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

Example 6 with DatabaseEntry

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

the class ExpressionExperimentServiceTest method testFindByAccession.

@Test
public final void testFindByAccession() {
    DatabaseEntry accessionEntry = DatabaseEntry.Factory.newInstance(ed);
    accessionEntry.setAccession(accession);
    Collection<ExpressionExperiment> expressionExperiment = expressionExperimentService.findByAccession(accessionEntry);
    assertTrue(expressionExperiment.size() > 0);
}

Example 7 with DatabaseEntry

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

the class ExpressionExperimentServiceTest method setup.

@Before
public void setup() {
    if (!persisted) {
        ee = this.getTestPersistentCompleteExpressionExperiment(false);
        ee.setName(ExpressionExperimentServiceTest.EE_NAME);
        DatabaseEntry accessionEntry = this.getTestPersistentDatabaseEntry();
        accession = accessionEntry.getAccession();
        ed = accessionEntry.getExternalDatabase();
        ee.setAccession(accessionEntry);
        Contact c = this.getTestPersistentContact();
        ee.setOwner(c);
        expressionExperimentService.update(ee);
        ee = expressionExperimentService.thaw(ee);
        persisted = true;
    } else {
        log.debug("Skipping making new ee for test");
    }
}

Example 8 with DatabaseEntry

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

the class GeneServiceTest method testFindByAccessionOther.

@Test
public void testFindByAccessionOther() {
    Gene gene = Gene.Factory.newInstance();
    Integer id = Integer.parseInt(RandomStringUtils.randomNumeric(5));
    gene.setNcbiGeneId(id);
    gene.setName(GeneServiceTest.TEST_GENE_NAME);
    ExternalDatabase ensembl = edbs.findByName("Ensembl");
    DatabaseEntry dbe = DatabaseEntry.Factory.newInstance();
    dbe.setAccession("E129458");
    dbe.setExternalDatabase(ensembl);
    gene.getAccessions().add(dbe);
    Taxon human = taxonService.findByCommonName("human");
    gene.setTaxon(human);
    geneDao.create(gene);
    Gene g = geneDao.findByAccession("E129458", ensembl);
    assertNotNull(g);
    assertEquals(g, gene);
    geneDao.remove(gene);
}

Example 9 with DatabaseEntry

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

the class GeoBrowserServiceImpl method filterGeoRecords.

private List<GeoRecord> filterGeoRecords(List<GeoRecord> records) {
    ExternalDatabase geo = externalDatabaseService.findByName("GEO");
    Collection<GeoRecord> toRemove = new HashSet<>();
    assert geo != null;
    rec: for (GeoRecord record : records) {
        if (record.getNumSamples() < GeoBrowserServiceImpl.MIN_SAMPLES) {
            toRemove.add(record);
        }
        Collection<String> organisms = record.getOrganisms();
        if (organisms == null || organisms.size() == 0) {
            continue;
        }
        int i = 0;
        for (String string : organisms) {
            Taxon t = taxonService.findByCommonName(string);
            if (t == null) {
                t = taxonService.findByScientificName(string);
                if (t == null) {
                    toRemove.add(record);
                    continue rec;
                }
            }
            String acc = record.getGeoAccession();
            if (organisms.size() > 1) {
                acc = acc + "." + i;
            }
            DatabaseEntry de = DatabaseEntry.Factory.newInstance();
            de.setExternalDatabase(geo);
            de.setAccession(acc);
            Collection<ExpressionExperiment> ee = expressionExperimentService.findByAccession(de);
            if (!ee.isEmpty()) {
                for (ExpressionExperiment expressionExperiment : ee) {
                    record.getCorrespondingExperiments().add(expressionExperiment.getId());
                }
            }
            record.setPreviousClicks(localInfo.containsKey(acc) ? localInfo.get(acc).getPreviousClicks() : 0);
            record.setUsable(!localInfo.containsKey(acc) || localInfo.get(acc).isUsable());
            i++;
        }
    }
    records.removeAll(toRemove);
    return records;
}

Example 10 with DatabaseEntry

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

the class GeoServiceImpl method fetchAndLoad.

/**
 * Given a GEO GSE or GDS (or GPL, but support might not be complete)
 * <ol>
 * <li>Check that it doesn't already exist in the system</li>
 * <li>Download and parse GDS files and GSE file needed</li>
 * <li>Convert the GDS and GSE into a ExpressionExperiment (or just the ArrayDesigns)
 * <li>Load the resulting ExpressionExperiment and/or ArrayDesigns into Gemma</li>
 * </ol>
 */
@Override
public Collection<?> fetchAndLoad(String geoAccession, boolean loadPlatformOnly, boolean doSampleMatching, boolean splitByPlatform, boolean allowSuperSeriesImport, boolean allowSubSeriesImport) {
    /*
         * We do this to get a fresh instantiation of GeoConverter (prototype scope)
         */
    GeoConverter geoConverter = (GeoConverter) this.beanFactory.getBean("geoConverter");
    if (this.geoDomainObjectGenerator == null) {
        this.geoDomainObjectGenerator = new GeoDomainObjectGenerator();
    } else {
        this.geoDomainObjectGenerator.initialize();
    }
    geoDomainObjectGenerator.setProcessPlatformsOnly(geoAccession.startsWith("GPL") || loadPlatformOnly);
    geoDomainObjectGenerator.setDoSampleMatching(doSampleMatching && !splitByPlatform);
    Collection<DatabaseEntry> projectedAccessions = geoDomainObjectGenerator.getProjectedAccessions(geoAccession);
    this.checkForExisting(projectedAccessions);
    if (loadPlatformOnly) {
        Collection<? extends GeoData> platforms = geoDomainObjectGenerator.generate(geoAccession);
        if (platforms.size() == 0) {
            AbstractGeoService.log.warn("GeoService.fetchAndLoad( targetPlatformAcc, true, false, false, false );t no results");
            return null;
        }
        geoConverter.setForceConvertElements(true);
        Collection<Object> arrayDesigns = geoConverter.convert(platforms);
        return persisterHelper.persist(arrayDesigns);
    }
    Collection<? extends GeoData> parseResult = geoDomainObjectGenerator.generate(geoAccession);
    if (parseResult.size() == 0) {
        AbstractGeoService.log.warn("Got no results");
        return null;
    }
    AbstractGeoService.log.debug("Generated GEO domain objects for " + geoAccession);
    Object obj = parseResult.iterator().next();
    if (!(obj instanceof GeoSeries)) {
        throw new RuntimeException("Got a " + obj.getClass().getName() + " instead of a " + GeoSeries.class.getName() + " (you may need to load platforms only).");
    }
    GeoSeries series = (GeoSeries) obj;
    String seriesAccession = series.getGeoAccession();
    if (series.isSuperSeries()) {
        if (allowSuperSeriesImport) {
            AbstractGeoService.log.info(" ========= SuperSeries Detected! =========");
            AbstractGeoService.log.info("Please make sure you want to import this as a superseries and not the individual subseries");
        } else {
            throw new IllegalStateException("SuperSeries detected, set 'allowSuperSeriesImport' to 'true' to allow this dataset to load");
        }
    }
    if (series.isSubSeries()) {
        if (allowSubSeriesImport) {
            AbstractGeoService.log.info(" ========= Subseries Detected! =========");
            AbstractGeoService.log.info("Please make sure you want to import this as a subseries and not the superseries");
        } else {
            throw new IllegalStateException("SubSeries detected, set 'allowSubSeriesImport' to 'true' to allow this dataset to load");
        }
    }
    this.confirmPlatformUniqueness(series, doSampleMatching && !splitByPlatform);
    ArrayDesignsForExperimentCache c = new ArrayDesignsForExperimentCache();
    this.matchToExistingPlatforms(geoConverter, series, c);
    this.checkSamplesAreNew(series);
    this.getSubSeriesInformation(series);
    geoConverter.clear();
    geoConverter.setSplitByPlatform(splitByPlatform);
    // noinspection unchecked
    Collection<ExpressionExperiment> result = (Collection<ExpressionExperiment>) geoConverter.convert(series);
    this.check(result);
    this.getPubMedInfo(result);
    AbstractGeoService.log.debug("Converted " + seriesAccession);
    assert persisterHelper != null;
    Collection<ExpressionExperiment> persistedResult = new HashSet<>();
    for (ExpressionExperiment ee : result) {
        c = expressionExperimentPrePersistService.prepare(ee, c);
        ee = persisterHelper.persist(ee, c);
        persistedResult.add(ee);
        AbstractGeoService.log.debug("Persisted " + seriesAccession);
    }
    this.updateReports(persistedResult);
    return persistedResult;
}