Java Experiment类代码示例

import gov.nih.nci.caarray.domain.project.Experiment; //导入依赖的package包/类
private void mergeExperimentContacts(Experiment originalExperiment, Experiment translatedExperiment) {
    for (final ExperimentContact translatedEc : translatedExperiment.getExperimentContacts()) {
        final List<ExperimentContact> originalExperimentContacts = originalExperiment.getExperimentContacts();
        boolean isNewEc = true;
        for (final ExperimentContact originalEc : originalExperimentContacts) {
            if (originalEc.equalsBaseContact(translatedEc)) {
                isNewEc = false;
                break;
            }
        }
        if (isNewEc) {
            translatedEc.setExperiment(originalExperiment);
            originalExperimentContacts.add(translatedEc);
        }
    }
}
 

import gov.nih.nci.caarray.domain.project.Experiment; //导入依赖的package包/类
private void lookupExperiments(CaArraySearchService service, DataRetrievalRequest request) {
    String[] experimentTitles = experimentTitlesCsv.split(",");
    if (experimentTitles == null) {
        return;
    }

    // Locate each experiment, and add its hybridizations to the request.
    Experiment exampleExperiment = new Experiment();
    for (int i = 0; i < experimentTitles.length; i++) {
        String experimentTitle = experimentTitles[i];
        exampleExperiment.setTitle(experimentTitle);
        List<Experiment> experimentList = service.search(exampleExperiment);
        Set<Hybridization> allHybs = getAllHybridizations(experimentList);
        request.getHybridizations().addAll(allHybs);
    }
}
 

import gov.nih.nci.caarray.domain.project.Experiment; //导入依赖的package包/类
@Test
public void testMultiDerived() {
    MageTabDocumentSet ds = getDocumentSet(TestMageTabSets.MULTI_DERIVED_1_INPUT_SET);
    CaArrayFileSet fileSet = TestMageTabSets.getFileSet(ds);
    CaArrayTranslationResult result = this.translator.translate(ds, fileSet);
    Experiment experiment = result.getInvestigations().iterator().next();
    Hybridization hyb = experiment.getHybridizations().iterator().next();
    checkPaCollection(hyb.getProtocolApplications(), "Scan");
    RawArrayData rad = hyb.getRawDataCollection().iterator().next();
    checkPaCollection(rad.getProtocolApplications(), "derived-data-protocol-1");
    for (DerivedArrayData d : hyb.getDerivedDataCollection()) {
        if (d.getName().equals("test.data")) {
            checkPaCollection(d.getProtocolApplications(), "derived-data-protocol-2");
        } else if (d.getName().equals("test2.data")) {
            checkPaCollection(d.getProtocolApplications());
        }
    }
}
 

import gov.nih.nci.caarray.domain.project.Experiment; //导入依赖的package包/类
private void parseResults(CQLQueryResults cqlResults) {
    if (cqlResults.getCountResult() != null) {
        System.out.println("Count was " + cqlResults.getCountResult().getCount());
        return;
    }        
    if (cqlResults.getObjectResult() == null) {
        System.out.println("Result was null.");
        return;
    }
    System.out.println("Retrieved " + cqlResults.getObjectResult().length + " experiments.");
    Iterator iter = new CQLQueryResultsIterator(cqlResults, CaArraySvcClient.class
            .getResourceAsStream("client-config.wsdd"));
    while (iter.hasNext()) {
        Experiment retrievedExperiment = (Experiment) (iter.next());
        System.out.println("Experiment title: " + retrievedExperiment.getTitle());
    }
}
 

import gov.nih.nci.caarray.domain.project.Experiment; //导入依赖的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; //导入依赖的package包/类
@Test
public void testBadArrayDesign() throws Exception {
    Experiment experiment = makeGoodExperiment();
    experiment.getArrayDesigns().clear();
    List<String> result = this.bean.validateForExport(experiment);
    assertEquals(1, result.size());
    assertEquals("No (Affymetrix) array design specified", result.get(0));

    experiment = makeGoodExperiment();
    final ArrayDesign ad = experiment.getArrayDesigns().iterator().next();
    ad.getProvider().setName("foo");
    ad.setGeoAccession(null);
    result = this.bean.validateForExport(experiment);
    assertEquals(1, result.size());
    assertEquals("Affymetrix is not the provider for array design test-ad", result.get(0));
}
 

import gov.nih.nci.caarray.domain.project.Experiment; //导入依赖的package包/类
private void onCollectionChange(Object collection) {
    if (collection instanceof PersistentCollection) {
        PersistentCollection pc = (PersistentCollection) collection;

        if (pc.getOwner() instanceof AccessProfile) {
            saveEntityForProcessing(PROFILES, new ArrayList<AccessProfile>(), (AccessProfile) pc.getOwner());
        }

        if (pc.getOwner() instanceof Experiment && pc.getRole() != null && pc.getRole().endsWith(".samples")) {
            // inefficient but seems to be the cleanest way possible: force an update of all the
            // access profiles associated with the project to make sure new or removed samples
            // are appropriately updated for
            Experiment experiment = (Experiment) pc.getOwner();
            Project proj = experiment.getProject();
            saveEntityForProcessing(BIOMATERIAL_CHANGES, new ArrayList<Project>(), proj);
        }
    }
}
 

import gov.nih.nci.caarray.domain.project.Experiment; //导入依赖的package包/类
private void reloadSupportingObjects() {
    final Transaction tx = this.hibernateHelper.beginTransaction();
    this.testOrganism =
            (Organism) this.hibernateHelper.getCurrentSession().load(Organism.class, getTestOrganism().getId());
    this.testOrganization =
            (Organization) this.hibernateHelper.getCurrentSession().load(Organization.class,
                    this.testOrganization.getId());
    this.testProject =
            (Project) this.hibernateHelper.getCurrentSession().load(Project.class, this.testProject.getId());
    this.testExperiment =
            (Experiment) this.hibernateHelper.getCurrentSession().load(Experiment.class,
                    this.testExperiment.getId());
    this.testTermSource =
            (TermSource) this.hibernateHelper.getCurrentSession().load(TermSource.class,
                    this.testTermSource.getId());
    this.testCategory =
            (Category) this.hibernateHelper.getCurrentSession().load(Category.class, this.testCategory.getId());
    this.testTerm = (Term) this.hibernateHelper.getCurrentSession().load(Term.class, this.testTerm.getId());
    tx.commit();
}
 

import gov.nih.nci.caarray.domain.project.Experiment; //导入依赖的package包/类
@Test
public void testNoScanWithNorm() {
    MageTabDocumentSet ds = getDocumentSet(TestMageTabSets.MULTI_NO_SCAN_2_INPUT_SET);
    CaArrayFileSet fileSet = TestMageTabSets.getFileSet(ds);
    CaArrayTranslationResult result = this.translator.translate(ds, fileSet);
    Experiment experiment = result.getInvestigations().iterator().next();
    Hybridization hyb = experiment.getHybridizations().iterator().next();
    checkPaCollection(hyb.getProtocolApplications(), "Scan");
    RawArrayData rad = hyb.getRawDataCollection().iterator().next();
    checkPaCollection(rad.getProtocolApplications(), "normalization-protocol-1", "normalization-protocol-2",
            "derived-data-protocol-1", "derived-data-protocol-2");
    for (DerivedArrayData d : hyb.getDerivedDataCollection()) {
        if (d.getName().equals("test.data")) {
            checkPaCollection(d.getProtocolApplications());
        } else if (d.getName().equals("test2.data")) {
            checkPaCollection(d.getProtocolApplications());
        } else {
            fail(d.getName());
        }
    }
}
 

import gov.nih.nci.caarray.domain.project.Experiment; //导入依赖的package包/类
@Test
public void testNormal_1() {
    MageTabDocumentSet ds = getDocumentSet(TestMageTabSets.NORMAL_1_INPUT_SET);
    CaArrayFileSet fileSet = TestMageTabSets.getFileSet(ds);
    CaArrayTranslationResult result = this.translator.translate(ds, fileSet);
    Experiment experiment = result.getInvestigations().iterator().next();
    Hybridization hyb = experiment.getHybridizations().iterator().next();
    checkPaCollection(hyb.getProtocolApplications(), "Scan");
    for (RawArrayData rad : hyb.getRawDataCollection()) {
        if (rad.getName().equals("test1.CEL")) {
            checkPaCollection(rad.getProtocolApplications());
        } else if(rad.getName().equals("test2.CEL")) {
            checkPaCollection(rad.getProtocolApplications(), "TRANPRTCL10656");
        } else {
            fail(rad.getName());
        }
    }        
    DerivedArrayData dad = hyb.getDerivedDataCollection().iterator().next();
    checkPaCollection(dad.getProtocolApplications());

}
 

import gov.nih.nci.caarray.domain.project.Experiment; //导入依赖的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; //导入依赖的package包/类
@Test
public void testBadSingleChannel() throws Exception {
    final Experiment experiment = makeGoodExperiment();
    final Hybridization h = experiment.getHybridizations().iterator().next();
    final RawArrayData rawData = new RawArrayData();
    final ProtocolApplication pa = new ProtocolApplication();
    rawData.setName("raw-array-data2");
    rawData.getHybridizations().add(h);
    final Protocol p = this.vocab.getProtocol("data processing", null);
    p.setDescription("data proc desc");
    pa.setProtocol(p);
    rawData.getProtocolApplications().add(pa);
    h.getRawDataCollection().add(rawData);
    final List<String> result = this.bean.validateForExport(experiment);
    assertEquals(result.toString(), 0, result.size());
}
 

import gov.nih.nci.caarray.domain.project.Experiment; //导入依赖的package包/类
private void translateSdrfElements(Experiment experiment, SdrfDocument sdrfDocument) {
    // Translate caArray domain biomaterial-data chains into MAGE-TAB biomaterial-data chains.
    for (final Source source : experiment.getSources()) {
        final AbstractSampleDataRelationshipNode sdrfSource = getOrCreateNode(source);
        addBiomaterialAttributes(source, (gov.nih.nci.caarray.magetab.sdrf.Source) sdrfSource);
        addSourceAttributes(source, sdrfSource);
        handleSamples(source, sdrfSource);
    }

    // Initialize the SDRF document with all the object graph nodes.
    final SdrfDocumentNodes sdrfDocumentNodes = new SdrfDocumentNodes();
    sdrfDocumentNodes.initNonDataNodes(this.allSources, this.allSamples, this.allExtracts, this.allLabeledExtracts,
            this.allHybridizations);
    sdrfDocumentNodes.initDataNodes(this.allArrayDataFiles, this.allArrayDataMatrixFiles,
            this.allDerivedArrayDataFiles, this.allDerivedArrayDataMatrixFiles);
    sdrfDocument.initializeNodes(sdrfDocumentNodes);

    // TODO Translate other SDRF elements, i.e., protocols, experimental factors.
}
 

import gov.nih.nci.caarray.domain.project.Experiment; //导入依赖的package包/类
/**
 * {@inheritDoc}
 */
public ActionForward execute(
        final ActionMapping mapping, final ActionForm form,
        final HttpServletRequest request,
        final HttpServletResponse response
    ) throws Exception {
	LOGGER.info("Fetching caArray experiment list...");
	CaArrayClient client = PageContext.getCaArrayClient(request);
	Collection<Experiment> experimentList = PageContext.getCaArrayExperimentList(request);
	String refresh = request.getParameter("refresh");
	
	if (experimentList == null || refresh != null){
			experimentList = client.getExperimentsWithSamples();
			PageContext.setCaArrayExperimentList(experimentList, request);
	}
	
	
	
	return mapping.findForward("success");
}