Java Experiment.setOrganism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 Experiment createExampleExperiment(String providerName, String organismName) {
    Experiment exampleExperiment = new Experiment();

    // Set the array provider.
    Organization organization = new Organization();
    organization.setName(providerName);
    organization.setProvider(true);
    exampleExperiment.setManufacturer(organization);

    // Set the organism.
    Organism organismCriterion = new Organism();
    organismCriterion.setCommonName(organismName);
    exampleExperiment.setOrganism(organismCriterion);

    // Set the assay type.
    // exampleExperiment.setAssayTypeEnum(AssayType.SNP);

    return exampleExperiment;
}
 

import gov.nih.nci.caarray.domain.project.Experiment; //导入方法依赖的package包/类
private Experiment createExampleExperiment(String providerName, String organismName) {
    Experiment exampleExperiment = new Experiment();

    Organization organization = new Organization();
    organization.setName(providerName);
    organization.setProvider(true);
    exampleExperiment.setManufacturer(organization);

    Organism organismCriterion = new Organism();
    organismCriterion.setCommonName(organismName);
    exampleExperiment.setOrganism(organismCriterion);

    return exampleExperiment;
}
 

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 fixAllExperiments(final SingleConnectionHibernateHelper hibernateHelper,
        final Organism organismToReplace, final Organism ncbiSourcedOrganism) {
    List<Experiment> allExperimentsWithBadOrganism = getAllExperimentsForOrganism(hibernateHelper,
            organismToReplace);
    for (Experiment experiment : allExperimentsWithBadOrganism) {
        experiment.setOrganism(ncbiSourcedOrganism);
        hibernateHelper.getCurrentSession().save(experiment);
    }
}
 

import gov.nih.nci.caarray.domain.project.Experiment; //导入方法依赖的package包/类
private Experiment createExampleExperiment(String manufacturerName, String organismName) {
    Experiment exampleExperiment = new Experiment();

    Organization organization = new Organization();
    organization.setName(manufacturerName);
    organization.setProvider(true);
    exampleExperiment.setManufacturer(organization);

    Organism organismCriterion = new Organism();
    organismCriterion.setCommonName(organismName);
    exampleExperiment.setOrganism(organismCriterion);

    return exampleExperiment;
}
 

import gov.nih.nci.caarray.domain.project.Experiment; //导入方法依赖的package包/类
private Experiment createExampleExperiment() {
    Experiment exampleExperiment = new Experiment();

    Organization organization = new Organization();
    organization.setName(manufacturer);
    organization.setProvider(true);
    exampleExperiment.setManufacturer(organization);

    Organism organismCriterion = new Organism();
    organismCriterion.setCommonName(organism);
    exampleExperiment.setOrganism(organismCriterion);

    return exampleExperiment;
}
 

import gov.nih.nci.caarray.domain.project.Experiment; //导入方法依赖的package包/类
private Experiment createExampleExperiment() {
    Experiment exampleExperiment = new Experiment();

    Organization organization = new Organization();
    organization.setName(manufacturer);
    exampleExperiment.setManufacturer(organization);

    Organism organismCriterion = new Organism();
    organismCriterion.setCommonName(organism);
    exampleExperiment.setOrganism(organismCriterion);

    return exampleExperiment;
}
 

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
@Override
protected void populateSearch(String[] input, ExampleSearch exampleSearch)
{
    ExperimentSearch search = (ExperimentSearch)exampleSearch;
    Experiment example = new Experiment();
    if (headerIndexMap.get(API) < input.length
            && !input[headerIndexMap.get(API)].equals(""))
    {
        search.setApi(input[headerIndexMap.get(API)].trim());
    }
    if (headerIndexMap.get(TEST_CASE) < input.length
            && !input[headerIndexMap.get(TEST_CASE)].equals(""))
        search.setTestCase(Float.parseFloat(input[headerIndexMap.get(TEST_CASE)]
                .trim()));
    if (headerIndexMap.get(LOGIN) < input.length
            && !input[headerIndexMap.get(LOGIN)].equals(""))
        search.setLogin(Boolean.parseBoolean(input[headerIndexMap.get(LOGIN)]
                .trim()));
    
    Organism organism = null;
    if (headerIndexMap.get(ORG_SCI_NAME) < input.length && !input[headerIndexMap.get(ORG_SCI_NAME)].equals(""))
    {
       organism = new Organism();
       organism.setScientificName(input[headerIndexMap.get(ORG_SCI_NAME)].trim());         
    }
    if (organism != null)
    {
        example.setOrganism(organism);
    }
    Organization organization = null;
    if (headerIndexMap.get(ARRAY_PROVIDER) < input.length && !input[headerIndexMap.get(ARRAY_PROVIDER)].equals(""))
    {
        organization = new Organization();
        organization.setName(input[headerIndexMap.get(ARRAY_PROVIDER)].trim());
        organization.setProvider(true);
        
    }
    if (organization != null)
    {
        example.setManufacturer(organization);
    }
    
    search.setExperiment(example);

    if (headerIndexMap.get(EXPECTED_RESULTS) < input.length
            && !input[headerIndexMap.get(EXPECTED_RESULTS)].equals(""))
        search.setExpectedResults(Integer
                .parseInt(input[headerIndexMap.get(EXPECTED_RESULTS)].trim()));
    if (headerIndexMap.get(MIN_RESULTS) < input.length
            && !input[headerIndexMap.get(MIN_RESULTS)].equals(""))
        search.setMinResults(Integer.parseInt(input[headerIndexMap.get(MIN_RESULTS)].trim()));
    
}