri = UriBuilder.fromUri(baseUri).path(PagesResource.class).build(wikiName, spaceName).toString(); </BUG> Link pagesLink = objectFacto...
String pagesUri = uri(baseUri, PagesResource.class, wikiName, spaceName);
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Link pagesLink = objectFactory.createLink(); pagesLink.setHref(pagesUri); pagesLink.setRel(Relations.PAGES); space.getLinks().add(pagesLink); if (home != null) { <BUG>String homeUri = UriBuilder.fromUri(baseUri).path(PageResource.class).build(wikiName, spaceName, home.getName()) .toString();</BUG> Link homeLink = obje...
String homeUri = uri(baseUri, PageResource.class, wikiName, spaceName, home.getName());
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.toString();</BUG> Link homeLink = objectFactory.createLink(); homeLink.setHref(homeUri); homeLink.setRel(Relations.HOME); space.getLinks().add(homeLink); <BUG>} String searchUri = UriBuilder.fromUri(baseUri).path(SpaceSearchResource.class).build(wikiName, spaceName).toString();</BUG> Link searchLink = objectFactory.cr...
Link pagesLink = objectFactory.createLink(); pagesLink.setHref(pagesUri); pagesLink.setRel(Relations.PAGES); space.getLinks().add(pagesLink); if (home != null) { String homeUri = uri(baseUri, PageResource.class, wikiName, spaceName, home.getName()); String searchUri = uri(baseUri, SpaceSearchResource.class, wikiName, s...
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if (!languages.isEmpty()) { if (!doc.getDefaultLanguage().equals("")) { translations.setDefault(doc.getDefaultLanguage()); Translation translation = objectFactory.createTranslation(); translation.setLanguage(doc.getDefaultLanguage()); <BUG>String pageTranslationUri = UriBuilder.fromUri(baseUri).path(PageResource.class)...
uri(baseUri, PageResource.class, doc.getWiki(), doc.getSpace(), doc.getName());
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} } for (String language : languages) { Translation translation = objectFactory.createTranslation(); translation.setLanguage(language); <BUG>String pageTranslationUri = UriBuilder.fromUri(baseUri).path(PageTranslationResource.class) .build(doc.getWiki(), doc.getSpace(), doc.getName(), language).toString();</BUG> Link p...
uri(baseUri, PageTranslationResource.class, doc.getWiki(), doc.getSpace(), doc.getName(), language);
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Link pageTranslationLink = objectFactory.createLink(); pageTranslationLink.setHref(pageTranslationUri); pageTranslationLink.setRel(Relations.PAGE); translation.getLinks().add(pageTranslationLink); String historyUri = <BUG>UriBuilder.fromUri(baseUri).path(PageTranslationHistoryResource.class) .build(doc.getWiki(), doc.g...
uri(baseUri, PageTranslationHistoryResource.class, doc.getWiki(), doc.getSpace(), doc.getName(), language); Link historyLink = objectFactory.createLink();
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pageSummary.setParent(doc.getParent()); if (parent != null && !parent.isNew()) { pageSummary.setParentId(parent.getPrefixedFullName()); } else { pageSummary.setParentId(""); <BUG>} String spaceUri = UriBuilder.fromUri(baseUri).path(SpaceResource.class).build(doc.getWiki(), doc.getSpace()).toString();</BUG> Link spaceLi...
String spaceUri = uri(baseUri, SpaceResource.class, doc.getWiki(), doc.getSpace());
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UriBuilder.fromUri(baseUri).path(SpaceResource.class).build(doc.getWiki(), doc.getSpace()).toString();</BUG> Link spaceLink = objectFactory.createLink(); spaceLink.setHref(spaceUri); spaceLink.setRel(Relations.SPACE); pageSummary.getLinks().add(spaceLink); <BUG>if (parent != null) { String parentUri = UriBuilder.fromUr...
pageSummary.setParent(doc.getParent()); if (parent != null && !parent.isNew()) { pageSummary.setParentId(parent.getPrefixedFullName()); } else { pageSummary.setParentId(""); } String spaceUri = uri(baseUri, SpaceResource.class, doc.getWiki(), doc.getSpace()); String parentUri = uri(baseUri, PageResource.class, parent.g...
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Link historyLink = objectFactory.createLink(); historyLink.setHref(historyUri); historyLink.setRel(Relations.HISTORY); pageSummary.getLinks().add(historyLink); if (!doc.getChildren().isEmpty()) { <BUG>String pageChildrenUri = UriBuilder.fromUri(baseUri).path(PageChildrenResource.class) .build(doc.getWiki(), doc.getSpac...
uri(baseUri, PageChildrenResource.class, doc.getWiki(), doc.getSpace(), doc.getName());
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objectsLink.setRel(Relations.OBJECTS); pageSummary.getLinks().add(objectsLink); } com.xpn.xwiki.api.Object tagsObject = doc.getObject("XWiki.TagClass", 0); if (tagsObject != null) { <BUG>if (tagsObject.getProperty("tags") != null) { String tagsUri = UriBuilder.fromUri(baseUri).path(PageTagsResource.class) .build(doc.ge...
String tagsUri = uri(baseUri, PageTagsResource.class, doc.getWiki(), doc.getSpace(), doc.getName());
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tagsLink.setHref(tagsUri); tagsLink.setRel(Relations.TAGS); pageSummary.getLinks().add(tagsLink); } } <BUG>String syntaxesUri = UriBuilder.fromUri(baseUri).path(SyntaxesResource.class).build().toString(); Link syntaxesLink = objectFactory.createLink();</BUG> syntaxesLink.setHref(syntaxesUri); syntaxesLink.setRel(Relati...
String syntaxesUri = uri(baseUri, SyntaxesResource.class); Link syntaxesLink = objectFactory.createLink();
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} return historySummary; } private static void fillAttachment(Attachment attachment, ObjectFactory objectFactory, URI baseUri, <BUG>com.xpn.xwiki.api.Attachment xwikiAttachment, String xwikiRelativeUrl, String xwikiAbsoluteUrl, XWiki xwikiApi, Boolean withPrettyNames) {</BUG> Document doc = xwikiAttachment.getDocument...
com.xpn.xwiki.api.Attachment xwikiAttachment, String xwikiRelativeUrl, String xwikiAbsoluteUrl, XWiki xwikiApi, {
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Calendar calendar = Calendar.getInstance(); calendar.setTime(xwikiAttachment.getDate()); attachment.setDate(calendar); attachment.setXwikiRelativeUrl(xwikiRelativeUrl); attachment.setXwikiAbsoluteUrl(xwikiAbsoluteUrl); <BUG>String pageUri = UriBuilder.fromUri(baseUri).path(PageResource.class).build(doc.getWiki(), doc.g...
String pageUri = uri(baseUri, PageResource.class, doc.getWiki(), doc.getSpace(), doc.getName());
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} return attachmentUri; }</BUG> public static Attachment createAttachment(ObjectFactory objectFactory, URI baseUri, <BUG>com.xpn.xwiki.api.Attachment xwikiAttachment, String xwikiRelativeUrl, String xwikiAbsoluteUrl, XWiki xwikiApi, Boolean withPrettyNames) {</BUG> Attachment attachment = objectFactory.createAttachmen...
com.xpn.xwiki.api.Attachment xwikiAttachment, String xwikiRelativeUrl, String xwikiAbsoluteUrl, XWiki xwikiApi, {
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attachmentLink.setRel(Relations.ATTACHMENT_DATA); attachment.getLinks().add(attachmentLink); return attachment; } public static Attachment createAttachmentAtVersion(ObjectFactory objectFactory, URI baseUri, <BUG>com.xpn.xwiki.api.Attachment xwikiAttachment, String xwikiRelativeUrl, String xwikiAbsoluteUrl, XWiki xwiki...
com.xpn.xwiki.api.Attachment xwikiAttachment, String xwikiRelativeUrl, String xwikiAbsoluteUrl, XWiki xwikiApi, {
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.build(doc.getWiki(), doc.getSpace(), doc.getName(), doc.getVersion(), xwikiObject.getClassName(), xwikiObject.getNumber()).toString();</BUG> } else { <BUG>propertiesUri = UriBuilder .fromUri(baseUri) .path(ObjectPropertiesResource.class) .build(doc.getWiki(), doc.getSpace(), doc.getName(), xwikiObject.getClassName(), ...
fillObjectSummary(objectSummary, objectFactory, baseUri, doc, xwikiObject, xwikiApi, withPrettyNames); Link objectLink = getObjectLink(objectFactory, baseUri, doc, xwikiObject, useVersion, Relations.OBJECT); objectSummary.getLinks().add(objectLink); String propertiesUri; if (useVersion) { uri(baseUri, ObjectPropertiesA...
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.build(doc.getWiki(), doc.getSpace(), doc.getName(), doc.getVersion(), xwikiObject.getClassName(), xwikiObject.getNumber(), propertyClass.getName()) .toString();</BUG> } else { <BUG>propertyUri = UriBuilder .fromUri(baseUri) .path(ObjectPropertyResource.class) .build(doc.getWiki(), doc.getSpace(), doc.getName(), xwikiO...
propertiesUri = uri(baseUri, ObjectPropertiesResource.class, doc.getWiki(), doc.getSpace(), doc.getName(), xwikiObject.getClassName(), xwikiObject.getNumber());
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.build(doc.getWiki(), doc.getSpace(), doc.getName(), doc.getVersion(), xwikiObject.getClassName(), xwikiObject.getNumber()).toString();</BUG> } else { <BUG>objectUri = UriBuilder .fromUri(baseUri) .path(ObjectResource.class) .build(doc.getWiki(), doc.getSpace(), doc.getName(), xwikiObject.getClassName(), xwikiObject.ge...
private static Link getObjectLink(ObjectFactory objectFactory, URI baseUri, Document doc, BaseObject xwikiObject, boolean useVersion, String relation) String objectUri; if (useVersion) { uri(baseUri, ObjectAtPageVersionResource.class, doc.getWiki(), doc.getSpace(), doc.getName(), doc.getVersion(), xwikiObject.getClassN...
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Link propertyLink = objectFactory.createLink(); propertyLink.setHref(propertyUri); propertyLink.setRel(Relations.SELF); property.getLinks().add(propertyLink); clazz.getProperties().add(property); <BUG>} String classUri = UriBuilder.fromUri(baseUri).path(ClassResource.class).build(wikiName, xwikiClass.getName()).toStrin...
String classUri = uri(baseUri, ClassResource.class, wikiName, xwikiClass.getName());
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String classUri = UriBuilder.fromUri(baseUri).path(ClassResource.class).build(wikiName, xwikiClass.getName()).toString();</BUG> Link classLink = objectFactory.createLink(); classLink.setHref(classUri); classLink.setRel(Relations.SELF); <BUG>clazz.getLinks().add(classLink); String propertiesUri = UriBuilder.fromUri(base...
propertyLink.setHref(propertyUri); propertyLink.setRel(Relations.SELF); property.getLinks().add(propertyLink); clazz.getProperties().add(property); } String classUri = uri(baseUri, ClassResource.class, wikiName, xwikiClass.getName()); String propertiesUri = uri(baseUri, ClassPropertiesResource.class, wikiName, xwikiCla...
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<BUG>package org.xwiki.rest.internal; import org.apache.commons.lang3.StringUtils;</BUG> import org.xwiki.component.manager.ComponentManager; import org.xwiki.context.Execution; import org.xwiki.model.reference.EntityReferenceSerializer;
import java.net.URI; import javax.ws.rs.core.UriBuilder; import org.apache.commons.httpclient.URIException; import org.apache.commons.httpclient.util.URIUtil; import org.apache.commons.lang3.StringUtils;
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if (!(SNodeOperations.isInstanceOf(arg, "jetbrains.mps.baseLanguage.structure.VoidType"))) { tmp = arg; continue with_meet; } } <BUG>return new _Quotations.QuotationClass_2().createNode(); </BUG> } if (SNodeOperations.isInstanceOf(tmp, "jetbrains.mps.baseLanguage.structure.ClassifierType")) { List<SNode> params = SLink...
return new _Quotations.QuotationClass_3().createNode();
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); } public static SNode call_getNormalizedTerminateType_1232036646585(SNode thisNode) { return ((FunctionType_Behavior.call_getTerminateType_1232032188607(thisNode) != null) ? ClassifierTypeUtil.getTypeCoercedToClassifierType(FunctionType_Behavior.call_getTerminateType_1232032188607(thisNode)) : <BUG>new _Quotations.Q...
new _Quotations.QuotationClass_8().createNode()
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public class RuntimeUtils { private static Map<String, SNode> runtimeClassifiers = null; public RuntimeUtils() { } public static SModel getRuntimeModel() { <BUG>return SNodeOperations.getModel(SLinkOperations.getTarget(new _Quotations.QuotationClass_9().createNode(), "classifier", false)); </BUG> } public static Map<St...
return SNodeOperations.getModel(SLinkOperations.getTarget(new _Quotations.QuotationClass_10().createNode(), "classifier", false));
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package jetbrains.mps.baseLanguage.closures.structure; import jetbrains.mps.baseLanguage.structure.Expression; import jetbrains.mps.baseLanguage.structure.IStatementListContainer; <BUG>import jetbrains.mps.baseLanguage.structure.IContainsStatementList; import jetbrains.mps.smodel.SNode;</BUG> import jetbrains.mps.baseL...
import jetbrains.mps.baseLanguage.structure.IMethodLike; import jetbrains.mps.smodel.SNode;
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import jetbrains.mps.baseLanguage.structure.ParameterDeclaration; import java.util.List; import jetbrains.mps.smodel.SModel; import jetbrains.mps.smodel.SModelUtil_new; import jetbrains.mps.project.GlobalScope; <BUG>public class ClosureLiteral extends Expression implements IStatementListContainer, IContainsStatementLis...
public class ClosureLiteral extends Expression implements IStatementListContainer, IContainsStatementList, IMethodLike {
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restSecurity.isSelfRegistration()); } throw new NotSupportedException("Self Registration is not enabled."); } HttpContext header = context.asContext(HttpContext.class); <BUG>String baseURL = baseURLProviderFactory.get(realm).getURL(header); </BUG> emailAddress = jVal.get(EMAIL).asString(); if (StringUtils.isBlank(email...
String baseURL = baseURLProviderFactory.get(realm).getRootURL(header);
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private static final String XUI_CONSOLE_BASE_PAGE = "{0}/XUI/#{1}"; private XuiRedirectHelper() { } public static void redirectToXui(HttpServletRequest request, String redirectRealm, String xuiHash) { String deploymentUri = InjectorHolder.getInstance(BaseURLProviderFactory.class).get(redirectRealm) <BUG>.getURL(request...
.getRootURL(request);
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import java.util.Map; import java.util.concurrent.ConcurrentHashMap; import javax.inject.Inject; import javax.inject.Named; import javax.inject.Singleton; <BUG>import javax.servlet.ServletContext; import org.forgerock.openam.core.guice.ServletContextCache;</BUG> import org.forgerock.openam.utils.OpenAMSettingsImpl; @Si...
import org.forgerock.openam.core.CoreWrapper; import org.forgerock.openam.core.guice.ServletContextCache;
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private static final String SERVICE_VERSION = "1.0"; private static final String PROVIDER_TYPE = "base-url-source"; private static final String CONTEXT_PATH = "base-url-context-path"; private final ServletContext servletContext; private final Debug debug = Debug.getInstance("amBaseURL"); <BUG>private final Map<String, ...
private final CoreWrapper coreWrapper; public BaseURLProviderFactory(@Named(ServletContextCache.CONTEXT_REFERENCE) ServletContext servletContext, CoreWrapper coreWrapper) { this.coreWrapper = coreWrapper; addListener();
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provider.init(settings, realmDN); provider.setContextPath(settings.getStringSetting(realmDN, CONTEXT_PATH)); } else { provider = new RequestValuesBaseURLProvider(); provider.setContextPath(servletContext.getContextPath()); <BUG>} providers.put(realmDN, provider); } catch (SMSException e) { debug.error("Unable to acces...
provider.setCoreWrapper(coreWrapper); } catch (SMSException | SSOException e) {
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debug.message("The globalConfigChanged ServiceListener method was invoked for service {}", serviceName); } public void organizationConfigChanged(String serviceName, String version, String orgName, String groupName, String serviceComponent, int type) { switch(type) { <BUG>case ServiceListener.ADDED: break;</BUG> case Se...
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public void testGetURL() throws Exception { OpenAMSettings settings = mock(OpenAMSettings.class); when(settings.getStringSetting("realm", "base-url-extension-class")).thenReturn(Extension.class.getName()); provider.init(settings, "realm"); provider.setContextPath(""); <BUG>String url = provider.getURL(mock(HttpServletR...
String url = provider.getRootURL(mock(HttpServletRequest.class));
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public void testGetURL() throws Exception { OpenAMSettings settings = mock(OpenAMSettings.class); when(settings.getStringSetting("realm", "base-url-fixed-value")).thenReturn("fred"); provider.init(settings, "realm"); provider.setContextPath(""); <BUG>String url = provider.getURL(mock(HttpServletRequest.class)); </BUG> ...
String url = provider.getRootURL(mock(HttpServletRequest.class));
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private SystemHandler systemHandler; private DeviceRegistry deviceRegistry; private DeviceActionHandler deviceActionHandler; private DeviceHistoryHandler deviceHistoryHandler; private ActionRegistry actionRegistry; <BUG>public ImperiHomeApiServlet() { GsonBuilder gsonBuilder = new GsonBuilder();</BUG> gsonBuilder.regis...
imperiHomeConfig = new ImperiHomeConfig(); GsonBuilder gsonBuilder = new GsonBuilder();
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logger.info("Started ImperiHome integration service at " + PATH); } catch (Exception e) { logger.error("Could not start ImperiHome integration service: {}", e.getMessage(), e); } } <BUG>protected void deactivate(ComponentContext componentContext) { try {</BUG> httpService.unregister(PATH); } catch (IllegalArgumentExcep...
protected void modified(Map<String, Object> config) { imperiHomeConfig.update(config); protected void deactivate() { try {
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protected final transient Logger logger = LoggerFactory.getLogger(getClass()); private String id; private String name; private String room; private DeviceType type; <BUG>private boolean inverted; private final DeviceParameters params; private transient String roomName;</BUG> private transient Item item; private final t...
private String defaultIcon; private transient boolean inverted; private transient String roomName;
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} else { AbstractDevice device = getDeviceInstance(deviceType, item); device.setId(getDeviceId(item)); device.setName(getLabel(item, issTags)); device.setInverted(isInverted(issTags)); <BUG>device.setActionRegistry(actionRegistry); setDeviceRoom(device, issTags);</BUG> setDeviceLinks(device, item, issTags); setMapping(...
setIcon(device, issTags); setDeviceRoom(device, issTags);
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package org.openhab.io.imperihome.internal.model.param; <BUG>public enum ParamType { GENERIC_VALUE("Value"),</BUG> TEMPERATURE_VALUE("Value"), TEMPERATURE_DUAL("temp"), LUMINOSITY_VALUE("Value"),
DEFAULT_ICON("defaultIcon"), GENERIC_VALUE("Value"),
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ROOM("room", false), TYPE("type", false), MAPPING("mapping", false), LINK("link", true), UNIT("unit", false), <BUG>INVERT("invert", false); private final String prefix;</BUG> private final boolean multiValue; TagType(String prefix, boolean multiValue) {
INVERT("invert", false), ICON("icon", false); private final String prefix;
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public class UserControllerTest { private static final Logger LOGGER = Logger.getLogger( UserControllerTest.class.getName() ); Properties properties = new Properties(); InputStream input = null; <BUG>private String neo4jServerPort = System.getProperty( "neo4j.server.port" ); private String neo4jRemoteShellPort = System...
private String dbmsConnectorHttpPort = System.getProperty( "dbms.connector.http.port" ); private String dbmsConnectorBoltPort = System.getProperty( "dbms.connector.bolt.port" ); private String dbmsShellPort = System.getProperty( "dbms.shell.port" ); private String dbmsDirectoriesData = System.getProperty( "dbms.directo...
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@Bean public Configuration getConfiguration() { if ( StringUtils.isEmpty( url ) ) { <BUG>url = "http://localhost:" + port; </BUG> } Configuration config = new Configuration(); config.driverConfiguration().setDriverClassName( HttpDriver.class.getName() )
url = "http://localhost:" + dbmsConnectorHttpPort;
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import com.compomics.util.experiment.massspectrometry.Spectrum; import com.compomics.util.experiment.massspectrometry.SpectrumFactory; import com.compomics.util.gui.waiting.waitinghandlers.ProgressDialogX; import com.compomics.util.preferences.IdentificationParameters; import com.compomics.util.experiment.identificatio...
import com.compomics.util.preferences.DigestionPreferences; import com.compomics.util.preferences.PTMScoringPreferences;
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waitingHandler.appendReportEndLine(); objectsCache = new ObjectsCache(); objectsCache.setAutomatedMemoryManagement(true); ProteomicAnalysis analysis = experiment.getAnalysisSet(sample).getProteomicAnalysis(replicateNumber); analysis.addIdentificationResults(IdentificationMethod.MS2_IDENTIFICATION, new Ms2Identification...
fileImporter = new FileImporter(this, waitingHandler, analysis, identificationParameters, metrics); fileImporter.importFiles(idFiles, spectrumFiles, processingPreferences, spectrumCountingPreferences, projectDetails, backgroundThread);
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PsmScoringPreferences psmScoringPreferences = identificationParameters.getPsmScoringPreferences(); ArrayList<Integer> usedAlgorithms = projectDetails.getIdentificationAlgorithms(); if (psmScoringPreferences.isScoringNeeded(usedAlgorithms)) { PsmScorer psmScorer = new PsmScorer(); waitingHandler.appendReport("Estimating...
psmScorer.estimateIntermediateScores(identification, inputMap, processingPreferences, identificationParameters, waitingHandler, exceptionHandler); if (psmScoringPreferences.isTargetDecoyNeededForPsmScoring(usedAlgorithms)) {
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waitingHandler.increasePrimaryProgressCounter(); if (waitingHandler.isRunCanceled()) { return; } waitingHandler.appendReport("Resolving protein inference issues, inferring peptide and protein PI status.", true, true); // could be slow <BUG>proteinInference.retainBestScoringGroups(identification, metrics, matchesValidat...
[DELETED]
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waitingHandler.appendReport("Validating identifications, quality control of matches.", true, true); } } else { waitingHandler.appendReport("No decoy sequences found. Impossible to estimate FDRs.", true, true); } <BUG>matchesValidator.validateIdentifications(identification, metrics, geneMaps, waitingHandler, exceptionHa...
matchesValidator.validateIdentifications(identification, metrics, geneMaps, waitingHandler, exceptionHandler, identificationParameters, identificationFeaturesGenerator, inputMap, spectrumCountingPreferences, processingPreferences); waitingHandler.increasePrimaryProgressCounter();
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timeWarp = new OwnLabel(getFormattedTimeWrap(), skin, "warp"); timeWarp.setName("time warp"); Container wrapWrapper = new Container(timeWarp); wrapWrapper.width(60f * GlobalConf.SCALE_FACTOR); wrapWrapper.align(Align.center); <BUG>VerticalGroup timeGroup = new VerticalGroup().align(Align.left).space(3 * GlobalConf.SCAL...
VerticalGroup timeGroup = new VerticalGroup().align(Align.left).columnAlign(Align.left).space(3 * GlobalConf.SCALE_FACTOR).padTop(3 * GlobalConf.SCALE_FACTOR);
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focusListScrollPane.setFadeScrollBars(false); focusListScrollPane.setScrollingDisabled(true, false); focusListScrollPane.setHeight(tree ? 200 * GlobalConf.SCALE_FACTOR : 100 * GlobalConf.SCALE_FACTOR); focusListScrollPane.setWidth(160); } <BUG>VerticalGroup objectsGroup = new VerticalGroup().align(Align.left).space(3 *...
VerticalGroup objectsGroup = new VerticalGroup().align(Align.left).columnAlign(Align.left).space(3 * GlobalConf.SCALE_FACTOR);
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headerGroup.addActor(expandIcon); headerGroup.addActor(detachIcon); addActor(headerGroup); expandIcon.setChecked(expanded); } <BUG>public void expand() { </BUG> if (!expandIcon.isChecked()) { expandIcon.setChecked(true); }
public void expandPane() {
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</BUG> if (!expandIcon.isChecked()) { expandIcon.setChecked(true); } } <BUG>public void collapse() { </BUG> if (expandIcon.isChecked()) { expandIcon.setChecked(false); }
headerGroup.addActor(expandIcon); headerGroup.addActor(detachIcon); addActor(headerGroup); expandIcon.setChecked(expanded); public void expandPane() { public void collapsePane() {
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}); playstop.addListener(new TextTooltip(txt("gui.tooltip.playstop"), skin)); TimeComponent timeComponent = new TimeComponent(skin, ui); timeComponent.initialize(); CollapsiblePane time = new CollapsiblePane(ui, txt("gui.time"), timeComponent.getActor(), skin, true, playstop); <BUG>time.align(Align.left); mainActors.ad...
time.align(Align.left).columnAlign(Align.left); mainActors.add(time);
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panes.put(visualEffectsComponent.getClass().getSimpleName(), visualEffects); ObjectsComponent objectsComponent = new ObjectsComponent(skin, ui); objectsComponent.setSceneGraph(sg); objectsComponent.initialize(); CollapsiblePane objects = new CollapsiblePane(ui, txt("gui.objects"), objectsComponent.getActor(), skin, fal...
objects.align(Align.left).columnAlign(Align.left); mainActors.add(objects);
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if (Constants.desktop) { MusicComponent musicComponent = new MusicComponent(skin, ui); musicComponent.initialize(); Actor[] musicActors = MusicActorsManager.getMusicActors() != null ? MusicActorsManager.getMusicActors().getActors(skin) : null; CollapsiblePane music = new CollapsiblePane(ui, txt("gui.music"), musicCompo...
music.align(Align.left).columnAlign(Align.left); mainActors.add(music);
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Bundle savedInstanceState) { final View rootView = inflater.inflate(R.layout.tab_qibla, container, false); final QiblaCompassView qiblaCompassView = (QiblaCompassView)rootView.findViewById(R.id.qibla_compass); qiblaCompassView.setConstants(((TextView)rootView.findViewById(R.id.bearing_north)), getText(R.string.bearing_...
sOrientationListener = new android.hardware.SensorListener() {
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package org.sonar.server.qualitygate; import com.google.common.base.Strings; <BUG>import org.apache.commons.lang.StringUtils; import org.sonar.core.permission.GlobalPermissions;</BUG> import org.sonar.core.properties.PropertiesDao; import org.sonar.core.properties.PropertyDto; import org.sonar.core.qualitygate.db.Quali...
import org.elasticsearch.common.collect.Lists; import org.sonar.api.measures.CoreMetrics; import org.sonar.api.measures.Metric; import org.sonar.api.measures.Metric.ValueType; import org.sonar.api.measures.MetricFinder; import org.sonar.core.permission.GlobalPermissions;
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import org.sonar.core.properties.PropertyDto; import org.sonar.core.qualitygate.db.QualityGateConditionDao; import org.sonar.core.qualitygate.db.QualityGateConditionDto; import org.sonar.core.qualitygate.db.QualityGateDao; import org.sonar.core.qualitygate.db.QualityGateDto; <BUG>import org.sonar.server.exceptions.BadR...
import org.sonar.server.exceptions.BadRequestException.Message; import org.sonar.server.exceptions.NotFoundException;
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private final PropertiesDao propertiesDao; public QualityGates(QualityGateDao dao, QualityGateConditionDao conditionDao, PropertiesDao propertiesDao) { </BUG> this.dao = dao; <BUG>this.conditionDao = conditionDao; this.propertiesDao = propertiesDao;</BUG> } public QualityGateDto create(String name) { checkPermission(Us...
public QualityGates(QualityGateDao dao, QualityGateConditionDao conditionDao, MetricFinder metricFinder, PropertiesDao propertiesDao) { this.metricFinder = metricFinder; this.propertiesDao = propertiesDao;
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dao.insert(newQualityGate); return newQualityGate; } public QualityGateDto rename(long idToRename, String name) { checkPermission(UserSession.get()); <BUG>QualityGateDto toRename = getNonNull(idToRename); </BUG> validateQualityGate(idToRename, name); toRename.setName(name); dao.update(toRename);
QualityGateDto toRename = getNonNullQgate(idToRename);
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public Collection<QualityGateDto> list() { return dao.selectAll(); } public void delete(long idToDelete) { checkPermission(UserSession.get()); <BUG>QualityGateDto qGate = getNonNull(idToDelete); </BUG> if (isDefault(qGate)) { throw new BadRequestException("Impossible to delete default quality gate."); }
QualityGateDto qGate = getNonNullQgate(idToDelete);
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public void setDefault(@Nullable Long idToUseAsDefault) { checkPermission(UserSession.get()); if (idToUseAsDefault == null) { propertiesDao.deleteGlobalProperty(SONAR_QUALITYGATE_PROPERTY); } else { <BUG>QualityGateDto newDefault = getNonNull(idToUseAsDefault); </BUG> propertiesDao.setProperty(new PropertyDto().setKey(...
QualityGateDto newDefault = getNonNullQgate(idToUseAsDefault);
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public void update(final AnActionEvent e) { super.update(e); final Presentation presentation = e.getPresentation(); if (presentation.isEnabled()) { final DataContext context = e.getDataContext(); <BUG>Module module = LangDataKeys.MODULE.getData(context); if (module == null || !PluginModuleType.isPluginModuleOrDependen...
final Module module = LangDataKeys.MODULE.getData(context); if (PluginModuleType.isPluginModuleOrDependency(module)) {
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final Project project = CommonDataKeys.PROJECT.getData(e.getDataContext()); if (view != null && project != null) { ProjectFileIndex projectFileIndex = ProjectRootManager.getInstance(project).getFileIndex(); PsiDirectory[] dirs = view.getDirectories(); for (PsiDirectory dir : dirs) { <BUG>if (projectFileIndex.isUnderSou...
if (projectFileIndex.isUnderSourceRootOfType(dir.getVirtualFile(), JavaModuleSourceRootTypes.SOURCES) &&
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import com.intellij.codeInspection.ProblemDescriptor; import com.intellij.codeInspection.ProblemHighlightType; import com.intellij.openapi.actionSystem.AnAction; import com.intellij.openapi.diagnostic.Logger; import com.intellij.openapi.module.Module; <BUG>import com.intellij.openapi.module.ModuleUtil; </BUG> import co...
import com.intellij.openapi.module.ModuleUtilCore;
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final PluginBuildConfiguration buildConfiguration = PluginBuildConfiguration.getInstance(module); if (buildConfiguration == null) return null; final ConfigFile configFile = buildConfiguration.getPluginXmlConfigFile(); return configFile != null ? configFile.getXmlFile() : null; } <BUG>public static boolean isPluginModul...
public static boolean isPluginModuleOrDependency(@Nullable Module module) { if (module == null) return false; if (isOfType(module)) return true;
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private static boolean isAllowed(ProblemsHolder holder) { if (PsiUtil.isIdeaProject(holder.getProject())) { return true; } Module module = ModuleUtilCore.findModuleForPsiElement(holder.getFile()); <BUG>if (module != null && PluginModuleType.isPluginModuleOrDependency(module)) { return true;</BUG> } return false; }
if (PluginModuleType.isPluginModuleOrDependency(module)) {
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import java.util.Iterator; import java.util.List; import java.util.Map; import org.alfresco.model.ContentModel; import org.alfresco.service.cmr.repository.StoreRef; <BUG>import org.alfresco.service.cmr.search.LimitBy; import org.alfresco.service.cmr.search.ResultSet;</BUG> import org.alfresco.service.cmr.search.ResultS...
import org.alfresco.service.cmr.search.PermissionEvaluationMode; import org.alfresco.service.cmr.search.ResultSet;
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import java.util.Iterator; import java.util.List; import java.util.Map; import org.alfresco.model.ContentModel; import org.alfresco.service.cmr.repository.StoreRef; <BUG>import org.alfresco.service.cmr.search.LimitBy; import org.alfresco.service.cmr.search.ResultSet;</BUG> import org.alfresco.service.cmr.search.ResultS...
import org.alfresco.service.cmr.search.PermissionEvaluationMode; import org.alfresco.service.cmr.search.ResultSet;
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import org.alfresco.service.cmr.dictionary.DictionaryService; import org.alfresco.service.cmr.dictionary.PropertyDefinition; import org.alfresco.service.cmr.repository.ContentData; import org.alfresco.service.cmr.repository.NodeService; import org.alfresco.service.cmr.repository.StoreRef; <BUG>import org.alfresco.servi...
import org.alfresco.service.cmr.search.PermissionEvaluationMode; import org.alfresco.service.cmr.search.ResultSet;
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searchParameters.setSkipCount((int) parameters.get(PARAMETER_SKIP)); searchParameters.addSort("@" + ContentModel.PROP_MODIFIED, true); searchParameters.addSort("@" + ContentModel.PROP_NODE_DBID, true); <BUG>searchParameters.setUseInMemorySort(false); searchParameters.setLimitBy(LimitBy.FINAL_SIZE); searchParameters.set...
[DELETED]
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} private static final String getQuery(Map<String, Object> parameters) { String query = ""; query += "(TYPE:\"" + parameters.get(PARAMETER_BASETYPE) + "\") "; query += "AND "; <BUG>query += "(@" + ContentModel.PROP_MODIFIED + ":[\"" + getDateAsString((Date) parameters.get(PARAMETER_DATE), DATE_FORMAT) + "T00:00:00.000Z...
query += "(@" + ContentModel.PROP_MODIFIED + ":[\"" + getDateAsString((Date) parameters.get(PARAMETER_DATE), DATE_FORMAT) + "\" TO MAX]) "; return query;
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import java.util.Iterator; import java.util.List; import java.util.Map; import org.alfresco.model.ContentModel; import org.alfresco.service.cmr.repository.StoreRef; <BUG>import org.alfresco.service.cmr.search.LimitBy; import org.alfresco.service.cmr.search.ResultSet;</BUG> import org.alfresco.service.cmr.search.ResultS...
import org.alfresco.service.cmr.search.PermissionEvaluationMode; import org.alfresco.service.cmr.search.ResultSet;
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import java.util.Iterator; import java.util.List; import java.util.Map; import org.alfresco.model.ContentModel; import org.alfresco.service.cmr.repository.StoreRef; <BUG>import org.alfresco.service.cmr.search.LimitBy; import org.alfresco.service.cmr.search.ResultSet;</BUG> import org.alfresco.service.cmr.search.ResultS...
import org.alfresco.service.cmr.search.PermissionEvaluationMode; import org.alfresco.service.cmr.search.ResultSet;
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import org.alfresco.service.cmr.dictionary.DictionaryService; import org.alfresco.service.cmr.dictionary.PropertyDefinition; import org.alfresco.service.cmr.repository.ContentData; import org.alfresco.service.cmr.repository.NodeService; import org.alfresco.service.cmr.repository.StoreRef; <BUG>import org.alfresco.servi...
import org.alfresco.service.cmr.search.PermissionEvaluationMode; import org.alfresco.service.cmr.search.ResultSet;
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searchParameters.setSkipCount((int) parameters.get(PARAMETER_SKIP)); searchParameters.addSort("@" + ContentModel.PROP_MODIFIED, true); searchParameters.addSort("@" + ContentModel.PROP_NODE_DBID, true); <BUG>searchParameters.setUseInMemorySort(false); searchParameters.setLimitBy(LimitBy.FINAL_SIZE); searchParameters.set...
[DELETED]
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} private static final String getQuery(Map<String, Object> parameters) { String query = ""; query += "(TYPE:\"" + parameters.get(PARAMETER_BASETYPE) + "\") "; query += "AND "; <BUG>query += "(@" + ContentModel.PROP_MODIFIED + ":[\"" + getDateAsString((Date) parameters.get(PARAMETER_DATE), DATE_FORMAT) + "T00:00:00.000Z...
query += "(@" + ContentModel.PROP_MODIFIED + ":[\"" + getDateAsString((Date) parameters.get(PARAMETER_DATE), DATE_FORMAT) + "\" TO MAX]) "; return query;
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import org.alfresco.service.cmr.dictionary.DictionaryService; import org.alfresco.service.cmr.dictionary.PropertyDefinition; import org.alfresco.service.cmr.repository.ContentData; import org.alfresco.service.cmr.repository.NodeService; import org.alfresco.service.cmr.repository.StoreRef; <BUG>import org.alfresco.servi...
import org.alfresco.service.cmr.search.PermissionEvaluationMode; import org.alfresco.service.cmr.search.ResultSet;
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package org.jclouds.glacier; import static com.google.common.util.concurrent.MoreExecutors.sameThreadExecutor; import static org.jclouds.Constants.PROPERTY_MAX_RETRIES; import static org.jclouds.Constants.PROPERTY_SO_TIMEOUT; <BUG>import static org.jclouds.glacier.util.TestUtils.buildPayload; import static org.testng.A...
import static com.google.common.base.Charsets.UTF_8; import static org.jclouds.util.Strings2.urlEncode; import static org.testng.Assert.assertEquals;
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this.queryLogger = Loggers.getLogger(logger, ".query"); this.fetchLogger = Loggers.getLogger(logger, ".fetch"); queryLogger.setLevel(level); fetchLogger.setLevel(level); indexSettingsService.addListener(new ApplySettings()); <BUG>} private long parseTimeSetting(String name, long defaultNanos) { try { return componentSe...
[DELETED]
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import java.util.stream.Collectors; public final class RedisManager { public static final RedisManager I = new RedisManager(); private RedisConnectionFactory factory = new RedisConnectionFactory(); public void init() { <BUG>Logs.Console.info("begin init redis..."); </BUG> RedisClusterManager clusterManager = new ZKRedi...
Logs.REDIS.info("begin init redis...");
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factory.setPoolConfig(CC.mp.redis.getPoolConfig(JedisPoolConfig.class)); factory.setRedisServers(clusterManager.getServers()); factory.setCluster(CC.mp.redis.isCluster()); factory.init(); test(); <BUG>Logs.Console.info("init redis success..."); </BUG> } private <R> R call(Function<JedisCommands, R> function, R d) { if ...
Logs.REDIS.info("init redis success...");
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import java.util.concurrent.Executor; public interface ExecutorFactory { String SERVER_BOSS = "sb"; String SERVER_WORK = "sw"; String HTTP_CLIENT_WORK = "hcw"; <BUG>String PUSH_CALLBACK = "pc"; String EVENT_BUS = "eb";</BUG> String MQ = "r"; String BIZ = "b"; Executor get(String name);
String PUSH_TIMER = "pt"; String EVENT_BUS = "eb";
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UNKNOWN(-1); Command(int cmd) { this.cmd = (byte) cmd; } public final byte cmd; <BUG>private static final Command[] values = values(); public static Command toCMD(byte b) { if (b > 0 && b < values.length) return values[b - 1];</BUG> return UNKNOWN; }
[DELETED]
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this.server = server; this.node = node; } @Override public void start() { <BUG>String serverName = server.getClass().getSimpleName(); ThreadPoolManager.I.newThread(serverName, () -> {</BUG> server.init(); server.start(new Listener() { @Override
[DELETED]
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import java.util.Set; import java.util.concurrent.Callable; import java.util.concurrent.Future; import java.util.concurrent.FutureTask; import java.util.concurrent.atomic.AtomicReference; <BUG>public class PushRequest extends FutureTask<Boolean> { </BUG> private static final Logger LOGGER = LoggerFactory.getLogger(Push...
public final class PushRequest extends FutureTask<Boolean> {
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.setUserId(userId) .setContent(content) .setClientType(location.getClientType()) .setTimeout(timeout - 500) .setTags(tags) <BUG>.addFlag(ackModel.flag); }, pushMessage -> { if (pushMessage != null) {</BUG> timeLine.addTimePoint("send-to-gateway-begin");
.addFlag(ackModel.flag)
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pushMessage -> { if (pushMessage != null) {</BUG> timeLine.addTimePoint("send-to-gateway-begin"); pushMessage.sendRaw(f -> { timeLine.addTimePoint("send-to-gateway-end"); <BUG>if (!f.isSuccess()) failure(); });</BUG> PushRequest.this.content = null;//释放内存 future = PushRequestBus.I.put(pushMessage.getSessionId(), PushR...
if (f.isSuccess()) { LOGGER.debug("send to gateway server success, location={}, conn={}", location, f.channel()); } else { LOGGER.error("send to gateway server failure, location={}, conn={}", location, f.channel(), f.cause()); } });
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submit(Status.offline); return this; } public FutureTask<Boolean> broadcast() { timeLine.begin(); <BUG>connectionFactory.broadcast( </BUG> connection -> GatewayPushMessage .build(connection) .setUserId(userId)
boolean success = connectionFactory.broadcast(
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future = PushRequestBus.I.put(pushMessage.getSessionId(), PushRequest.this); } else { success(); } } <BUG>); return this;</BUG> } public void timeout() { submit(Status.timeout);
if (!success) { LOGGER.error("get gateway connection failure when broadcast."); failure(); return this;
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package com.mpush.cache.redis.mq; import com.mpush.cache.redis.listener.ListenerDispatcher; import com.mpush.tools.Jsons; import com.mpush.tools.log.Logs; import redis.clients.jedis.JedisPubSub; <BUG>public class Subscriber extends JedisPubSub { private static ListenerDispatcher dispatcher = ListenerDispatcher.I; pub...
public final class Subscriber extends JedisPubSub { private ListenerDispatcher dispatcher = ListenerDispatcher.I();
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import static com.mpush.api.event.Topics.ONLINE_CHANNEL; public class UserStatusChangeListener implements MessageListener { private static final Logger LOGGER = LoggerFactory.getLogger(UserStatusChangeListener.class); public UserStatusChangeListener() { if ("127.0.0.1".equals(Utils.getLocalIp())) { <BUG>ListenerDispatc...
ListenerDispatcher.I().subscribe(ONLINE_CHANNEL, this); ListenerDispatcher.I().subscribe(OFFLINE_CHANNEL, this);
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package org.mule.routing; import org.mule.DefaultMuleEvent; import org.mule.OptimizedRequestContext; import org.mule.api.DefaultMuleException; <BUG>import org.mule.api.ExceptionPayload; import org.mule.api.MuleEvent;</BUG> import org.mule.api.MuleException; import org.mule.api.MuleMessage; import org.mule.api.MuleMessa...
import org.mule.api.MessagingException; import org.mule.api.MuleEvent;
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public ReportElement getBase() { return base; } @Override public float print(PDDocument document, PDPageContentStream stream, int pageNumber, float startX, float startY, float allowedWidth) throws IOException { <BUG>PDPage currPage = (PDPage) document.getDocumentCatalog().getPages().get(pageNo); PDPageContentStream pag...
PDPage currPage = document.getDocumentCatalog().getPages().get(pageNo); PDPageContentStream pageStream = new PDPageContentStream(document, currPage, PDPageContentStream.AppendMode.APPEND, false);
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public PdfTextStyle(String config) { Assert.hasText(config); String[] split = config.split(","); Assert.isTrue(split.length == 3, "config must look like: 10,Times-Roman,#000000"); fontSize = Integer.parseInt(split[0]); <BUG>font = resolveStandard14Name(split[1]); color = new Color(Integer.valueOf(split[2].substring(1),...
font = getFont(split[1]); color = new Color(Integer.valueOf(split[2].substring(1), 16));