Examples with DifferentialExpressionAnalysisTaskCommand ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskCommand used on opensource projects

Example 1 with DifferentialExpressionAnalysisTaskCommand

use of ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskCommand in project Gemma by PavlidisLab.

the class DifferentialExpressionAnalysisController method run.

/**
 * AJAX entry point when running completely automatically.
 *
 * @param id id
 * @return string
 */
public String run(Long id) {
    ExpressionExperiment ee = expressionExperimentService.load(id);
    if (ee == null) {
        throw new IllegalArgumentException("Cannot access experiment with id=" + id);
    }
    this.experimentReportService.evictFromCache(ee.getId());
    ee = expressionExperimentService.thawLite(ee);
    DifferentialExpressionAnalysisTaskCommand cmd = new DifferentialExpressionAnalysisTaskCommand(ee);
    boolean rnaSeq = expressionExperimentService.isRNASeq(ee);
    cmd.setUseWeights(rnaSeq);
    cmd.setFactors(ExperimentalDesignUtils.factorsWithoutBatch(ee.getExperimentalDesign().getExperimentalFactors()));
    // if possible, might get dropped.
    cmd.setIncludeInteractions(true);
    return taskRunningService.submitRemoteTask(cmd);
}

Example 2 with DifferentialExpressionAnalysisTaskCommand

use of ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskCommand in project Gemma by PavlidisLab.

the class DifferentialExpressionAnalysisController method refreshStats.

public String refreshStats(Long eeId, Long id) {
    ExpressionExperiment ee = expressionExperimentService.load(eeId);
    if (ee == null) {
        throw new IllegalArgumentException("Cannot access experiment with id=" + eeId);
    }
    DifferentialExpressionAnalysis toRefresh = differentialExpressionAnalysisService.load(id);
    if (toRefresh == null) {
        throw new IllegalArgumentException("Cannot access analysis with id=" + id);
    }
    this.experimentReportService.evictFromCache(ee.getId());
    DifferentialExpressionAnalysisTaskCommand cmd = new DifferentialExpressionAnalysisTaskCommand(ee, toRefresh);
    return taskRunningService.submitLocalTask(cmd);
}

Example 3 with DifferentialExpressionAnalysisTaskCommand

use of ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskCommand in project Gemma by PavlidisLab.

the class DifferentialExpressionAnalysisController method redo.

/**
 * AJAX entry point to redo an analysis.
 *
 * @param eeId ee id
 * @param id   id
 * @return string
 * @throws Exception exception
 */
public String redo(Long eeId, Long id) {
    ExpressionExperiment ee = expressionExperimentService.load(eeId);
    if (ee == null) {
        throw new IllegalArgumentException("Cannot access experiment with id=" + eeId);
    }
    DifferentialExpressionAnalysis toRedo = differentialExpressionAnalysisService.load(id);
    if (toRedo == null) {
        throw new IllegalArgumentException("Cannot access analysis with id=" + id);
    }
    this.experimentReportService.evictFromCache(ee.getId());
    DifferentialExpressionAnalysisTaskCommand cmd = new DifferentialExpressionAnalysisTaskCommand(ee, toRedo);
    return taskRunningService.submitRemoteTask(cmd);
}

Example 4 with DifferentialExpressionAnalysisTaskCommand

use of ubic.gemma.core.tasks.analysis.diffex.DifferentialExpressionAnalysisTaskCommand in project Gemma by PavlidisLab.

the class DifferentialExpressionAnalysisController method runCustom.

public String runCustom(Long id, Collection<Long> factorids, boolean includeInteractions, Long subsetFactorId) {
    if (factorids.isEmpty()) {
        throw new IllegalArgumentException("You must provide at least one factor to analyze");
    }
    ExpressionExperiment ee = expressionExperimentService.load(id);
    if (ee == null) {
        throw new IllegalArgumentException("Cannot access experiment with id=" + id);
    }
    ee = expressionExperimentService.thawLite(ee);
    /*
         * Get the factors matching the factorids
         */
    Collection<ExperimentalFactor> factors = new HashSet<>();
    for (ExperimentalFactor ef : ee.getExperimentalDesign().getExperimentalFactors()) {
        if (factorids.contains(ef.getId())) {
            factors.add(ef);
        }
    }
    if (factors.size() != factorids.size()) {
        throw new IllegalArgumentException("Unknown factors?");
    }
    ExperimentalFactor subsetFactor = null;
    if (subsetFactorId != null) {
        for (ExperimentalFactor ef : ee.getExperimentalDesign().getExperimentalFactors()) {
            if (subsetFactorId.equals(ef.getId())) {
                subsetFactor = ef;
                break;
            }
        }
        if (subsetFactor == null) {
            throw new IllegalArgumentException("Unknown subset factor?");
        }
        if (factors.contains(subsetFactor)) {
            throw new IllegalArgumentException("Subset factor must not be one of the factors used in the analysis");
        }
    }
    DifferentialExpressionAnalysisTaskCommand cmd = new DifferentialExpressionAnalysisTaskCommand(ee);
    boolean rnaSeq = expressionExperimentService.isRNASeq(ee);
    cmd.setUseWeights(rnaSeq);
    cmd.setFactors(factors);
    cmd.setSubsetFactor(subsetFactor);
    for (ExperimentalFactor ef : factors) {
        if (BatchInfoPopulationServiceImpl.isBatchFactor(ef)) {
            /*
                 * This is a policy and I am pretty sure it makes sense!
                 */
            DifferentialExpressionAnalysisController.log.warn("Removing interaction term because it includes 'batch'");
            includeInteractions = false;
        }
    }
    cmd.setIncludeInteractions(includeInteractions);
    DifferentialExpressionAnalysisController.log.info("Initializing analysis");
    this.experimentReportService.evictFromCache(ee.getId());
    return taskRunningService.submitRemoteTask(cmd);
}