Exemplo n.º 1
0
  private void setGeneticProfiles(HttpServletRequest request) throws DaoException {
    CancerStudy cancerStudy = (CancerStudy) request.getAttribute(CANCER_STUDY);
    GeneticProfile mutProfile = cancerStudy.getMutationProfile();
    if (mutProfile != null) {
      request.setAttribute(MUTATION_PROFILE, mutProfile);
    }

    GeneticProfile cnaProfile = cancerStudy.getCopyNumberAlterationProfile(true);
    if (cnaProfile != null) {
      request.setAttribute(CNA_PROFILE, cnaProfile);
    }
  }
Exemplo n.º 2
0
  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;
  }
Exemplo n.º 3
0
  /**
   * 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());
  }
Exemplo n.º 4
0
  public static CancerStudy loadCancerStudy(File file, boolean strict, boolean addStudyToDb)
      throws IOException, DaoException {
    TrimmedProperties properties = new TrimmedProperties();
    properties.load(new FileInputStream(file));

    CancerStudy cancerStudy = getCancerStudy(properties);

    if (strict && null == DaoTypeOfCancer.getTypeOfCancerById(cancerStudy.getTypeOfCancerId())) {
      throw new IllegalArgumentException(
          cancerStudy.getTypeOfCancerId() + " is not a supported cancer type.");
    }

    if (addStudyToDb) {
      DaoCancerStudy.addCancerStudy(cancerStudy, true); // overwrite if exist
    }

    return cancerStudy;
  }
Exemplo n.º 5
0
  /**
   * 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());
  }
Exemplo n.º 6
0
  private static CancerStudy getCancerStudy(TrimmedProperties properties) {
    String cancerStudyIdentifier = properties.getProperty("cancer_study_identifier");
    if (cancerStudyIdentifier == null) {
      throw new IllegalArgumentException("cancer_study_identifier is not specified.");
    }

    String name = properties.getProperty("name");
    if (name == null) {
      throw new IllegalArgumentException("name is not specified.");
    }

    String description = properties.getProperty("description");
    if (description == null) {
      throw new IllegalArgumentException("description is not specified.");
    }

    String typeOfCancer = properties.getProperty("type_of_cancer").toLowerCase();
    if (typeOfCancer == null) {
      throw new IllegalArgumentException("type of cancer is not specified.");
    }

    String shortName = properties.getProperty("short_name");
    if (shortName == null) {
      throw new IllegalArgumentException("short_name is not specified.");
    }

    CancerStudy cancerStudy =
        new CancerStudy(
            name, description, cancerStudyIdentifier, typeOfCancer, publicStudy(properties));
    cancerStudy.setPmid(properties.getProperty("pmid"));
    cancerStudy.setCitation(properties.getProperty("citation"));
    cancerStudy.setGroupsInUpperCase(properties.getProperty("groups"));
    cancerStudy.setShortName(shortName);

    return cancerStudy;
  }
Exemplo n.º 7
0
  /**
   * 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);
    }
  }
Exemplo n.º 9
0
  /**
   * Processes requests for both HTTP <code>GET</code> and <code>POST</code> methods.
   *
   * @param request servlet request
   * @param response servlet response
   * @throws javax.servlet.ServletException if a servlet-specific error occurs
   * @throws java.io.IOException if an I/O error occurs
   */
  protected void doGet(HttpServletRequest request, HttpServletResponse response)
      throws IOException, ServletException {
    XDebug xdebug = new XDebug();
    xdebug.startTimer();

    response.setContentType("application/json");
    PrintWriter writer = response.getWriter();

    try {
      List resultsList = new LinkedList();

      // Get the gene list
      String geneList = request.getParameter(QueryBuilder.GENE_LIST);
      if (request instanceof XssRequestWrapper) {
        geneList = ((XssRequestWrapper) request).getRawParameter(QueryBuilder.GENE_LIST);
      }
      String cancerStudyIdListString = request.getParameter(QueryBuilder.CANCER_STUDY_LIST);
      String[] cancerStudyIdList = cancerStudyIdListString.split(",");

      // Get the priority
      Integer dataTypePriority;
      try {
        dataTypePriority =
            Integer.parseInt(request.getParameter(QueryBuilder.DATA_PRIORITY).trim());
      } catch (NumberFormatException e) {
        dataTypePriority = 0;
      }

      //  Cancer All Cancer Studies
      List<CancerStudy> cancerStudiesList = accessControl.getCancerStudies();
      HashMap<String, Boolean> studyMap = new HashMap<>();
      for (String studyId : cancerStudyIdList) {
        studyMap.put(studyId, Boolean.TRUE);
      }
      for (CancerStudy cancerStudy : cancerStudiesList) {
        String cancerStudyId = cancerStudy.getCancerStudyStableId();
        if (!studyMap.containsKey(cancerStudyId)) {
          continue;
        }
        if (cancerStudyId.equalsIgnoreCase("all")) continue;

        Map cancerMap = new LinkedHashMap();
        cancerMap.put("studyId", cancerStudyId);
        cancerMap.put("typeOfCancer", cancerStudy.getTypeOfCancerId());

        //  Get all Genetic Profiles Associated with this Cancer Study ID.
        ArrayList<GeneticProfile> geneticProfileList =
            GetGeneticProfiles.getGeneticProfiles(cancerStudyId);

        //  Get all Patient Lists Associated with this Cancer Study ID.
        ArrayList<SampleList> sampleSetList = GetSampleLists.getSampleLists(cancerStudyId);

        //  Get the default patient set
        AnnotatedSampleSets annotatedSampleSets =
            new AnnotatedSampleSets(sampleSetList, dataTypePriority);
        SampleList defaultSampleSet = annotatedSampleSets.getDefaultSampleList();
        if (defaultSampleSet == null) {
          continue;
        }

        List<String> sampleIds = defaultSampleSet.getSampleList();

        //  Get the default genomic profiles
        CategorizedGeneticProfileSet categorizedGeneticProfileSet =
            new CategorizedGeneticProfileSet(geneticProfileList);
        HashMap<String, GeneticProfile> defaultGeneticProfileSet = null;
        switch (dataTypePriority) {
          case 2:
            defaultGeneticProfileSet = categorizedGeneticProfileSet.getDefaultCopyNumberMap();
            break;
          case 1:
            defaultGeneticProfileSet = categorizedGeneticProfileSet.getDefaultMutationMap();
            break;
          case 0:
          default:
            defaultGeneticProfileSet =
                categorizedGeneticProfileSet.getDefaultMutationAndCopyNumberMap();
        }

        String mutationProfile = "", cnaProfile = "";
        for (GeneticProfile geneticProfile : defaultGeneticProfileSet.values()) {
          GeneticAlterationType geneticAlterationType = geneticProfile.getGeneticAlterationType();
          if (geneticAlterationType.equals(GeneticAlterationType.COPY_NUMBER_ALTERATION)) {
            cnaProfile = geneticProfile.getStableId();
          } else if (geneticAlterationType.equals(GeneticAlterationType.MUTATION_EXTENDED)) {
            mutationProfile = geneticProfile.getStableId();
          }
        }

        cancerMap.put("mutationProfile", mutationProfile);
        cancerMap.put("cnaProfile", cnaProfile);

        cancerMap.put("caseSetId", defaultSampleSet.getStableId());
        cancerMap.put("caseSetLength", sampleIds.size());

        ProfileDataSummary genomicData =
            getGenomicData(
                cancerStudyId,
                defaultGeneticProfileSet,
                defaultSampleSet,
                geneList,
                sampleSetList,
                request,
                response);

        ArrayList<GeneWithScore> geneFrequencyList = genomicData.getGeneFrequencyList();
        ArrayList<String> genes = new ArrayList<String>();
        for (GeneWithScore geneWithScore : geneFrequencyList) genes.add(geneWithScore.getGene());
        int noOfMutated = 0,
            noOfCnaUp = 0,
            noOfCnaDown = 0,
            noOfCnaLoss = 0,
            noOfCnaGain = 0,
            noOfOther = 0,
            noOfAll = 0;

        boolean skipStudy = defaultGeneticProfileSet.isEmpty();
        if (!skipStudy) {

          for (String sampleId : sampleIds) {
            if (sampleId == null) {
              continue;
            }
            if (!genomicData.isCaseAltered(sampleId)) continue;

            boolean isAnyMutated = false,
                isAnyCnaUp = false,
                isAnyCnaDown = false,
                isAnyCnaLoss = false,
                isAnyCnaGain = false;

            for (String gene : genes) {
              isAnyMutated |= genomicData.isGeneMutated(gene, sampleId);
              GeneticTypeLevel cnaLevel = genomicData.getCNALevel(gene, sampleId);
              boolean isCnaUp = cnaLevel != null && cnaLevel.equals(GeneticTypeLevel.Amplified);
              isAnyCnaUp |= isCnaUp;
              boolean isCnaDown =
                  cnaLevel != null && cnaLevel.equals(GeneticTypeLevel.HomozygouslyDeleted);
              isAnyCnaDown |= isCnaDown;
              boolean isCnaLoss =
                  cnaLevel != null && cnaLevel.equals(GeneticTypeLevel.HemizygouslyDeleted);
              isAnyCnaLoss |= isCnaLoss;
              boolean isCnaGain = cnaLevel != null && cnaLevel.equals(GeneticTypeLevel.Gained);
              isAnyCnaGain |= isCnaGain;
            }

            boolean isAnyCnaChanged = isAnyCnaUp || isAnyCnaDown;
            if (isAnyMutated && !isAnyCnaChanged) noOfMutated++;
            else if (isAnyMutated && isAnyCnaChanged) noOfOther++;
            else if (isAnyCnaUp) noOfCnaUp++;
            else if (isAnyCnaDown) noOfCnaDown++;
            else if (isAnyCnaGain) noOfCnaGain++;
            else if (isAnyCnaLoss) noOfCnaLoss++;

            noOfAll++;
          }
        }

        Map alterations = new LinkedHashMap();
        cancerMap.put("alterations", alterations);
        alterations.put("all", noOfAll);
        alterations.put("mutation", noOfMutated);
        alterations.put("cnaUp", noOfCnaUp);
        alterations.put("cnaDown", noOfCnaDown);
        alterations.put("cnaLoss", noOfCnaLoss);
        alterations.put("cnaGain", noOfCnaGain);
        alterations.put("other", noOfOther);
        cancerMap.put("genes", genes);
        cancerMap.put("skipped", skipStudy);

        resultsList.add(cancerMap);
      }

      JSONValue.writeJSONString(resultsList, writer);
    } catch (DaoException e) {
      throw new ServletException(e);
    } catch (ProtocolException e) {
      throw new ServletException(e);
    } finally {
      writer.close();
    }
  }