/**
* 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());
}
private void processRequestStatistics(
HttpServletRequest request, HttpServletResponse response, String type)
throws ServletException, IOException {
String cancerStudyIds = request.getParameter(QueryBuilder.CANCER_STUDY_ID);
try {
boolean includeMut = "mut".equalsIgnoreCase(type);
boolean includeCna = "cna".equalsIgnoreCase(type);
Map<String, Map<String, Object>> data = new HashMap<String, Map<String, Object>>();
// get list of cancer studies
AccessControl accessControl = getaccessControl();
List<CancerStudy> cancerStudies;
if (cancerStudyIds == null || cancerStudyIds.isEmpty()) {
cancerStudies = accessControl.getCancerStudies();
} else {
cancerStudies = new ArrayList<CancerStudy>();
for (String studyId : cancerStudyIds.split("[ ,]+")) {
CancerStudy study = DaoCancerStudy.getCancerStudyByStableId(studyId);
if (study != null && !accessControl.isAccessibleCancerStudy(studyId).isEmpty()) {
cancerStudies.add(study);
}
}
}
for (CancerStudy cancerStudy : cancerStudies) {
if (cancerStudy.getCancerStudyStableId().equalsIgnoreCase("all")) {
continue;
}
Map<String, Object> row = new HashMap<String, Object>();
data.put(cancerStudy.getCancerStudyStableId(), row);
if (!includeMut && !includeMut) {
row.put("name", cancerStudy.getName());
String pmid = cancerStudy.getPmid();
if (pmid != null) {
row.put("pmid", pmid);
}
String citation = cancerStudy.getCitation();
if (citation != null) {
row.put("citation", citation);
}
row.put(
"cases", DaoPatient.getPatientsByCancerStudyId(cancerStudy.getInternalId()).size());
}
if (includeMut) {
GeneticProfile mutProfile = cancerStudy.getMutationProfile();
if (mutProfile == null) {
row.put("mut", 0);
} else {
int mutEvents = DaoMutation.countMutationEvents(mutProfile.getGeneticProfileId());
int samplesWithMut =
DaoSampleProfile.countSamplesInProfile(mutProfile.getGeneticProfileId());
row.put("mut", 1.0 * mutEvents / samplesWithMut);
}
}
if (includeCna) {
GeneticProfile cnaProfile = cancerStudy.getCopyNumberAlterationProfile(false);
if (cnaProfile == null) {
row.put("cna", 0);
} else {
List<Integer> samples =
DaoSampleProfile.getAllSampleIdsInProfile(cnaProfile.getGeneticProfileId());
Map<Integer, Double> fracs =
DaoCopyNumberSegment.getCopyNumberActeredFraction(
samples,
cnaProfile.getCancerStudyId(),
GlobalProperties.getPatientViewGenomicOverviewCnaCutoff()[0]);
double aveFrac = 0;
for (double frac : fracs.values()) {
aveFrac += frac;
}
aveFrac /= samples.size();
row.put("cna", aveFrac);
}
}
}
response.setContentType("application/json");
PrintWriter out = response.getWriter();
try {
JSONValue.writeJSONString(data, out);
} finally {
out.close();
}
} catch (DaoException ex) {
throw new ServletException(ex);
} catch (ProtocolException ex) {
throw new ServletException(ex);
}
}