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

Example 86 with StopWatch

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

the class ExpressionExperimentController method showExpressionExperiment.

@RequestMapping({ "/showExpressionExperiment.html", "/", "/show" })
public ModelAndView showExpressionExperiment(HttpServletRequest request, HttpServletResponse response) {
    StopWatch timer = new StopWatch();
    timer.start();
    ModelAndView mav = new ModelAndView("expressionExperiment.detail");
    BioAssaySet expExp = this.getExpressionExperimentFromRequest(request);
    mav.addObject("expressionExperiment", expExp);
    mav.addObject("eeId", expExp.getId());
    mav.addObject("eeClass", ExpressionExperiment.class.getName());
    if (timer.getTime() > 200) {
        ExpressionExperimentController.log.info("Show Experiment was slow: id=" + expExp.getId() + " " + timer.getTime() + "ms");
    }
    return mav;
}

Example 87 with StopWatch

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

the class ExpressionExperimentController method loadStatusSummaries.

/**
 * AJAX. Data summarizing the status of experiments.
 *
 * @param taxonId    can be null
 * @param limit      If >0, get the most recently updated N experiments, where N <= limit; or if < 0, get the least
 *                   recently updated; if 0, or null, return all.
 * @param filter     if non-null, limit data sets to ones meeting criteria.
 * @param showPublic return user's public datasets too
 * @return ee details vos
 */
public Collection<ExpressionExperimentDetailsValueObject> loadStatusSummaries(Long taxonId, List<Long> ids, Integer limit, Integer filter, Boolean showPublic) {
    StopWatch timer = new StopWatch();
    timer.start();
    Collection<ExpressionExperimentDetailsValueObject> vos;
    if (!SecurityUtil.isUserLoggedIn()) {
        throw new AccessDeniedException("User does not have access to experiment management");
    }
    if (limit == null) {
        limit = 50;
    }
    vos = this.getEEVOsForManager(taxonId, ids, limit, filter, showPublic);
    if (vos.isEmpty()) {
        return new HashSet<>();
    }
    if (timer.getTime() > 1000) {
        ExpressionExperimentController.log.info("Fetching basic data took: " + timer.getTime() + "ms");
    }
    timer.reset();
    timer.start();
    expressionExperimentReportService.getAnnotationInformation(vos);
    expressionExperimentReportService.populateEventInformation(vos);
    if (timer.getTime() > 1000) {
        ExpressionExperimentController.log.info("Filling in report data for " + vos.size() + " EEs: " + timer.getTime() + "ms");
    }
    // We need to convert the VOs to detailVos and add array designs so trouble info can be correctly displayed.
    for (ExpressionExperimentDetailsValueObject vo : vos) {
        vo.setArrayDesigns(arrayDesignService.loadValueObjectsForEE(vo.getId()));
    }
    return vos;
}

Example 88 with StopWatch

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

the class ExpressionExperimentSetController method showExpressionExperimentSet.

@RequestMapping(value = "/showExpressionExperimentSet.html", method = RequestMethod.GET)
public ModelAndView showExpressionExperimentSet(HttpServletRequest request, HttpServletResponse response) {
    ModelAndView mav = new ModelAndView("expressionExperimentSet.detail");
    StopWatch timer = new StopWatch();
    timer.start();
    ExpressionExperimentSetValueObject eesvo = this.getExpressionExperimentSetFromRequest(request);
    mav.addObject("eeSetId", eesvo.getId());
    mav.addObject("eeSetName", eesvo.getName());
    if (timer.getTime() > 200) {
        log.info("Show experiment set was slow: id=" + eesvo.getId() + " " + timer.getTime() + "ms");
    }
    return mav;
}

Example 89 with StopWatch

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

the class GeneController method handleRequestInternal.

@RequestMapping("/downloadGeneList.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> geneSetIds = ControllerUtils.extractIds(request.getParameter("gs"));
    // might not be there
    String geneSetName = request.getParameter("gsn");
    ModelAndView mav = new ModelAndView(new TextView());
    if ((geneIds == null || geneIds.isEmpty()) && (geneSetIds == null || geneSetIds.isEmpty())) {
        mav.addObject("text", "Could not find genes to match gene ids: {" + geneIds + "} or gene set ids {" + geneSetIds + "}");
        return mav;
    }
    Collection<GeneValueObject> genes = new ArrayList<>();
    if (geneIds != null) {
        for (Long id : geneIds) {
            genes.add(geneService.loadValueObjectById(id));
        }
    }
    if (geneSetIds != null) {
        for (Long id : geneSetIds) {
            genes.addAll(geneSetService.getGenesInGroup(new GeneSetValueObject(id)));
        }
    }
    mav.addObject("text", format4File(genes, geneSetName));
    watch.stop();
    Long time = watch.getTime();
    if (time > 100) {
        log.info("Retrieved and Formated" + genes.size() + " genes in : " + time + " ms.");
    }
    return mav;
}

Example 90 with StopWatch

use of org.apache.commons.lang3.time.StopWatch in project nd4j by deeplearning4j.

the class BinarySerdeTest method timeOldVsNew.

@Test
public void timeOldVsNew() throws Exception {
    int numTrials = 1000;
    long oldTotal = 0;
    long newTotal = 0;
    INDArray arr = Nd4j.create(100000);
    Nd4j.getCompressor().compressi(arr, "GZIP");
    for (int i = 0; i < numTrials; i++) {
        StopWatch oldStopWatch = new StopWatch();
        BufferedOutputStream bos = new BufferedOutputStream(new ByteArrayOutputStream(arr.length()));
        DataOutputStream dos = new DataOutputStream(bos);
        oldStopWatch.start();
        Nd4j.write(arr, dos);
        oldStopWatch.stop();
        // System.out.println("Old " + oldStopWatch.getNanoTime());
        oldTotal += oldStopWatch.getNanoTime();
        StopWatch newStopWatch = new StopWatch();
        newStopWatch.start();
        BinarySerde.toByteBuffer(arr);
        newStopWatch.stop();
        // System.out.println("New " + newStopWatch.getNanoTime());
        newTotal += newStopWatch.getNanoTime();
    }
    oldTotal /= numTrials;
    newTotal /= numTrials;
    System.out.println("Old avg " + oldTotal + " New avg " + newTotal);
}