@Before
public void setUp() throws DaoException {
DaoCancerStudy.reCacheAll();
DaoGeneOptimized.getInstance().reCache();
ProgressMonitor.resetWarnings();
studyId = DaoCancerStudy.getCancerStudyByStableId("study_tcga_pub").getInternalId();
GeneticProfile newGeneticProfile = new GeneticProfile();
newGeneticProfile.setCancerStudyId(studyId);
newGeneticProfile.setGeneticAlterationType(GeneticAlterationType.COPY_NUMBER_ALTERATION);
newGeneticProfile.setStableId("study_tcga_pub_test");
newGeneticProfile.setProfileName("Barry CNA Results");
newGeneticProfile.setDatatype("test");
DaoGeneticProfile.addGeneticProfile(newGeneticProfile);
geneticProfileId =
DaoGeneticProfile.getGeneticProfileByStableId("study_tcga_pub_test").getGeneticProfileId();
sample1 =
DaoSample.getSampleByCancerStudyAndSampleId(studyId, "TCGA-A1-A0SB-01").getInternalId();
sample2 =
DaoSample.getSampleByCancerStudyAndSampleId(studyId, "TCGA-A1-A0SD-01").getInternalId();
sample3 =
DaoSample.getSampleByCancerStudyAndSampleId(studyId, "TCGA-A1-A0SE-01").getInternalId();
sample4 =
DaoSample.getSampleByCancerStudyAndSampleId(studyId, "TCGA-A1-A0SF-01").getInternalId();
sample5 =
DaoSample.getSampleByCancerStudyAndSampleId(studyId, "TCGA-A1-A0SG-01").getInternalId();
}
private boolean validate(HttpServletRequest request) throws DaoException {
String cancerStudyID = request.getParameter(ID);
if (cancerStudyID == null) {
cancerStudyID = request.getParameter(QueryBuilder.CANCER_STUDY_ID);
}
CancerStudy cancerStudy = DaoCancerStudy.getCancerStudyByStableId(cancerStudyID);
if (cancerStudy == null) {
try {
cancerStudy = DaoCancerStudy.getCancerStudyByInternalId(Integer.parseInt(cancerStudyID));
} catch (NumberFormatException ex) {
}
}
if (cancerStudy == null) {
request.setAttribute(ERROR, "No such cancer study");
return false;
}
String cancerStudyIdentifier = cancerStudy.getCancerStudyStableId();
if (accessControl.isAccessibleCancerStudy(cancerStudyIdentifier).size() != 1) {
request.setAttribute(
ERROR,
"You are not authorized to view the cancer study with id: '"
+ cancerStudyIdentifier
+ "'. ");
return false;
} else {
UserDetails ud = accessControl.getUserDetails();
if (ud != null) {
logger.info("CancerStudyView.validate: Query initiated by user: "******"_all";
request.setAttribute(QueryBuilder.CASE_SET_ID, sampleListId);
}
SampleList sampleList = daoSampleList.getSampleListByStableId(sampleListId);
if (sampleList == null) {
request.setAttribute(ERROR, "Could not find sample list of '" + sampleListId + "'. ");
return false;
}
request.setAttribute(QueryBuilder.CASE_IDS, sampleList.getSampleList());
request.setAttribute(CANCER_STUDY, cancerStudy);
request.setAttribute(QueryBuilder.HTML_TITLE, cancerStudy.getName());
return true;
}
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);
}
}