예제 #1
0
  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());
  }
예제 #2
0
  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);
    }
  }