Java Experiment.getSamples方法代码示例

import gov.nih.nci.caarray.domain.project.Experiment; //导入方法依赖的package包/类
@Test
public void testTranslateValid_Feature13141() throws Exception {
    final CaArrayFileSet fileSet = TestMageTabSets.getFileSet(TestMageTabSets.VALID_FEATURE_13141_INPUT_SET);
    final MageTabDocumentSet docSet = MageTabParser.INSTANCE.parse(TestMageTabSets.VALID_FEATURE_13141_INPUT_SET);
    final ValidationResult vResult = this.translator.validate(docSet, fileSet);
    assertTrue(vResult.getMessages().isEmpty());
    final CaArrayTranslationResult tResult = this.translator.translate(docSet, fileSet);
    assertEquals(1, tResult.getInvestigations().size());
    final Experiment e = tResult.getInvestigations().iterator().next();
    assertEquals(6, e.getSamples().size());
    for (final Sample s : e.getSamples()) {
        assertNotNull(s.getExternalId());
    }
    boolean wasFound = false;
    for (final Source source : e.getSources()) {
        if (!(StringUtils.isEmpty(source.getDescription()))) {
            assertEquals(2000, source.getDescription().length());
            wasFound = true;
        }
    }
    assertTrue("the 2000 char source description was not found.", wasFound);
    final Set<Publication> publicationsSet = e.getPublications();
    assertEquals(1, publicationsSet.size());
    final Publication publication = publicationsSet.iterator().next();
    assertEquals(2000, publication.getAuthors().length());
}
 

import gov.nih.nci.caarray.domain.project.Experiment; //导入方法依赖的package包/类
@Test
public void testTranslateInvalid_Feature13141() throws Exception {
    final CaArrayFileSet fileSet = TestMageTabSets.getFileSet(TestMageTabSets.INVALID_FEATURE_13141_INPUT_SET);
    final MageTabDocumentSet docSet = MageTabParser.INSTANCE.parse(TestMageTabSets.INVALID_FEATURE_13141_INPUT_SET);
    final ValidationResult vResult = this.translator.validate(docSet, fileSet);
    assertFalse(vResult.getMessages().isEmpty());
    assertEquals(3, vResult.getMessages(ValidationMessage.Type.WARNING).size());
    final String string = "[ExternalSampleId] value '%s"
        + "' is referenced multiple times (ExternalSampleId must be unique). "
        + "Existing value will be reused.";
    assertEquals(String.format(string, "345"), vResult.getMessages(ValidationMessage.Type.WARNING).get(0)
            .getMessage());
    assertEquals(String.format(string, "234"), vResult.getMessages(ValidationMessage.Type.WARNING).get(1)
            .getMessage());
    assertEquals(String.format(string, "123"), vResult.getMessages(ValidationMessage.Type.WARNING).get(2)
            .getMessage());
    final CaArrayTranslationResult result = this.translator.translate(docSet, fileSet);

    assertEquals(1, result.getInvestigations().size());
    final Experiment e = result.getInvestigations().iterator().next();
    assertEquals(6, e.getSamples().size());
    for (final Sample s : e.getSamples()) {
        assertNotNull(s.getExternalId());
    }
}
 

import gov.nih.nci.caarray.domain.project.Experiment; //导入方法依赖的package包/类
private Set<Hybridization> getAllHybridizationsForSamples(CaArraySearchService service,
		Experiment experiment, List<String> specimenList) {
	Set<Hybridization> allHybridizations = new HashSet<Hybridization>();
	Set<Sample> allSamples = experiment.getSamples();
	//Sample->Extract->LabeledExtract->Hybridization->RawArrayData or DerivedArrayData.
	for (Sample sample : allSamples) {
		for (String specimenName : specimenList) {
			if (sample != null && sample.getName() != null
					&& sample.getName().contains(specimenName.trim())) {
				Sample populatedSample = service.search(sample).get(0);
				System.out.println("Sample Name: "+populatedSample.getName());
				Set<Extract> allExtracts = populatedSample.getExtracts();
				for(Extract extract:allExtracts){
					Extract populatedExtract = service.search(extract).get(0);
					Set<LabeledExtract> allLabeledExtracts = populatedExtract.getLabeledExtracts();
					for(LabeledExtract labeledExtract:allLabeledExtracts){
						LabeledExtract populatedLabeledExtract = service.search(labeledExtract).get(0);
						allHybridizations.addAll(populatedLabeledExtract.getHybridizations());
					}
				}
			}
		}
	}
	return allHybridizations;
}
 

import gov.nih.nci.caarray.domain.project.Experiment; //导入方法依赖的package包/类
private Experiment createExperimentWithBiomaterialCharacteristics() {
    // Create an experiment with biomaterials.
    Experiment experiment = createExperimentWithOneToOneChains();

    // Create ontology categories for the predefined characteristics.
    Set<ExperimentOntologyCategory> allOntologyCategories = new HashSet<ExperimentOntologyCategory>();
    allOntologyCategories.add(ExperimentOntologyCategory.MATERIAL_TYPE);
    allOntologyCategories.add(ExperimentOntologyCategory.CELL_TYPE);
    allOntologyCategories.add(ExperimentOntologyCategory.DISEASE_STATE);
    allOntologyCategories.add(ExperimentOntologyCategory.ORGANISM_PART);
    Set<ExperimentOntologyCategory> oneOntologyCategory = new HashSet<ExperimentOntologyCategory>();
    oneOntologyCategory.add(ExperimentOntologyCategory.DISEASE_STATE);

    // Add Source provider and predefined characteristics.
    Organization provider = new Organization();
    provider.setName(PROVIDER_ORGANIZATION);
    for (Source source : experiment.getSources()) {
        source.getProviders().add(provider);
        addPredefinedCharacteristics(source, allOntologyCategories);
        source.setExternalId(TEST_EXTERNAL_ID);
    }

    // Add Sample predefined characteristics and special characteristics with a term source.
    for (Sample sample : experiment.getSamples()) {
        addPredefinedCharacteristics(sample, oneOntologyCategory);
        addSpecialCharacteristics(sample, true);
        addMeasurementCharacteristic(sample);
    }

    // Leave Extracts with no characteristics.

    // Add LabeledExtract label and special characteristics without a term source.
    Term label = new Term();
    label.setValue(LABEL_VALUE);
    Category category = new Category();
    category.setName(MageTabOntologyCategory.LABEL_COMPOUND.getCategoryName());
    label.setCategory(category);
    for (LabeledExtract labeledExtract : experiment.getLabeledExtracts()) {
        labeledExtract.setLabel(label);
        addSpecialCharacteristics(labeledExtract, false);
    }
    return experiment;
}