Java Experiment.getHybridizations方法代码示例

import gov.nih.nci.caarray.domain.project.Experiment; //导入方法依赖的package包/类
private void lookupExperiment(CaArraySvcClient client, DataRetrievalRequest request, String experimentName)
        throws RemoteException {
    CQLQuery cqlQuery = new CQLQuery();
    gov.nih.nci.cagrid.cqlquery.Object target = new gov.nih.nci.cagrid.cqlquery.Object();
    target.setName("gov.nih.nci.caarray.domain.project.Experiment");
    Attribute titleAttribute = new Attribute();
    titleAttribute.setName("title");
    titleAttribute.setValue(experimentName);
    titleAttribute.setPredicate(Predicate.EQUAL_TO);
    target.setAttribute(titleAttribute);
    cqlQuery.setTarget(target);
    CQLQueryResults cqlResults = client.query(cqlQuery);
    CQLQueryResultsIterator iter = new CQLQueryResultsIterator(cqlResults, CaArraySvcClient.class
            .getResourceAsStream("client-config.wsdd"));
    if (!(iter.hasNext())) {
        System.out.println("Could not find experiment.");
        return;
    }
    Experiment experiment = (Experiment) iter.next();
    Set<Hybridization> allHybs = experiment.getHybridizations();
    if (allHybs.isEmpty()) {
        return;
    }
    request.getHybridizations().addAll(allHybs);
}
 

import gov.nih.nci.caarray.domain.project.Experiment; //导入方法依赖的package包/类
private static void writeSeriesSection(Experiment experiment, String permaLinkUrl, PrintWriter out) {
    out.print("^SERIES=");
    out.println(experiment.getPublicIdentifier());
    out.print("!Series_title=");
    out.println(experiment.getTitle());
    out.print("!Series_summary=");
    final String desc =
            StringUtils.isNotBlank(experiment.getDescription()) ? experiment.getDescription() : experiment
                    .getTitle();
    out.println(desc);
    writeExperimentDesignTypes(experiment, desc, out);
    for (final Publication pub : experiment.getPublications()) {
        out.print("!Series_pubmed_id=");
        out.println(pub.getPubMedId());
    }
    for (final ExperimentContact c : experiment.getExperimentContacts()) {
        writeExperimentContact(c, out);
    }
    out.print("!Series_web_link=");
    out.println(permaLinkUrl);
    for (final Hybridization h : experiment.getHybridizations()) {
        out.print("!Series_sample_id=");
        out.println(h.getName());
    }
}
 

import gov.nih.nci.caarray.domain.project.Experiment; //导入方法依赖的package包/类
private long getEstimatedPackageSize(Experiment experiment) {
    long size = 0;
    for (final Hybridization h : experiment.getHybridizations()) {
        for (final RawArrayData rad : h.getRawDataCollection()) {
            size += rad.getDataFile().getCompressedSize();
        }
        for (final DerivedArrayData dad : h.getDerivedDataCollection()) {
            size += dad.getDataFile().getCompressedSize();
        }
    }
    for (final CaArrayFile f : experiment.getProject().getUserVisibleSupplementalFiles()) {
        size += f.getCompressedSize();
    }

    // estimate GEO SOFT file size and zip entry overhead.
    size += experiment.getHybridizations().size() * ONE_KB;
    return size;
}
 

import gov.nih.nci.caarray.domain.project.Experiment; //导入方法依赖的package包/类
@Test
public void testSpecificationDocuments() throws Exception {
    final CaArrayFileSet fileSet = TestMageTabSets.getFileSet(TestMageTabSets.MAGE_TAB_SPECIFICATION_INPUT_SET);
    final MageTabDocumentSet docSet = MageTabParser.INSTANCE
    .parse(TestMageTabSets.MAGE_TAB_SPECIFICATION_INPUT_SET);
    final CaArrayTranslationResult result = this.translator.translate(docSet, fileSet);
    final Experiment experiment = result.getInvestigations().iterator().next();
    assertNotNull(experiment.getDescription());
    assertTrue(experiment.getDescription().startsWith("<>Gene expression of TK6"));
    assertEquals(8, experiment.getExperimentContacts().size());
    assertEquals(1, experiment.getExperimentDesignTypes().size());
    assertEquals("genetic_modification_design", experiment.getExperimentDesignTypes().iterator().next().getValue());
    assertEquals(6, experiment.getSources().size());
    assertEquals(6, experiment.getSamples().size());
    assertEquals(6, experiment.getExtracts().size());
    assertEquals(6, experiment.getLabeledExtracts().size());
    assertEquals(6, experiment.getHybridizations().size());
    for (final Hybridization hyb : experiment.getHybridizations()) {
        assertNotNull(hyb.getArray().getDesign());
        assertEquals(6, hyb.getDerivedDataCollection().iterator().next().getDerivedFromArrayDataCollection().size());
    }
}
 

import gov.nih.nci.caarray.domain.project.Experiment; //导入方法依赖的package包/类
@Test
public void testSpecificationDocumentsNoExpDesc() throws Exception {
    final CaArrayFileSet fileSet = TestMageTabSets
    .getFileSet(TestMageTabSets.MAGE_TAB_SPECIFICATION_NO_EXP_DESC_INPUT_SET);
    final MageTabDocumentSet docSet = MageTabParser.INSTANCE
    .parse(TestMageTabSets.MAGE_TAB_SPECIFICATION_NO_EXP_DESC_INPUT_SET);
    final CaArrayTranslationResult result = this.translator.translate(docSet, fileSet);
    final Experiment experiment = result.getInvestigations().iterator().next();
    assertNull(experiment.getDescription());
    assertEquals(8, experiment.getExperimentContacts().size());
    assertEquals(1, experiment.getExperimentDesignTypes().size());
    assertEquals("genetic_modification_design", experiment.getExperimentDesignTypes().iterator().next().getValue());
    assertEquals(6, experiment.getSources().size());
    assertEquals(6, experiment.getSamples().size());
    assertEquals(6, experiment.getExtracts().size());
    assertEquals(6, experiment.getLabeledExtracts().size());
    assertEquals(6, experiment.getHybridizations().size());
    for (final Hybridization hyb : experiment.getHybridizations()) {
        assertNotNull(hyb.getArray().getDesign());
    }
}
 

import gov.nih.nci.caarray.domain.project.Experiment; //导入方法依赖的package包/类
@Test
public void testSpecificationDocumentsNoArrayDesignRef() throws Exception {
    final CaArrayFileSet fileSet = TestMageTabSets
    .getFileSet(TestMageTabSets.MAGE_TAB_SPECIFICATION_NO_ARRAY_DESIGN_INPUT_SET);
    final MageTabDocumentSet docSet = MageTabParser.INSTANCE
    .parse(TestMageTabSets.MAGE_TAB_SPECIFICATION_NO_ARRAY_DESIGN_INPUT_SET);
    final CaArrayTranslationResult result = this.translator.translate(docSet, fileSet);
    final Experiment experiment = result.getInvestigations().iterator().next();
    assertNotNull(experiment.getDescription());
    assertTrue(experiment.getDescription().startsWith("<>Gene expression of TK6"));
    assertFalse(experiment.getDescription().contains("<"));
    assertEquals(8, experiment.getExperimentContacts().size());
    assertEquals(1, experiment.getExperimentDesignTypes().size());
    assertEquals("genetic_modification_design", experiment.getExperimentDesignTypes().iterator().next().getValue());
    assertEquals(6, experiment.getSources().size());
    assertEquals(6, experiment.getSamples().size());
    assertEquals(6, experiment.getExtracts().size());
    assertEquals(6, experiment.getLabeledExtracts().size());
    assertEquals(6, experiment.getHybridizations().size());
    for (final Hybridization hyb : experiment.getHybridizations()) {
        assertNull(hyb.getArray().getDesign().getName());
    }
}
 

import gov.nih.nci.caarray.domain.project.Experiment; //导入方法依赖的package包/类
private void lookupExperiment(CaArraySearchService service, DataRetrievalRequest request, String experimentName) {
    // Locate the experiment and add its hybridizations to the request.
    Experiment exampleExperiment = new Experiment();
    exampleExperiment.setTitle(experimentName);
    Experiment experiment = service.search(exampleExperiment).get(0);
    Set<Hybridization> allHybs = experiment.getHybridizations();
    request.getHybridizations().addAll(allHybs);
}
 

import gov.nih.nci.caarray.domain.project.Experiment; //导入方法依赖的package包/类
private Hybridization getFirstHybridization(CaArraySearchService service, Experiment experiment) {
    Set<Hybridization> allHybridizations = experiment.getHybridizations();
    for (Hybridization hybridization : allHybridizations) {
        Hybridization populatedHybridization = service.search(hybridization).get(0);
        // Yes, we're returning only the first hybridization.
        return populatedHybridization;
    }
    return null;
}
 

import gov.nih.nci.caarray.domain.project.Experiment; //导入方法依赖的package包/类
private static void addHybsByExperiment(CaArraySvcClient client, DataRetrievalRequest request, 
        String experimentName) throws QueryProcessingExceptionType, MalformedQueryExceptionType, RemoteException {
    Experiment experiment = (Experiment) get(client, "gov.nih.nci.caarray.domain.project.Experiment", "title",
            experimentName);
    Set<Hybridization> allHybs = experiment.getHybridizations();
    request.getHybridizations().addAll(allHybs);
}
 

import gov.nih.nci.caarray.domain.project.Experiment; //导入方法依赖的package包/类
/**
 * {@inheritDoc}
 */
@Override
@TransactionAttribute(TransactionAttributeType.SUPPORTS)
public List<String> validateForExport(Experiment experiment) {

    final List<String> errors = new ArrayList<String>();
    final boolean stop = checkArrayDesigns(errors, experiment);
    if (stop) {
        return errors;
    }

    final Set<String> protocolErrors = new HashSet<String>();
    for (final Hybridization hyb : experiment.getHybridizations()) {
        final Set<Source> sources = new HashSet<Source>();
        final Set<Sample> samples = new HashSet<Sample>();
        final Set<Extract> extracts = new HashSet<Extract>();
        final Set<LabeledExtract> labeledExtracts = new HashSet<LabeledExtract>();
        GeoSoftFileWriterUtil.collectBioMaterials(hyb, sources, samples, extracts, labeledExtracts);

        checkRawData(errors, hyb);
        checkDerivedDataFileType(errors, hyb);

        checkBioProtocol(protocolErrors, samples, "nucleic_acid_extraction");
        checkBioProtocol(protocolErrors, extracts, "labeling");
        checkBioProtocol(protocolErrors, labeledExtracts, "hybridization");
        checkProtocol(protocolErrors, hyb.getProtocolApplications(), "scan", "image_acquisition");
        checkDataProcessingProtocol(protocolErrors, hyb.getRawDataCollection());
        checkCharOrFactorValue(errors, hyb, labeledExtracts, extracts, samples, sources);
        checkLabeledExtract(errors, labeledExtracts, extracts);

    }
    errors.addAll(protocolErrors);

    return errors;
}
 

import gov.nih.nci.caarray.domain.project.Experiment; //导入方法依赖的package包/类
private void addDataFiles(Experiment experiment, ArchiveOutputStream zout) throws IOException {
    for (final Hybridization h : experiment.getHybridizations()) {
        addDataFiles(h.getRawDataCollection(), zout);
        addDataFiles(h.getDerivedDataCollection(), zout);
    }
    for (final CaArrayFile f : experiment.getProject().getUserVisibleSupplementalFiles()) {
        this.fileAccessHelper.addFileToArchive(f, zout);
    }
}
 

import gov.nih.nci.caarray.domain.project.Experiment; //导入方法依赖的package包/类
private void checkTcgaBroadHybridizations(Experiment investigation) {
    assertEquals(1, investigation.getArrayDesigns().size());
    final ArrayDesign arrayDesign = investigation.getArrayDesigns().iterator().next();
    for (final LabeledExtract labeledExtract : investigation.getLabeledExtracts()) {
        final Hybridization hybridization = labeledExtract.getHybridizations().iterator().next();
        assertEquals(arrayDesign, hybridization.getArray().getDesign());
        final RawArrayData celData = hybridization.getRawDataCollection().iterator().next();
        assertEquals(celData.getDataFile().getName(), celData.getName());
    }
    final Set<Hybridization> hybridizations = investigation.getHybridizations();
    assertEquals(26, hybridizations.size());
    checkHybridizationsHaveRawDataAndFiles(hybridizations);
}
 

import gov.nih.nci.caarray.domain.project.Experiment; //导入方法依赖的package包/类
@Test
public void testTranslateDataMatrixCopyNumberData() throws Exception {
    final CaArrayFileSet fileSet = TestMageTabSets.getFileSet(TestMageTabSets.GOOD_DATA_MATRIX_COPY_NUMBER_INPUT_SET);
    final MageTabDocumentSet docSet = MageTabParser.INSTANCE.parse(TestMageTabSets.GOOD_DATA_MATRIX_COPY_NUMBER_INPUT_SET);
    final CaArrayTranslationResult result = this.translator.translate(docSet, fileSet);
    assertEquals(1, result.getInvestigations().size());
    final Experiment investigation = result.getInvestigations().iterator().next();
    final Set<Hybridization> hybridizations = investigation.getHybridizations();
    assertEquals(3, hybridizations.size());
    for (final Hybridization hybridization : hybridizations) {
        assertTrue(hybridization.getRawDataCollection().isEmpty());
        assertFalse(hybridization.getDerivedDataCollection().isEmpty());
        assertNotNull(hybridization.getDerivedDataCollection().iterator().next().getDataFile());
    }
}
 

import gov.nih.nci.caarray.domain.project.Experiment; //导入方法依赖的package包/类
private Hybridization getFirstHybridization(CaArraySearchService service, Experiment experiment) {
    Set<Hybridization> allHybridizations = experiment.getHybridizations();
    logForSilverCompatibility(TRAVERSE_OBJECT_GRAPH, "Experiment.getHybridizations().size(): "
            + experiment.getHybridizations().size());
    for (Hybridization hybridization : allHybridizations) {
        Hybridization populatedHybridization = service.search(hybridization).get(0);
        logForSilverCompatibility(API_CALL, "CaArraySearchService.search(Hybridization)");
        // Yes, we're returning only the first hybridization.
        return populatedHybridization;
    }
    return null;
}
 

import gov.nih.nci.caarray.domain.project.Experiment; //导入方法依赖的package包/类
private void lookupExperiment(DataRetrievalRequest request, String experimentName)
throws RemoteException {
    CQLQuery cqlQuery = new CQLQuery();
    gov.nih.nci.cagrid.cqlquery.Object target = new gov.nih.nci.cagrid.cqlquery.Object();
    target.setName("gov.nih.nci.caarray.domain.project.Experiment");
    Attribute titleAttribute = new Attribute();
    titleAttribute.setName("title");
    titleAttribute.setValue(experimentName);
    titleAttribute.setPredicate(Predicate.EQUAL_TO);
    target.setAttribute(titleAttribute);
    cqlQuery.setTarget(target);
    CQLQueryResults cqlResults = gridClient.query(cqlQuery);
    logForSilverCompatibility(API_CALL, "Grid query(CQLQuery)");
    CQLQueryResultsIterator iter = new CQLQueryResultsIterator(cqlResults, CaArraySvcClient.class
            .getResourceAsStream("client-config.wsdd"));
    if (!(iter.hasNext())) {
        return;
    }
    Experiment experiment = (Experiment) iter.next();
    Set<Hybridization> allHybs = experiment.getHybridizations();
    logForSilverCompatibility(TRAVERSE_OBJECT_GRAPH, "Experiment.getHybridizations().size(): "
            + experiment.getHybridizations().size());
    if (allHybs.isEmpty()) {
        return;
    }
    request.getHybridizations().addAll(allHybs);
}