List of usage examples for java.util LinkedHashSet isEmpty
boolean isEmpty();
From source file:com.geewhiz.pacify.filter.PacifyVelocityFilter.java
@Override public LinkedHashSet<Defect> filter(PFile pFile, Map<String, String> propertyValues) { LinkedHashSet<Defect> defects = new LinkedHashSet<Defect>(); if (!BEGIN_TOKEN.equals(pFile.getBeginToken())) { defects.add(new WrongTokenDefinedDefect(pFile, "If you use the PacifyVelocityFilter class, only \"" + BEGIN_TOKEN + "\" is allowed as start token.")); }// w w w .ja v a2 s . c o m if (!END_TOKEN.equals(pFile.getEndToken())) { defects.add(new WrongTokenDefinedDefect(pFile, "If you use the PacifyVelocityFilter class, only \"" + END_TOKEN + "\" is allowed as end token.")); } if (!defects.isEmpty()) { return defects; } File fileToFilter = pFile.getFile(); File tmpFile = FileUtils.createEmptyFileWithSamePermissions(fileToFilter); Template template = getTemplate(fileToFilter, pFile.getEncoding()); Context context = getContext(propertyValues, fileToFilter); try { FileWriterWithEncoding fw = new FileWriterWithEncoding(tmpFile, pFile.getEncoding()); template.merge(context, fw); fw.close(); if (!fileToFilter.delete()) { throw new RuntimeException("Couldn't delete file [" + fileToFilter.getPath() + "]... Aborting!"); } if (!tmpFile.renameTo(fileToFilter)) { throw new RuntimeException("Couldn't rename filtered file from [" + tmpFile.getPath() + "] to [" + fileToFilter.getPath() + "]... Aborting!"); } } catch (IOException e) { throw new RuntimeException(e); } return defects; }
From source file:com.hp.autonomy.searchcomponents.idol.parametricvalues.IdolParametricValuesService.java
@Override public Set<QueryTagInfo> getAllParametricValues(final IdolParametricRequest parametricRequest) throws AciErrorException { final Collection<String> fieldNames = new HashSet<>(); fieldNames.addAll(parametricRequest.getFieldNames()); if (fieldNames.isEmpty()) { fieldNames.addAll(fieldsService.getParametricFields(new IdolFieldsRequest.Builder().build())); }/*from w w w. j a v a 2s . c o m*/ final Set<QueryTagInfo> results; if (fieldNames.isEmpty()) { results = Collections.emptySet(); } else { final AciParameters aciParameters = new AciParameters(TagActions.GetQueryTagValues.name()); parameterHandler.addSearchRestrictions(aciParameters, parametricRequest.getQueryRestrictions()); if (parametricRequest.isModified()) { parameterHandler.addQmsParameters(aciParameters, parametricRequest.getQueryRestrictions()); } aciParameters.add(GetQueryTagValuesParams.DocumentCount.name(), true); aciParameters.add(GetQueryTagValuesParams.MaxValues.name(), parametricRequest.getMaxValues()); aciParameters.add(GetQueryTagValuesParams.FieldName.name(), StringUtils.join(fieldNames.toArray(), ',')); aciParameters.add(GetQueryTagValuesParams.Sort.name(), SortParam.DocumentCount.name()); final GetQueryTagValuesResponseData responseData = contentAciService.executeAction(aciParameters, queryTagValuesResponseProcessor); final List<FlatField> fields = responseData.getField(); results = new LinkedHashSet<>(fields.size()); for (final FlatField field : fields) { final List<JAXBElement<? extends Serializable>> valueElements = field.getValueOrSubvalueOrValues(); final LinkedHashSet<QueryTagCountInfo> values = new LinkedHashSet<>(valueElements.size()); for (final JAXBElement<?> element : valueElements) { if (VALUE_NODE_NAME.equals(element.getName().getLocalPart())) { final TagValue tagValue = (TagValue) element.getValue(); values.add(new QueryTagCountInfo(tagValue.getValue(), tagValue.getCount())); } } final String fieldName = getFieldNameFromPath(field.getName().get(0)); if (!values.isEmpty()) { results.add(new QueryTagInfo(fieldName, values)); } } } return results; }
From source file:net.sf.taverna.t2.activities.beanshell.BeanshellActivityHealthChecker.java
public VisitReport visit(BeanshellActivity activity, List<Object> ancestors) { Object subject = (Processor) VisitReport.findAncestor(ancestors, Processor.class); if (subject == null) { // Fall back to using the activity itself as the subject of the reports subject = activity;//from w ww.ja v a 2 s.co m } List<VisitReport> reports = new ArrayList<VisitReport>(); String script = activity.getConfiguration().get("script").textValue(); if (!script.trim().endsWith(";")) { /** Missing ; on last line is not allowed by Parser, * but is allowed by Interpreter.eval() used at runtime */ script = script + ";"; } Parser parser = new Parser(new StringReader(script)); try { while (!parser.Line()) ; reports.add(new VisitReport(HealthCheck.getInstance(), subject, "Script OK", HealthCheck.NO_PROBLEM, Status.OK)); } catch (ParseException e) { VisitReport report = new VisitReport(HealthCheck.getInstance(), subject, e.getMessage(), HealthCheck.INVALID_SCRIPT, Status.SEVERE); report.setProperty("exception", e); reports.add(report); } // Check if we can find all the Beanshell's dependencies if (activity.getConfiguration().has("localDependency")) { LinkedHashSet<String> localDependencies = new LinkedHashSet<>(); for (JsonNode localDependency : activity.getConfiguration().get("localDependency")) { localDependencies.add(localDependency.textValue()); } String[] jarArray = activity.libDir.list(new FileExtFilter(".jar")); if (jarArray != null) { List<String> jarFiles = Arrays.asList(jarArray); // URLs of all jars found in the lib directory for (String jar : localDependencies) { if (jarFiles.contains(jar)) { localDependencies.remove(jar); } } } if (localDependencies.isEmpty()) { // all dependencies found reports.add(new VisitReport(HealthCheck.getInstance(), subject, "Beanshell dependencies found", HealthCheck.NO_PROBLEM, Status.OK)); } else { VisitReport vr = new VisitReport(HealthCheck.getInstance(), subject, "Beanshell dependencies missing", HealthCheck.MISSING_DEPENDENCY, Status.SEVERE); vr.setProperty("dependencies", localDependencies); vr.setProperty("directory", activity.libDir); reports.add(vr); } } Status status = VisitReport.getWorstStatus(reports); VisitReport report = new VisitReport(HealthCheck.getInstance(), subject, "Beanshell report", HealthCheck.NO_PROBLEM, status, reports); return report; }
From source file:com.geewhiz.pacify.managers.FilterManager.java
public LinkedHashSet<Defect> doFilter() { LinkedHashSet<Defect> defects = new LinkedHashSet<Defect>(); for (Object entry : pMarker.getFilesAndArchives()) { if (entry instanceof PFile) { defects.addAll(filterPFile((PFile) entry)); } else if (entry instanceof PArchive) { defects.addAll(filterPArchive((PArchive) entry)); } else {/*from ww w. j a v a 2 s .c o m*/ throw new NotImplementedException( "Filter implementation for " + entry.getClass().getName() + " not implemented."); } } CheckForNotReplacedTokens checker = new CheckForNotReplacedTokens(); defects.addAll(checker.checkForErrors(pMarker)); if (defects.isEmpty()) { pMarker.getFile().delete(); } return defects; }
From source file:com.qwazr.server.configuration.ServerConfiguration.java
protected ServerConfiguration(final Map<?, ?>... propertiesMaps) throws IOException { // Merge the maps. properties = new HashMap<>(); if (propertiesMaps != null) { for (Map<?, ?> props : propertiesMaps) if (props != null) props.forEach((key, value) -> { if (key != null && value != null) properties.put(key.toString(), value.toString()); });// w ww. ja va 2 s. co m } //Set the data directory dataDirectory = getDataDirectory(getStringProperty(QWAZR_DATA, null)); if (dataDirectory == null) throw new IOException("The data directory has not been set."); if (!Files.exists(dataDirectory)) throw new IOException("The data directory does not exists: " + dataDirectory.toAbsolutePath()); if (!Files.isDirectory(dataDirectory)) throw new IOException("The data directory is not a directory: " + dataDirectory.toAbsolutePath()); //Set the temp directory tempDirectory = getTempDirectory(dataDirectory, getStringProperty(QWAZR_TEMP, null)); if (!Files.exists(tempDirectory)) Files.createDirectories(tempDirectory); if (!Files.exists(tempDirectory)) throw new IOException("The temp directory does not exists: " + tempDirectory.toAbsolutePath()); if (!Files.isDirectory(tempDirectory)) throw new IOException("The temp directory is not a directory: " + tempDirectory.toAbsolutePath()); //Set the configuration directories etcDirectories = getEtcDirectories(getStringProperty(QWAZR_ETC_DIR, null)); etcFileFilter = buildEtcFileFilter(getStringProperty(QWAZR_ETC, null)); //Set the listen address listenAddress = findListenAddress(getStringProperty(LISTEN_ADDR, null)); //Set the public address publicAddress = findPublicAddress(getStringProperty(PUBLIC_ADDR, null), this.listenAddress); //Set the connectors webAppConnector = new WebConnector(publicAddress, getIntegerProperty(WEBAPP_PORT, null), 9090, getStringProperty(WEBAPP_AUTHENTICATION, null), getStringProperty(WEBAPP_REALM, null)); webServiceConnector = new WebConnector(publicAddress, getIntegerProperty(WEBSERVICE_PORT, null), 9091, getStringProperty(WEBSERVICE_AUTHENTICATION, null), getStringProperty(WEBSERVICE_REALM, null)); multicastConnector = new WebConnector(getStringProperty(MULTICAST_ADDR, null), getIntegerProperty(MULTICAST_PORT, null), 9091, null, null); // Collect the master address. final LinkedHashSet<String> set = new LinkedHashSet<>(); try { findMatchingAddress(getStringProperty(QWAZR_MASTERS, null), set); } catch (SocketException e) { LOGGER.warning("Failed in extracting IP information. No master server is configured."); } this.masters = set.isEmpty() ? null : Collections.unmodifiableSet(set); this.groups = buildSet(getStringProperty(QWAZR_GROUPS, null), ",; \t", true); }
From source file:cz.incad.kramerius.pdf.impl.FirstPagePDFServiceImpl.java
String templateParent(PreparedDocument rdoc, ObjectPidsPath path) throws IOException, ParserConfigurationException, SAXException, XPathExpressionException, JAXBException { ResourceBundle resourceBundle = resourceBundleService.getResourceBundle("base", localesProvider.get()); StringTemplate template = new StringTemplate(IOUtils.readAsString( this.getClass().getResourceAsStream("templates/_first_page.st"), Charset.forName("UTF-8"), true)); FirstPageViewObject fpvo = prepareViewObject(resourceBundle); // tistena polozka GeneratedItem itm = new GeneratedItem(); // detaily/*from w ww . j a v a 2 s .c o m*/ Map<String, LinkedHashSet<String>> detailItemValues = new HashMap<String, LinkedHashSet<String>>(); Map<String, Map<String, List<String>>> mods = processModsFromPath(path, null); // Hlavni nazev String rootPid = path.getRoot(); if (mods.get(rootPid).containsKey(TitleBuilder.MODS_TITLE)) { List<String> list = mods.get(rootPid).get(TitleBuilder.MODS_TITLE); if (!list.isEmpty()) { String key = TitleBuilder.MODS_TITLE; itemVals(detailItemValues, list, key); } } // pouze jeden root String[] rProps = renderedProperties(true); String[] fromRootToLeaf = path.getPathFromRootToLeaf(); for (int i = 0; i < fromRootToLeaf.length; i++) { String pidPath = fromRootToLeaf[i]; for (String prop : rProps) { if (mods.get(pidPath).containsKey(prop)) { List<String> list = mods.get(pidPath).get(prop); itemVals(detailItemValues, list, prop); } } } // hlavni nazev List<DetailItem> details = new ArrayList<FirstPagePDFServiceImpl.DetailItem>(); LinkedHashSet<String> maintitles = detailItemValues.get(TitleBuilder.MODS_TITLE); String key = maintitles != null && maintitles.size() > 1 ? resourceBundle.getString("pdf.fp.titles") : resourceBundle.getString("pdf.fp.title"); if (maintitles != null && (!maintitles.isEmpty())) { details.add(new DetailItem(key, vals(maintitles).toString())); } String[] props = renderedProperties(true); for (String prop : props) { LinkedHashSet<String> vals = detailItemValues.get(prop); key = vals != null && vals.size() > 1 ? resourceBundle.getString(i18nKey(prop) + "s") : resourceBundle.getString(i18nKey(prop)); if (vals != null && (!vals.isEmpty())) { details.add(new DetailItem(key, vals(vals).toString())); } } pagesInParentPdf(rdoc, resourceBundle, details); itm.setDetailItems((DetailItem[]) details.toArray(new DetailItem[details.size()])); fpvo.setGeneratedItems(new GeneratedItem[] { itm }); template.setAttribute("viewinfo", fpvo); String templateText = template.toString(); return templateText; }
From source file:cz.incad.kramerius.pdf.impl.FirstPagePDFServiceImpl.java
String templateSelection(PreparedDocument rdoc, String... pids)
throws XPathExpressionException, IOException, ParserConfigurationException, SAXException {
ResourceBundle resourceBundle = resourceBundleService.getResourceBundle("base", localesProvider.get());
StringTemplate template = new StringTemplate(IOUtils.readAsString(
this.getClass().getResourceAsStream("templates/_first_page.st"), Charset.forName("UTF-8"), true));
FirstPageViewObject fpvo = prepareViewObject(resourceBundle);
// tistena polozka
GeneratedItem itm = new GeneratedItem();
Map<String, LinkedHashSet<String>> detailItemValues = new HashMap<String, LinkedHashSet<String>>();
Map<String, ObjectPidsPath> pathsMapping = new HashMap<String, ObjectPidsPath>();
LinkedHashSet<String> roots = new LinkedHashSet<String>();
for (String pid : pids) {
ObjectPidsPath sPath = selectOnePath(pid);
pathsMapping.put(pid, sPath);//from w ww . j a va 2s.com
roots.add(sPath.getRoot());
}
for (String pid : pids) {
ObjectPidsPath path = pathsMapping.get(pid);
Map<String, Map<String, List<String>>> mods = processModsFromPath(path, null);
String rootPid = path.getRoot();
if (mods.get(rootPid).containsKey(TitleBuilder.MODS_TITLE)) {
List<String> list = mods.get(rootPid).get(TitleBuilder.MODS_TITLE);
if (!list.isEmpty()) {
String key = TitleBuilder.MODS_TITLE;
itemVals(detailItemValues, list, key);
}
}
String[] rProps = renderedProperties(roots.size() == 1);
String[] fromRootToLeaf = path.getPathFromRootToLeaf();
for (int i = 0; i < fromRootToLeaf.length; i++) {
String pidPath = fromRootToLeaf[i];
for (String prop : rProps) {
if (mods.get(pidPath).containsKey(prop)) {
List<String> list = mods.get(pidPath).get(prop);
itemVals(detailItemValues, list, prop);
}
}
}
}
// hlavni nazev
List<DetailItem> details = new ArrayList<FirstPagePDFServiceImpl.DetailItem>();
LinkedHashSet<String> maintitles = detailItemValues.get(TitleBuilder.MODS_TITLE);
String key = maintitles != null && maintitles.size() > 1 ? resourceBundle.getString("pdf.fp.titles")
: resourceBundle.getString("pdf.fp.title");
if (maintitles != null && (!maintitles.isEmpty())) {
details.add(new DetailItem(key, vals(maintitles).toString()));
}
for (String prop : renderedProperties(roots.size() == 1)) {
LinkedHashSet<String> vals = detailItemValues.get(prop);
key = vals != null && vals.size() > 1 ? resourceBundle.getString(i18nKey(prop) + "s")
: resourceBundle.getString(i18nKey(prop));
if (vals != null && (!vals.isEmpty())) {
details.add(new DetailItem(key, vals(vals).toString()));
}
}
// stranky v pdfku
pagesInSelectiontPdf(rdoc, resourceBundle, details);
itm.setDetailItems((DetailItem[]) details.toArray(new DetailItem[details.size()]));
fpvo.setGeneratedItems(new GeneratedItem[] { itm });
template.setAttribute("viewinfo", fpvo);
String templateText = template.toString();
return templateText;
}
From source file:org.objectweb.proactive.extensions.dataspaces.vfs.VFSSpacesMountManagerImpl.java
/** * Mounts the first available VFS file system on the given dataspace * @param spaceInfo space information// ww w . j a va 2 s. c o m * @throws FileSystemException if no file system could be mounted */ private void mountFirstAvailableFileSystem(final SpaceInstanceInfo spaceInfo) throws FileSystemException { final DataSpacesURI mountingPoint = spaceInfo.getMountingPoint(); try { writeLock.lock(); if (!mountedSpaces.containsKey(mountingPoint)) { mountedSpaces.put(mountingPoint, new ConcurrentHashMap<String, FileObject>()); } ConcurrentHashMap<String, FileObject> fileSystems = mountedSpaces.get(mountingPoint); if (spaceInfo.getUrls().size() == 0) { throw new IllegalStateException("Empty Space configuration"); } DataSpacesURI spacePart = mountingPoint.getSpacePartOnly(); ArrayList<String> urls = new ArrayList<String>(spaceInfo.getUrls()); if (urls.size() == 1) { urls.add(0, Utils.getLocalAccessURL(urls.get(0), spaceInfo.getPath(), spaceInfo.getHostname())); } logger.debug("[VFSMountManager] Request mounting VFS root list : " + urls); try { VFSMountManagerHelper.mountAny(urls, fileSystems); if (!accessibleFileObjectUris.containsKey(mountingPoint)) { LinkedHashSet<String> srl = new LinkedHashSet<String>(); accessibleFileObjectUris.put(mountingPoint, srl); } LinkedHashSet<String> srl = accessibleFileObjectUris.get(mountingPoint); for (String uri : urls) { if (fileSystems.containsKey(uri)) { srl.add(uri); } } if (srl.isEmpty()) { throw new IllegalStateException("Invalid empty size list when trying to mount " + urls + " mounted map content is " + fileSystems); } accessibleFileObjectUris.put(mountingPoint, srl); if (logger.isDebugEnabled()) logger.debug( String.format("[VFSMountManager] Mounted space: %s (access URL: %s)", spacePart, srl)); mountedSpaces.put(mountingPoint, fileSystems); } catch (org.apache.commons.vfs.FileSystemException e) { mountedSpaces.remove(mountingPoint); throw new FileSystemException("An error occurred while trying to mount " + spaceInfo.getName(), e); } } finally { writeLock.unlock(); } }
From source file:org.mskcc.cbio.oncokb.quest.VariantAnnotationXML.java
public static String annotate(Alteration alt, String tumorType) { // GeneBo geneBo = ApplicationContextSingleton.getGeneBo(); StringBuilder sb = new StringBuilder(); Gene gene = alt.getGene();//from w w w . j a va2 s . c o m // Set<Gene> genes = new HashSet<Gene>(); // if (gene.getEntrezGeneId() > 0) { // genes.add(gene); // } else { // fake gene... could be a fusion gene // Set<String> aliases = gene.getGeneAliases(); // for (String alias : aliases) { // Gene g = geneBo.findGeneByHugoSymbol(alias); // if (g != null) { // genes.add(g); // } // } // } List<TumorType> relevantTumorTypes = TumorTypeUtils.getMappedOncoTreeTypesBySource(tumorType, "quest"); AlterationUtils.annotateAlteration(alt, alt.getAlteration()); AlterationBo alterationBo = ApplicationContextSingleton.getAlterationBo(); LinkedHashSet<Alteration> alterations = alterationBo.findRelevantAlterations(alt, true); // In previous logic, we do not include alternative alleles List<Alteration> alternativeAlleles = AlterationUtils.getAlleleAlterations(alt); alterations.removeAll(alternativeAlleles); EvidenceBo evidenceBo = ApplicationContextSingleton.getEvidenceBo(); // find all drugs //List<Drug> drugs = evidenceBo.findDrugsByAlterations(alterations); // find tumor types Set<String> tumorTypes = new HashSet<>(); if (alterations != null && alterations.size() > 0) { List<Object> tumorTypesEvidence = evidenceBo .findTumorTypesWithEvidencesForAlterations(new ArrayList<>(alterations)); for (Object evidence : tumorTypesEvidence) { if (evidence != null) { Object[] evidences = (Object[]) evidence; if (evidences.length > 0 && evidences[0] != null) { tumorTypes.add((String) evidences[0]); } } } } // sortTumorType(tumorTypes, tumorType); Query query = new Query(alt); query.setTumorType(tumorType); // summary sb.append("<annotation_summary>"); sb.append(SummaryUtils.fullSummary(gene, alt, alterations.isEmpty() ? Collections.singletonList(alt) : new ArrayList<>(alterations), query, relevantTumorTypes)); sb.append("</annotation_summary>\n"); // gene background List<Evidence> geneBgEvs = evidenceBo.findEvidencesByGene(Collections.singleton(gene), Collections.singleton(EvidenceType.GENE_BACKGROUND)); if (!geneBgEvs.isEmpty()) { Evidence ev = geneBgEvs.get(0); sb.append("<gene_annotation>\n"); sb.append(" <description>"); sb.append(StringEscapeUtils.escapeXml10(ev.getDescription()).trim()); sb.append("</description>\n"); exportRefereces(ev, sb, " "); sb.append("</gene_annotation>\n"); } if (alterations.isEmpty()) { sb.append("<!-- There is no information about the function of this variant in the MSKCC OncoKB. -->"); return sb.toString(); } List<Evidence> mutationEffectEbs = evidenceBo.findEvidencesByAlteration(alterations, Collections.singleton(EvidenceType.MUTATION_EFFECT)); for (Evidence ev : mutationEffectEbs) { sb.append("<variant_effect>\n"); sb.append(" <effect>"); if (ev != null) { sb.append(ev.getKnownEffect()); } sb.append("</effect>\n"); if (ev.getDescription() != null) { sb.append(" <description>"); sb.append(StringEscapeUtils.escapeXml10(ev.getDescription()).trim()); sb.append("</description>\n"); } if (ev != null) { exportRefereces(ev, sb, " "); } sb.append("</variant_effect>\n"); } for (String tt : tumorTypes) { TumorType oncoTreeType = TumorTypeUtils.getMappedOncoTreeTypesBySource(tt, "quest").get(0); boolean isRelevant = relevantTumorTypes.contains(oncoTreeType); StringBuilder sbTumorType = new StringBuilder(); sbTumorType.append("<cancer_type type=\"").append(tt).append("\" relevant_to_patient_disease=\"") .append(isRelevant ? "Yes" : "No").append("\">\n"); int nEmp = sbTumorType.length(); // find prognostic implication evidence blob Set<Evidence> prognosticEbs = new HashSet<Evidence>(evidenceBo.findEvidencesByAlteration(alterations, Collections.singleton(EvidenceType.PROGNOSTIC_IMPLICATION), Collections.singleton(oncoTreeType))); if (!prognosticEbs.isEmpty()) { sbTumorType.append(" <prognostic_implications>\n"); sbTumorType.append(" <description>\n"); for (Evidence ev : prognosticEbs) { String description = ev.getDescription(); if (description != null) { sbTumorType.append(" ").append(StringEscapeUtils.escapeXml10(description).trim()) .append("\n"); } } sbTumorType.append("</description>\n"); for (Evidence ev : prognosticEbs) { exportRefereces(ev, sbTumorType, " "); } sbTumorType.append(" </prognostic_implications>\n"); } // STANDARD_THERAPEUTIC_IMPLICATIONS List<Evidence> stdImpEbsSensitivity = evidenceBo.findEvidencesByAlteration(alterations, Collections.singleton(EvidenceType.STANDARD_THERAPEUTIC_IMPLICATIONS_FOR_DRUG_SENSITIVITY), Collections.singleton(oncoTreeType)); List<Evidence> stdImpEbsResisitance = evidenceBo.findEvidencesByAlteration(alterations, Collections.singleton(EvidenceType.STANDARD_THERAPEUTIC_IMPLICATIONS_FOR_DRUG_RESISTANCE), Collections.singleton(oncoTreeType)); //Remove level_0 stdImpEbsSensitivity = filterLevelZeroEvidence(stdImpEbsSensitivity); //Remove level_R3 stdImpEbsResisitance = filterResistanceEvidence(stdImpEbsResisitance); exportTherapeuticImplications(relevantTumorTypes, stdImpEbsSensitivity, stdImpEbsResisitance, "standard_therapeutic_implications", sbTumorType, " ", isRelevant); // INVESTIGATIONAL_THERAPEUTIC_IMPLICATIONS List<Evidence> invImpEbsSensitivity = evidenceBo.findEvidencesByAlteration(alterations, Collections.singleton(EvidenceType.INVESTIGATIONAL_THERAPEUTIC_IMPLICATIONS_DRUG_SENSITIVITY), Collections.singleton(oncoTreeType)); List<Evidence> invImpEbsResisitance = evidenceBo.findEvidencesByAlteration(alterations, Collections.singleton(EvidenceType.INVESTIGATIONAL_THERAPEUTIC_IMPLICATIONS_DRUG_RESISTANCE), Collections.singleton(oncoTreeType)); //Remove level_R3 invImpEbsResisitance = filterResistanceEvidence(invImpEbsResisitance); exportTherapeuticImplications(relevantTumorTypes, invImpEbsSensitivity, invImpEbsResisitance, "investigational_therapeutic_implications", sbTumorType, " ", isRelevant); if (sbTumorType.length() > nEmp) { sbTumorType.append("</cancer_type>\n"); sb.append(sbTumorType); } } return sb.toString(); }
From source file:eionet.cr.web.util.columns.ReferringPredicatesColumn.java
@Override public String format(Object object) { if (object instanceof SubjectDTO) { SubjectDTO subjectDTO = (SubjectDTO) object; // Collect labels of all predicates pointing to referringToHash (ignore derived object values). LinkedHashSet<String> labels = new LinkedHashSet<String>(); Map<String, Collection<ObjectDTO>> predicatesObjects = subjectDTO.getPredicates(); if (predicatesObjects != null && !predicatesObjects.isEmpty()) { for (String predicate : predicatesObjects.keySet()) { Collection<ObjectDTO> objects = predicatesObjects.get(predicate); if (objects != null && !objects.isEmpty()) { for (ObjectDTO objectDTO : objects) { if (objectDTO.getSourceObjectHash() == 0 && objectDTO.getHash() == referringToHash) { String predicateLabel = JstlFunctions .getPredicateLabel(actionBean.getPredicateLabels(), predicate); labels.add(predicateLabel); }// w w w. j av a 2 s.c o m } } } } // Return the above-found labels as a comma-separated list. return labels.isEmpty() ? StringUtils.EMPTY : Util.toCSV(labels); } else { return object == null ? StringUtils.EMPTY : object.toString(); } }