/**
   * Test importing of Clinical Data File.
   *
   * @throws DaoException Database Access Error.
   * @throws IOException IO Error.
   */
  @Test
  @Ignore("To be fixed")
  public void testImportClinicalDataSurvival() throws Exception {

    // TBD: change this to use getResourceAsStream()
    File clinicalFile = new File("target/test-classes/clinical_data.txt");
    ImportClinicalData importClinicalData = new ImportClinicalData(study, clinicalFile);
    importClinicalData.importData();

    LinkedHashSet<String> caseSet = new LinkedHashSet<String>();
    caseSet.add("TCGA-A1-A0SB");
    caseSet.add("TCGA-A1-A0SI");
    caseSet.add("TCGA-A1-A0SE");

    List<Patient> clinicalCaseList =
        DaoClinicalData.getSurvivalData(study.getInternalId(), caseSet);
    assertEquals(3, clinicalCaseList.size());

    Patient clinical0 = clinicalCaseList.get(0);
    assertEquals(new Double(79.04), clinical0.getAgeAtDiagnosis());
    assertEquals("DECEASED", clinical0.getOverallSurvivalStatus());
    assertEquals("Recurred/Progressed", clinical0.getDiseaseFreeSurvivalStatus());
    assertEquals(new Double(43.8), clinical0.getOverallSurvivalMonths());
    assertEquals(new Double(15.05), clinical0.getDiseaseFreeSurvivalMonths());

    Patient clinical1 = clinicalCaseList.get(1);
    assertEquals(new Double(55.53), clinical1.getAgeAtDiagnosis());
    assertEquals("LIVING", clinical1.getOverallSurvivalStatus());
    assertEquals("DiseaseFree", clinical1.getDiseaseFreeSurvivalStatus());
    assertEquals(new Double(49.02), clinical1.getOverallSurvivalMonths());
    assertEquals(new Double(49.02), clinical1.getDiseaseFreeSurvivalMonths());

    Patient clinical2 = clinicalCaseList.get(2);
    assertEquals(null, clinical2.getDiseaseFreeSurvivalMonths());
  }
  /**
   * Test importing of Clinical Data File.
   *
   * @throws DaoException Database Access Error.
   * @throws IOException IO Error.
   */
  @Test
  @Ignore("To be fixed")
  public void testImportClinicalDataParameters() throws Exception {

    // TBD: change this to use getResourceAsStream()
    File clinicalFile = new File("target/test-classes/clinical_data.txt");
    ImportClinicalData importClinicalData = new ImportClinicalData(study, clinicalFile);
    importClinicalData.importData();

    Set<String> paramSet = DaoClinicalData.getDistinctParameters(study.getInternalId());
    assertEquals(9, paramSet.size());
  }
  /**
   * Test importing of Clinical Data File.
   *
   * @throws DaoException Database Access Error.
   * @throws IOException IO Error.
   */
  @Test
  @Ignore("To be fixed")
  public void testImportClinicalDataSlice() throws Exception {

    // TBD: change this to use getResourceAsStream()
    File clinicalFile = new File("target/test-classes/clinical_data.txt");
    ImportClinicalData importClinicalData = new ImportClinicalData(study, clinicalFile);
    importClinicalData.importData();

    List<ClinicalParameterMap> slice =
        DaoClinicalData.getDataSlice(study.getInternalId(), Arrays.asList("PLATINUMSTATUS"));
    assertTrue(slice.size() >= 1);

    ClinicalParameterMap paramMap = slice.get(0);
    assertEquals("PLATINUMSTATUS", paramMap.getName());
    assertEquals("Sensitive", paramMap.getValue("TCGA-A1-A0SD"));
    assertEquals("NA", paramMap.getValue("TCGA-A1-A0SE"));
    assertEquals(2, paramMap.getDistinctCategories().size());
  }