Java Experiment.getPublications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 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
@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
/**
 * Compare 2 experiments to check if they are the same.
 * 
 * @return true if the 2 experiments are the same and false otherwise.
 */
@SuppressWarnings("PMD")
private boolean compareExperiments(Experiment retrievedInv, Experiment dummyInv) {
    checkBioMaterials(dummyInv, retrievedInv);
    checkHybridizations(dummyInv, retrievedInv);

    // Experiment summary.
    if (!dummyInv.getTitle().equals(retrievedInv.getTitle())) {
        return false;
    }
    // Contacts
    final Collection<ExperimentContact> contacts = retrievedInv.getExperimentContacts();
    if (contacts.isEmpty() || contacts.size() != 1) {
        return false;
    }
    final Iterator<ExperimentContact> i = contacts.iterator();
    final Person person = i.next().getContact();
    if (!DUMMY_PERSON.getFirstName().equals(person.getFirstName())) {
        return false;
    }
    // Annotations
    final Collection<Term> retrievedNormTypes = retrievedInv.getNormalizationTypes();
    if (retrievedNormTypes.isEmpty() || retrievedNormTypes.size() != 1) {
        return false;
    }
    final Iterator<Term> i2 = retrievedNormTypes.iterator();
    final Term retrievedNormType = i2.next();
    if (!DUMMY_NORMALIZATION_TYPE.getValue().equals(retrievedNormType.getValue())) {
        return false;
    }
    // Factors
    final Collection<Factor> factors = retrievedInv.getFactors();
    if (factors.isEmpty() || factors.size() != 2) {
        return false;
    }

    // Publications
    final Collection<Publication> publications = retrievedInv.getPublications();
    if (publications.isEmpty() || publications.size() != 2) {
        return false;
    }
    return true;
}