Example usage for org.springframework.util StopWatch start

List of usage examples for org.springframework.util StopWatch start

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Introduction

In this page you can find the example usage for org.springframework.util StopWatch start.

Prototype

public void start() throws IllegalStateException

Source Link

Document

Start an unnamed task.

Usage

From source file:org.springframework.statemachine.recipes.support.RunnableAction.java

@Override
public final void execute(StateContext<String, String> context) {
    if (!shouldExecute(id, context)) {
        return;/* w w w. j  a va 2 s.  c o  m*/
    }
    StopWatch watch = new StopWatch();
    String logId = (id == null ? "" : (" id=" + id));
    log.info("Executing runnable" + logId);
    if (log.isDebugEnabled()) {
        watch.start();
    }
    try {
        onPreExecute(id, context);
        runnable.run();
        onSuccess(id, context);
    } catch (Exception e) {
        onError(id, context, e);
    } finally {
        onPostExecute(id, context);
    }
    if (log.isDebugEnabled()) {
        watch.stop();
        log.debug("Runnable execution took " + watch.getTotalTimeMillis() + " ms" + logId);
    }
}

From source file:ubic.gemma.core.tasks.visualization.DifferentialExpressionSearchTaskImpl.java

/**
 * Retrieve the details (contrasts) for results which meet the criterion. (PVALUE_CONTRAST_SELECT_THRESHOLD).
 * Requires a database hit./*from w w w.j  a  va  2  s . c  o  m*/
 *
 * @param diffExResults results
 * @return map
 */
private Map<Long, ContrastsValueObject> getDetailsForContrasts(
        Collection<DiffExprGeneSearchResult> diffExResults) {

    StopWatch timer = new StopWatch();
    timer.start();
    List<Long> resultsWithContrasts = new ArrayList<>();

    for (DiffExprGeneSearchResult r : diffExResults) {
        if (r.getResultId() == null) {
            // it is a dummy result. It means there is no result for this gene in this resultset.
            continue;
        }

        /*
         * this check will not be needed if we only store the 'good' results, but we do store everything.
         */
        // Here I am trying to avoid fetching them when there is no hope that the results will be interesting.
        if (r instanceof MissingResult || r instanceof NonRetainedResult || r
                .getCorrectedPvalue() > DifferentialExpressionSearchTaskImpl.PVALUE_CONTRAST_SELECT_THRESHOLD) {
            // Then it won't have contrasts; no need to fetch.
            continue;
        }

        resultsWithContrasts.add(r.getResultId());
    }

    Map<Long, ContrastsValueObject> detailedResults = new HashMap<>();
    if (!resultsWithContrasts.isEmpty()) {
        // uses a left join so it will have all the results.
        detailedResults = differentialExpressionResultService
                .loadContrastDetailsForResults(resultsWithContrasts);
    }

    timer.stop();
    if (timer.getTotalTimeMillis() > 1) {
        DifferentialExpressionSearchTaskImpl.log.info("Fetch contrasts for " + resultsWithContrasts.size()
                + " results: " + timer.getTotalTimeMillis() + "ms");
    }
    return detailedResults;
}

From source file:ubic.gemma.persistence.util.monitor.MonitorAdvice.java

@Around("@annotation(ubic.gemma.persistence.util.monitor.Monitored)")
public Object profile(ProceedingJoinPoint pjp) throws Throwable {

    StopWatch stopWatch = new StopWatch();

    stopWatch.start();
    Object retVal = pjp.proceed();

    stopWatch.stop();/*from ww w  .j  a va2s  .  c o m*/

    log.info(pjp.getSignature().toString() + " took " + stopWatch.getLastTaskTimeMillis() + "ms.");

    return retVal;

}

From source file:ubic.gemma.tasks.visualization.DifferentialExpressionSearchTaskImpl.java

/**
 * Staging for getting the diff ex results.
 * //from w w  w .j  ava2s  .  c  o m
 * @param resultSets to be searched
 * @param geneIds to be searched
 * @param searchResult holds the results
 */
private void fetchDifferentialExpressionResults(List<ExpressionAnalysisResultSet> resultSets,
        List<Long> geneIds, DifferentialExpressionGenesConditionsValueObject searchResult) {

    Map<ExpressionAnalysisResultSet, Collection<Long>> resultSetIdsToArrayDesignsUsed = new HashMap<ExpressionAnalysisResultSet, Collection<Long>>();

    StopWatch timer = new StopWatch();
    timer.start();
    // DATABASE CALL HERE, but should be quite fast.
    for (ExpressionAnalysisResultSet rs : resultSets) {
        resultSetIdsToArrayDesignsUsed.put(rs,
                EntityUtils.getIds(eeService.getArrayDesignsUsed(rs.getAnalysis().getExperimentAnalyzed())));
    }
    timer.stop();
    if (timer.getTotalTimeMillis() > 100) {
        log.info("Fetch array designs used: " + timer.getTotalTimeMillis() + "ms");
    }

    fetchDifferentialExpressionResults(resultSetIdsToArrayDesignsUsed, geneIds, searchResult);

}

From source file:ubic.gemma.tasks.visualization.DifferentialExpressionSearchTaskImpl.java

/**
 * Retrieve the details (contrasts) for results which meet the criterion. (PVALUE_CONTRAST_SELECT_THRESHOLD)
 * /*w w w.j  a v a 2  s.c o m*/
 * @param geneToProbeResult
 * @return
 */
private Map<Long, ContrastsValueObject> getDetailsForContrasts(
        Collection<DiffExprGeneSearchResult> diffExResults) {

    StopWatch timer = new StopWatch();
    timer.start();
    List<Long> resultsWithContrasts = new ArrayList<Long>();

    for (DiffExprGeneSearchResult r : diffExResults) {
        if (r.getResultId() == null) {
            // it is a dummy result. It means there is no result for this gene in this resultset.
            continue;
        }

        /*
         * this check will not be needed if we only store the 'good' results?
         */
        // Here I am trying to avoid fetching them when there is no hope that the results will be interesting.
        if (r instanceof MissingResult || r instanceof NonRetainedResult
                || r.getCorrectedPvalue() > PVALUE_CONTRAST_SELECT_THRESHOLD) {
            // Then it won't have contrasts; no need to fetch.
            continue;
        }

        resultsWithContrasts.add(r.getResultId());
    }

    Map<Long, ContrastsValueObject> detailedResults = new HashMap<Long, ContrastsValueObject>();
    if (!resultsWithContrasts.isEmpty()) {
        // uses a left join so it will have all the results.
        detailedResults = differentialExpressionResultService
                .loadContrastDetailsForResults(resultsWithContrasts);
    }

    timer.stop();
    if (timer.getTotalTimeMillis() > 1) {
        log.info("Fetch contrasts for " + resultsWithContrasts.size() + " results: "
                + timer.getTotalTimeMillis() + "ms");
    }
    return detailedResults;
}

From source file:uk.ac.ebi.atlas.experimentimport.analyticsindex.baseline.BaselineAnalyticsIndexerService.java

public int index(BaselineExperiment experiment) {
    String experimentAccession = experiment.getAccession();
    ExperimentType experimentType = experiment.getType();

    String defaultQueryFactorType = experiment.getExperimentalFactors().getDefaultQueryFactorType();
    ExperimentDesign experimentDesign = experiment.getExperimentDesign();

    ImmutableMap<String, String> ensemblSpeciesGroupedByAssayGroupId = SpeciesGrouper
            .buildEnsemblSpeciesGroupedByAssayGroupId(experiment);

    ImmutableSetMultimap<String, String> ontologyTermIdsByAssayAccession = expandOntologyTerms(
            experimentDesign.getAllOntologyTermIdsByAssayAccession());

    ImmutableSetMultimap<String, String> conditionSearchTermsByAssayGroupId = buildConditionSearchTermsByAssayGroupId(
            experiment, ontologyTermIdsByAssayAccession);

    checkArgument(StringUtils.isNotBlank(defaultQueryFactorType));

    LOGGER.info("Start indexing " + experimentAccession);
    StopWatch stopWatch = new StopWatch(getClass().getSimpleName());
    stopWatch.start();

    //TODO: move this to another class
    ObjectInputStream<BaselineAnalytics> inputStream = (experimentType == ExperimentType.PROTEOMICS_BASELINE)
            ? proteomicsBaselineAnalyticsInputStreamFactory.create(experimentAccession)
            : baselineAnalyticsInputStreamFactory.create(experimentAccession);

    int count = indexRnaSeqBaselineExperimentAnalytics(experimentAccession, experimentType,
            defaultQueryFactorType, conditionSearchTermsByAssayGroupId, ensemblSpeciesGroupedByAssayGroupId,
            inputStream);//ww  w  .  ja  va  2s  . co m

    stopWatch.stop();
    LOGGER.info(String.format("Done indexing %s, indexed %,d documents in %s seconds", experimentAccession,
            count, stopWatch.getTotalTimeSeconds()));

    return count;
}

From source file:uk.ac.ebi.atlas.search.baseline.BaselineExperimentAssayGroupSearchService.java

public SortedSet<BaselineExperimentAssayGroup> query(Set<String> geneIds, Optional<String> condition,
        Optional<String> species) {
    LOGGER.info(String.format("<query> geneIds=%s, condition=%s", Joiner.on(", ").join(geneIds), condition));
    StopWatch stopWatch = new StopWatch(getClass().getSimpleName());
    stopWatch.start();

    String conditionString = condition.isPresent() ? condition.get() : "";
    String speciesString = species.isPresent() ? species.get() : "";

    Optional<ImmutableSet<IndexedAssayGroup>> indexedAssayGroups = fetchAssayGroupsForCondition(
            conditionString);//from   w  w w . j  a  v  a 2  s . co  m

    SetMultimap<String, String> assayGroupsWithExpressionByExperiment = baselineExperimentAssayGroupsDao
            .fetchExperimentAssayGroupsWithNonSpecificExpression(indexedAssayGroups, Optional.of(geneIds));

    SortedSet<BaselineExperimentAssayGroup> baselineExperimentAssayGroups = searchedForConditionButGotNoResults(
            conditionString, indexedAssayGroups) ? emptySortedSet()
                    : buildResults(assayGroupsWithExpressionByExperiment, !StringUtils.isBlank(conditionString),
                            speciesString);

    stopWatch.stop();
    LOGGER.info(String.format("<query> %s results, took %s seconds", baselineExperimentAssayGroups.size(),
            stopWatch.getTotalTimeSeconds()));

    return baselineExperimentAssayGroups;
}

From source file:uk.ac.ebi.atlas.search.baseline.BaselineExperimentAssayGroupSearchService.java

@Deprecated
public SortedSet<BaselineExperimentAssayGroup> query(String geneQuery, String condition, String specie,
        boolean isExactMatch) {
    LOGGER.info(String.format("<query> geneQuery=%s, condition=%s", geneQuery, condition));
    StopWatch stopWatch = new StopWatch(getClass().getSimpleName());
    stopWatch.start();

    Optional<ImmutableSet<IndexedAssayGroup>> indexedAssayGroups = fetchAssayGroupsForCondition(condition);

    String species = StringUtils.isNotBlank(specie) ? specie : "";

    //TODO: move outside into caller, because this is called twice, here and in DiffAnalyticsSearchService
    Optional<Set<String>> geneIds = solrQueryService.expandGeneQueryIntoGeneIds(geneQuery, species,
            isExactMatch);//ww  w .  j a  v  a  2  s .  c  o  m

    SetMultimap<String, String> assayGroupsWithExpressionByExperiment = baselineExperimentAssayGroupsDao
            .fetchExperimentAssayGroupsWithNonSpecificExpression(indexedAssayGroups, geneIds);

    boolean conditionSearch = !isEmpty(indexedAssayGroups);

    SortedSet<BaselineExperimentAssayGroup> baselineExperimentAssayGroups = Sets.newTreeSet();
    if (conditionSearch || StringUtils.isNotEmpty(geneQuery) && StringUtils.isEmpty(condition)) {
        baselineExperimentAssayGroups = buildResults(assayGroupsWithExpressionByExperiment, conditionSearch,
                species);
    }

    stopWatch.stop();
    LOGGER.info(String.format("<query> %s results, took %s seconds", baselineExperimentAssayGroups.size(),
            stopWatch.getTotalTimeSeconds()));

    return baselineExperimentAssayGroups;
}