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

Example 1 with MedicOntologyService

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

the class ExternalDatabaseEvidenceImporterAbstractCLI method loadServices.

// load all needed services
private synchronized void loadServices(String[] args) throws Exception {
    // this gets the context, so we can access beans
    Exception err = this.processCommandLine(args);
    if (err != null)
        throw err;
    OntologyService ontologyService = this.getBean(OntologyService.class);
    this.diseaseOntologyService = ontologyService.getDiseaseOntologyService();
    this.humanPhenotypeOntologyService = ontologyService.getHumanPhenotypeOntologyService();
    this.geneService = this.getBean(GeneService.class);
    while (!this.diseaseOntologyService.isOntologyLoaded()) {
        this.wait(3000);
        AbstractCLI.log.info("waiting for the Disease Ontology to load");
    }
    while (!this.humanPhenotypeOntologyService.isOntologyLoaded()) {
        this.wait(3000);
        AbstractCLI.log.info("waiting for the HP Ontology to load");
    }
    this.medicOntologyService = new MedicOntologyService();
}