Examples with StopWatch org.apache.commons.lang3.time.StopWatch used on opensource projects

Example 81 with StopWatch

use of org.apache.commons.lang3.time.StopWatch in project Gemma by PavlidisLab.

the class DEDVController method getDEDVForVisualization.

/**
 * AJAX exposed method
 */
public VisualizationValueObject[] getDEDVForVisualization(Collection<Long> eeIds, Collection<Long> geneIds) {
    StopWatch watch = new StopWatch();
    watch.start();
    Collection<ExpressionExperiment> ees = expressionExperimentService.load(eeIds);
    if (ees == null || ees.isEmpty())
        return null;
    Collection<DoubleVectorValueObject> dedvs;
    if (geneIds == null || geneIds.isEmpty()) {
        dedvs = processedExpressionDataVectorService.getProcessedDataArrays(ees.iterator().next(), SAMPLE_SIZE);
    } else {
        if (geneIds.size() > MAX_RESULTS_TO_RETURN) {
            log.warn(geneIds.size() + " genes for visualization. Too many.  Only using first " + MAX_RESULTS_TO_RETURN + " genes. ");
            List<Long> reducedGeneIds = new ArrayList<>(geneIds);
            geneIds = reducedGeneIds.subList(0, MAX_RESULTS_TO_RETURN);
        }
        dedvs = processedExpressionDataVectorService.getProcessedDataArrays(ees, geneIds);
    }
    if (dedvs.isEmpty()) {
        return null;
    }
    Long time = watch.getTime();
    watch.reset();
    watch.start();
    if (time > 100) {
        log.info("Retrieved " + dedvs.size() + " DEDVs for " + eeIds.size() + " EEs" + (geneIds == null ? " sample" : " for " + geneIds.size() + " genes ") + " in " + time + " ms (times <100ms not reported).");
    }
    Map<Long, LinkedHashMap<BioAssayValueObject, LinkedHashMap<ExperimentalFactor, Double>>> layouts = experimentalDesignVisualizationService.sortVectorDataByDesign(dedvs);
    time = watch.getTime();
    watch.reset();
    watch.start();
    if (time > 100) {
        log.info("Ran sortVectorDataByDesign on " + dedvs.size() + " DEDVs for " + eeIds.size() + " EEs" + " in " + time + " ms (times <100ms not reported).");
    }
    watch.stop();
    time = watch.getTime();
    if (time > 100) {
        log.info("Ran sortLayoutSamplesByFactor on " + layouts.size() + " layouts" + " in " + time + " ms (times <100ms not reported).");
    }
    return makeVisCollection(dedvs, geneIds, null, layouts);
}

Example 82 with StopWatch

use of org.apache.commons.lang3.time.StopWatch in project Gemma by PavlidisLab.

the class DEDVController method makeDiffVisCollection.

/**
 * Takes the DEDVs and put them in point objects and normalize the values. returns a map of eeid to visValueObject.
 * Currently removes multiple hits for same gene. Tries to pick best DEDV. Organizes the experiments from lowest to
 * higest p-value
 *
 * @param validatedProbes (bad name)
 */
private VisualizationValueObject[] makeDiffVisCollection(Collection<DoubleVectorValueObject> dedvs, List<Long> genes, Map<Long, Collection<DifferentialExpressionValueObject>> validatedProbes, Map<Long, LinkedHashMap<BioAssayValueObject, LinkedHashMap<ExperimentalFactor, Double>>> layouts) {
    StopWatch watch = new StopWatch();
    watch.start();
    Map<Long, Collection<DoubleVectorValueObject>> vvoMap = new HashMap<>();
    Map<Long, ExpressionExperimentValueObject> eeMap = new HashMap<>();
    // Organize by expression experiment
    for (DoubleVectorValueObject dvvo : dedvs) {
        ExpressionExperimentValueObject ee = dvvo.getExpressionExperiment();
        eeMap.put(ee.getId(), ee);
        if (!vvoMap.containsKey(ee.getId())) {
            vvoMap.put(ee.getId(), new HashSet<DoubleVectorValueObject>());
        }
        vvoMap.get(ee.getId()).add(dvvo);
    }
    class EE2PValue implements Comparable<EE2PValue> {

        Long EEId;

        double pValue;

        public EE2PValue() {
            super();
        }

        public EE2PValue(Long eeid, double pValue) {
            this();
            this.EEId = eeid;
            this.pValue = pValue;
        }

        @Override
        public int compareTo(EE2PValue o) {
            if (this.pValue > o.getPValue())
                return 1;
            else if (this.pValue > o.getPValue())
                return -1;
            else
                return 0;
        }

        public Long getEEId() {
            return EEId;
        }

        public double getPValue() {
            return pValue;
        }
    }
    List<EE2PValue> sortedEE = new ArrayList<>();
    // Need to sort the expression experiments by lowest p-value
    for (Long eeId : vvoMap.keySet()) {
        Collection<DifferentialExpressionValueObject> devos = validatedProbes.get(eeId);
        double minP = 1;
        if (devos != null && !devos.isEmpty()) {
            for (DifferentialExpressionValueObject devo : devos) {
                if (minP > devo.getP()) {
                    minP = devo.getP();
                }
            }
        }
        sortedEE.add(new EE2PValue(eeId, minP));
    }
    Collections.sort(sortedEE);
    VisualizationValueObject[] result = new VisualizationValueObject[vvoMap.keySet().size()];
    List<GeneValueObject> geneValueObjects = getGeneValueObjectList(genes);
    // Create collection of visualizationValueObject for flotr on js side
    int i = 0;
    for (EE2PValue ee2P : sortedEE) {
        VisualizationValueObject vvo = new VisualizationValueObject(vvoMap.get(ee2P.getEEId()), geneValueObjects, ee2P.getPValue(), validatedProbes.get(ee2P.getEEId()));
        getSampleNames(vvoMap.get(ee2P.getEEId()), vvo, layouts);
        if (layouts != null && !layouts.isEmpty() && layouts.containsKey(ee2P.getEEId())) {
            LinkedHashMap<BioAssayValueObject, LinkedHashMap<ExperimentalFactor, Double>> layout = layouts.get(ee2P.getEEId());
            this.prepareFactorsForFrontEndDisplay(vvo, layout);
        }
        if (layouts != null) {
            ExpressionExperimentValueObject ee = eeMap.get(ee2P.getEEId());
            log.debug("setup experimental design layout profiles for " + ee);
            vvo.setUpFactorProfiles(layouts.get(ee.getId()));
        }
        result[i] = vvo;
        i++;
    }
    Long time = watch.getTime();
    if (time > 1000) {
        log.info("Created vis value objects in: " + time);
    }
    return result;
}

Example 83 with StopWatch

use of org.apache.commons.lang3.time.StopWatch in project Gemma by PavlidisLab.

the class DEDVController method handleRequestInternal.

/**
 * Handle case of text export of the results.
 */
@RequestMapping("/downloadDEDV.html")
protected ModelAndView handleRequestInternal(HttpServletRequest request) {
    StopWatch watch = new StopWatch();
    watch.start();
    // might not be any
    Collection<Long> geneIds = ControllerUtils.extractIds(request.getParameter("g"));
    // might not be there
    Collection<Long> eeIds = ControllerUtils.extractIds(request.getParameter("ee"));
    ModelAndView mav = new ModelAndView(new TextView());
    if (eeIds == null || eeIds.isEmpty()) {
        mav.addObject("text", "Input empty for finding DEDVs: " + geneIds + " and " + eeIds);
        return mav;
    }
    String threshSt = request.getParameter("thresh");
    String resultSetIdSt = request.getParameter("rs");
    Double thresh = 100.0;
    if (StringUtils.isNotBlank(threshSt)) {
        try {
            thresh = Double.parseDouble(threshSt);
        } catch (NumberFormatException e) {
            throw new RuntimeException("Threshold was not a valid value: " + threshSt);
        }
    }
    Map<ExpressionExperimentValueObject, Map<Long, Collection<DoubleVectorValueObject>>> result;
    if (request.getParameter("pca") != null) {
        int component = Integer.parseInt(request.getParameter("component"));
        Long eeId = eeIds.iterator().next();
        Map<ProbeLoading, DoubleVectorValueObject> topLoadedVectors = this.svdService.getTopLoadedVectors(eeId, component, thresh.intValue());
        if (topLoadedVectors == null)
            return null;
        mav.addObject("text", format4File(topLoadedVectors.values()));
        return mav;
    }
    /*
         * The following should be set if we're viewing diff. ex results.
         */
    Long resultSetId = null;
    if (StringUtils.isNumeric(resultSetIdSt)) {
        resultSetId = Long.parseLong(resultSetIdSt);
    }
    if (resultSetId != null) {
        /*
             * Diff ex case.
             */
        Long eeId = eeIds.iterator().next();
        Collection<DoubleVectorValueObject> diffExVectors = processedExpressionDataVectorService.getDiffExVectors(resultSetId, thresh, MAX_RESULTS_TO_RETURN);
        if (diffExVectors == null || diffExVectors.isEmpty()) {
            mav.addObject("text", "No results");
            return mav;
        }
        /*
             * Organize the vectors in the same way expected by the ee+gene type of request.
             */
        ExpressionExperimentValueObject ee = expressionExperimentService.loadValueObject(expressionExperimentService.load(eeId));
        result = new HashMap<>();
        Map<Long, Collection<DoubleVectorValueObject>> gmap = new HashMap<>();
        for (DoubleVectorValueObject dv : diffExVectors) {
            for (Long g : dv.getGenes()) {
                if (!gmap.containsKey(g)) {
                    gmap.put(g, new HashSet<DoubleVectorValueObject>());
                }
                gmap.get(g).add(dv);
            }
        }
        result.put(ee, gmap);
    } else {
        // Generic listing.
        result = getDEDV(eeIds, geneIds);
    }
    if (result == null || result.isEmpty()) {
        mav.addObject("text", "No results");
        return mav;
    }
    mav.addObject("text", format4File(result));
    watch.stop();
    Long time = watch.getTime();
    if (time > 100) {
        log.info("Retrieved and Formated" + result.keySet().size() + " DEDVs for eeIDs: " + eeIds + " and GeneIds: " + geneIds + " in : " + time + " ms.");
    }
    return mav;
}

Example 84 with StopWatch

use of org.apache.commons.lang3.time.StopWatch in project Gemma by PavlidisLab.

the class DEDVController method getDEDVForDiffExVisualization.

/**
 * AJAX exposed method - for ProbeLevelDiffExGrid, VisualizationDifferentialWindow,
 * DifferentialExpressionAnalysesSummaryTree
 *
 * @param eeIds     FIXME accommodate ExpressionExperimentSubSets. Currently we pass in the "source experiment" so we
 *                  don't get the slice.
 * @param geneIds   (could be just one)
 * @param threshold for 'significance'
 * @param factorMap Collection of DiffExpressionSelectedFactorCommand showing which factors to use.
 */
public VisualizationValueObject[] getDEDVForDiffExVisualization(Collection<Long> eeIds, Collection<Long> geneIds, Double threshold, Collection<DiffExpressionSelectedFactorCommand> factorMap) {
    if (eeIds.isEmpty() || geneIds.isEmpty())
        return null;
    StopWatch watch = new StopWatch();
    watch.start();
    Collection<? extends BioAssaySet> ees = expressionExperimentService.load(eeIds);
    if (ees == null || ees.isEmpty())
        return null;
    Collection<Gene> genes = geneService.load(geneIds);
    if (genes == null || genes.isEmpty())
        return null;
    Collection<DoubleVectorValueObject> dedvs = processedExpressionDataVectorService.getProcessedDataArrays(ees, geneIds);
    watch.stop();
    Long time = watch.getTime();
    log.info("Retrieved " + dedvs.size() + " DEDVs for " + eeIds.size() + " EEs and " + geneIds.size() + " genes in " + time + " ms.");
    watch = new StopWatch();
    watch.start();
    Map<Long, LinkedHashMap<BioAssayValueObject, LinkedHashMap<ExperimentalFactor, Double>>> layouts;
    layouts = experimentalDesignVisualizationService.sortVectorDataByDesign(dedvs);
    time = watch.getTime();
    if (time > 100) {
        log.info("Ran sortVectorDataByDesign on " + dedvs.size() + " DEDVs for 1 EE" + " in " + time + " ms (times <100ms not reported).");
    }
    // layouts = experimentalDesignVisualizationService.sortLayoutSamplesByFactor( layouts ); // required? yes, see
    // GSE11859
    time = watch.getTime();
    if (time > 100) {
        log.info("Ran sortLayoutSamplesByFactor on " + layouts.size() + " layouts" + " in " + time + " ms (times <100ms not reported).");
    }
    watch = new StopWatch();
    watch.start();
    Map<Long, Collection<DifferentialExpressionValueObject>> validatedProbes = getProbeDiffExValidation(genes, threshold, factorMap);
    watch.stop();
    time = watch.getTime();
    log.info("Retrieved " + validatedProbes.size() + " valid probes in " + time + " ms.");
    return makeDiffVisCollection(dedvs, new ArrayList<>(geneIds), validatedProbes, layouts);
}

Example 85 with StopWatch

use of org.apache.commons.lang3.time.StopWatch in project Gemma by PavlidisLab.

the class DEDVController method getProbeLinkValidation.

/**
 * Identify which probes were 'responsible' for the coexpression links.
 * FIXME change this to actually compute the correlations.
 *
 * @return map of EEID -> collection ProbeIDs which underlie the stored coexpression links.
 */
private Map<Long, Collection<Long>> getProbeLinkValidation(Collection<ExpressionExperiment> ees, Gene queryGene, Gene coexpressedGene, Collection<DoubleVectorValueObject> dedvs) {
    StopWatch watch = new StopWatch();
    watch.start();
    Map<Long, Collection<Long>> coexpressedEE2ProbeIds = new HashMap<>();
    Map<Long, Collection<Long>> queryEE2ProbeIds = new HashMap<>();
    /*
         * Get the probes for the vectors, organize by ee.
         */
    for (DoubleVectorValueObject dedv : dedvs) {
        ExpressionExperimentValueObject ee = dedv.getExpressionExperiment();
        if (dedv.getGenes().contains(queryGene.getId())) {
            if (!queryEE2ProbeIds.containsKey(ee.getId())) {
                queryEE2ProbeIds.put(ee.getId(), new HashSet<Long>());
            }
            queryEE2ProbeIds.get(ee.getId()).add(dedv.getDesignElement().getId());
        } else if (dedv.getGenes().contains(coexpressedGene.getId())) {
            if (!coexpressedEE2ProbeIds.containsKey(ee.getId())) {
                coexpressedEE2ProbeIds.put(ee.getId(), new HashSet<Long>());
            }
            coexpressedEE2ProbeIds.get(ee.getId()).add(dedv.getDesignElement().getId());
        } else {
            log.error("Dedv doesn't belong to coexpressed or query gene. QueryGene= " + queryGene + "CoexpressedGene= " + coexpressedGene + "DEDV " + dedv.getId() + " has genes: " + dedv.getGenes());
        }
    }
    Map<Long, Collection<Long>> validatedProbes = new HashMap<>();
    for (ExpressionExperiment ee : ees) {
        Collection<Long> queryProbeIds = queryEE2ProbeIds.get(ee.getId());
        Collection<Long> coexpressedProbeIds = coexpressedEE2ProbeIds.get(ee.getId());
        if (queryProbeIds == null || queryProbeIds.isEmpty()) {
            log.warn("Unexpectedly no probes for " + queryGene + " in " + ee);
            continue;
        }
        if (coexpressedProbeIds == null || coexpressedProbeIds.isEmpty()) {
            log.warn("Unexpectedly no probes for " + coexpressedGene + " in " + ee);
        }
    /*
             * Note: this does a probe-level query FIXME if we don't store data at probe-level we can't do this.
             */
    // Collection<Long> probesInLinks = this.geneCoexpressionService.getCoexpressedProbes( queryProbeIds,
    // coexpressedProbeIds, ee, queryGene.getTaxon().getCommonName() );
    // if ( probesInLinks.isEmpty() ) {
    // log.warn( "Unexpectedly no probes for link between " + queryGene + " -and- " + coexpressedGene + " in "
    // + ee );
    // }
    // 
    // validatedProbes.put( ee.getId(), probesInLinks );
    // FIXME FIXME
    }
    watch.stop();
    Long time = watch.getTime();
    if (time > 1000) {
        log.info("Validation of probes for " + ees.size() + " experiments in " + time + "ms.");
    }
    return validatedProbes;
}