/** * Grabs the appropriate stuff from a request and returns a list of case_ids * * @param request * @return * @throws ProtocolException * @throws DaoException */ public static ArrayList<String> getSampleIds(HttpServletRequest request) throws ProtocolException, DaoException { String samples = request.getParameter(WebService.CASE_LIST); String sampleSetId = request.getParameter(WebService.CASE_SET_ID); String sampleIdsKey = request.getParameter(WebService.CASE_IDS_KEY); if (sampleIdsKey != null) { samples = SampleSetUtil.getSampleIds(sampleIdsKey); } ArrayList<String> sampleList = new ArrayList<String>(); if (sampleSetId != null && !(sampleSetId.equals("-1"))) { DaoSampleList dao = new DaoSampleList(); SampleList selectedSampleList = dao.getSampleListByStableId(sampleSetId); if (selectedSampleList == null) { throw new ProtocolException( "Invalid " + WebService.CASE_SET_ID + ": " + sampleSetId + "."); } sampleList = selectedSampleList.getSampleList(); } else if (samples != null) { for (String _sample : samples.split("[\\s,]+")) { _sample = _sample.trim(); if (_sample.length() == 0) continue; sampleList.add(_sample); } } else if (samples != null) { // todo: this is a hack, samples is just another word for patients return new ArrayList(Arrays.asList(samples.split(" "))); } else { throw new ProtocolException( WebService.CASE_SET_ID + " or " + WebService.CASE_LIST + " must be specified."); } return sampleList; }
/** * Given an HttpServletRequest, determine all cancer_study_ids associated with it. cancer study * identifiers can be inferred from profile_ids, case_list_ids, or case_ids. this returns the set * of ALL POSSIBLE cancer study identifiers * * @param request * @return the cancer_study_ids associated with the request, which will be empty if none can be * determined; or empty set if a problem arises. * @throws DaoException * @throws ProtocolException */ public static HashSet<String> getCancerStudyIDs(HttpServletRequest request) throws DaoException, ProtocolException { HashSet<String> cancerStudies = new HashSet<String>(); // a CANCER_STUDY_ID is explicitly provided, as in getGeneticProfiles, getCaseLists, etc. // make sure the cancer_study_id provided in the request points to a real study String studyIDstring = getCancerStudyId(request); if (studyIDstring != null) { if (DaoCancerStudy.doesCancerStudyExistByStableId(studyIDstring)) { cancerStudies.add(studyIDstring); } return cancerStudies; } // a genetic_profile_id is explicitly provided, as in getProfileData if (null != request.getParameter(WebService.GENETIC_PROFILE_ID)) { ArrayList<String> geneticProfileIds = getGeneticProfileId(request); for (String geneticProfileId : geneticProfileIds) { // that's the point of this code?? // if (geneticProfileId == null) { // return cancerStudies; // } GeneticProfile aGeneticProfile = DaoGeneticProfile.getGeneticProfileByStableId(geneticProfileId); if (aGeneticProfile != null && DaoCancerStudy.doesCancerStudyExistByInternalId( aGeneticProfile.getCancerStudyId())) { cancerStudies.add( DaoCancerStudy.getCancerStudyByInternalId(aGeneticProfile.getCancerStudyId()) .getCancerStudyStableId()); } } return cancerStudies; } // a patient_set_id is explicitly provided, as in getProfileData, getMutationData, // getClinicalData, etc. String sampleSetId = request.getParameter(WebService.CASE_SET_ID); if (sampleSetId != null) { DaoSampleList aDaoSampleList = new DaoSampleList(); SampleList aSampleList = aDaoSampleList.getSampleListByStableId(sampleSetId); if (aSampleList != null && DaoCancerStudy.doesCancerStudyExistByInternalId(aSampleList.getCancerStudyId())) { cancerStudies.add( DaoCancerStudy.getCancerStudyByInternalId(aSampleList.getCancerStudyId()) .getCancerStudyStableId()); } return cancerStudies; } return cancerStudies; }