/** 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; }
/** * 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()); }