private void runImportCnaData() throws DaoException, IOException {
DaoGeneticAlteration dao = DaoGeneticAlteration.getInstance();
DaoGeneOptimized daoGene = DaoGeneOptimized.getInstance();
// the largest current true Entrez gene ID counts 8 digits
daoGene.addGene(new CanonicalGene(999999207, "TESTAKT1"));
daoGene.addGene(new CanonicalGene(999999208, "TESTAKT2"));
daoGene.addGene(new CanonicalGene(999910000, "TESTAKT3"));
daoGene.addGene(new CanonicalGene(999999369, "TESTARAF"));
daoGene.addGene(new CanonicalGene(999999472, "TESTATM"));
daoGene.addGene(new CanonicalGene(999999673, "TESTBRAF"));
daoGene.addGene(new CanonicalGene(999999672, "TESTBRCA1"));
daoGene.addGene(new CanonicalGene(999999675, "TESTBRCA2"));
ProgressMonitor.setConsoleMode(false);
// TBD: change this to use getResourceAsStream()
File file = new File("src/test/resources/cna_test.txt");
ImportTabDelimData parser = new ImportTabDelimData(file, "Barry", geneticProfileId, null);
int numLines = FileUtil.getNumLines(file);
parser.importData(numLines);
String value = dao.getGeneticAlteration(geneticProfileId, sample1, 999999207);
assertEquals("0", value);
value = dao.getGeneticAlteration(geneticProfileId, sample4, 999999207);
assertEquals("-1", value);
value = dao.getGeneticAlteration(geneticProfileId, sample2, 999999207);
assertEquals("0", value);
value = dao.getGeneticAlteration(geneticProfileId, sample2, 999910000);
assertEquals("2", value);
value = dao.getGeneticAlteration(geneticProfileId, sample3, 999910000);
assertEquals("2", value);
int cnaStatus =
Integer.parseInt(dao.getGeneticAlteration(geneticProfileId, sample3, 999910000));
assertEquals(CopyNumberStatus.COPY_NUMBER_AMPLIFICATION, cnaStatus);
cnaStatus = Integer.parseInt(dao.getGeneticAlteration(geneticProfileId, sample2, 999910000));
assertEquals(CopyNumberStatus.COPY_NUMBER_AMPLIFICATION, cnaStatus);
cnaStatus = Integer.parseInt(dao.getGeneticAlteration(geneticProfileId, sample4, 999999207));
assertEquals(CopyNumberStatus.HEMIZYGOUS_DELETION, cnaStatus);
Patient patient = DaoPatient.getPatientByCancerStudyAndPatientId(studyId, "TCGA-A1-A0SB");
Sample sample =
DaoSample.getSampleByPatientAndSampleId(patient.getInternalId(), "TCGA-A1-A0SB-01");
assertTrue(
DaoSampleProfile.sampleExistsInGeneticProfile(sample.getInternalId(), geneticProfileId));
patient = DaoPatient.getPatientByCancerStudyAndPatientId(studyId, "TCGA-A1-A0SJ");
sample = DaoSample.getSampleByPatientAndSampleId(patient.getInternalId(), "TCGA-A1-A0SJ-01");
assertTrue(
DaoSampleProfile.sampleExistsInGeneticProfile(sample.getInternalId(), geneticProfileId));
ArrayList caseIds = DaoSampleProfile.getAllSampleIdsInProfile(geneticProfileId);
assertEquals(14, caseIds.size());
}
@Before
public void setUp() throws DaoException {
study = DaoCancerStudy.getCancerStudyByStableId("study_tcga_pub");
DaoGeneticProfile.reCache();
DaoPatient.reCache();
DaoSample.reCache();
}
private void runImportCnaData2() throws DaoException, IOException {
DaoGeneticAlteration dao = DaoGeneticAlteration.getInstance();
ProgressMonitor.setConsoleMode(false);
// TBD: change this to use getResourceAsStream()
File file = new File("src/test/resources/cna_test2.txt");
ImportTabDelimData parser = new ImportTabDelimData(file, geneticProfileId, null);
int numLines = FileUtil.getNumLines(file);
parser.importData(numLines);
String value = dao.getGeneticAlteration(geneticProfileId, sample1, 207);
assertEquals(value, "0");
value = dao.getGeneticAlteration(geneticProfileId, sample4, 207);
assertEquals(value, "-1");
value = dao.getGeneticAlteration(geneticProfileId, sample2, 207);
assertEquals(value, "0");
value = dao.getGeneticAlteration(geneticProfileId, sample2, 10000);
assertEquals(value, "2");
value = dao.getGeneticAlteration(geneticProfileId, sample3, 10000);
assertEquals(value, "2");
int cnaStatus = Integer.parseInt(dao.getGeneticAlteration(geneticProfileId, sample3, 10000));
assertEquals(CopyNumberStatus.COPY_NUMBER_AMPLIFICATION, cnaStatus);
cnaStatus = Integer.parseInt(dao.getGeneticAlteration(geneticProfileId, sample2, 10000));
assertEquals(CopyNumberStatus.COPY_NUMBER_AMPLIFICATION, cnaStatus);
cnaStatus = Integer.parseInt(dao.getGeneticAlteration(geneticProfileId, sample4, 207));
assertEquals(CopyNumberStatus.HEMIZYGOUS_DELETION, cnaStatus);
Patient patient = DaoPatient.getPatientByCancerStudyAndPatientId(studyId, "TCGA-A1-A0SB");
Sample sample =
DaoSample.getSampleByPatientAndSampleId(patient.getInternalId(), "TCGA-A1-A0SB-01");
assertTrue(
DaoSampleProfile.sampleExistsInGeneticProfile(sample.getInternalId(), geneticProfileId));
patient = DaoPatient.getPatientByCancerStudyAndPatientId(studyId, "TCGA-A1-A0SJ");
sample = DaoSample.getSampleByPatientAndSampleId(patient.getInternalId(), "TCGA-A1-A0SJ-01");
assertTrue(
DaoSampleProfile.sampleExistsInGeneticProfile(sample.getInternalId(), geneticProfileId));
ArrayList sampleIds = DaoSampleProfile.getAllSampleIdsInProfile(geneticProfileId);
assertEquals(14, sampleIds.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);
}
}