Exemplo n.º 1
0
  /** Gets all Genomic Data. */
  private ProfileDataSummary getGenomicData(
      String cancerStudyId,
      HashMap<String, GeneticProfile> defaultGeneticProfileSet,
      SampleList defaultSampleSet,
      String geneListStr,
      ArrayList<SampleList> sampleList,
      HttpServletRequest request,
      HttpServletResponse response)
      throws IOException, ServletException, DaoException {

    // parse geneList, written in the OncoPrintSpec language (except for changes by XSS clean)
    double zScore =
        ZScoreUtil.getZScore(
            new HashSet<String>(defaultGeneticProfileSet.keySet()),
            new ArrayList<GeneticProfile>(defaultGeneticProfileSet.values()),
            request);
    double rppaScore = ZScoreUtil.getRPPAScore(request);

    ParserOutput theOncoPrintSpecParserOutput =
        OncoPrintSpecificationDriver.callOncoPrintSpecParserDriver(
            geneListStr,
            new HashSet<String>(defaultGeneticProfileSet.keySet()),
            new ArrayList<GeneticProfile>(defaultGeneticProfileSet.values()),
            zScore,
            rppaScore);

    ArrayList<String> geneList = new ArrayList<String>();
    geneList.addAll(theOncoPrintSpecParserOutput.getTheOncoPrintSpecification().listOfGenes());

    ArrayList<ProfileData> profileDataList = new ArrayList<ProfileData>();
    Set<String> warningUnion = new HashSet<String>();

    for (GeneticProfile profile : defaultGeneticProfileSet.values()) {
      try {
        GetProfileData remoteCall =
            new GetProfileData(
                profile, geneList, StringUtils.join(defaultSampleSet.getSampleList(), " "));
        ProfileData pData = remoteCall.getProfileData();
        warningUnion.addAll(remoteCall.getWarnings());
        profileDataList.add(pData);
      } catch (IllegalArgumentException e) {
        e.getStackTrace();
      }
    }

    ProfileMerger merger = new ProfileMerger(profileDataList);
    ProfileData mergedProfile = merger.getMergedProfile();

    ProfileDataSummary dataSummary =
        new ProfileDataSummary(
            mergedProfile,
            theOncoPrintSpecParserOutput.getTheOncoPrintSpecification(),
            zScore,
            rppaScore);
    return dataSummary;
  }
Exemplo n.º 2
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());
  }