Examples with ExperimentalFactorOntologyService ubic.basecode.ontology.providers.ExperimentalFactorOntologyService used on opensource projects

Example 1 with ExperimentalFactorOntologyService

use of ubic.basecode.ontology.providers.ExperimentalFactorOntologyService in project Gemma by PavlidisLab.

the class ExperimentalDesignImportCli method doWork.

@Override
protected Exception doWork(String[] args) {
    Exception e = this.processCommandLine(args);
    if (e != null)
        return e;
    ExperimentalFactorOntologyService mos = this.getBean(OntologyService.class).getExperimentalFactorOntologyService();
    mos.startInitializationThread(true);
    while (!mos.isOntologyLoaded()) {
        try {
            Thread.sleep(5000);
        } catch (InterruptedException e1) {
        // 
        }
        AbstractCLI.log.info("Waiting for EFO to load");
    }
    ExperimentalDesignImporter edImp = this.getBean(ExperimentalDesignImporter.class);
    ExpressionExperimentService ees = this.getBean(ExpressionExperimentService.class);
    expressionExperiment = ees.thawBioAssays(expressionExperiment);
    try {
        edImp.importDesign(expressionExperiment, inputStream);
    } catch (IOException e1) {
        return e1;
    }
    return null;
}