Examples with SVDService ubic.gemma.core.analysis.preprocess.svd.SVDService used on opensource projects

Example 1 with SVDService

use of ubic.gemma.core.analysis.preprocess.svd.SVDService in project Gemma by PavlidisLab.

the class SVDCli method doWork.

@Override
protected Exception doWork(String[] args) {
    Exception err = super.processCommandLine(args);
    if (err != null)
        return err;
    SVDService svdService = this.getBean(SVDService.class);
    for (BioAssaySet bas : this.expressionExperiments) {
        if (!force && this.noNeedToRun(bas, PCAAnalysisEvent.class)) {
            this.errorObjects.add(bas + ": Already has PCA; use -force to override");
            continue;
        }
        try {
            AbstractCLI.log.info("Processing: " + bas);
            ExpressionExperiment ee = (ExpressionExperiment) bas;
            svdService.svd(ee.getId());
            this.successObjects.add(bas.toString());
        } catch (Exception e) {
            AbstractCLI.log.error(e, e);
            this.errorObjects.add(bas + ": " + e.getMessage());
        }
    }
    this.summarizeProcessing();
    return null;
}