List of usage examples for java.util LinkedHashSet addAll
boolean addAll(Collection<? extends E> c);
From source file:org.jahia.services.content.JCRPublicationService.java
public void publishByInfoList(final List<PublicationInfo> publicationInfos, final String sourceWorkspace, final String destinationWorkspace, boolean checkPermissions, final List<String> comments) throws RepositoryException { LinkedHashSet<String> allIds = new LinkedHashSet<String>(); for (PublicationInfo publicationInfo : publicationInfos) { allIds.addAll(publicationInfo.getAllUuids(false, false, false)); for (PublicationInfo subtree : publicationInfo.getAllReferences()) { allIds.addAll(subtree.getAllUuids(false, false, false)); }/*from w w w.ja v a 2s . com*/ } publish(new ArrayList<String>(allIds), sourceWorkspace, destinationWorkspace, checkPermissions, comments); }
From source file:uk.ac.ebi.intact.dataexchange.cvutils.model.CvObjectOntologyBuilder.java
/** * The main method which converts the OBOOBject * toCVObject.//from w w w . j a va 2 s .c om * */ public <T extends CvObject> T toCvObject(OBOObject oboObj, OboCategory... categories) { T cvObject; Class<T> cvClass = null; try { if (log.isTraceEnabled()) log.trace("ID ->" + oboObj.getID() + " Name ->" + oboObj.getName()); /* first check if it has more than one parents * it true, get all the children * and add to the map4misWithMoreParent but with a new * LinkedHashset same as that of the parent */ if (this.isHavingMoreThanOneParent(oboObj.getID())) { String[] children = getChildren4MisWithMoreParent(oboObj); for (String child : children) { Set<String> linkedSet4child = map4misWithMoreParent.get(oboObj.getID()); if (linkedSet4child != null) { LinkedHashSet<String> newLinkedSet4child = new LinkedHashSet<String>(); newLinkedSet4child.addAll(linkedSet4child); map4misWithMoreParent.put(child, newLinkedSet4child); } } /* * map4misWithMoreParent stores the mi id and a * LinkedHashSet that contains all the root parent class * as we have to create cvterms for each root, for each * iteration take one parent root assign to cv class * and remove it from the set...otherwise we don't know * which parent class was assigned when * * */ String rootclass = null; Set<String> linkedSet = map4misWithMoreParent.get(oboObj.getID()); if (linkedSet != null && linkedSet.size() > 0) { rootclass = (String) linkedSet.toArray()[0]; cvClass = getRootClass(rootclass); } if (rootclass != null) { linkedSet.remove(rootclass); } if (log.isTraceEnabled()) { log.trace("More than One Parent True " + oboObj.getID()); } /* * if more than one parent is true and cvClass is still null means it has parents that are from same root class eg: 3 parents 2 root class so when it iterates third time and as the set contains one two classes, it returns null * */ if (cvClass == null) { cvClass = findCvClassforMI(oboObj.getID()); if (cvClass != null) { String processedKey_ = createCvKey(cvClass, oboObj.getID()); if (processed.containsKey(processedKey_)) { return (T) processed.get(processedKey_); } } } } else { //find the CvClass for any given MI identifier cvClass = findCvClassforMI(oboObj.getID()); } //if CvClass is null then CvTopic.class is taken as default if (cvClass == null) { cvClass = (Class<T>) CvTopic.class; } if (log.isTraceEnabled()) log.trace("cvClass ->" + cvClass.getName()); //Checks if the given object is already mi2cv. If so, returns the CvObject String processedKey = createCvKey(cvClass, oboObj.getID()); if (processed.containsKey(processedKey)) { return (T) processed.get(processedKey); } final Institution institution = IntactContext.getCurrentInstance().getInstitution(); //Short label look for EXACT PSI-MI-short in synonym tag OBO 1.2 String shortLabel = calculateShortLabel(oboObj); cvObject = CvObjectUtils.createCvObject(institution, cvClass, null, shortLabel); if (log.isTraceEnabled()) log.trace("shortLabel ->" + shortLabel); //Identity xref is added to all the cvs cvObject.addXref(createIdentityXref(cvObject, oboObj.getID())); cvObject.setIdentifier(oboObj.getID()); cvObject.setFullName(oboObj.getName()); /******************************** *Database and Qualifier Cv ********************************/ Set<Dbxref> defDbXrefSet = oboObj.getDefDbxrefs(); Object[] dbxrefArray = defDbXrefSet.toArray(); //check if Unique Resid boolean uniqueResid; uniqueResid = checkIfUniqueResid(dbxrefArray); if (dbxrefArray != null) { CvObjectXref xref; //more than one dbxreference //add the first one boolean firstDatabasexref = false; int firstPubmedIndex = getPubmedIndex(dbxrefArray); //add xrefs for (int i = 0; i < dbxrefArray.length; i++) { if (i == firstPubmedIndex) { firstDatabasexref = true; } Dbxref defDbxref = (Dbxref) dbxrefArray[i]; CvTermXref cvtermXref = addQualifiersForOtherDbXreferences(defDbxref, firstDatabasexref, uniqueResid); if (cvtermXref != null) { xref = toXref(cvObject, cvtermXref.getId(), cvtermXref.getQualifier(), cvtermXref.getDatabase()); if (xref != null) { cvObject.addXref(xref); } } } } else { log.debug("No dbxreference"); } /******************************** *Definitions ********************************/ // definition if (oboObj.getDefinition() != null) { String definition = oboObj.getDefinition(); if (definition.contains("\n")) { String[] defArray = definition.split("\n"); String prefixString = ""; String suffixString = ""; if (defArray.length == 2) { prefixString = defArray[0]; suffixString = defArray[1]; } else if (defArray.length > 2) { prefixString = defArray[0]; for (int i = 1; i < defArray.length; i++) { if (i == 1) { suffixString = defArray[i]; } else { suffixString = suffixString + "\n" + defArray[i]; } } } if (suffixString.startsWith("OBSOLETE") || oboObj.isObsolete()) { Annotation annot = toAnnotation(CvTopic.OBSOLETE, suffixString); if (annot != null) { cvObject.addAnnotation(annot); } CvTopic definitionTopicDef = CvObjectUtils.createCvObject(institution, CvTopic.class, null, CvTopic.DEFINITION); cvObject.addAnnotation(new Annotation(institution, definitionTopicDef, prefixString)); } else if (suffixString.startsWith("http")) { Annotation annot = toAnnotation(CvTopic.URL, suffixString); if (annot != null) { cvObject.addAnnotation(annot); } CvTopic definitionTopicDef = CvObjectUtils.createCvObject(institution, CvTopic.class, null, CvTopic.DEFINITION); cvObject.addAnnotation(new Annotation(institution, definitionTopicDef, prefixString)); } else { if (log.isDebugEnabled()) log.debug(" Line Break in Definition--special case MI: " + oboObj.getID() + " Defintion: " + oboObj.getDefinition()); CvTopic definitionTopic = CvObjectUtils.createCvObject(institution, CvTopic.class, null, CvTopic.DEFINITION); cvObject.addAnnotation( new Annotation(institution, definitionTopic, oboObj.getDefinition())); } } else { CvTopic definitionTopic = CvObjectUtils.createCvObject(institution, CvTopic.class, null, CvTopic.DEFINITION); cvObject.addAnnotation(new Annotation(institution, definitionTopic, oboObj.getDefinition())); } } //end of definition /******************************** *XREF ANNOTATIONS ********************************/ Set<Dbxref> dbxrefSet = oboObj.getDbxrefs(); for (Dbxref dbxref : dbxrefSet) { String xref = dbxref.toString(); if (xref.contains(CvTopic.XREF_VALIDATION_REGEXP)) { int firstIndex = xref.indexOf('"'); int lastIndex = xref.lastIndexOf('"'); String annotationText = firstIndex > -1 && lastIndex > -1 ? xref.substring(firstIndex + 1, lastIndex) : xref; Annotation annot = toAnnotation(CvTopic.XREF_VALIDATION_REGEXP, annotationText); if (annot != null) { cvObject.addAnnotation(annot); } } else if (xref.contains(CvTopic.SEARCH_URL)) { Annotation annot = toAnnotation(CvTopic.SEARCH_URL, dbxref.getDesc()); if (annot != null) { cvObject.addAnnotation(annot); } } } /******************************** * comment ********************************/ if (oboObj.getComment() != null && oboObj.getComment().length() > 0) { Annotation annot = toAnnotation(CvTopic.COMMENT, oboObj.getComment()); if (annot != null) { cvObject.addAnnotation(annot); } } //end comment /******************************** * Alias ********************************/ Set<Synonym> syn = oboObj.getSynonyms(); CvObjectAlias alias_; for (Synonym aSyn : syn) { SynonymType synCat = aSyn.getSynonymType(); if (synCat != null && synCat.getID() != null && synCat.getID().equalsIgnoreCase(CvObjectOntologyBuilder.ALIAS_IDENTIFIER)) { String aliasName = aSyn.getText(); alias_ = (CvObjectAlias) toAlias(cvObject, aliasName); cvObject.addAlias(alias_); } } processed.put(processedKey, cvObject); if (log.isTraceEnabled()) log.trace("--Processed size " + processed.size()); if (cvObject instanceof CvDagObject) { Collection<Link> childLinks = oboObj.getChildren(); for (Link childLink1 : childLinks) { CvDagObject dagObject = (CvDagObject) cvObject; OBOObject childObj = (OBOObject) childLink1.getChild(); //check for subset if (categories == null || categories.length == 0) { dagObject.addChild((CvDagObject) toCvObject(childObj, categories)); } else { for (OboCategory category : categories) { for (TermSubset oboCat : childObj.getSubsets()) { if (category.getName().equalsIgnoreCase(oboCat.getName())) { if (log.isTraceEnabled()) { log.trace("Adding child after subset check: " + childObj.getID() + " " + childObj.getName()); } dagObject.addChild((CvDagObject) toCvObject(childObj, categories)); } } } } } } } catch (Exception ex) { throw new IntactException("Exception converting to CvObject from OBOObject: " + oboObj.getID(), ex); } return cvObject; }
From source file:se.unlogic.hierarchy.core.servlets.CoreServlet.java
private void appendLinks(Document doc, ForegroundModuleResponse moduleResponse) { Element links = doc.createElement("links"); doc.getDocumentElement().appendChild(links); LinkedHashSet<LinkTag> linkSet = new LinkedHashSet<LinkTag>(); if (moduleResponse.getLinks() != null) { linkSet.addAll(moduleResponse.getLinks()); }/*from w w w.j a va2 s . c om*/ if (moduleResponse.getBackgroundModuleResponses() != null) { for (BackgroundModuleResponse backgroundModuleResponse : moduleResponse .getBackgroundModuleResponses()) { if (backgroundModuleResponse.getLinks() != null) { linkSet.addAll(backgroundModuleResponse.getLinks()); } } } XMLUtils.append(doc, links, linkSet); }
From source file:se.unlogic.hierarchy.core.servlets.CoreServlet.java
private void appendScripts(Document doc, ForegroundModuleResponse moduleResponse) { Element scripts = doc.createElement("scripts"); doc.getDocumentElement().appendChild(scripts); LinkedHashSet<ScriptTag> scriptsSet = new LinkedHashSet<ScriptTag>(); if (moduleResponse.getScripts() != null) { scriptsSet.addAll(moduleResponse.getScripts()); }//from w w w . ja v a 2 s .c o m if (moduleResponse.getBackgroundModuleResponses() != null) { for (BackgroundModuleResponse backgroundModuleResponse : moduleResponse .getBackgroundModuleResponses()) { if (backgroundModuleResponse.getScripts() != null) { scriptsSet.addAll(backgroundModuleResponse.getScripts()); } } } XMLUtils.append(doc, scripts, scriptsSet); }
From source file:cross.io.InputDataFactory.java
/** * Create a collection of files from the given string resource paths. * * @param input the string resource paths * @return a collection of files/*from w w w. ja v a 2 s . c o m*/ */ @Override public Collection<File> getInputFiles(String[] input) { LinkedHashSet<File> files = new LinkedHashSet<>(); for (String inputString : input) { log.debug("Processing input string {}", inputString); //separate wildcards from plain files String name = FilenameUtils.getName(inputString); boolean isWildcard = name.contains("?") || name.contains("*"); String fullPath = FilenameUtils.getFullPath(inputString); File path = new File(fullPath); File baseDirFile = new File(this.basedir); if (!baseDirFile.exists()) { throw new ExitVmException("Input base directory '" + baseDirFile + "' does not exist!"); } if (!baseDirFile.isDirectory()) { throw new ExitVmException("Input base directory '" + baseDirFile + "' is not a directory!"); } log.debug("Path is absolute: {}", path.isAbsolute()); //identify absolute and relative files if (!path.isAbsolute()) { log.info("Resolving relative file against basedir: {}", this.basedir); path = new File(this.basedir, fullPath); } //normalize filenames fullPath = FilenameUtils.normalize(path.getAbsolutePath()); log.debug("After normalization: {}", fullPath); IOFileFilter dirFilter = this.recurse ? TrueFileFilter.INSTANCE : null; if (isWildcard) { log.debug("Using wildcard matcher for {}", name); files.addAll(FileUtils.listFiles(new File(fullPath), new WildcardFileFilter(name, IOCase.INSENSITIVE), dirFilter)); } else { log.debug("Using name for {}", name); File f = new File(fullPath, name); if (!f.exists()) { throw new ExitVmException("Input file '" + f + "' does not exist!"); } files.add(f); } } return files; }
From source file:istata.service.StataService.java
/** * produce a list with possible sidebar suggestions for the current context * /*from w w w . ja v a 2 s . c om*/ * @param filter * @param pos * @param from * @param to * @return */ public List<ContentLine> suggest(String filter, int pos, int from, int to) { LinkedHashSet<ContentLine> res = new LinkedHashSet<ContentLine>(); ArrayList<ContentLine> rescmd = new ArrayList<ContentLine>(); { int i = 0; for (ContentLine cl : cmdRepository.findAll()) { if (cl.getContent().startsWith(filter)) { ContentLine srl = new ContentLine(); Map<String, Object> model = new HashMap<String, Object>(); model.put("cmd", cl); model.put("from", from); model.put("to", to); String text = VelocityEngineUtils.mergeTemplateIntoString(velocityEngine, "items/cmd.vm", "UTF-8", model); srl.setContent(text); srl.setLine(i++); rescmd.add(srl); } } } Collections.reverse(rescmd); res.addAll(rescmd.subList(0, Math.min(10, rescmd.size()))); List<ContentLine> out = new ArrayList<ContentLine>(); try { IStata stata = stataFactory.getInstance(); /* * get files */ Collection<ContentLine> filesNames = filteredFiles(filter, pos, from, to); res.addAll(filesNames); /* * get VARS, should be a mothod call probably */ // current token StringBuilder token = new StringBuilder(""); StringBuilder rest = new StringBuilder(filter); int p = (pos == -1 || pos > filter.length()) ? filter.length() : pos; char ch = 'x'; while (p > 0 && (CharUtils.isAsciiAlphanumeric(ch = filter.charAt(p - 1)) || ch == '_')) { token.insert(0, ch); rest.deleteCharAt(p - 1); p--; } // remove rest of potential token while (rest.length() > 0 && p > 0 && p < rest.length() && (CharUtils.isAsciiAlphanumeric(rest.charAt(p)) || rest.charAt(p) == '_')) { rest.deleteCharAt(p); } String t = token.toString(); List<StataVar> list = new ArrayList<StataVar>(); List<StataVar> listfull = stata.getVars("", false); if (t.length() > 0) { for (StataVar sv : listfull) { if (sv.getName().startsWith(t)) { list.add(sv); } } } else { list = listfull; } for (int i = 0; i < list.size(); i++) { ContentLine srl = new ContentLine(); srl.setLine(i + 100); String vname = list.get(i).getName(); String cl = new StringBuilder(rest).insert(p, " ").insert(p, vname).toString(); try { String cc = URLEncoder.encode(cl, "UTF-8"); Map<String, Object> model = new HashMap<String, Object>(); model.put("var", vname); model.put("repl", cc); model.put("focuspos", p + 1 + vname.length()); model.put("from", from); model.put("to", to); String text = VelocityEngineUtils.mergeTemplateIntoString(velocityEngine, "items/var.vm", "UTF-8", model); srl.setContent(text); res.add(srl); } catch (UnsupportedEncodingException e) { // TODO Auto-generated catch block e.printStackTrace(); } } } catch (StataNotRunningException e) { ContentLine srl = new ContentLine(); srl.setLine(1); srl.setContent( "<div class='list-group-item sidebaritem error' >" + "Stata not running, you can try to start " + "an instance by clicking " + "<a target='_blank' href='/start'>here</a>" + "</div>"); out.add(srl); } catch (StataBusyException e1) { ContentLine srl = new ContentLine(); srl.setLine(1); srl.setContent("<div class='list-group-item sidebaritem error' >" + "Stata appears to by busy or not running, you can try to " + "start a new instance by clicking " + "<a target='_blank' href='/start'>here</a> " + "or wait for the current job to complete</div>"); out.add(srl); } out.addAll(res); return out; }
From source file:se.unlogic.hierarchy.core.servlets.CoreServlet.java
private void appendScripts(Document doc, List<BackgroundModuleResponse> moduleResponses) { if (moduleResponses != null) { Element scripts = doc.createElement("scripts"); doc.getDocumentElement().appendChild(scripts); LinkedHashSet<ScriptTag> scriptsSet = new LinkedHashSet<ScriptTag>(); for (BackgroundModuleResponse backgroundModuleResponse : moduleResponses) { if (backgroundModuleResponse.getScripts() != null) { scriptsSet.addAll(backgroundModuleResponse.getScripts()); }// www . j a v a 2 s . c o m } XMLUtils.append(doc, scripts, scriptsSet); } }
From source file:org.mskcc.cbio.importer.converter.internal.ConverterImpl.java
/** * Generates case lists for the given portal. * * @param portal String//w w w.j a v a2s. c om * @throws Exception */ @Override public void generateCaseLists(String portal) throws Exception { if (LOG.isInfoEnabled()) { LOG.info("generateCaseLists()"); } // check args if (portal == null) { throw new IllegalArgumentException("portal must not be null"); } // get portal metadata PortalMetadata portalMetadata = config.getPortalMetadata(portal).iterator().next(); if (portalMetadata == null) { if (LOG.isInfoEnabled()) { LOG.info("convertData(), cannot find PortalMetadata, returning"); } return; } // get CaseListMetadata Collection<CaseListMetadata> caseListMetadatas = config.getCaseListMetadata(Config.ALL); // iterate over all cancer studies for (CancerStudyMetadata cancerStudyMetadata : config.getCancerStudyMetadata(portalMetadata.getName())) { // iterate over case lists for (CaseListMetadata caseListMetadata : caseListMetadatas) { if (LOG.isInfoEnabled()) { LOG.info("generateCaseLists(), processing cancer study: " + cancerStudyMetadata + ", case list: " + caseListMetadata.getCaseListFilename()); } // how many staging files are we working with? String[] stagingFilenames = null; // setup union/intersection bools boolean unionCaseList = caseListMetadata.getStagingFilenames() .contains(CaseListMetadata.CASE_LIST_UNION_DELIMITER); boolean intersectionCaseList = caseListMetadata.getStagingFilenames() .contains(CaseListMetadata.CASE_LIST_INTERSECTION_DELIMITER); // union (like all cases) if (unionCaseList) { stagingFilenames = caseListMetadata.getStagingFilenames() .split("\\" + CaseListMetadata.CASE_LIST_UNION_DELIMITER); } // intersection (like complete or cna-seq) else if (intersectionCaseList) { stagingFilenames = caseListMetadata.getStagingFilenames() .split("\\" + CaseListMetadata.CASE_LIST_INTERSECTION_DELIMITER); } // just a single staging file else { stagingFilenames = new String[] { caseListMetadata.getStagingFilenames() }; } if (LOG.isInfoEnabled()) { LOG.info("generateCaseLists(), stagingFilenames: " + java.util.Arrays.toString(stagingFilenames)); } // this is the set we will pass to writeCaseListFile LinkedHashSet<String> caseSet = new LinkedHashSet<String>(); // this indicates the number of staging files processed - // used to verify that an intersection should be written int numStagingFilesProcessed = 0; for (String stagingFilename : stagingFilenames) { if (LOG.isInfoEnabled()) { LOG.info("generateCaseLists(), processing stagingFile: " + stagingFilename); } // compute the case set List<String> caseList = fileUtils.getCaseListFromStagingFile(caseIDs, portalMetadata, cancerStudyMetadata, stagingFilename); // we may not have this datatype in study if (caseList.size() == 0) { if (LOG.isInfoEnabled()) { LOG.info("generateCaseLists(), stagingFileHeader is empty: " + stagingFilename + ", skipping..."); } continue; } // intersection if (intersectionCaseList) { if (caseSet.isEmpty()) { caseSet.addAll(caseList); } else { caseSet.retainAll(caseList); } } // otherwise union or single staging (treat the same) else { caseSet.addAll(caseList); } ++numStagingFilesProcessed; } // write the case list file (don't make empty case lists) if (caseSet.size() > 0) { if (LOG.isInfoEnabled()) { LOG.info("generateCaseLists(), calling writeCaseListFile()..."); } // do not write out complete cases file unless we've processed all the files required if (intersectionCaseList && (numStagingFilesProcessed != stagingFilenames.length)) { if (LOG.isInfoEnabled()) { LOG.info( "generateCaseLists(), number of staging files processed != number staging files required for cases_complete.txt, skipping call to writeCaseListFile()..."); } continue; } fileUtils.writeCaseListFile(portalMetadata, cancerStudyMetadata, caseListMetadata, caseSet.toArray(new String[0])); } else if (LOG.isInfoEnabled()) { LOG.info("generateCaseLists(), caseSet.size() <= 0, skipping call to writeCaseListFile()..."); } // if union, write out the cancer study metadata file if (caseSet.size() > 0 && caseListMetadata.getCaseListFilename().equals(ALL_CASES_FILENAME)) { if (LOG.isInfoEnabled()) { LOG.info( "generateCaseLists(), processed all cases list, we can now update cancerStudyMetadata file()..."); } fileUtils.writeCancerStudyMetadataFile(portalMetadata, cancerStudyMetadata, caseSet.size()); } } } }
From source file:se.unlogic.hierarchy.core.servlets.CoreServlet.java
private void appendLinks(Document doc, List<BackgroundModuleResponse> moduleResponses) { if (moduleResponses != null) { Element links = doc.createElement("links"); doc.getDocumentElement().appendChild(links); LinkedHashSet<LinkTag> linkSet = new LinkedHashSet<LinkTag>(); // Only add links from background modules that are not previously added for (BackgroundModuleResponse moduleResponse : moduleResponses) { if (moduleResponse.getLinks() != null) { linkSet.addAll(moduleResponse.getLinks()); }/* w w w. j a va 2 s . com*/ } XMLUtils.append(doc, links, linkSet); } }
From source file:org.apache.ws.scout.registry.BusinessLifeCycleManagerImpl.java
protected BulkResponse deleteOperation(Collection<Key> keys, String op) throws JAXRException { if (keys == null) throw new JAXRException("Keys provided to " + op + " are null"); //Now we need to convert the collection into a vector for juddi BulkResponseImpl bulk = new BulkResponseImpl(); String[] keyarr = new String[keys.size()]; Result[] keyResultArr;//from w w w . j a va 2s.c om LinkedHashSet<Key> coll = new LinkedHashSet<Key>(); Collection<Exception> exceptions = new ArrayList<Exception>(); try { Iterator iter = keys.iterator(); int currLoc = 0; while (iter.hasNext()) { Key key = (Key) iter.next(); keyarr[currLoc] = key.getId(); currLoc++; } // Save business DispositionReport bd = (DispositionReport) executeOperation(keyarr, op); List<Result> resultList = bd.getResult(); keyResultArr = new Result[resultList.size()]; resultList.toArray(keyResultArr); log.debug("After deleting Business. Obtained vector size:" + keyResultArr != null ? keyResultArr.length : 0); for (int i = 0; keyResultArr != null && i < keyResultArr.length; i++) { Result result = (Result) keyResultArr[i]; int errno = result.getErrno(); if (errno == 0) { coll.addAll(keys); } else { ErrInfo errinfo = result.getErrInfo(); DeleteException de = new DeleteException(errinfo.getErrCode() + ":" + errinfo.getValue()); bulk.setStatus(JAXRResponse.STATUS_FAILURE); exceptions.add(de); } } } catch (RegistryException regExcept) { /* * jUDDI (and prollie others) throw an exception on any fault in * the transaction w/ the registry, so we don't get any partial * success */ DeleteException de = new DeleteException(regExcept.getFaultCode() + ":" + regExcept.getFaultString(), regExcept); bulk.setStatus(JAXRResponse.STATUS_FAILURE); exceptions.add(de); } catch (JAXRException tran) { exceptions.add(new JAXRException("Apache JAXR Impl:", tran)); bulk.setStatus(JAXRResponse.STATUS_FAILURE); } bulk.setCollection(coll); bulk.setExceptions(exceptions); return bulk; }