/**
* 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;
}
public static void main(String[] args) throws Exception {
ProgressMonitor.setConsoleMode(true);
DaoSampleList daoSampleList = new DaoSampleList();
ArrayList<SampleList> sampleListMaster = daoSampleList.getAllSampleLists();
for (SampleList sampleList : sampleListMaster) {
System.out.println(
sampleList.getSampleListId()
+ ": "
+ sampleList.getStableId()
+ ": "
+ sampleList.getName());
}
}
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;
}
/** 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;
}
/**
* 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();
}
}