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

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

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

Prototype

public StopWatch()

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Constructor.

Usage

From source file:com.liferay.portal.search.elasticsearch.internal.ElasticsearchQuerySuggester.java

protected Suggest doSuggest(Suggester suggester, SearchContext searchContext) {

    StopWatch stopWatch = new StopWatch();

    stopWatch.start();//  w  w w  .j  a  v  a2 s. c  o  m

    Client client = elasticsearchConnectionManager.getClient();

    SuggestRequestBuilder suggestRequestBuilder = client
            .prepareSuggest(indexNameBuilder.getIndexName(searchContext.getCompanyId()));

    SuggestBuilder suggestBuilder = suggesterTranslator.translate(suggester, searchContext);

    for (SuggestBuilder.SuggestionBuilder<?> suggestionBuilder : suggestBuilder.getSuggestion()) {

        suggestRequestBuilder.addSuggestion(suggestionBuilder);
    }

    if (suggester instanceof AggregateSuggester) {
        AggregateSuggester aggregateSuggester = (AggregateSuggester) suggester;

        suggestRequestBuilder.setSuggestText(aggregateSuggester.getValue());
    }

    SuggestResponse suggestResponse = suggestRequestBuilder.get();

    Suggest suggest = suggestResponse.getSuggest();

    if (_log.isInfoEnabled()) {
        stopWatch.stop();

        _log.info("Spell checked keywords in " + stopWatch.getTime() + "ms");
    }

    return suggest;
}

From source file:de.griffel.confluence.plugins.plantuml.PlantUmlMacro.java

protected final String executeInternal(Map<String, String> params, final String body,
        final RenderContext renderContext) throws MacroException, IOException,
        UnauthorizedDownloadResourceException, DownloadResourceNotFoundException {

    final StopWatch stopWatch = new StopWatch();
    stopWatch.start();//from w  w w  .  ja v  a2  s .co  m

    final PlantUmlMacroParams macroParams = new PlantUmlMacroParams(params);

    if (!(renderContext instanceof PageContext)) {
        throw new MacroException("This macro can only be used in Confluence pages. (ctx="
                + renderContext.getClass().getName() + ")");
    }

    final PageContext pageContext = (PageContext) renderContext;
    final UmlSourceLocator umlSourceLocator = new UmlSourceLocatorConfluence(pageContext);
    final PreprocessingContext preprocessingContext = new MyPreprocessingContext(pageContext);

    final DiagramType diagramType = macroParams.getDiagramType();
    final boolean dropShadow = macroParams.getDropShadow();
    final boolean separation = macroParams.getSeparation();
    final PlantUmlConfiguration configuration = configurationManager.load();
    final UmlSourceBuilder builder = new UmlSourceBuilder(diagramType, dropShadow, separation, configuration)
            .append(new StringReader(body));
    final PlantUmlPreprocessor preprocessor = new PlantUmlPreprocessor(builder.build(), umlSourceLocator,
            preprocessingContext);
    final String umlBlock = preprocessor.toUmlBlock();

    final String result = render(umlBlock, pageContext, macroParams, preprocessor);

    stopWatch.stop();
    logger.info(String.format("Rendering %s diagram on page %s:%s took %d ms.", diagramType,
            pageContext.getSpaceKey(), pageContext.getPageTitle(), stopWatch.getTime()));

    return result;
}

From source file:ch.systemsx.cisd.openbis.generic.server.authorization.DefaultReturnValueFilter.java

public final Object applyFilter(final IAuthSession session, final Method method,
        final Object returnValueOrNull) {
    assert session != null : "Unspecified session";
    assert method != null : "Unspecified method";
    final StopWatch stopWatch = new StopWatch();
    stopWatch.start();//  w  ww  .j av a 2 s . c  om
    try {
        if (returnValueOrNull == null) {
            operationLog.debug(String.format(NULL_RETURN_VALUE_MSG_FORMAT, MethodUtils.describeMethod(method)));
            return returnValueOrNull;
        }
        final ReturnValueFilter annotation = method.getAnnotation(ReturnValueFilter.class);
        if (annotation == null) {
            operationLog.debug(String.format(NO_ANNOTATION_FOUND_MSG_FORMAT, MethodUtils.describeMethod(method),
                    ReturnValueFilter.class.getSimpleName()));
            return returnValueOrNull;
        }
        final IValidator<?> validator = getValidator(annotation);
        return proceed(session.tryGetPerson(), method, returnValueOrNull, validator);
    } finally {
        logTimeTaken(stopWatch, method);
    }
}

From source file:au.org.theark.lims.util.BioCollectionSpecimenUploader.java

/**
 * //  w  w  w  .  ja va  2s. com
 * Upload the biocollection file data.
 * 
 * Where N is any number of columns
 * 
 * @param fileInputStream
 *           is the input stream of a file
 * @param inLength
 *           is the length of a file
 * @throws FileFormatException
 *            file format Exception
 * @throws ArkBaseException
 *            general ARK Exception
 * @return the upload report detailing the upload process
 */
public StringBuffer uploadAndReportMatrixBiocollectionFile(InputStream fileInputStream, long inLength,
        String inFileFormat, char inDelimChr) throws FileFormatException, ArkSystemException {
    delimiterCharacter = inDelimChr;
    uploadReport = new StringBuffer();
    curPos = 0;

    InputStreamReader inputStreamReader = null;
    CsvReader csvReader = null;
    DecimalFormat decimalFormat = new DecimalFormat("0.00");

    // If Excel, convert to CSV for validation
    if (inFileFormat.equalsIgnoreCase("XLS")) {
        Workbook w;
        try {
            w = Workbook.getWorkbook(fileInputStream);
            delimiterCharacter = ',';
            XLStoCSV xlsToCsv = new XLStoCSV(delimiterCharacter);
            fileInputStream = xlsToCsv.convertXlsToCsv(w);
            fileInputStream.reset();
        } catch (BiffException e) {
            log.error(e.getMessage());
        } catch (IOException e) {
            log.error(e.getMessage());
        }
    }

    try {
        inputStreamReader = new InputStreamReader(fileInputStream);
        csvReader = new CsvReader(inputStreamReader, delimiterCharacter);

        srcLength = inLength;
        if (srcLength <= 0) {
            uploadReport.append("The input size was not greater than 0. Actual length reported: ");
            uploadReport.append(srcLength);
            uploadReport.append("\n");
            throw new FileFormatException(
                    "The input size was not greater than 0. Actual length reported: " + srcLength);
        }
        timer = new StopWatch();
        timer.start();
        csvReader.readHeaders();
        srcLength = inLength - csvReader.getHeaders().toString().length();
        log.debug("Header length: " + csvReader.getHeaders().toString().length());
        // Loop through all rows in file
        while (csvReader.readRecord()) {
            log.info("At record: " + recordCount);
            String subjectUID = csvReader.get("SUBJECTUID");
            String biocollectionUID = csvReader.get("BIOCOLLECTIONUID");
            LinkSubjectStudy linkSubjectStudy = iArkCommonService.getSubjectByUIDAndStudy(subjectUID, study);
            //this is validated in prior step and should never happen
            if (linkSubjectStudy == null) {
                log.error(
                        "\n\n\n\n\n\n\n\n\n\n\n\nUnexpected subject? a shouldnt happen...we should have errored this in validation");
                break;//TODO : log appropriately or do some handling
            }
            BioCollection bioCollection = iLimsService.getBioCollectionForStudySubjectByUID(biocollectionUID,
                    study, linkSubjectStudy);
            if (bioCollection == null) {
                bioCollection = new BioCollection();
                if (study.getAutoGenerateBiocollectionUid()) {
                    // if biocollection not in the system we have to create a new biocollection uid.
                    bioCollection.setBiocollectionUid(iLimsService.getNextGeneratedBiospecimenUID(study));
                } else {
                    bioCollection.setBiocollectionUid(biocollectionUID);
                }
            } else {// if exsists we do not want to auto genetared the uid.
                bioCollection.setBiocollectionUid(biocollectionUID);
            }
            bioCollection.setStudy(study);
            bioCollection.setLinkSubjectStudy(linkSubjectStudy);

            if (csvReader.getIndex("NAME") > 0) {
                String name = csvReader.get("NAME");
                bioCollection.setName(name);
            }
            if (csvReader.getIndex("COLLECTIONDATE") > 0) {
                String collectionDate = csvReader.get("COLLECTIONDATE");
                bioCollection.setCollectionDate(simpleDateFormat.parse(collectionDate));
            }
            if (csvReader.getIndex("COMMENTS") > 0) {
                String comments = csvReader.get("COMMENTS");
                bioCollection.setComments(comments);
            }
            //validation SHOULD make sure these cases will work.  TODO:  test scripts

            if (bioCollection.getId() == null) {
                insertBiocollections.add(bioCollection);
                StringBuffer sb = new StringBuffer();
                sb.append("BioCollectionUID: ");
                sb.append(bioCollection.getBiocollectionUid());
                sb.append(" has been created successfully.");
                sb.append("\n");
                uploadReport.append(sb);
                insertCount++;
            } else {
                updateBiocollections.add(bioCollection);
                StringBuffer sb = new StringBuffer();
                sb.append("BioCollectionUID: ");
                sb.append(bioCollection.getBiocollectionUid());
                sb.append(" has been updated successfully.");
                sb.append("\n");
                uploadReport.append(sb);
                updateCount++;
            }
            recordCount++;
        }
    } catch (IOException ioe) {
        uploadReport.append("Unexpected I/O exception whilst reading the biospecimen data file\n");
        log.error("processMatrixBiospecimenFile IOException stacktrace:", ioe);
        throw new ArkSystemException("Unexpected I/O exception whilst reading the biospecimen data file");
    } catch (Exception ex) {
        uploadReport.append("Unexpected exception whilst reading the biospecimen data file\n");
        log.error("processMatrixBiospecimenFile Exception stacktrace:", ex);
        throw new ArkSystemException(
                "Unexpected exception occurred when trying to process biospecimen data file");
    } finally {
        // Clean up the IO objects
        timer.stop();
        uploadReport.append("\n");
        uploadReport.append("Total elapsed time: ");
        uploadReport.append(timer.getTime());
        uploadReport.append(" ms or ");
        uploadReport.append(decimalFormat.format(timer.getTime() / 1000.0));
        uploadReport.append(" s");
        uploadReport.append("\n");
        uploadReport.append("Total file size: ");
        uploadReport.append(inLength);
        uploadReport.append(" B or ");
        uploadReport.append(decimalFormat.format(inLength / 1024.0 / 1024.0));
        uploadReport.append(" MB");
        uploadReport.append("\n");

        if (timer != null)
            timer = null;

        if (csvReader != null) {
            try {
                csvReader.close();
            } catch (Exception ex) {
                log.error("Cleanup operation failed: csvRdr.close()", ex);
            }
        }
        if (inputStreamReader != null) {
            try {
                inputStreamReader.close();
            } catch (Exception ex) {
                log.error("Cleanup operation failed: isr.close()", ex);
            }
        }
        // Restore the state of variables
        srcLength = -1;
    }
    uploadReport.append("Processed ");
    uploadReport.append(recordCount);
    uploadReport.append(" records.");
    uploadReport.append("\n");
    uploadReport.append("Inserted ");
    uploadReport.append(insertCount);
    uploadReport.append(" records.");
    uploadReport.append("\n");
    uploadReport.append("Updated ");
    uploadReport.append(updateCount);
    uploadReport.append(" records.");
    uploadReport.append("\n");

    // Batch insert/update
    iLimsService.batchInsertBiocollections(insertBiocollections);
    iLimsService.batchUpdateBiocollections(updateBiocollections);

    return uploadReport;
}

From source file:net.nan21.dnet.core.web.controller.data.AbstractAsgnController.java

/**
 * Default handler for find action./*from ww w  .  j a  v a 2s  .c om*/
 * 
 * @param resourceName
 * @param dataformat
 * @param dataString
 * @param paramString
 * @param resultStart
 * @param resultSize
 * @param orderByCol
 * @param orderBySense
 * @return
 * @throws Exception
 */
@RequestMapping(method = RequestMethod.POST, params = Constants.REQUEST_PARAM_ACTION + "="
        + Constants.ASGN_ACTION_QUERY_RIGHT)
@ResponseBody
public String findRight(@PathVariable String resourceName, @PathVariable String dataFormat,
        @RequestParam(value = Constants.REQUEST_PARAM_ASGN_OBJECT_ID, required = true) String objectId,
        @RequestParam(value = Constants.REQUEST_PARAM_ASGN_SELECTION_ID, required = true) String selectionId,
        @RequestParam(value = Constants.REQUEST_PARAM_FILTER, required = false, defaultValue = "{}") String dataString,
        @RequestParam(value = Constants.REQUEST_PARAM_PARAMS, required = false, defaultValue = "{}") String paramString,
        @RequestParam(value = Constants.REQUEST_PARAM_START, required = false, defaultValue = "0") int resultStart,
        @RequestParam(value = Constants.REQUEST_PARAM_SIZE, required = false, defaultValue = "500") int resultSize,
        @RequestParam(value = Constants.REQUEST_PARAM_SORT, required = false, defaultValue = "") String orderByCol,
        @RequestParam(value = Constants.REQUEST_PARAM_SENSE, required = false, defaultValue = "") String orderBySense,
        @RequestParam(value = Constants.REQUEST_PARAM_ORDERBY, required = false, defaultValue = "") String orderBy,
        HttpServletRequest request, HttpServletResponse response) throws Exception {
    try {

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

        if (logger.isInfoEnabled()) {
            logger.info("Processing request: {}.{} -> action = {} ",
                    new String[] { resourceName, dataFormat, Constants.ASGN_ACTION_QUERY_RIGHT });
        }

        if (logger.isDebugEnabled()) {
            logger.debug("  --> request-filter: objectId={}, selectionId={} data={}",
                    new String[] { objectId, selectionId, dataString });
            logger.debug("  --> request-params: {} ", new String[] { paramString });
            logger.debug("  --> request-orderBy: sort={}, sense={}, orderBy={}",
                    new String[] { orderByCol, orderBySense, orderBy });
            logger.debug("  --> request-result-range: {} ",
                    new String[] { resultStart + "", (resultStart + resultSize) + "" });
        }

        this.prepareRequest(request, response);

        this.authorizeAsgnAction(resourceName, "find");

        IAsgnService<M, F, P> service = this.findAsgnService(this.serviceNameFromResourceName(resourceName));

        IDsMarshaller<M, F, P> marshaller = service.createMarshaller(dataFormat);

        IQueryBuilder<M, F, P> builder = service.createQueryBuilder().addFetchLimit(resultStart, resultSize);

        if (orderBy != null && !orderBy.equals("")) {
            List<SortToken> sortTokens = marshaller.readListFromString(orderBy, SortToken.class);
            builder.addSortInfo(sortTokens);
        } else {
            builder.addSortInfo(orderByCol, orderBySense);
        }

        F filter = marshaller.readFilterFromString(dataString);
        P params = marshaller.readParamsFromString(paramString);

        List<M> list = service.findRight(selectionId, filter, params, builder);
        long totalCount = service.countRight(selectionId, filter, params, builder);

        IActionResultFind result = this.packfindResult(list, params, totalCount);
        stopWatch.stop();
        result.setExecutionTime(stopWatch.getTime());

        return marshaller.writeResultToString(result);
    } catch (Exception e) {
        return this.handleException(e, response);
    } finally {
        this.finishRequest();
    }
}

From source file:com.liferay.portal.events.ServicePreActionExt.java

public void run(HttpServletRequest request, HttpServletResponse response) throws ActionException {

    StopWatch stopWatch = null;/*from   www . java  2  s .  c  o m*/

    if (_log.isDebugEnabled()) {
        stopWatch = new StopWatch();

        stopWatch.start();
    }

    try {
        servicePre(request, response);
    } catch (Exception e) {
        throw new ActionException(e);
    }

    if (_log.isDebugEnabled()) {
        _log.debug("Running takes " + stopWatch.getTime() + " ms");
    }
}

From source file:com.liferay.portlet.documentlibrary.util.VideoProcessorImpl.java

private void _generateThumbnailXuggler(FileVersion fileVersion, File file, int height, int width)
        throws Exception {

    StopWatch stopWatch = null;//from   w  w w  . j  a  v a  2  s . c om

    if (_log.isInfoEnabled()) {
        stopWatch = new StopWatch();

        stopWatch.start();
    }

    String tempFileId = DLUtil.getTempFileId(fileVersion.getFileEntryId(), fileVersion.getVersion());

    File thumbnailTempFile = getThumbnailTempFile(tempFileId);

    try {
        try {
            if (PropsValues.DL_FILE_ENTRY_PREVIEW_FORK_PROCESS_ENABLED) {
                ProcessCallable<String> processCallable = new LiferayVideoThumbnailProcessCallable(
                        ServerDetector.getServerId(), PropsUtil.get(PropsKeys.LIFERAY_HOME),
                        Log4JUtil.getCustomLogSettings(), file.getCanonicalPath(), thumbnailTempFile,
                        THUMBNAIL_TYPE, height, width,
                        PropsValues.DL_FILE_ENTRY_THUMBNAIL_VIDEO_FRAME_PERCENTAGE);

                ProcessExecutor.execute(processCallable, ClassPathUtil.getPortalClassPath());
            } else {
                LiferayConverter liferayConverter = new LiferayVideoThumbnailConverter(file.getCanonicalPath(),
                        thumbnailTempFile, THUMBNAIL_TYPE, height, width,
                        PropsValues.DL_FILE_ENTRY_THUMBNAIL_VIDEO_FRAME_PERCENTAGE);

                liferayConverter.convert();
            }
        } catch (Exception e) {
            _log.error(e, e);
        }

        storeThumbnailImages(fileVersion, thumbnailTempFile);

        if (_log.isInfoEnabled()) {
            _log.info("Xuggler generated a thumbnail for " + fileVersion.getTitle() + " in " + stopWatch);
        }
    } catch (Exception e) {
        throw new SystemException(e);
    } finally {
        FileUtil.delete(thumbnailTempFile);
    }
}

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

public UIVOCluster getUISFromApplicationContext(Map<String, String> parameters) throws GWTServiceException {
    if (getServletContext().getAttribute("init_failure") != null) {
        Throwable throwable = (Throwable) getServletContext().getAttribute("init_failure");
        getServletContext().removeAttribute("init_failure");
        getServletContext().removeAttribute("init_failure_message");
        throw handleException(throwable);
    } else {/*from ww  w .j  a  v a2 s  .co m*/
        try {
            Iterator<ApplicationIdentifier> contextItr = ApplicationCluster.getInstance().keysIterator();
            String appId = null;
            String windowSession = null;
            UIVOCluster cluster = new UIVOCluster();
            cluster.setExternalProperties(ApplicationClusterUtil.getExternalProperties());
            cluster.setDebugMode(ContextLoaderHelper.isDebugMode());
            cluster.setShowLog(ContextLoaderHelper.showLog());
            cluster.setGlobalDateFormat(ApplicationClusterUtil.getGlobalDateFormat());
            cluster.setReloadable(ContextLoaderHelper.isReloadable(getThreadLocalRequest()));
            cluster.setUseDockMode(ContextLoaderHelper.isDockMode());
            cluster.setClientSideEventEnabled(ApplicationCluster.getInstance().isClientSideEventEnabled());

            UIGVO uiGVO = service.getSystemApplication(
                    ApplicationCluster.getInstance().getSystemApplicationContext(), appId, windowSession,
                    getLocale(), parameters);
            cluster.setSystemMenuApplication(uiGVO);
            List<UIGVO> gvoList = new ArrayList<UIGVO>();

            StopWatch stopWatch = new StopWatch();

            while (contextItr.hasNext()) {
                ApplicationIdentifier key = contextItr.next();
                if (!ApplicationClusterUtil.isSystemApplication(key)) {
                    stopWatch.start();

                    UIGVO uigvo = null;
                    ApplicationContext context = ApplicationCluster.getInstance().get(key);

                    if (context.getLoadException() == null) {
                        try {
                            uigvo = service.getUI(context.getId(), appId, windowSession, getLocale(),
                                    parameters);
                        } catch (Exception e) {
                            String errorMessage = e != null ? "(" + e.getMessage() + ")" : "";
                            String message = key.toString() + " caused exception : <br>" + errorMessage;
                            cluster.getMessages().add(message);
                        }

                    }

                    if (uigvo != null) {
                        uigvo.setAppId(context.getId().toString());
                        uigvo.setDebug(Boolean.valueOf(context.getConfigurationItem(/*
                                                                                    * Configuration.
                                                                                    * DEVELOPMENT_MODE
                                                                                    */"")));

                        uigvo.setTitle(context.getName());
                        stopWatch.stop();
                        uigvo.setTime(Long.valueOf(stopWatch.getTime()));
                        logger.info("Application -" + context.getName() + " is rendered in  "
                                + stopWatch.getTime() + "ms");

                        stopWatch.reset();
                        gvoList.add(uigvo);
                    } else {
                        stopWatch.stop();
                        stopWatch.reset();
                        String errorMessage = context.getLoadException() != null
                                ? context.getLoadException().getMessage()
                                : "";
                        String message = "Application [" + key.toString()
                                + "] is not loaded, because of the following:<br>" + errorMessage;

                        cluster.getMessages().add(message);
                    }

                    if (context.getWarningMessages() != null) {
                        for (String strMsg : context.getWarningMessages()) {
                            cluster.getMessages().add(strMsg);
                        }
                    }

                }
            }

            cluster.setVos(gvoList.toArray(new UIGVO[] {}));
            cluster = service.stripCluster(cluster);
            return cluster;

        } catch (Exception e) {
            throw handleException(e);

        }
    }

}

From source file:chibi.gemmaanalysis.ArrayDesignStatCli.java

@Override
protected Exception doWork(String[] args) {
    Collection<String> failedAds = new ArrayList<>();
    Exception err = processCommandLine(args);
    if (err != null)
        return err;
    if (arrayDesignsToProcess == null || arrayDesignsToProcess.size() == 0) {
        this.arrayDesignsToProcess = adService.loadAll();
    }/*from  w  w  w .  j  a va  2 s .c o m*/
    Map<Taxon, Collection<ArrayDesign>> taxon2arraydesign = new HashMap<Taxon, Collection<ArrayDesign>>();
    Collection<Long> adIds = new HashSet<Long>();
    for (ArrayDesign ad : this.arrayDesignsToProcess) {

        Taxon taxon = ad.getPrimaryTaxon();
        if (taxon == null) {
            System.err.println("ArrayDesign " + ad.getName() + " doesn't have a taxon");
            continue;
        }
        taxon = taxonService.load(taxon.getId());

        if (taxon != null && taxon.getCommonName() == null) {
            log.warn(ad.getShortName() + " taxon common name is null");
            failedAds.add(ad.getShortName());
            continue;
        }

        // filter out taxon
        if (this.taxon != null && this.taxon.getCommonName() != null
                && !taxon.getCommonName().equalsIgnoreCase(this.taxon.getCommonName())) {
            continue;
        }

        adIds.add(ad.getId());

        Collection<ArrayDesign> ads = null;
        ads = taxon2arraydesign.get(taxon);
        if (ads == null) {
            ads = new HashSet<ArrayDesign>();
            taxon2arraydesign.put(taxon, ads);
        }
        ads.add(ad);
    }
    Map<Long, Boolean> isMerged = adService.isMerged(adIds);
    Map<Long, Boolean> isSubsumed = adService.isSubsumed(adIds);
    StopWatch timer = new StopWatch();
    timer.start();
    int lineCount = 0;
    try (FileWriter out = new FileWriter(new File(this.outFile));) {
        String header = "taxon\tshortName\tname\tisTroubled\texperiments\tmergees\tsubsumes\tsubsumedBy\tgenes\tprobes\tcsWithGenes\tcsBioSequences\tcsBlatResults\tP2G_0";
        out.write(header);
        for (int i = 1; i <= MAXIMUM_COUNT; i++)
            out.write("\tP2G_" + i);
        for (int i = 1; i <= MAXIMUM_COUNT; i++)
            out.write("\tG2P_" + i);
        out.write("\n");
        System.err.print(header + "\n");
        for (Taxon taxon : taxon2arraydesign.keySet()) {
            Collection<ArrayDesign> ads = taxon2arraydesign.get(taxon);
            Collection<Gene> allGenes = geneService.getGenesByTaxon(taxon);
            for (Gene gene : allGenes) {
                geneIds.add(gene.getId());

            }
            for (ArrayDesign ad : ads) {

                try {
                    Status status = statusService.getStatus(ad);
                    String isTroubled = status != null ? Boolean.toString(status.getTroubled().booleanValue())
                            : NA;
                    ad = arrayDesignService.thawLite(ad);
                    long mergees = ad.getMergees().size();
                    long subsumes = ad.getSubsumedArrayDesigns().size();
                    String subsumedBy = ad.getSubsumingArrayDesign() != null
                            ? ad.getSubsumingArrayDesign().getShortName()
                            : NA;
                    long numEEs = arrayDesignService.getExpressionExperiments(ad).size();
                    // boolean merged = isMerged.get( ad.getId() );
                    // if ( merged ) continue;
                    // boolean subsumed = isSubsumed.get( ad.getId() );
                    // if ( subsumed ) continue;
                    long numProbes = getArrayDesignService().getCompositeSequenceCount(ad).longValue();
                    long numCsBioSequences = getArrayDesignService().numCompositeSequenceWithBioSequences(ad);
                    long numCsBlatResults = getArrayDesignService().numCompositeSequenceWithBlatResults(ad);
                    long numCsGenes = getArrayDesignService().numCompositeSequenceWithGenes(ad);
                    long numGenes = getArrayDesignService().numGenes(ad);
                    Collection<CompositeSequence> allCSs = getArrayDesignService().getCompositeSequences(ad);
                    Collection<Long> csIds = new HashSet<Long>();
                    for (CompositeSequence cs : allCSs)
                        csIds.add(cs.getId());
                    // FIXME this used to provide only known genes.
                    Map<Long, Collection<Long>> csId2geneIds = this.getCs2GeneMap(csIds);
                    Map<Long, Collection<Long>> geneId2csIds = getGeneId2CSIdsMap(csId2geneIds);
                    int[] csStats = getStats(csId2geneIds, false);
                    int[] geneStats = getStats(geneId2csIds, true);
                    int cs2NoneGene = allCSs.size() - csId2geneIds.keySet().size();
                    String line = taxon.getCommonName() + "\t" + ad.getShortName() + "\t" + ad.getName() + "\t"
                            + isTroubled + "\t" + numEEs + "\t" + mergees + "\t" + subsumes + "\t" + subsumedBy
                            + "\t" + numGenes + "\t" + numProbes + "\t" + numCsGenes + "\t" + numCsBioSequences
                            + "\t" + numCsBlatResults + "\t" + cs2NoneGene;
                    out.write(line);
                    for (int i = 0; i < MAXIMUM_COUNT; i++) {
                        out.write("\t" + csStats[i]);
                    }
                    for (int i = 0; i < MAXIMUM_COUNT; i++) {
                        out.write("\t" + geneStats[i]);
                    }
                    out.write("\n");
                    System.err.print(line + "\n");

                    lineCount++;
                } catch (Exception e) {
                    log.error(e, e);
                    failedAds.add(ad.getShortName());
                    continue;
                }
            }
        }
        out.close();
        log.info("Skipped " + failedAds.size() + " array designs : " + Arrays.toString(failedAds.toArray()));
        log.info("Finished running in " + timer.getTime() + " ms.");
        log.info("Wrote " + lineCount + " lines to " + outFile);

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

From source file:com.liferay.portal.search.elasticsearch.internal.ElasticsearchIndexSearcher.java

@Override
public long searchCount(SearchContext searchContext, Query query) throws SearchException {

    StopWatch stopWatch = new StopWatch();

    stopWatch.start();//from  ww  w .ja v a  2  s .  c o m

    try {
        return doSearchCount(searchContext, query);
    } catch (Exception e) {
        if (_log.isWarnEnabled()) {
            _log.warn(e, e);
        }

        if (!_logExceptionsOnly) {
            throw new SearchException(e.getMessage(), e);
        }

        return 0;
    } finally {
        if (_log.isInfoEnabled()) {
            stopWatch.stop();

            _log.info(StringBundler.concat("Searching ", query.toString(), " took ",
                    String.valueOf(stopWatch.getTime()), " ms"));
        }
    }
}