Example usage for org.apache.commons.lang.time StopWatch start

List of usage examples for org.apache.commons.lang.time StopWatch start

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Introduction

In this page you can find the example usage for org.apache.commons.lang.time StopWatch start.

Prototype

public void start()

Source Link

Document

Start the stopwatch.

This method starts a new timing session, clearing any previous values.

Usage

From source file:edu.utah.further.i2b2.hook.further.FurtherInterceptionFilter.java

/**
 * Send the i2b2 query request message to the FURTHeR FQE. Must be run after the i2b2
 * processing chain, because it depends on the i2b2 query ID generated by the i2b2
 * server.//from  w ww  .j a va2s  . c o m
 * 
 * @param request
 * @param i2b2QueryId
 *            i2b2 query ID, obtained from the i2b2 response
 */
private void spawnFurtherRequest(final HttpServletRequest request, final long i2b2QueryId) {
    if (log.isDebugEnabled()) {
        log.debug("Read i2b2QueryId from request: " + i2b2QueryId);
    }
    try {
        // Need to read create from request.getInputStream() multiple times
        // in this method ==> save a copy in a buffer first
        // inputStream is already at the end of the file.
        final InputStream inputStream = request.getInputStream();
        final byte[] buffer = CoreUtil.readBytesFromStream(inputStream);
        inputStream.close();

        // Decide whether to fork or not
        if (StringUtil.isValidLong(i2b2QueryId) && isProcessRequest(buffer)) {
            // Read the FURTHeR section of the i2b2 request body
            final String requestXml = new String(buffer);
            // Request contains an FQE processing flag, send to FURTHeR
            if (log.isDebugEnabled()) {
                ServletUtil.printRequestHeaders(request);
                ServletUtil.printRequestParameters(request);
                ServletUtil.printRequestAttributes(request);
            }

            // TODO: read query instance id from i2b2 response and pass to the
            // following call
            final QueryContextIdentifier id = furtherServices.i2b2QueryRequest(requestXml, i2b2QueryId);

            // Make available to response through the request, ensures thread safety
            // instead of using instance var
            request.setAttribute(QUERY_ID, id);

            QueryState state = furtherServices.getQueryState(id).getState();

            final StopWatch stopWatch = new StopWatch();

            final int interval = 10;
            int i = 0;
            stopWatch.start();
            // Poll state every sec
            final long maxQueryTimeMillis = furtherServices.getMaxQueryTime() * 1000;
            while (state != QueryState.COMPLETED && state != QueryState.STOPPED && state != QueryState.FAILED
                    && state != QueryState.INVALID && state != null
                    && stopWatch.getTime() < maxQueryTimeMillis) {
                Thread.yield();
                state = furtherServices.getQueryState(id).getState();

                if (log.isDebugEnabled() && ((i % interval) == 0)) {
                    log.debug("QueryState for query " + id.getId() + ": " + state);
                }

                i++;
            }
            stopWatch.stop();
        } else {
            if (log.isDebugEnabled()) {
                log.info("Ignoring unrecognized/irrelvant requestXml");
            }
        }
    } catch (final Throwable throwable) {
        if (log.isDebugEnabled()) {
            log.error("Caught " + throwable + ", ignoring", throwable);
        }
    }
}

From source file:com.qualogy.qafe.mgwt.server.RPCServiceImpl.java

public GDataObject executeEvent(EventDataGVO eventData) throws GWTServiceException {
    StopWatch stopWatch = new StopWatch();
    try {//from ww  w .  j a v a  2  s .com

        stopWatch.start();

        String appIdUUID = eventData.getUuid().substring(eventData.getUuid().lastIndexOf('|') + 1);// uuid.substring(uuid.lastIndexOf('|')+1);
        ApplicationIdentifier appId = service.getApplicationId(appIdUUID);
        GDataObject gDataObject = null;
        if (appId != null) {
            eventData.setContext(appId.toString());
            resolveRequest(eventData);
            gDataObject = eventProcessor.execute(eventData, appId,
                    new SessionContainer(getLocale(), eventData.getParameters()));
        }
        stopWatch.stop();

        if (gDataObject != null) {
            gDataObject.setTime(Long.valueOf(stopWatch.getTime()));
        }
        return gDataObject;
    } catch (Exception e) {
        GWTServiceException gWTServiceException = handleException(e);
        gWTServiceException.setGDataObject(ExceptionProcessor.handle(eventData, e));
        stopWatch.stop();
        if (gWTServiceException.getGDataObject() != null) {
            gWTServiceException.getGDataObject().setTime(Long.valueOf(stopWatch.getTime()));
        }
        throw gWTServiceException;
    }
}

From source file:com.liferay.journal.util.impl.JournalContentImpl.java

@Override
public JournalArticleDisplay getDisplay(JournalArticle article, String ddmTemplateKey, String viewMode,
        String languageId, int page, PortletRequestModel portletRequestModel, ThemeDisplay themeDisplay) {

    StopWatch stopWatch = new StopWatch();

    stopWatch.start();

    long groupId = article.getGroupId();
    String articleId = article.getArticleId();
    double version = article.getVersion();

    articleId = StringUtil.toUpperCase(GetterUtil.getString(articleId));
    ddmTemplateKey = StringUtil.toUpperCase(GetterUtil.getString(ddmTemplateKey));

    long layoutSetId = 0;
    boolean secure = false;

    if (themeDisplay != null) {
        try {/*from w  ww.  j av a  2  s  .  co m*/
            if (!JournalArticlePermission.contains(themeDisplay.getPermissionChecker(), article,
                    ActionKeys.VIEW)) {

                return null;
            }
        } catch (Exception e) {
        }

        LayoutSet layoutSet = themeDisplay.getLayoutSet();

        layoutSetId = layoutSet.getLayoutSetId();

        secure = themeDisplay.isSecure();
    }

    if (Validator.isNull(ddmTemplateKey)) {
        ddmTemplateKey = article.getDDMTemplateKey();
    }

    JournalContentKey journalContentKey = new JournalContentKey(groupId, articleId, version, ddmTemplateKey,
            layoutSetId, viewMode, languageId, page, secure);

    JournalArticleDisplay articleDisplay = _portalCache.get(journalContentKey);

    boolean lifecycleRender = false;

    if (portletRequestModel != null) {
        lifecycleRender = RenderRequest.RENDER_PHASE.equals(portletRequestModel.getLifecycle());
    }

    if ((articleDisplay == null) || !lifecycleRender) {
        articleDisplay = getArticleDisplay(article, ddmTemplateKey, viewMode, languageId, page,
                portletRequestModel, themeDisplay);

        if ((articleDisplay != null) && articleDisplay.isCacheable() && lifecycleRender) {

            _portalCache.put(journalContentKey, articleDisplay);
        }
    }

    if (_log.isDebugEnabled()) {
        _log.debug(StringBundler.concat("getDisplay for {", String.valueOf(groupId), ", ", articleId, ", ",
                ddmTemplateKey, ", ", viewMode, ", ", languageId, ", ", String.valueOf(page), "} takes ",
                String.valueOf(stopWatch.getTime()), " ms"));
    }

    return articleDisplay;
}

From source file:ch.systemsx.cisd.openbis.generic.server.business.bo.samplelister.SampleListingWorker.java

/**
 * Load the samples defined by the criteria given to the constructor. The samples will be
 * enriched with sample properties and dependencies to parents and container will be resolved.
 *///from w  w w.  jav a2 s.  co m
public List<Sample> load() {
    final StopWatch watch = new StopWatch();
    watch.start();
    final Experiment expOrNull = tryLoadExperiment();
    final boolean oneGroupPerSample = isOneGroupPerSamples();
    final Group groupOrNull;
    if (oneGroupPerSample) {
        groupOrNull = null;
        final Group[] groups = referencedEntityDAO.getAllGroups(databaseInstanceId);
        for (Group group : groups) {
            group.setInstance(databaseInstance);
            groupMap.put(group.getId(), group);
        }
    } else {
        groupOrNull = tryLoadGroup(expOrNull);
        if (groupOrNull != null) {
            // For use by dependent samples.
            groupMap.put(groupOrNull.getId(), groupOrNull);
        }
    }
    loadSampleTypes();
    retrievePrimaryBasicSamples(tryGetIteratorForSamplesByIds(), groupOrNull, oneGroupPerSample);
    retrievePrimaryBasicSamples(tryGetIteratorForGroupSamples(), groupOrNull, oneGroupPerSample);
    retrievePrimaryBasicSamples(tryGetIteratorForSharedSamples(), groupOrNull, oneGroupPerSample);
    retrievePrimaryBasicSamples(tryGetIteratorForExperimentSamples(), groupOrNull, oneGroupPerSample);
    retrievePrimaryBasicSamples(tryGetIteratorForContainedSamples(), groupOrNull, oneGroupPerSample);
    if (operationLog.isDebugEnabled()) {
        watch.stop();
        operationLog.debug(
                String.format("Basic retrieval of %d samples took %s s", sampleList.size(), watch.toString()));
        watch.reset();
        watch.start();
    }

    // Only enrich the "primary" samples (matching the criteria) with properties, not
    // dependent samples.
    if (samplePropertiesEnricherOrNull != null) {
        samplePropertiesEnricherOrNull.enrich(sampleMap.keySet(), new IEntityPropertiesHolderResolver() {
            public Sample get(long id) {
                return sampleMap.get(id);
            }
        });
        if (operationLog.isDebugEnabled()) {
            watch.stop();
            operationLog.debug(String.format("Enrichment with properties took %s s", watch.toString()));
        }
    }

    retrieveDependentSamplesRecursively();
    resolveParents();
    resolveContainers();

    return sampleList;
}

From source file:com.microsoft.exchange.integration.AbstractIntegrationTest.java

/**
 * Create a single {@link CalendarItemType} and submit with {@link ExchangeWebServicesClient#createItem(CreateItem)}.
 * @throws JAXBException //from  ww  w .  j  a  va 2 s  .  c om
 */
@Test
public void testCreateCalendarItem() throws JAXBException {
    NonEmptyArrayOfBaseItemIdsType createdIds = new NonEmptyArrayOfBaseItemIdsType();
    try {
        initializeCredentials();

        CalendarItemType calendarItem = new CalendarItemType();
        final Date start = DateHelp.parseDateTimePhrase("20121109-1200");
        final Date end = DateHelp.parseDateTimePhrase("20121109-1300");

        calendarItem.setStart(DateHelp.convertDateToXMLGregorianCalendar(start));
        calendarItem.setEnd(DateHelp.convertDateToXMLGregorianCalendar(end));
        calendarItem.setSubject("integration test: testCreateCalendarItem");
        calendarItem.setLocation("test location");
        BodyType body = new BodyType();
        body.setBodyType(BodyTypeType.TEXT);
        body.setValue("test ran at " + new Date());
        calendarItem.setBody(body);

        CreateItem request = new CreateItem();
        request.setSendMeetingInvitations(CalendarItemCreateOrDeleteOperationType.SEND_TO_ALL_AND_SAVE_COPY);

        NonEmptyArrayOfAllItemsType arrayOfItems = new NonEmptyArrayOfAllItemsType();
        arrayOfItems.getItemsAndMessagesAndCalendarItems().add(calendarItem);
        request.setItems(arrayOfItems);
        DistinguishedFolderIdType folder = new DistinguishedFolderIdType();
        folder.setId(DistinguishedFolderIdNameType.CALENDAR);
        TargetFolderIdType target = new TargetFolderIdType();
        target.setDistinguishedFolderId(folder);
        request.setSavedItemFolderId(target);

        StopWatch stopWatch = new StopWatch();
        stopWatch.start();
        CreateItemResponse response = ewsClient.createItem(request);
        stopWatch.stop();
        Assert.assertNotNull(response);
        String captured = capture(response);
        log.debug("CreateItem request (1 CalendarItem) completed in " + stopWatch + ", response: " + captured);

        ArrayOfResponseMessagesType responseMessages = response.getResponseMessages();
        Assert.assertNotNull(responseMessages);
        Assert.assertEquals(1, responseMessages
                .getCreateItemResponseMessagesAndDeleteItemResponseMessagesAndGetItemResponseMessages().size());
        JAXBElement<? extends ResponseMessageType> m = responseMessages
                .getCreateItemResponseMessagesAndDeleteItemResponseMessagesAndGetItemResponseMessages().get(0);
        Assert.assertEquals(ResponseCodeType.NO_ERROR, m.getValue().getResponseCode());

        ItemInfoResponseMessageType itemType = (ItemInfoResponseMessageType) m.getValue();
        ArrayOfRealItemsType itemArray = itemType.getItems();
        ItemType item = itemArray.getItemsAndMessagesAndCalendarItems().get(0);
        createdIds.getItemIdsAndOccurrenceItemIdsAndRecurringMasterItemIds().add(item.getItemId());

    } finally {
        deleteItems(createdIds);
    }
}

From source file:com.microsoft.exchange.integration.AbstractIntegrationTest.java

/**
 * Create 3 {@link CalendarItemType}s and submit with 1 {@link ExchangeWebServicesClient#createItem(CreateItem)} invocation.
 *///from   www  . jav a  2  s  .co  m
@Test
public void testCreate3CalendarItems() {
    NonEmptyArrayOfBaseItemIdsType createdIds = new NonEmptyArrayOfBaseItemIdsType();
    try {
        initializeCredentials();

        CalendarItemType item1 = constructCalendarItem(DateHelp.parseDateTimePhrase("20121109-1300"),
                DateHelp.parseDateTimePhrase("20121109-1400"),
                "integration test: testCreate3CalendarItems, item1", "test location",
                "test ran at " + new Date());
        CalendarItemType item2 = constructCalendarItem(DateHelp.parseDateTimePhrase("20121109-1400"),
                DateHelp.parseDateTimePhrase("20121109-1500"),
                "integration test: testCreate3CalendarItems, item2", "test location",
                "test ran at " + new Date());
        CalendarItemType item3 = constructCalendarItem(DateHelp.parseDateTimePhrase("20121109-1500"),
                DateHelp.parseDateTimePhrase("20121109-1600"),
                "integration test: testCreate3CalendarItems, item3", "test location",
                "test ran at " + new Date());

        CreateItem request = new CreateItem();
        request.setSendMeetingInvitations(CalendarItemCreateOrDeleteOperationType.SEND_TO_ALL_AND_SAVE_COPY);

        NonEmptyArrayOfAllItemsType arrayOfItems = new NonEmptyArrayOfAllItemsType();
        arrayOfItems.getItemsAndMessagesAndCalendarItems().add(item1);
        arrayOfItems.getItemsAndMessagesAndCalendarItems().add(item2);
        arrayOfItems.getItemsAndMessagesAndCalendarItems().add(item3);
        request.setItems(arrayOfItems);
        DistinguishedFolderIdType folder = new DistinguishedFolderIdType();
        folder.setId(DistinguishedFolderIdNameType.CALENDAR);
        TargetFolderIdType target = new TargetFolderIdType();
        target.setDistinguishedFolderId(folder);
        request.setSavedItemFolderId(target);

        StopWatch stopWatch = new StopWatch();
        stopWatch.start();
        CreateItemResponse response = ewsClient.createItem(request);
        stopWatch.stop();
        log.debug("CreateItem request (3 CalendarItems) completed in " + stopWatch);
        Assert.assertNotNull(response);
        ArrayOfResponseMessagesType responseMessages = response.getResponseMessages();
        Assert.assertNotNull(responseMessages);
        Assert.assertEquals(3, responseMessages
                .getCreateItemResponseMessagesAndDeleteItemResponseMessagesAndGetItemResponseMessages().size());
        for (JAXBElement<? extends ResponseMessageType> m : responseMessages
                .getCreateItemResponseMessagesAndDeleteItemResponseMessagesAndGetItemResponseMessages()) {
            Assert.assertEquals(ResponseCodeType.NO_ERROR, m.getValue().getResponseCode());

            ItemInfoResponseMessageType itemType = (ItemInfoResponseMessageType) m.getValue();
            ArrayOfRealItemsType itemArray = itemType.getItems();
            ItemType item = itemArray.getItemsAndMessagesAndCalendarItems().get(0);
            createdIds.getItemIdsAndOccurrenceItemIdsAndRecurringMasterItemIds().add(item.getItemId());
        }
    } finally {
        deleteItems(createdIds);
    }
}

From source file:chibi.gemmaanalysis.ExperimentMetaDataExtractorCli.java

public void generateExperimentMetaData(Collection<BioAssaySet> expressionExperiments) throws IOException {

    File file = getOutputFile(this.viewFile);

    try (Writer writer = new OutputStreamWriter(new GZIPOutputStream(new FileOutputStream(file)));) {

        String[] colNames = { "ShortName", "Taxon", "DateUpload", "IsPublic", "NumPlatform", "Platform",
                "Channel", "IsExonArray", "QtIsRatio", "QtIsNormalized", "QtScale", "NumProfiles",
                "NumFilteredProfiles", "NumSamples", "NumConditions", "NumReplicatesPerCondition",
                "PossibleOutliers", "CuratedOutlier", "IsTroubled", "PubTroubled", "PubYear", "PubJournal",
                "Batch.PC1.Var", "Batch.PC2.Var", "Batch.PC3.Var", "Batch.PC1.Pval", "Batch.PC2.Pval",
                "Batch.PC3.Pval", "NumFactors", "FactorNames", "FactorCategories", "NumFactorValues" };
        // log.info( StringUtils.join( colNames, "\t" ) + "\n" );
        writer.write(StringUtils.join(colNames, "\t") + "\n");

        int i = 0;
        Collection<String> failedEEs = new ArrayList<>();

        StopWatch timer = new StopWatch();
        timer.start();

        for (BioAssaySet bas : expressionExperiments) {
            /*//from  ww  w. j  a v a2 s  .  co m
             * Skip subsets
             */
            if (bas instanceof ExpressionExperimentSubSet)
                return;

            try {

                ExpressionExperiment ee = (ExpressionExperiment) bas;
                ee = eeService.thawLite(ee);
                ExpressionExperimentValueObject vo = eeService.loadValueObject(ee.getId());
                vo.setIsPublic(!securityService.isPrivate(ee));
                log.info("Processing (" + ++i + "/" + expressionExperiments.size() + ") : " + ee);

                BibliographicReference primaryPublication = ee.getPrimaryPublication();
                Status pubStatus = primaryPublication != null ? statusService.getStatus(primaryPublication)
                        : null;
                Collection<ArrayDesign> arrayDesignsUsed = eeService.getArrayDesignsUsed(ee);

                Collection<String> arrayDesignIsExon = new ArrayList<>();
                Collection<String> arrayDesignTechTypes = new ArrayList<>();
                Collection<String> arrayDesignShortNames = new ArrayList<>();

                // for multiple platforms e.g. GSE5949
                for (ArrayDesign ad : arrayDesignsUsed) {
                    arrayDesignShortNames.add(ad.getShortName());
                    arrayDesignTechTypes.add(ad.getTechnologyType().getValue());
                    arrayDesignIsExon.add(ad.getName().toLowerCase().contains("exon") + "");
                }

                QuantitationType qt = null;
                for (QuantitationType q : ee.getQuantitationTypes()) {
                    if (q.getIsPreferred().booleanValue()) {
                        qt = q;
                        break;
                    }
                }

                int manualOutlierCount = 0;
                for (BioAssay ba : ee.getBioAssays()) {
                    if (ba.getIsOutlier().booleanValue()) {
                        manualOutlierCount++;
                    }
                }

                ExperimentalDesign experimentalDesign = edService.load(vo.getExperimentalDesign());

                // Batch PCs
                int maxcomp = 3;
                BatchEffectDetails batchEffectPC1 = null;
                BatchEffectDetails batchEffectPC2 = null;
                BatchEffectDetails batchEffectPC3 = null;
                Collection<BatchEffectDetails> batchEffects = getBatchEffect(ee, maxcomp);
                Iterator<BatchEffectDetails> batchEffectsIterator;
                if (batchEffects == null || batchEffects.size() == 0) {
                    log.warn("No batch effect info");
                } else {
                    batchEffectsIterator = batchEffects.iterator();
                    if (batchEffectsIterator.hasNext()) {
                        batchEffectPC1 = batchEffectsIterator.next();
                    }
                    if (batchEffectsIterator.hasNext()) {
                        batchEffectPC2 = batchEffectsIterator.next();
                    }
                    if (batchEffectsIterator.hasNext()) {
                        batchEffectPC3 = batchEffectsIterator.next();
                    }
                }

                // eeService.getExperimentsWithOutliers();
                StopWatch timerOutlier = new StopWatch();
                timerOutlier.start();
                // log.info( "Outlier detection service started " + timer.getTime() + "ms" );
                Collection<OutlierDetails> possibleOutliers = outlierDetectionService.identifyOutliers(ee);
                if (timerOutlier.getTime() > 10000) {
                    log.info("Automatic outlier detection took " + timerOutlier.getTime() + "ms");
                }
                // Collection<OutlierDetails> possibleOutliers = null;

                // samples per condition
                boolean removeBatchFactor = false;
                Collection<String> samplesPerConditionCount = new ArrayList<>();
                CountingMap<FactorValueVector> assayCount = ExperimentalDesignUtils.getDesignMatrix(ee,
                        removeBatchFactor);
                List<FactorValueVector> keys = assayCount.sortedKeyList(true);
                for (FactorValueVector key : keys) {
                    samplesPerConditionCount.add(Integer.toString(assayCount.get(key).intValue()));
                }

                // factor names
                Collection<ExperimentalFactor> factors = ee.getExperimentalDesign().getExperimentalFactors();
                Collection<String> factorNames = new ArrayList<>();
                Collection<String> factorCategories = new ArrayList<>();
                Collection<Integer> factorValues = new ArrayList<>();
                for (ExperimentalFactor f : factors) {
                    factorNames.add(f.getName());
                    String cat = f.getCategory() != null ? f.getCategory().getCategory() : NA;
                    factorCategories.add(cat);
                    factorValues.add(Integer.valueOf(f.getFactorValues().size()));
                }

                int filteredProfilesCount = -1;

                try {
                    FilterConfig filterConfig = new FilterConfig();
                    filterConfig.setIgnoreMinimumSampleThreshold(true);
                    filteredProfilesCount = expressionDataMatrixService.getFilteredMatrix(ee, filterConfig,
                            expressionDataMatrixService.getProcessedExpressionDataVectors(ee)).rows();
                } catch (Exception e) {
                    log.error(e.getMessage(), e);
                }

                String val[] = { vo.getShortName(), vo.getTaxon(),
                        DateFormat.getDateInstance(DateFormat.MEDIUM).format(vo.getDateCreated()),
                        vo != null ? Boolean.toString(vo.getIsPublic()) : NA,
                        Integer.toString(arrayDesignsUsed.size()), StringUtils.join(arrayDesignShortNames, ','),
                        StringUtils.join(arrayDesignTechTypes, ','), // arrayDesign.getTechnologyType().getValue(),
                        // ONE-COLOR, TWO-COLOR, NONE (RNA-seq
                        // GSE37646), DUAL-MODE (one or two color)
                        StringUtils.join(arrayDesignIsExon, ','), // exon GSE28383
                        qt != null ? Boolean.toString(qt.getIsRatio().booleanValue()) : NA,
                        qt != null ? Boolean.toString(qt.getIsNormalized().booleanValue()) : NA,
                        qt != null ? qt.getScale().getValue() : NA,
                        Integer.toString(vo.getProcessedExpressionVectorCount().intValue()), // NumProfiles
                        Integer.toString(filteredProfilesCount), // NumFilteredProfiles
                        Integer.toString(vo.getBioAssayCount().intValue()), // NumSamples
                        Integer.toString(assayCount.size()), // NumConditions
                        StringUtils.join(samplesPerConditionCount, ","),
                        possibleOutliers != null ? Integer.toString(possibleOutliers.size()) : NA,
                        Integer.toString(manualOutlierCount), Boolean.toString(vo.getTroubled()),
                        pubStatus != null ? Boolean.toString(pubStatus.getTroubled().booleanValue()) : NA,
                        primaryPublication != null ? DateFormat.getDateInstance(DateFormat.MEDIUM)
                                .format(primaryPublication.getPublicationDate()) : NA,
                        primaryPublication != null ? primaryPublication.getPublication() : NA,

                        batchEffectPC1 != null
                                ? Double.toString(batchEffectPC1.getComponentVarianceProportion())
                                : NA,
                        batchEffectPC2 != null
                                ? Double.toString(batchEffectPC2.getComponentVarianceProportion())
                                : NA,
                        batchEffectPC3 != null
                                ? Double.toString(batchEffectPC3.getComponentVarianceProportion())
                                : NA,

                        batchEffectPC1 != null ? Double.toString(batchEffectPC1.getPvalue()) : NA,
                        batchEffectPC2 != null ? Double.toString(batchEffectPC2.getPvalue()) : NA,
                        batchEffectPC3 != null ? Double.toString(batchEffectPC3.getPvalue()) : NA,

                        // factors
                        factors != null ? Integer.toString(factors.size()) : NA, // NumFactors
                        factorNames != null ? StringUtils.join(factorNames, ",") : NA,
                        factorCategories != null ? StringUtils.join(factorCategories, ",") : NA,
                        factorValues != null ? StringUtils.join(factorValues, ",") : NA,

                };

                // log.info( StringUtils.join( val, "\t" ) + "\n" );
                writer.write(StringUtils.join(val, "\t") + "\n");

            } catch (Exception e) {
                failedEEs.add(((ExpressionExperiment) bas).getShortName());
                StringWriter sw = new StringWriter();
                e.printStackTrace(new PrintWriter(sw));
                log.error(sw.toString());
            }
        }

        log.info("Finished processing " + expressionExperiments.size() + " datasets in " + timer.getTime()
                + " ms. ");
        log.info("Writen to " + file);
        log.info("Number of failed experiment metadata extraction(s): " + failedEEs.size() + " / "
                + expressionExperiments.size());

        if (failedEEs.size() > 0) {
            log.info("Skipped experiments:");
            log.info(StringUtils.join(failedEEs, ","));
        }
    }
}

From source file:eu.annocultor.tagger.vocabularies.AbstractVocabulary.java

private void loadTerms(String query, boolean isSesame, File cacheDir, String baseDirName,
        String... filePatterns) throws Exception {
    VocabularySerializer handler = new VocabularySerializer(this, this.getVocabularyName());
    File baseDir = new File(baseDirName);

    List<String> locations = new ArrayList<String>();

    // normalizing files to prevent problems with hashes in cache file names
    // when run from a different environment
    for (String pattern : filePatterns) {
        for (File file : Utils.expandFileTemplateFrom(baseDir, pattern)) {
            locations.add(file.getCanonicalPath());
        }//from   ww w . ja va 2s  . c  o  m
    }

    String locationDescriptionForExceptionLogging = "Expanded from dir " + baseDirName + " pattern "
            + StringUtils.join(filePatterns, ",") + " to " + StringUtils.join(locations, ";");

    if (baseDirName.startsWith("http://") && filePatterns.length == 0) {
        locations.add(baseDirName);
        locationDescriptionForExceptionLogging += "Loading from SPARQL endpoint " + baseDirName;
    }
    loadMap(locations, locationDescriptionForExceptionLogging, this.name, query, isSesame, cacheDir, handler);

    reconstructParents(handler);

    if (codeSet().size() == 0)
        throw new Exception("No terms loaded to vocabulary " + name);

    StopWatch timeElapsed = new StopWatch();
    timeElapsed.start();

    timeElapsed.stop();
    // log.info("Parsed " + name + " in " + timeElapsed + " ms");
}

From source file:eu.europeana.enrichment.tagger.vocabularies.AbstractVocabulary.java

private void loadTerms(String query, boolean isSesame, File cacheDir, String baseDirName,
        String... filePatterns) throws Exception {
    VocabularySerializer handler = new VocabularySerializer(this, this.getVocabularyName());
    File baseDir = new File(baseDirName);

    List<String> locations = new ArrayList<String>();

    // normalizing files to prevent problems with hashes in cache file names
    // when run from a different environment
    for (String pattern : filePatterns) {
        for (File file : Utils.expandFileTemplateFrom(baseDir, pattern)) {
            locations.add(file.getCanonicalPath());
        }/*from  w ww . ja  v a2s. com*/

    }

    String locationDescriptionForExceptionLogging = "Expanded from dir " + baseDirName + " pattern "
            + StringUtils.join(filePatterns, ",") + " to " + StringUtils.join(locations, ";");

    if (baseDirName.startsWith("http://") && filePatterns.length == 0) {
        locations.add(baseDirName);
        locationDescriptionForExceptionLogging += "Loading from SPARQL endpoint " + baseDirName;
    }
    loadMap(locations, locationDescriptionForExceptionLogging, this.name, query, isSesame, cacheDir, handler);

    reconstructParents(handler);

    // if (codeSet().size() == 0)
    // throw new Exception("No terms loaded to vocabulary " + name);

    StopWatch timeElapsed = new StopWatch();
    timeElapsed.start();

    timeElapsed.stop();
    // log.info("Parsed " + name + " in " + timeElapsed + " ms");
}

From source file:eu.annocultor.tagger.vocabularies.AbstractVocabulary.java

boolean loadFromCache(List<String> locations, String locationDescriptionForExceptionLogging,
        VocabularySerializer handler, File cacheFileTerms, File cacheFileParents) throws Exception {
    long lastModified = 0;
    for (String location : locations) {
        File file = new File(location);
        if (file.lastModified() > lastModified) {
            lastModified = file.lastModified();
        }//from ww w  . j ava 2s  .  co m
    }

    if (cacheFileTerms.exists() && cacheFileTerms.lastModified() > lastModified && cacheFileParents.exists()) {
        logMessage("Recovered cached query result from file " + cacheFileTerms);
        StopWatch timeElapsed = new StopWatch();
        timeElapsed.start();

        VocabularySerializer.SerializedProperties props = new VocabularySerializer.SerializedProperties();
        props.getTerms().load(new BufferedInputStream(new FileInputStream(cacheFileTerms), 1024 * 10));
        props.getParents().load(new BufferedInputStream(new FileInputStream(cacheFileParents), 1024 * 10));
        handler.deserializeFromProperties(props);

        timeElapsed.stop();
        logMessage("Loaded " + props.getTerms().size() + " term codes in " + timeElapsed + " ms");
        return true;
    }

    if (!cacheFileTerms.exists() || !cacheFileParents.exists()) {
        logMessage("No cache file " + cacheFileTerms.getCanonicalPath()
                + " found, loading RDF from the following files");
        logMessage(locationDescriptionForExceptionLogging);
    }

    if (cacheFileTerms.exists() && !(cacheFileTerms.lastModified() > lastModified)) {
        logMessage("Cache file " + cacheFileTerms.getCanonicalPath()
                + " is older than RDF files, loading RDF from the following files");
    }
    return false;
}