List of usage examples for java.util Collection clear
void clear();
From source file:ubic.gemma.persistence.service.common.auditAndSecurity.AuditEventDaoImpl.java
private Map<Auditable, AuditEvent> getLastEvent(final Collection<? extends Auditable> auditables, Class<? extends AuditEventType> type) { Map<Auditable, AuditEvent> result = new HashMap<>(); if (auditables.size() == 0) return result; final Map<AuditTrail, Auditable> atMap = this.getAuditTrailMap(auditables); List<String> classes = this.getClassHierarchy(type); //language=HQL final String queryString = "select trail, ae from AuditTrailImpl trail " + "inner join trail.events ae inner join ae.eventType et inner join fetch ae.performer where trail in (:trails) " + "and et.class in (:classes) order by ae.date desc, ae.id desc "; StopWatch timer = new StopWatch(); timer.start();//ww w. j a v a 2s . c o m Collection<AuditTrail> batch = new ArrayList<>(); int batchSize = 100; for (AuditTrail at : atMap.keySet()) { batch.add(at); if (batch.size() == batchSize) { org.hibernate.Query queryObject = this.getSessionFactory().getCurrentSession() .createQuery(queryString); queryObject.setParameterList("trails", batch); queryObject.setParameterList("classes", classes); queryObject.setReadOnly(true); List<?> qr = queryObject.list(); if (qr == null || qr.isEmpty()) { batch.clear(); continue; } this.putAllQrs(result, qr, atMap); batch.clear(); } } if (!batch.isEmpty()) { org.hibernate.Query queryObject = this.getSessionFactory().getCurrentSession().createQuery(queryString); queryObject.setParameterList("trails", batch); // if too many will fail. queryObject.setParameterList("classes", classes); queryObject.setReadOnly(true); List<?> qr = queryObject.list(); if (qr == null || qr.isEmpty()) return result; this.putAllQrs(result, qr, atMap); } timer.stop(); if (timer.getTime() > 500) { AbstractDao.log.info("Last event of type " + type.getSimpleName() + " retrieved for " + auditables.size() + " items in " + timer.getTime() + "ms"); } return result; }
From source file:com.screenslicer.core.nlp.Person.java
public static String extractName(String src, boolean strict, boolean dictionaryOnly) { NameFinderME nameFinder = new NameFinderME(nameModel); String[] sentences = NlpUtil.sentences(src); Collection<String> nlpNames = new HashSet<String>(); Collection<String> nlpFallbacks = new HashSet<String>(); Collection<String> dictionaryNames = new HashSet<String>(); Collection<String> dictionaryFallbacks = new HashSet<String>(); for (int i = 0; i < sentences.length; i++) { String[] tokens = NlpUtil.tokensFromSentence(sentences[i]); for (int j = 0; j < tokens.length; j++) { String first = tokens[j]; String last = null;/*from w w w . ja va 2 s . com*/ if (j + 1 < tokens.length) { last = tokens[j + 1]; } if (isFirstName(first, strict) && isLastName(last) && isFullName(first + " " + last, strict)) { dictionaryNames.add(first + " " + last); } else if (!strict && isFirstName(first, strict)) { dictionaryFallbacks.add(first); } } Span[] spans = nameFinder.find(tokens); for (int j = 0; !dictionaryOnly && j < spans.length; j++) { List<String> curNames = Arrays.asList(Span.spansToStrings(spans, tokens)); for (String curName : curNames) { if (curName.contains(" ") && isFullName(curName, strict)) { nlpNames.add(curName); } else if (isFirstName(curName, strict)) { nlpFallbacks.add(curName); } } } } if (nlpNames.isEmpty()) { nlpNames = nlpFallbacks; } if (dictionaryNames.isEmpty()) { dictionaryNames = dictionaryFallbacks; } if ((dictionaryOnly || nlpNames.size() != 1) && dictionaryNames.size() != 1) { nlpNames.clear(); nlpFallbacks.clear(); dictionaryNames.clear(); dictionaryFallbacks.clear(); nameFinder.clearAdaptiveData(); for (int s = 0; s < sentences.length; s++) { String[] tokens = sentences[s].split("[\\W\\s]|$|^"); for (int i = 0; i < tokens.length; i++) { String first = tokens[i]; String last = null; if (i + 1 < tokens.length) { last = tokens[i + 1]; } if (isFirstName(first, strict) && isLastName(last) && isFullName(first + " " + last, strict)) { dictionaryNames.add(first + " " + last); } else if (!strict && isFirstName(first, strict)) { dictionaryFallbacks.add(first); } } Span[] spans = nameFinder.find(tokens); for (int j = 0; !dictionaryOnly && j < spans.length; j++) { List<String> curNames = Arrays.asList(Span.spansToStrings(spans, tokens)); for (String curName : curNames) { if (curName.contains(" ") && isFullName(curName, strict)) { nlpNames.add(curName); } else if (isFirstName(curName, strict)) { nlpFallbacks.add(curName); } } } } } if (nlpNames.isEmpty()) { nlpNames = nlpFallbacks; } if (dictionaryNames.isEmpty()) { dictionaryNames = dictionaryFallbacks; } if (nlpNames.size() == 1) { return nlpNames.iterator().next(); } if (nlpFallbacks.size() == 1) { return nlpFallbacks.iterator().next(); } if (dictionaryNames.size() == 1) { return dictionaryNames.iterator().next(); } if (dictionaryFallbacks.size() == 1) { return dictionaryFallbacks.iterator().next(); } return null; }
From source file:fr.paris.lutece.plugins.document.web.DocumentServiceJspBean.java
/** * Return the html form for portlet selection. * * @param request The HTTP request// w w w . j a v a 2 s .c o m * @return The html form of the portlet selection page */ public String getSelectPortlet(HttpServletRequest request) { init(request); String strPageId = request.getParameter(PARAMETER_PAGE_ID); if ((strPageId == null) || !strPageId.matches(REGEX_ID)) { return AdminMessageService.getMessageUrl(request, Messages.MANDATORY_FIELDS, AdminMessage.TYPE_STOP); } Page page = PageHome.findByPrimaryKey(IntegerUtils.convert(strPageId)); Collection<Portlet> listPortletsAll = page.getPortlets(); Collection<Portlet> listPortlets = new ArrayList<Portlet>(); for (Portlet portlet : listPortletsAll) { if (portlet.getPortletTypeId().equals(DocumentListPortletHome.getInstance().getPortletTypeId())) { if (StringUtils.isNotBlank(getTypeFilter())) { // filter by type if (getTypeFilter().equals(((DocumentListPortlet) portlet).getDocumentTypeCode())) { listPortlets.add(portlet); } } else { // no type filter listPortlets.add(portlet); } } } listPortletsAll.clear(); Map<String, Object> model = getDefaultModel(); model.put(MARK_PORTLETS_LIST, listPortlets); HtmlTemplate template = AppTemplateService.getTemplate(TEMPLATE_SELECTOR_PORTLET, _user.getLocale(), model); return template.getHtml(); }
From source file:org.apache.openjpa.enhance.PCDataGenerator.java
/** * Set the collection of {@link JumpInstruction}s to the given instruction, * clearing the collection in the process. *///from w ww . ja va 2s. c o m protected void setTarget(Instruction ins, Collection<Instruction> jumps) { for (Iterator<Instruction> it = jumps.iterator(); it.hasNext();) ((JumpInstruction) it.next()).setTarget(ins); jumps.clear(); }
From source file:com.datatorrent.lib.io.block.AbstractBlockReader.java
/** * <b>Note:</b> This partitioner does not support parallel partitioning.<br/><br/> * {@inheritDoc}// ww w.ja v a 2 s. c o m */ @SuppressWarnings("unchecked") @Override public Collection<Partition<AbstractBlockReader<R, B, STREAM>>> definePartitions( Collection<Partition<AbstractBlockReader<R, B, STREAM>>> partitions, PartitioningContext context) { if (partitions.iterator().next().getStats() == null) { //First time when define partitions is called return partitions; } List<Partition<AbstractBlockReader<R, B, STREAM>>> newPartitions = Lists.newArrayList(); //Create new partitions for (Partition<AbstractBlockReader<R, B, STREAM>> partition : partitions) { newPartitions.add(new DefaultPartition<>(partition.getPartitionedInstance())); } partitions.clear(); int morePartitionsToCreate = partitionCount - newPartitions.size(); List<BasicCounters<MutableLong>> deletedCounters = Lists.newArrayList(); if (morePartitionsToCreate < 0) { //Delete partitions Iterator<Partition<AbstractBlockReader<R, B, STREAM>>> partitionIterator = newPartitions.iterator(); while (morePartitionsToCreate++ < 0) { Partition<AbstractBlockReader<R, B, STREAM>> toRemove = partitionIterator.next(); deletedCounters.add(toRemove.getPartitionedInstance().counters); LOG.debug("partition removed {}", toRemove.getPartitionedInstance().operatorId); partitionIterator.remove(); } } else { KryoCloneUtils<AbstractBlockReader<R, B, STREAM>> cloneUtils = KryoCloneUtils.createCloneUtils(this); while (morePartitionsToCreate-- > 0) { DefaultPartition<AbstractBlockReader<R, B, STREAM>> partition = new DefaultPartition<>( cloneUtils.getClone()); newPartitions.add(partition); } } DefaultPartition.assignPartitionKeys(Collections.unmodifiableCollection(newPartitions), blocksMetadataInput); int lPartitionMask = newPartitions.iterator().next().getPartitionKeys().get(blocksMetadataInput).mask; //transfer the state here for (Partition<AbstractBlockReader<R, B, STREAM>> newPartition : newPartitions) { AbstractBlockReader<R, B, STREAM> reader = newPartition.getPartitionedInstance(); reader.partitionKeys = newPartition.getPartitionKeys().get(blocksMetadataInput).partitions; reader.partitionMask = lPartitionMask; LOG.debug("partitions {},{}", reader.partitionKeys, reader.partitionMask); } //transfer the counters AbstractBlockReader<R, B, STREAM> targetReader = newPartitions.iterator().next().getPartitionedInstance(); for (BasicCounters<MutableLong> removedCounter : deletedCounters) { addCounters(targetReader.counters, removedCounter); } return newPartitions; }
From source file:com.haulmont.cuba.gui.data.impl.CollectionPropertyDatasourceImpl.java
protected void doSort() { Collection<T> collection = getCollection(); if (collection == null) return;/*w w w. j av a 2 s . c o m*/ List<T> list = new LinkedList<>(collection); list.sort(createEntityComparator()); collection.clear(); collection.addAll(list); }
From source file:ubic.gemma.persistence.service.expression.designElement.CompositeSequenceDaoImpl.java
@Override public Map<CompositeSequence, Collection<Gene>> getGenes(Collection<CompositeSequence> compositeSequences) { Map<CompositeSequence, Collection<Gene>> returnVal = new HashMap<>(); int BATCH_SIZE = 2000; if (compositeSequences.size() == 0) return returnVal; /*/*w w w .j av a2 s. c om*/ * Get the cs->gene mapping */ final String nativeQuery = "SELECT CS, GENE FROM GENE2CS WHERE CS IN (:csids) "; for (CompositeSequence cs : compositeSequences) { returnVal.put(cs, new HashSet<Gene>()); } List<Object> csGene = new ArrayList<>(); Session session = this.getSessionFactory().getCurrentSession(); org.hibernate.SQLQuery queryObject = session.createSQLQuery(nativeQuery); queryObject.addScalar("cs", new LongType()); queryObject.addScalar("gene", new LongType()); Collection<Long> csIdBatch = new HashSet<>(); for (CompositeSequence cs : compositeSequences) { csIdBatch.add(cs.getId()); if (csIdBatch.size() == BATCH_SIZE) { queryObject.setParameterList("csids", csIdBatch); csGene.addAll(queryObject.list()); session.clear(); csIdBatch.clear(); } } if (csIdBatch.size() > 0) { queryObject.setParameterList("csids", csIdBatch); csGene.addAll(queryObject.list()); session.clear(); } StopWatch watch = new StopWatch(); watch.start(); int count = 0; Collection<Long> genesToFetch = new HashSet<>(); Map<Long, Collection<Long>> cs2geneIds = new HashMap<>(); for (Object object : csGene) { Object[] ar = (Object[]) object; Long cs = (Long) ar[0]; Long gene = (Long) ar[1]; if (!cs2geneIds.containsKey(cs)) { cs2geneIds.put(cs, new HashSet<Long>()); } cs2geneIds.get(cs).add(gene); genesToFetch.add(gene); } // nothing found? if (genesToFetch.size() == 0) { returnVal.clear(); return returnVal; } if (AbstractDao.log.isDebugEnabled()) AbstractDao.log.debug("Built cs -> gene map in " + watch.getTime() + " ms; fetching " + genesToFetch.size() + " genes."); // fetch the genes Collection<Long> batch = new HashSet<>(); Collection<Gene> genes = new HashSet<>(); String geneQuery = "from Gene g where g.id in ( :gs )"; org.hibernate.Query geneQueryObject = this.getSessionFactory().getCurrentSession().createQuery(geneQuery) .setFetchSize(1000); for (Long gene : genesToFetch) { batch.add(gene); if (batch.size() == BATCH_SIZE) { AbstractDao.log.debug("Processing batch ... "); geneQueryObject.setParameterList("gs", batch); //noinspection unchecked genes.addAll(geneQueryObject.list()); batch.clear(); } } if (batch.size() > 0) { geneQueryObject.setParameterList("gs", batch); //noinspection unchecked genes.addAll(geneQueryObject.list()); } if (AbstractDao.log.isDebugEnabled()) AbstractDao.log.debug("Got information on " + genes.size() + " genes in " + watch.getTime() + " ms"); Map<Long, Gene> geneIdMap = new HashMap<>(); for (Gene g : genes) { Hibernate.initialize(g); Long id = g.getId(); geneIdMap.put(id, g); } // fill in the return value. for (CompositeSequence cs : compositeSequences) { Long csId = cs.getId(); assert csId != null; Collection<Long> genesToAttach = cs2geneIds.get(csId); if (genesToAttach == null) { // this means there was no gene for that cs; we should remove it from the result returnVal.remove(cs); continue; } for (Long geneId : genesToAttach) { returnVal.get(cs).add(geneIdMap.get(geneId)); } ++count; } if (AbstractDao.log.isDebugEnabled()) AbstractDao.log.debug("Done, " + count + " result rows processed, " + returnVal.size() + "/" + compositeSequences.size() + " probes are associated with genes"); return returnVal; }
From source file:com.haulmont.cuba.core.sys.EntityManagerImpl.java
/** * Copies all property values from source to dest excluding null values. *//* w ww . j av a2 s . c om*/ protected void deepCopyIgnoringNulls(Entity source, Entity dest, Set<Entity> visited) { if (visited.contains(source)) return; visited.add(source); MetadataTools metadataTools = metadata.getTools(); for (MetaProperty srcProperty : source.getMetaClass().getProperties()) { String name = srcProperty.getName(); if (!PersistenceHelper.isLoaded(source, name)) { continue; } if (srcProperty.isReadOnly()) { continue; } Object value = source.getValue(name); if (value == null) { continue; } if (srcProperty.getRange().isClass() && !metadataTools.isEmbedded(srcProperty)) { if (!metadataTools.isOwningSide(srcProperty)) continue; Class refClass = srcProperty.getRange().asClass().getJavaClass(); if (!metadataTools.isPersistent(refClass)) continue; if (srcProperty.getRange().getCardinality().isMany()) { if (!metadataTools.isOwningSide(srcProperty)) continue; //noinspection unchecked Collection<Entity> srcCollection = (Collection) value; Collection<Entity> dstCollection = dest.getValue(name); if (dstCollection == null) throw new RuntimeException("Collection is null: " + srcProperty); boolean equal = srcCollection.size() == dstCollection.size(); if (equal) { if (srcProperty.getRange().isOrdered()) { equal = Arrays.equals(srcCollection.toArray(), dstCollection.toArray()); } else { equal = CollectionUtils.isEqualCollection(srcCollection, dstCollection); } } if (!equal) { dstCollection.clear(); for (Entity srcRef : srcCollection) { Entity reloadedRef = findOrCreate(refClass, srcRef.getId()); dstCollection.add(reloadedRef); deepCopyIgnoringNulls(srcRef, reloadedRef, visited); } } } else { Entity srcRef = (Entity) value; Entity destRef = dest.getValue(name); if (srcRef.equals(destRef)) { deepCopyIgnoringNulls(srcRef, destRef, visited); } else { Entity reloadedRef = findOrCreate(refClass, srcRef.getId()); dest.setValue(name, reloadedRef); deepCopyIgnoringNulls(srcRef, reloadedRef, visited); } } } else if (metadataTools.isEmbedded(srcProperty)) { Entity srcRef = (Entity) value; Entity destRef = dest.getValue(name); if (destRef != null) { deepCopyIgnoringNulls(srcRef, destRef, visited); } else { Entity newRef = (Entity) metadata.create(srcProperty.getRange().asClass().getJavaClass()); dest.setValue(name, newRef); deepCopyIgnoringNulls(srcRef, newRef, visited); } } else { dest.setValue(name, value); } } }
From source file:org.jactr.entry.iterative.IterativeMain.java
public void iteration(final int index, int total, Document environment, URL envURL, final Collection<IIterativeRunListener> listeners, final PrintWriter log) throws TerminateIterativeRunException { ExecutorServices.initialize();/* w ww. j ava2 s . c om*/ if (LOGGER.isDebugEnabled()) { long totalMem = Runtime.getRuntime().totalMemory(); long freeMem = Runtime.getRuntime().freeMemory(); LOGGER.debug("Running iteration " + index + "/" + total + " [" + freeMem / 1024 + "k free : " + (totalMem - freeMem) / 1024 + "k used of " + totalMem / 1024 + "k]"); } for (IIterativeRunListener listener : listeners) try { listener.preLoad(index, total); } catch (Exception e) { LOGGER.error("listener " + listener + " threw an exception ", e); } /* * first we use the environment to load all the model descriptors */ EnvironmentParser ep = new EnvironmentParser(); Collection<CommonTree> modelDescriptors = ep.getModelDescriptors(environment, envURL); for (IIterativeRunListener listener : listeners) try { listener.preBuild(index, total, modelDescriptors); } catch (TerminateIterativeRunException tire) { throw tire; } catch (Exception e) { LOGGER.error("listener " + listener + " threw an exception ", e); } /* * now we actually do that vodoo that we do to set up the environment this * will build the models, instruments, and set up common reality.. */ ep.process(environment, modelDescriptors); modelDescriptors.clear(); ACTRRuntime runtime = ACTRRuntime.getRuntime(); Collection<IModel> models = runtime.getModels(); for (IModel model : models) model.addListener(new ModelListenerAdaptor() { long startTime = 0; long simStartTime = 0; boolean closed = false; @Override public void modelStarted(ModelEvent event) { startTime = event.getSystemTime(); simStartTime = (long) (event.getSimulationTime() * 1000); } protected String header(ModelEvent event) { StringBuilder sb = new StringBuilder(" <model name=\""); sb.append(event.getSource()).append("\" simulated=\""); sb.append(duration(simStartTime, (long) (event.getSimulationTime() * 1000))); sb.append("\" actual=\""); sb.append(duration(startTime, event.getSystemTime())); sb.append("\" factor=\""); double factor = (event.getSimulationTime() * 1000 - simStartTime) / (event.getSystemTime() - startTime); NumberFormat format = NumberFormat.getNumberInstance(); format.setMaximumFractionDigits(3); sb.append(format.format(factor)).append("\""); return sb.toString(); } @Override public void modelStopped(ModelEvent event) { if (!closed) synchronized (log) { log.println(header(event) + "/>"); } } @Override public void exceptionThrown(ModelEvent event) { synchronized (log) { closed = true; log.println(header(event) + ">"); event.getException().printStackTrace(log); log.println(" </model>"); for (IIterativeRunListener listener : listeners) try { listener.exceptionThrown(index, event.getSource(), event.getException()); } catch (TerminateIterativeRunException tire) { } /* * from here we try to stop the runtime, but do not block.. that * would be disasterous */ IController controller = ACTRRuntime.getRuntime().getController(); controller.stop(); } } }, ExecutorServices.INLINE_EXECUTOR); for (IIterativeRunListener listener : listeners) try { listener.preRun(index, total, models); } catch (TerminateIterativeRunException tire) { throw tire; } catch (Exception e) { LOGGER.error("listener " + listener + " threw an exception ", e); } try { /* * start 'er up! */ IController controller = runtime.getController(); /* * we do the model check in case the listener is monkeying around with the * models (adding, removing) the controller will not ever complete if no * models are executed. */ if (models.size() != 0) try { controller.start().get(); controller.complete().get(); } catch (InterruptedException ie) { LOGGER.error("Interrupted while waiting for completion", ie); } /* * all done - time to notify and clean up */ for (IIterativeRunListener listener : listeners) try { listener.postRun(index, total, models); } catch (TerminateIterativeRunException tire) { throw tire; } catch (Exception e) { LOGGER.error("listener " + listener + " threw an exception ", e); } } catch (TerminateIterativeRunException tire) { throw tire; } catch (Throwable e) { throw new RuntimeException("Failed to run iteration " + index + " ", e); } finally { cleanUp(runtime); } }
From source file:org.apache.shindig.gadgets.http.HttpResponseBuilder.java
public HttpResponseBuilder setEncoding(Charset charset) { Collection<String> values = headers.get("Content-Type"); if (!values.isEmpty()) { String contentType = values.iterator().next(); StringBuilder newContentTypeBuilder = new StringBuilder(""); // Remove previously set charset: String[] parts = StringUtils.split(contentType, ';'); for (String part : parts) { if (!part.contains("charset=")) { if (newContentTypeBuilder.length() > 0) { newContentTypeBuilder.append("; "); }/*from w ww . j av a 2 s .c o m*/ newContentTypeBuilder.append(part); } } if (charset != null) { if (newContentTypeBuilder.length() > 0) { newContentTypeBuilder.append("; "); } newContentTypeBuilder.append("charset=").append(charset.name()); } values.clear(); String newContentType = newContentTypeBuilder.toString(); values.add(newContentType); if (!(values.size() == 1 && !contentType.equals(newContentType))) { incrementNumChanges(); } } return this; }