Examples with ArrayDesignsForExperimentCache ubic.gemma.persistence.util.ArrayDesignsForExperimentCache used on opensource projects

Example 1 with ArrayDesignsForExperimentCache

use of ubic.gemma.persistence.util.ArrayDesignsForExperimentCache in project Gemma by PavlidisLab.

the class PersistentDummyObjectHelper method getTestExpressionExperimentWithAllDependencies.

public ExpressionExperiment getTestExpressionExperimentWithAllDependencies(ExpressionExperiment prototype) {
    ExpressionExperiment ee = ExpressionExperiment.Factory.newInstance();
    ee.setShortName(RandomStringUtils.randomNumeric(PersistentDummyObjectHelper.RANDOM_STRING_LENGTH));
    ee.setName("Expression Experiment " + RandomStringUtils.randomNumeric(PersistentDummyObjectHelper.RANDOM_STRING_LENGTH));
    ee.setDescription("A test expression experiment");
    ee.setSource("https://www.ncbi.nlm.nih.gov/geo/");
    DatabaseEntry de1 = this.getTestPersistentDatabaseEntry(PersistentDummyObjectHelper.geo);
    ee.setAccession(de1);
    LocalFile file = LocalFile.Factory.newInstance();
    try {
        file.setLocalURL(new URL("file:///just/a/placeholder/" + ee.getShortName()));
    } catch (MalformedURLException e) {
        log.error("Malformed URL");
    }
    ee.setRawDataFile(file);
    Collection<FactorValue> allFactorValues = new HashSet<>();
    ExperimentalDesign ed = this.getExperimentalDesign(allFactorValues);
    Collection<BioMaterial> bioMaterials = this.getBioMaterials(allFactorValues);
    ee.setExperimentalDesign(ed);
    ee.setOwner(this.getTestPersistentContact());
    List<ArrayDesign> arrayDesignsUsed = new ArrayList<>(eeService.getArrayDesignsUsed(prototype));
    Collection<BioAssay> bioAssays = new HashSet<>();
    Collection<QuantitationType> quantitationTypes = this.addQuantitationTypes(new HashSet<QuantitationType>());
    eeService.thaw(prototype);
    Collection<RawExpressionDataVector> vectors = new HashSet<>();
    for (ArrayDesign ad : arrayDesignsUsed) {
        List<BioAssay> bas = this.getBioAssays(bioMaterials, ad);
        bioAssays.addAll(bas);
        ad = this.adService.thaw(ad);
        vectors.addAll(this.getDesignElementDataVectors(ee, quantitationTypes, bas, ad));
    }
    ee.setBioAssays(bioAssays);
    assert quantitationTypes.size() > 0;
    ee.setQuantitationTypes(quantitationTypes);
    ee.setRawExpressionDataVectors(vectors);
    ArrayDesignsForExperimentCache c = persisterHelper.prepare(ee);
    ee = persisterHelper.persist(ee, c);
    return ee;
}

Example 2 with ArrayDesignsForExperimentCache

use of ubic.gemma.persistence.util.ArrayDesignsForExperimentCache in project Gemma by PavlidisLab.

the class PersistentDummyObjectHelper method getTestExpressionExperimentWithAllDependencies.

/**
 * Add an expressionExperiment to the database for testing purposes. Includes associations
 *
 * @param doSequence Should the array design get all the sequence information filled in? (true = slower)
 * @return EE
 */
public ExpressionExperiment getTestExpressionExperimentWithAllDependencies(boolean doSequence) {
    ExpressionExperiment ee = ExpressionExperiment.Factory.newInstance();
    ee.setShortName(RandomStringUtils.randomAlphanumeric(PersistentDummyObjectHelper.RANDOM_STRING_LENGTH));
    ee.setName("Expression Experiment " + RandomStringUtils.randomNumeric(PersistentDummyObjectHelper.RANDOM_STRING_LENGTH));
    ee.setDescription("A test expression experiment");
    ee.setSource("https://www.ncbi.nlm.nih.gov/geo/");
    DatabaseEntry de1 = this.getTestPersistentDatabaseEntry(PersistentDummyObjectHelper.geo);
    ee.setAccession(de1);
    LocalFile file = LocalFile.Factory.newInstance();
    try {
        file.setLocalURL(new URL("file:///just/a/placeholder/" + ee.getShortName()));
    } catch (MalformedURLException e) {
        log.error("Malformed URL");
    }
    ee.setRawDataFile(file);
    ArrayDesign adA = this.getTestPersistentArrayDesign(this.getTestElementCollectionSize(), false, doSequence);
    ArrayDesign adB = this.getTestPersistentArrayDesign(this.getTestElementCollectionSize(), false, doSequence);
    Collection<FactorValue> allFactorValues = new HashSet<>();
    ExperimentalDesign ed = this.getExperimentalDesign(allFactorValues);
    ee.setExperimentalDesign(ed);
    ee.setOwner(this.getTestPersistentContact());
    Collection<BioAssay> bioAssays = new HashSet<>();
    Collection<BioMaterial> bioMaterials = this.getBioMaterials(allFactorValues);
    List<BioAssay> bioAssaysA = this.getBioAssays(bioMaterials, adA);
    List<BioAssay> bioAssaysB = this.getBioAssays(bioMaterials, adB);
    bioAssays.addAll(bioAssaysA);
    bioAssays.addAll(bioAssaysB);
    ee.setBioAssays(bioAssays);
    log.debug("expression experiment => design element data vectors");
    Collection<RawExpressionDataVector> vectors = new HashSet<>();
    Collection<QuantitationType> quantitationTypes = this.addQuantitationTypes(new HashSet<QuantitationType>());
    assert quantitationTypes.size() > 0;
    vectors.addAll(this.getDesignElementDataVectors(ee, quantitationTypes, bioAssaysA, adA));
    vectors.addAll(this.getDesignElementDataVectors(ee, quantitationTypes, bioAssaysB, adB));
    ee.setQuantitationTypes(quantitationTypes);
    ee.setRawExpressionDataVectors(vectors);
    ArrayDesignsForExperimentCache c = persisterHelper.prepare(ee);
    ee = persisterHelper.persist(ee, c);
    return ee;
}

Example 3 with ArrayDesignsForExperimentCache

use of ubic.gemma.persistence.util.ArrayDesignsForExperimentCache 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;
}

Example 4 with ArrayDesignsForExperimentCache

use of ubic.gemma.persistence.util.ArrayDesignsForExperimentCache in project Gemma by PavlidisLab.

the class PersistentDummyObjectHelper method getTestPersistentExpressionExperiment.

/**
 * Convenience method to provide an ExpressionExperiment that can be used to fill non-nullable associations in test
 * objects. This implementation does NOT fill in associations of the created object except for the creation of
 * persistent BioMaterials and BioAssays so that database taxon lookups for this experiment will work.
 *
 * @param taxon the experiment will have this taxon
 * @return EE
 */
public ExpressionExperiment getTestPersistentExpressionExperiment(Taxon taxon) {
    BioAssay ba;
    BioMaterial bm;
    ArrayDesign ad;
    bm = this.getTestPersistentBioMaterial(taxon);
    ad = this.getTestPersistentArrayDesign(4, true, true);
    ba = this.getTestPersistentBioAssay(ad, bm);
    Set<BioAssay> bas1 = new HashSet<>();
    bas1.add(ba);
    ExpressionExperiment ee = ExpressionExperiment.Factory.newInstance();
    ee.setName(RandomStringUtils.randomNumeric(PersistentDummyObjectHelper.RANDOM_STRING_LENGTH) + "_testee");
    ee.setShortName(RandomStringUtils.randomNumeric(PersistentDummyObjectHelper.RANDOM_STRING_LENGTH) + "_testee");
    ee.setBioAssays(bas1);
    Collection<FactorValue> allFactorValues = new HashSet<>();
    ExperimentalDesign ed = this.getExperimentalDesign(allFactorValues);
    ee.setExperimentalDesign(ed);
    ee.setOwner(this.getTestPersistentContact());
    log.debug("expression experiment => design element data vectors");
    Collection<RawExpressionDataVector> vectors = new HashSet<>();
    Collection<QuantitationType> quantitationTypes = this.addQuantitationTypes(new HashSet<QuantitationType>());
    assert quantitationTypes.size() > 0;
    ee.setQuantitationTypes(quantitationTypes);
    ee.setRawExpressionDataVectors(vectors);
    ArrayDesignsForExperimentCache c = persisterHelper.prepare(ee);
    return persisterHelper.persist(ee, c);
}

Example 5 with ArrayDesignsForExperimentCache

use of ubic.gemma.persistence.util.ArrayDesignsForExperimentCache in project Gemma by PavlidisLab.

the class ExpressionPersister method persist.

@Override
public Object persist(Object entity) {
    if (entity == null)
        return null;
    if (entity instanceof ExpressionExperiment) {
        AbstractPersister.log.warn("Consider doing the 'setup' step in a separate transaction");
        this.getSessionFactory().getCurrentSession().setFlushMode(FlushMode.AUTO);
        ArrayDesignsForExperimentCache c = expressionExperimentPrePersistService.prepare((ExpressionExperiment) entity);
        return this.persist((ExpressionExperiment) entity, c);
    } else if (entity instanceof BioAssayDimension) {
        return this.persistBioAssayDimension((BioAssayDimension) entity, null);
    } else if (entity instanceof BioMaterial) {
        return this.persistBioMaterial((BioMaterial) entity);
    } else if (entity instanceof BioAssay) {
        return this.persistBioAssay((BioAssay) entity, null);
    } else if (entity instanceof Compound) {
        return this.persistCompound((Compound) entity);
    } else if (entity instanceof ExpressionExperimentSubSet) {
        return this.persistExpressionExperimentSubSet((ExpressionExperimentSubSet) entity);
    }
    return super.persist(entity);
}