/**
* 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());
}