Examples with ExternalDatabase ubic.gemma.model.common.description.ExternalDatabase used on opensource projects

Example 21 with ExternalDatabase

use of ubic.gemma.model.common.description.ExternalDatabase in project Gemma by PavlidisLab.

the class LoadExpressionDataCli method removeIfExists.

/**
 * Delete previous version of the experiment.
 *
 * @param accession accession
 */
private void removeIfExists(String accession) {
    DatabaseEntry acDbe = DatabaseEntry.Factory.newInstance();
    acDbe.setAccession(accession);
    ExternalDatabase geo = ExternalDatabase.Factory.newInstance();
    geo.setName("GEO");
    acDbe.setExternalDatabase(geo);
    Collection<ExpressionExperiment> existing = eeService.findByAccession(acDbe);
    if (!existing.isEmpty()) {
        AbstractCLI.log.info("Deleting existing version of " + accession);
        for (ExpressionExperiment expressionExperiment : existing) {
            eeService.remove(expressionExperiment);
        }
    }
}

Example 22 with ExternalDatabase

use of ubic.gemma.model.common.description.ExternalDatabase in project Gemma by PavlidisLab.

the class GeneServiceTest method testFindByAccessionNcbiWithSource.

@Test
public void testFindByAccessionNcbiWithSource() {
    Gene gene = Gene.Factory.newInstance();
    Integer id = Integer.parseInt(RandomStringUtils.randomNumeric(5));
    gene.setNcbiGeneId(id);
    gene.setName(GeneServiceTest.TEST_GENE_NAME);
    ExternalDatabase ncbi = edbs.findByName("Entrez Gene");
    DatabaseEntry dbe = DatabaseEntry.Factory.newInstance();
    // this gets ignored, because the ncbi id is part of the object.
    dbe.setAccession("12345");
    dbe.setExternalDatabase(ncbi);
    gene.getAccessions().add(dbe);
    Taxon human = taxonService.findByCommonName("human");
    gene.setTaxon(human);
    geneDao.create(gene);
    Gene g = geneDao.findByAccession("12345", ncbi);
    assertNotNull(g);
    assertEquals(g, gene);
    geneDao.remove(gene);
}

Example 23 with ExternalDatabase

use of ubic.gemma.model.common.description.ExternalDatabase in project Gemma by PavlidisLab.

the class ArrayDesignServiceTest method assignExternalReference.

private void assignExternalReference(ArrayDesign toFind, String accession) {
    ExternalDatabase geo = externalDatabaseService.findByName("GEO");
    assert geo != null;
    DatabaseEntry de = DatabaseEntry.Factory.newInstance();
    de.setExternalDatabase(geo);
    de.setAccession(accession);
    toFind.getExternalReferences().add(de);
}