Java Code Examples for org.apache.commons.collections4.ListUtils#union()

public CoveragePerContigCollection(final LocatableMetadata metadata,
                                   final List<CoveragePerContig> coveragePerContigs,
                                   final List<String> contigs) {
    super(
            metadata,
            coveragePerContigs,
            new TableColumnCollection(ListUtils.union(Collections.singletonList(SAMPLE_NAME_TABLE_COLUMN), contigs)),
            dataLine -> new CoveragePerContig(
                    dataLine.get(SAMPLE_NAME_TABLE_COLUMN),
                    contigs.stream().collect(Collectors.toMap(
                            Function.identity(),
                            dataLine::getInt,
                            (u, v) -> {
                                throw new GATKException.ShouldNeverReachHereException("Cannot have duplicate contigs.");
                            },   //contigs should already be distinct
                            LinkedHashMap::new))),
            (coveragePerContig, dataLine) -> {
                dataLine.append(coveragePerContig.getSampleName());
                contigs.stream().map(coveragePerContig::getCoverage).forEach(dataLine::append);
            });
}
 

@Override
public List<ComRecipientHistory> getStatusHistory(int recipientId, int companyId) {
    List<RecipientBindingHistory> recipientBindingHistory = getBindingHistory(recipientId, companyId);
    List<ComRecipientHistory> convertedBindingHistory = recipientHistoryConverter.convert(recipientBindingHistory);
    List<ComRecipientHistory> recipientProfileHistory = getProfileHistory(recipientId, companyId);
    List<ComRecipientHistory> unitedList = ListUtils.union(convertedBindingHistory, recipientProfileHistory);
    unitedList.sort(Comparator.comparing(ComRecipientHistory::getChangeDate,
            Comparator.nullsFirst(Comparator.naturalOrder())).reversed());
    return unitedList;
}
 

public ScalarHMMSegmenter(final List<SimpleInterval> positions, final List<DATA> data,
                          final List<Double> constantHiddenStates, final List<Double> initialNonConstantHiddenStates) {
    super(positions, data, ListUtils.union(constantHiddenStates, initialNonConstantHiddenStates),
            uniformWeights(constantHiddenStates.size() + initialNonConstantHiddenStates.size()),
            DEFAULT_INITIAL_CONCENTRATION, DEFAULT_MEMORY_LENGTH);
    numConstantStates = constantHiddenStates.size();
}
 

/**
 * Extra step required for backwards compatibility (see {@link DeployedMtaEnvDetector})
 *
 * @param mtasByMetadata
 * @param mtasByEnv
 * @return
 */
private List<DeployedMta> combineMetadataAndEnvMtas(List<DeployedMta> mtasByMetadata, List<DeployedMta> mtasByEnv) {

    List<DeployedMta> missedMtas = mtasByEnv.stream()
                                            .filter(mta -> !mtasByMetadata.contains(mta))
                                            .collect(Collectors.toList());

    return ListUtils.union(mtasByMetadata, missedMtas);
}
 

void delete_item(Business business, Process process, boolean onlyRemoveNotCompleted) throws Exception {
	List<String> jobs = business.work().listJobWithProcess(process.getId());
	if (!onlyRemoveNotCompleted) {
		jobs = ListUtils.union(jobs, business.workCompleted().listJobWithProcess(process.getId()));
	}
	EntityManagerContainer emc = business.entityManagerContainer();
	for (String job : jobs) {
		emc.beginTransaction(Item.class);
		for (Item o : business.item().listObjectWithJob(job)) {
			emc.remove(o);
		}
		emc.commit();
	}
}
 

private void delete_dataItem(Business business, Application application, boolean onlyRemoveNotCompleted)
		throws Exception {
	List<String> jobs = business.work().listJobWithApplication(application.getId());
	if (!onlyRemoveNotCompleted) {
		jobs = ListUtils.union(jobs, business.workCompleted().listJobWithApplication(application.getId()));
	}
	EntityManagerContainer emc = business.entityManagerContainer();
	for (String job : jobs) {
		emc.beginTransaction(Item.class);
		for (Item o : business.item().listObjectWithJob(job)) {
			emc.remove(o);
		}
		emc.commit();
	}
}
 

public static AlleleLikelihoods<GATKRead, Allele> makeLikelihoods(final String sample,
                                                      final List<GATKRead> refReads,
                                                      final List<GATKRead> altReads,
                                                      final List<GATKRead> uninformativeReads,
                                                      final double refReadAltLikelihood,
                                                      final double altReadRefLikelihood,
                                                      final double badReadAltLikelihood,
                                                      final Allele refAllele,
                                                      final Allele altAllele) {
    final List<GATKRead> reads = ListUtils.union(ListUtils.union(refReads, altReads), uninformativeReads);
    final AlleleLikelihoods<GATKRead, Allele> likelihoods = initializeReadLikelihoods(sample, new IndexedAlleleList<>(Arrays.asList(refAllele, altAllele)), reads);

    final LikelihoodMatrix<GATKRead, Allele> matrix = likelihoods.sampleMatrix(0);
    int readIndex = 0;
    for (int i = 0; i < refReads.size(); i++) {
        matrix.set(0, readIndex, MATCH_LIKELIHOOD);
        matrix.set(1, readIndex, refReadAltLikelihood);
        readIndex++;
    }

    for (int i = 0; i < altReads.size(); i++) {
        matrix.set(0, readIndex, altReadRefLikelihood);
        matrix.set(1, readIndex, MATCH_LIKELIHOOD);
        readIndex++;
    }

    for (int i = 0; i < uninformativeReads.size(); i++) {
        matrix.set(0, readIndex, MATCH_LIKELIHOOD);
        matrix.set(1, readIndex, badReadAltLikelihood);
        readIndex++;
    }

    return likelihoods;
}
 

ActionResult<Wo<WoObject>> execute(EffectivePerson effectivePerson, String id, String callback, byte[] bytes,
		FormDataContentDisposition disposition) throws Exception {
	try (EntityManagerContainer emc = EntityManagerContainerFactory.instance().create()) {
		ActionResult<Wo<WoObject>> result = new ActionResult<>();
		Attachment attachment = emc.find(id, Attachment.class);
		if (null == attachment) {
			throw new ExceptionAttachmentNotExistCallback(callback, id);
		}
		if ((!StringUtils.equals(effectivePerson.getDistinguishedName(), attachment.getPerson()))
				&& (!attachment.getEditorList().contains(effectivePerson.getDistinguishedName()))) {
			throw new ExceptionAttachmentAccessDeniedCallback(effectivePerson, callback, attachment);
		}
		StorageMapping mapping = ThisApplication.context().storageMappings().get(Attachment.class,
				attachment.getStorage());
		if (null == mapping) {
			throw new ExceptionStorageNotExistCallback(callback, attachment.getStorage());
		}
		attachment.setLastUpdatePerson(effectivePerson.getDistinguishedName());
		/** 禁止不带扩展名的文件上传 */
		/** 文件名编码转换 */
		String fileName = new String(disposition.getFileName().getBytes(DefaultCharset.charset_iso_8859_1),
				DefaultCharset.charset);
		fileName = FilenameUtils.getName(fileName);

		if (StringUtils.isEmpty(FilenameUtils.getExtension(fileName))) {
			throw new ExceptionEmptyExtensionCallback(callback, fileName);
		}
		/** 不允许不同的扩展名上传 */
		if (!Objects.equals(StringUtils.lowerCase(FilenameUtils.getExtension(fileName)),
				attachment.getExtension())) {
			throw new ExceptionExtensionNotMatchCallback(callback, fileName, attachment.getExtension());
		}
		emc.beginTransaction(Attachment.class);
		attachment.updateContent(mapping, bytes);
		emc.check(attachment, CheckPersistType.all);
		emc.commit();
		/** 通知所有的共享和共享编辑人员 */
		List<String> people = new ArrayList<>();
		people = ListUtils.union(attachment.getShareList(), attachment.getEditorList());
		people.add(attachment.getPerson());
		for (String o : ListTools.trim(people, true, true)) {
			if (!StringUtils.equals(o, effectivePerson.getDistinguishedName())) {
				this.message_send_attachment_editorModify(attachment, effectivePerson.getDistinguishedName(), o);
			}
		}
		ApplicationCache.notify(Attachment.class, attachment.getId());
		WoObject woObject = new WoObject();
		woObject.setId(attachment.getId());
		Wo<WoObject> wo = new Wo<>(callback, woObject);
		result.setData(wo);
		return result;
	}
}
 

ActionResult<Wo> execute(EffectivePerson effectivePerson, String id, byte[] bytes,
		FormDataContentDisposition disposition) throws Exception {
	try (EntityManagerContainer emc = EntityManagerContainerFactory.instance().create()) {
		ActionResult<Wo> result = new ActionResult<>();
		Attachment attachment = emc.find(id, Attachment.class);
		if (null == attachment) {
			throw new ExceptionAttachmentNotExist(id);
		}
		if ((!StringUtils.equals(effectivePerson.getDistinguishedName(), attachment.getPerson()))
				&& (!attachment.getEditorList().contains(effectivePerson.getDistinguishedName()))) {
			throw new ExceptionAttachmentAccessDenied(effectivePerson, attachment);
		}
		StorageMapping mapping = ThisApplication.context().storageMappings().get(Attachment.class,
				attachment.getStorage());
		if (null == mapping) {
			throw new ExceptionStorageNotExist(attachment.getStorage());
		}
		attachment.setLastUpdatePerson(effectivePerson.getDistinguishedName());
		/** 禁止不带扩展名的文件上传 */
		/** 文件名编码转换 */
		String fileName = new String(disposition.getFileName().getBytes(DefaultCharset.charset_iso_8859_1),
				DefaultCharset.charset);
		fileName = FilenameUtils.getName(fileName);

		if (StringUtils.isEmpty(FilenameUtils.getExtension(fileName))) {
			throw new ExceptionEmptyExtension(fileName);
		}
		/** 不允许不同的扩展名上传 */
		if (!Objects.equals(StringUtils.lowerCase(FilenameUtils.getExtension(fileName)),
				attachment.getExtension())) {
			throw new ExceptionExtensionNotMatch(fileName, attachment.getExtension());
		}
		emc.beginTransaction(Attachment.class);
		attachment.updateContent(mapping, bytes);
		emc.check(attachment, CheckPersistType.all);
		emc.commit();
		/** 通知所有的共享和共享编辑人员 */
		List<String> people = new ArrayList<>();
		people = ListUtils.union(attachment.getShareList(), attachment.getEditorList());
		people.add(attachment.getPerson());
		for (String o : ListTools.trim(people, true, true)) {
			if (!StringUtils.equals(o, effectivePerson.getDistinguishedName())) {
				this.message_send_attachment_editorModify(attachment, effectivePerson.getDistinguishedName(), o);
			}
		}
		ApplicationCache.notify(Attachment.class, attachment.getId());
		Wo wo = new Wo();
		wo.setId(attachment.getId());
		result.setData(wo);
		return result;
	}
}
 

private static TableColumnCollection getColumns(final List<AnnotationKey<?>> annotationKeys) {
    return new TableColumnCollection(
            ListUtils.union(
                    AnnotatedIntervalTableColumn.STANDARD_COLUMNS.names(),
                    annotationKeys.stream().map(AnnotationKey::getName).collect(Collectors.toList())));
}
 

ActionResult<Wo> execute(EffectivePerson effectivePerson, String id, byte[] bytes,
		FormDataContentDisposition disposition) throws Exception {
	try (EntityManagerContainer emc = EntityManagerContainerFactory.instance().create()) {
		ActionResult<Wo> result = new ActionResult<>();
		Attachment attachment = emc.find(id, Attachment.class);
		if (null == attachment) {
			throw new ExceptionAttachmentNotExist(id);
		}
		if ((!StringUtils.equals(effectivePerson.getDistinguishedName(), attachment.getPerson()))
				&& (!attachment.getEditorList().contains(effectivePerson.getDistinguishedName()))) {
			throw new ExceptionAttachmentAccessDenied(effectivePerson, attachment);
		}
		StorageMapping mapping = ThisApplication.context().storageMappings().get(Attachment.class,
				attachment.getStorage());
		if (null == mapping) {
			throw new ExceptionStorageNotExist(attachment.getStorage());
		}
		attachment.setLastUpdatePerson(effectivePerson.getDistinguishedName());
		/** 禁止不带扩展名的文件上传 */
		/** 文件名编码转换 */
		String fileName = new String(disposition.getFileName().getBytes(DefaultCharset.charset_iso_8859_1),
				DefaultCharset.charset);
		fileName = FilenameUtils.getName(fileName);

		if (StringUtils.isEmpty(FilenameUtils.getExtension(fileName))) {
			throw new ExceptionEmptyExtension(fileName);
		}
		/** 不允许不同的扩展名上传 */
		if (!Objects.equals(StringUtils.lowerCase(FilenameUtils.getExtension(fileName)),
				attachment.getExtension())) {
			throw new ExceptionExtensionNotMatch(fileName, attachment.getExtension());
		}
		emc.beginTransaction(Attachment.class);
		attachment.updateContent(mapping, bytes);
		emc.check(attachment, CheckPersistType.all);
		emc.commit();
		/** 通知所有的共享和共享编辑人员 */
		List<String> people = new ArrayList<>();
		people = ListUtils.union(attachment.getShareList(), attachment.getEditorList());
		people.add(attachment.getPerson());
		for (String o : ListTools.trim(people, true, true)) {
			if (!StringUtils.equals(o, effectivePerson.getDistinguishedName())) {
				this.message_send_attachment_editorModify(attachment, effectivePerson.getDistinguishedName(), o);
			}
		}
		ApplicationCache.notify(Attachment.class, attachment.getId());
		Wo wo = new Wo();
		wo.setId(attachment.getId());
		result.setData(wo);
		return result;
	}
}
 

@Override
public Object apply(List<Object> args, Context context) throws ParseException {
  SensorEnrichmentConfig config = getSensorEnrichmentConfig(args, 0);

  ThreatIntelConfig tiConfig = (ThreatIntelConfig) getConfig(config, EnrichmentConfigFunctions.Type.THREAT_INTEL);
  if(tiConfig == null) {
    tiConfig = new ThreatIntelConfig();
    config.setThreatIntel(tiConfig);
  }

  org.apache.metron.common.configuration.enrichment.threatintel.ThreatTriageConfig triageConfig = tiConfig.getTriageConfig();
  if(triageConfig == null) {
    triageConfig = new org.apache.metron.common.configuration.enrichment.threatintel.ThreatTriageConfig();
    tiConfig.setTriageConfig(triageConfig);
  }

  // build the new rules
  List<RiskLevelRule> newRules = new ArrayList<>();
  for(Map<String, Object> newRule : getNewRuleDefinitions(args)) {

    if(newRule != null && newRule.containsKey("rule") && newRule.containsKey("score")) {

      // create the rule
      RiskLevelRule ruleToAdd = new RiskLevelRule();
      ruleToAdd.setRule((String) newRule.get(RULE_EXPR_KEY));
      ruleToAdd.setScoreExpression(newRule.get(RULE_SCORE_KEY));

      // add optional rule fields
      if (newRule.containsKey(RULE_NAME_KEY)) {
        ruleToAdd.setName((String) newRule.get(RULE_NAME_KEY));
      }
      if (newRule.containsKey(RULE_COMMENT_KEY)) {
        ruleToAdd.setComment((String) newRule.get(RULE_COMMENT_KEY));
      }
      if (newRule.containsKey(RULE_REASON_KEY)) {
        ruleToAdd.setReason((String) newRule.get(RULE_REASON_KEY));
      }
      newRules.add(ruleToAdd);
    }
  }

  // combine the new and existing rules
  List<RiskLevelRule> allRules = ListUtils.union(triageConfig.getRiskLevelRules(), newRules);
  triageConfig.setRiskLevelRules(allRules);

  return toJSON(config);
}
 

ActionResult<Wo<WoObject>> execute(EffectivePerson effectivePerson, String id, String callback, byte[] bytes,
		FormDataContentDisposition disposition) throws Exception {
	try (EntityManagerContainer emc = EntityManagerContainerFactory.instance().create()) {
		ActionResult<Wo<WoObject>> result = new ActionResult<>();
		Attachment attachment = emc.find(id, Attachment.class);
		if (null == attachment) {
			throw new ExceptionAttachmentNotExistCallback(callback, id);
		}
		if ((!StringUtils.equals(effectivePerson.getDistinguishedName(), attachment.getPerson()))
				&& (!attachment.getEditorList().contains(effectivePerson.getDistinguishedName()))) {
			throw new ExceptionAttachmentAccessDeniedCallback(effectivePerson, callback, attachment);
		}
		StorageMapping mapping = ThisApplication.context().storageMappings().get(Attachment.class,
				attachment.getStorage());
		if (null == mapping) {
			throw new ExceptionStorageNotExistCallback(callback, attachment.getStorage());
		}
		attachment.setLastUpdatePerson(effectivePerson.getDistinguishedName());
		/** 禁止不带扩展名的文件上传 */
		/** 文件名编码转换 */
		String fileName = new String(disposition.getFileName().getBytes(DefaultCharset.charset_iso_8859_1),
				DefaultCharset.charset);
		fileName = FilenameUtils.getName(fileName);

		if (StringUtils.isEmpty(FilenameUtils.getExtension(fileName))) {
			throw new ExceptionEmptyExtensionCallback(callback, fileName);
		}
		/** 不允许不同的扩展名上传 */
		if (!Objects.equals(StringUtils.lowerCase(FilenameUtils.getExtension(fileName)),
				attachment.getExtension())) {
			throw new ExceptionExtensionNotMatchCallback(callback, fileName, attachment.getExtension());
		}
		emc.beginTransaction(Attachment.class);
		attachment.updateContent(mapping, bytes);
		emc.check(attachment, CheckPersistType.all);
		emc.commit();
		/** 通知所有的共享和共享编辑人员 */
		List<String> people = new ArrayList<>();
		people = ListUtils.union(attachment.getShareList(), attachment.getEditorList());
		people.add(attachment.getPerson());
		for (String o : ListTools.trim(people, true, true)) {
			if (!StringUtils.equals(o, effectivePerson.getDistinguishedName())) {
				this.message_send_attachment_editorModify(attachment, effectivePerson.getDistinguishedName(), o);
			}
		}
		ApplicationCache.notify(Attachment.class, attachment.getId());
		WoObject woObject = new WoObject();
		woObject.setId(attachment.getId());
		Wo<WoObject> wo = new Wo<>(callback, woObject);
		result.setData(wo);
		return result;
	}
}
 

ActionResult<Wo> execute(EffectivePerson effectivePerson, String id, byte[] bytes,
		FormDataContentDisposition disposition) throws Exception {
	try (EntityManagerContainer emc = EntityManagerContainerFactory.instance().create()) {
		ActionResult<Wo> result = new ActionResult<>();
		Attachment attachment = emc.find(id, Attachment.class);
		if (null == attachment) {
			throw new ExceptionAttachmentNotExist(id);
		}
		if ((!StringUtils.equals(effectivePerson.getDistinguishedName(), attachment.getPerson()))
				&& (!attachment.getEditorList().contains(effectivePerson.getDistinguishedName()))) {
			throw new ExceptionAttachmentAccessDenied(effectivePerson, attachment);
		}
		StorageMapping mapping = ThisApplication.context().storageMappings().get(Attachment.class,
				attachment.getStorage());
		if (null == mapping) {
			throw new ExceptionStorageNotExist(attachment.getStorage());
		}
		attachment.setLastUpdatePerson(effectivePerson.getDistinguishedName());
		/** 禁止不带扩展名的文件上传 */
		/** 文件名编码转换 */
		String fileName = new String(disposition.getFileName().getBytes(DefaultCharset.charset_iso_8859_1),
				DefaultCharset.charset);
		fileName = FilenameUtils.getName(fileName);

		if (StringUtils.isEmpty(FilenameUtils.getExtension(fileName))) {
			throw new ExceptionEmptyExtension(fileName);
		}
		/** 不允许不同的扩展名上传 */
		if (!Objects.equals(StringUtils.lowerCase(FilenameUtils.getExtension(fileName)),
				attachment.getExtension())) {
			throw new ExceptionExtensionNotMatch(fileName, attachment.getExtension());
		}
		emc.beginTransaction(Attachment.class);
		attachment.updateContent(mapping, bytes);
		emc.check(attachment, CheckPersistType.all);
		emc.commit();
		/** 通知所有的共享和共享编辑人员 */
		List<String> people = new ArrayList<>();
		people = ListUtils.union(attachment.getShareList(), attachment.getEditorList());
		people.add(attachment.getPerson());
		for (String o : ListTools.trim(people, true, true)) {
			if (!StringUtils.equals(o, effectivePerson.getDistinguishedName())) {
				this.message_send_attachment_editorModify(attachment, effectivePerson.getDistinguishedName(), o);
			}
		}
		ApplicationCache.notify(Attachment.class, attachment.getId());
		Wo wo = new Wo();
		wo.setId(attachment.getId());
		result.setData(wo);
		return result;
	}
}
 

public static List<Object> usingApacheCommons(List<Object> first, List<Object> second) {
    List<Object> combined = ListUtils.union(first, second);
    return combined;
}
 

private List<String> prepareServicesToBind() {
    if (input.application.shouldKeepServiceBindings) {
        return ListUtils.union(input.application.services, input.existingApplication.services);
    }
    return input.application.services;
}
 

public List<? extends DmgMessage> getMessages() {
    return ListUtils.union(ListUtils.union(this.lists, this.inscriptions), ListUtils.union(this.closures, this.extensions));
}
 

private VariantContext addNonRefSymbolicAllele(final VariantContext mergedVC) {
    final List<Allele> alleleList = ListUtils.union(mergedVC.getAlleles(), Arrays.asList(GATKVCFConstants.NON_REF_SYMBOLIC_ALLELE));
    return new VariantContextBuilder(mergedVC).alleles(alleleList).make();
}
 

public static VariantContext addNonRefSymbolicAllele(final VariantContext mergedVC) {
    final List<Allele> alleleList = ListUtils.union(mergedVC.getAlleles(), Arrays.asList(Allele.NON_REF_ALLELE));
    return new VariantContextBuilder(mergedVC).alleles(alleleList).make();
}
 

public static List<String> getParametersForTag(final String tagName) {
	return ListUtils.union(getMandatoryParametersForTag(tagName), getOptionalParametersForTag(tagName));
}