Java Experiment.setTitle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 lookupExperiments(CaArraySearchService service, DataRetrievalRequest request, String experimentName) {
    String[] experimentTitles = experimentName.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);
        logForSilverCompatibility(API_CALL, "CaArraySearchService.search(Experiment)");
        Set<Hybridization> allHybs = getAllHybridizations(experimentList);
        request.getHybridizations().addAll(allHybs);
    }
}
 

import gov.nih.nci.caarray.domain.project.Experiment; //导入方法依赖的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 Experiment lookupExperiment(CaArraySearchService service, String experimentName) {
    Experiment exampleExperiment = new Experiment();
    exampleExperiment.setTitle(experimentName);

    List<Experiment> experimentList = service.search(exampleExperiment);
    if (experimentList.size() == 0) {
        return null;
    }
    Experiment experiment = experimentList.get(0);
    return experiment;
}
 

import gov.nih.nci.caarray.domain.project.Experiment; //导入方法依赖的package包/类
private Experiment lookupExperiment(CaArraySearchService service, String experimentName) {
    Experiment exampleExperiment = new Experiment();
    exampleExperiment.setTitle(experimentName);

    List<Experiment> experimentList = service.search(exampleExperiment);
    if (experimentList.size() == 0) {
        return null;
    }
    return experimentList.get(0);
}
 

import gov.nih.nci.caarray.domain.project.Experiment; //导入方法依赖的package包/类
@Test
public void updateExperiment() {
    Transaction tx = this.hibernateHelper.beginTransaction();

    // setup
    setupHelper();
    int initLogMessages = getLogMessages().size();
    
    // update experiment fields
    Project p = ProjectTestHelper.getDummyProject();
    Experiment e = p.getExperiment();
    e.setTitle("title new");
    e.setDescription("description new");
    e.getAssayTypes().add(ProjectTestHelper.getDummyAssayType2());
    e.setManufacturer(ProjectTestHelper.getDummyOrganization2());
    e.getArrayDesigns().add(ProjectTestHelper.getDummyArrayDesign());
    e.setOrganism(ProjectTestHelper.getDummyOrganism2());
    this.hibernateHelper.getCurrentSession().saveOrUpdate(p);
    this.hibernateHelper.getCurrentSession().flush();

    // check logs
    List<String> messages = getLogMessages();
    assertEquals(7, messages.size() - initLogMessages);
    assertTrue(messages.contains("Experiment " + e.getTitle() + ":"));
    assertTrue(messages.contains(" - Title updated"));
    assertTrue(messages.contains(" - Description updated"));
    assertTrue(messages.contains(" - Assay Types updated"));
    assertTrue(messages.contains(" - Provider updated"));
    assertTrue(messages.contains(" - Array Designs updated"));
    assertTrue(messages.contains(" - Organism updated"));

    tx.commit();
}
 

import gov.nih.nci.caarray.domain.project.Experiment; //导入方法依赖的package包/类
@Override
protected void setValues(CaArrayFile caArrayFile) {
    super.setValues(caArrayFile);
    caArrayFile.setFileStatus(getNextValue(FileStatus.values(), caArrayFile.getFileStatus()));
    caArrayFile.setName(getUniqueStringValue());
    if (caArrayFile.getProject() == null) {
        final TermSource ts = new TermSource();
        ts.setName("Dummy TS");
        ts.setVersion("1.0");
        final Organism org = new Organism();
        org.setScientificName("Foo");
        org.setTermSource(ts);
        Project p = new Project();
        Experiment e = p.getExperiment();
        e.setProject(p);
        caArrayFile.setProject(p);
        e.setTitle("TestFileExperiment1");
        final SortedSet<AssayType> assayTypes = new TreeSet<AssayType>();
        final AssayType assayType = new AssayType("aCGH");
        assayTypes.add(assayType);
        save(assayType);
        e.setAssayTypes(assayTypes);
        e.setOrganism(org);
        e.setManufacturer(new Organization());
        save(p);
    }
    caArrayFile.setFileType(FileTypeRegistry.MAGE_TAB_IDF);
    caArrayFile.setDataHandle(DUMMY_HANDLE);
    caArrayFile.setValidationResult(new FileValidationResult());
}
 

import gov.nih.nci.caarray.domain.project.Experiment; //导入方法依赖的package包/类
private void translateInvestigationSummary(gov.nih.nci.caarray.magetab.idf.Investigation idfInvestigation,
        Experiment investigation) {
    investigation.setTitle(idfInvestigation.getTitle());
    // WC: temporary fix.  this should be constrained on the db.
    String desc = idfInvestigation.getDescription();
    if (desc != null && desc.length() > LARGE_TEXT_FIELD_LENGTH) {
        desc = desc.substring(0, LARGE_TEXT_FIELD_LENGTH);
    }
    investigation.setDescription(desc);
    investigation.setDate(idfInvestigation.getDateOfExperiment());
    investigation.setPublicReleaseDate(idfInvestigation.getPublicReleaseDate());
}
 

import gov.nih.nci.caarray.domain.project.Experiment; //导入方法依赖的package包/类
@Test
public void testImportDoesntOverwriteExistingExperiment() {
    final Project project = getTgaBroadTestProject();
    final Experiment experiment = new Experiment();
    final String title = "title" + System.currentTimeMillis();
    experiment.setTitle(title);
    project.setExperiment(experiment);
    this.fileManagementService.importFiles(project, project.getFileSet(),
            DataImportOptions.getAutoCreatePerFileOptions());
    assertEquals(title, project.getExperiment().getTitle());
}
 

import gov.nih.nci.caarray.domain.project.Experiment; //导入方法依赖的package包/类
private Experiment lookupExperiment(CaArraySearchService service, String experimentName) {
    Experiment exampleExperiment = new Experiment();
    exampleExperiment.setTitle(experimentName);

    List<Experiment> experimentList = service.search(exampleExperiment);
    logForSilverCompatibility(API_CALL, "CaArraySearchService.search(Experiment)");
    if (experimentList.size() == 0) {
        return null;
    }
    Experiment experiment = experimentList.get(0);
    return experiment;
}
 

import gov.nih.nci.caarray.domain.project.Experiment; //导入方法依赖的package包/类
private Experiment lookupExperiment(CaArraySearchService service, String experimentName) {
    Experiment exampleExperiment = new Experiment();
    exampleExperiment.setTitle(experimentName);

    List<Experiment> experimentList = service.search(exampleExperiment);
    logForSilverCompatibility(API_CALL, "CaArraySearchService.search(Experiment)");
    if (experimentList.size() == 0) {
        return null;
    }
    return experimentList.get(0);
}
 

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

    ArrayDesign ad = null;
    
    // 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);
        
        Experiment exp = experimentList.iterator().next();
        
        // TODO: For now assume it's just one experiment
        experiment = exp;
        Set<ArrayDesign> arrDesigns = exp.getArrayDesigns();
        ad = arrDesigns.iterator().next();
        Set<Hybridization> allHybs = getAllHybridizations(experimentList);
        request.getHybridizations().addAll(allHybs);
    }
    
    arrayDesignName = ad.getName();        
    System.out.println("****Array desing name = " + ad.getName());
}
 

import gov.nih.nci.caarray.domain.project.Experiment; //导入方法依赖的package包/类
@Test
public void testSearchByExampleLimitOffset() {
    Transaction tx = hibernateHelper.beginTransaction();

    AssayType at1 = new AssayType("AT1");        
    AssayType at2 = new AssayType("AT2");
    SEARCH_DAO.save(Arrays.asList(at1, at2));
    
    TermSource ts1 = new TermSource();
    ts1.setName("TS1");
    SEARCH_DAO.save(ts1);
    
    Organism o1 = new Organism();
    o1.setScientificName("Foo");
    o1.setTermSource(ts1);
    SEARCH_DAO.save(o1);
    
    Experiment e1 = new Experiment();
    e1.setTitle("e1");
    e1.setOrganism(o1);
    e1.getAssayTypes().add(at1);
    e1.getAssayTypes().add(at2);
    Project p1 = new Project();
    p1.setExperiment(e1);
    e1.setProject(p1);

    Experiment e2 = new Experiment();
    e2.setTitle("e2");
    e2.setOrganism(o1);
    e2.getAssayTypes().add(at1);
    Project p2 = new Project();
    p2.setExperiment(e2);
    e2.setProject(p2);

    Experiment e3 = new Experiment();
    e3.setTitle("e3");
    e3.setOrganism(o1);
    e3.getAssayTypes().add(at2);
    Project p3 = new Project();
    p3.setExperiment(e3);
    e3.setProject(p3);

    Experiment e4 = new Experiment();
    e4.setTitle("e4");
    e4.setOrganism(o1);
    e4.getAssayTypes().add(at2);
    Project p4 = new Project();
    p4.setExperiment(e4);
    e4.setProject(p4);
    
    SEARCH_DAO.save(Arrays.asList(p1, p2, p3, p4));

    tx.commit();
    tx = hibernateHelper.beginTransaction();
    @SuppressWarnings("unchecked")
    List<Experiment> results = (List<Experiment>) hibernateHelper.doUnfiltered(new UnfilteredCallback() {
        public Object doUnfiltered(Session s) {
            return SEARCH_DAO.queryEntityByExample(ExampleSearchCriteria.forEntity(new Experiment()), 3, 0, Order
                    .asc("title"));
        }
    });
    assertEquals(3, results.size());
    assertEquals("e1", results.get(0).getTitle());
    assertEquals("e2", results.get(1).getTitle());
    assertEquals("e3", results.get(2).getTitle());
    tx.commit();
}
 

import gov.nih.nci.caarray.domain.project.Experiment; //导入方法依赖的package包/类
private Experiment createExperimentWithOverviewInformation() {
    Experiment experiment = new Experiment();
    experiment.setTitle(EXPERIMENT_TITLE);
    experiment.setDescription(EXPERIMENT_DESCRIPTION);
    return experiment;
}