/**
* 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;
}
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;
}
