private void setGeneticProfiles(HttpServletRequest request) throws DaoException {
CancerStudy cancerStudy = (CancerStudy) request.getAttribute(CANCER_STUDY);
GeneticProfile mutProfile = cancerStudy.getMutationProfile();
if (mutProfile != null) {
request.setAttribute(MUTATION_PROFILE, mutProfile);
}
GeneticProfile cnaProfile = cancerStudy.getCopyNumberAlterationProfile(true);
if (cnaProfile != null) {
request.setAttribute(CNA_PROFILE, cnaProfile);
}
}
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;
}
/**
* Test importing of Clinical Data File.
*
* @throws DaoException Database Access Error.
* @throws IOException IO Error.
*/
@Test
@Ignore("To be fixed")
public void testImportClinicalDataSurvival() 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();
LinkedHashSet<String> caseSet = new LinkedHashSet<String>();
caseSet.add("TCGA-A1-A0SB");
caseSet.add("TCGA-A1-A0SI");
caseSet.add("TCGA-A1-A0SE");
List<Patient> clinicalCaseList =
DaoClinicalData.getSurvivalData(study.getInternalId(), caseSet);
assertEquals(3, clinicalCaseList.size());
Patient clinical0 = clinicalCaseList.get(0);
assertEquals(new Double(79.04), clinical0.getAgeAtDiagnosis());
assertEquals("DECEASED", clinical0.getOverallSurvivalStatus());
assertEquals("Recurred/Progressed", clinical0.getDiseaseFreeSurvivalStatus());
assertEquals(new Double(43.8), clinical0.getOverallSurvivalMonths());
assertEquals(new Double(15.05), clinical0.getDiseaseFreeSurvivalMonths());
Patient clinical1 = clinicalCaseList.get(1);
assertEquals(new Double(55.53), clinical1.getAgeAtDiagnosis());
assertEquals("LIVING", clinical1.getOverallSurvivalStatus());
assertEquals("DiseaseFree", clinical1.getDiseaseFreeSurvivalStatus());
assertEquals(new Double(49.02), clinical1.getOverallSurvivalMonths());
assertEquals(new Double(49.02), clinical1.getDiseaseFreeSurvivalMonths());
Patient clinical2 = clinicalCaseList.get(2);
assertEquals(null, clinical2.getDiseaseFreeSurvivalMonths());
}
public static CancerStudy loadCancerStudy(File file, boolean strict, boolean addStudyToDb)
throws IOException, DaoException {
TrimmedProperties properties = new TrimmedProperties();
properties.load(new FileInputStream(file));
CancerStudy cancerStudy = getCancerStudy(properties);
if (strict && null == DaoTypeOfCancer.getTypeOfCancerById(cancerStudy.getTypeOfCancerId())) {
throw new IllegalArgumentException(
cancerStudy.getTypeOfCancerId() + " is not a supported cancer type.");
}
if (addStudyToDb) {
DaoCancerStudy.addCancerStudy(cancerStudy, true); // overwrite if exist
}
return cancerStudy;
}
/**
* 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());
}
private static CancerStudy getCancerStudy(TrimmedProperties properties) {
String cancerStudyIdentifier = properties.getProperty("cancer_study_identifier");
if (cancerStudyIdentifier == null) {
throw new IllegalArgumentException("cancer_study_identifier is not specified.");
}
String name = properties.getProperty("name");
if (name == null) {
throw new IllegalArgumentException("name is not specified.");
}
String description = properties.getProperty("description");
if (description == null) {
throw new IllegalArgumentException("description is not specified.");
}
String typeOfCancer = properties.getProperty("type_of_cancer").toLowerCase();
if (typeOfCancer == null) {
throw new IllegalArgumentException("type of cancer is not specified.");
}
String shortName = properties.getProperty("short_name");
if (shortName == null) {
throw new IllegalArgumentException("short_name is not specified.");
}
CancerStudy cancerStudy =
new CancerStudy(
name, description, cancerStudyIdentifier, typeOfCancer, publicStudy(properties));
cancerStudy.setPmid(properties.getProperty("pmid"));
cancerStudy.setCitation(properties.getProperty("citation"));
cancerStudy.setGroupsInUpperCase(properties.getProperty("groups"));
cancerStudy.setShortName(shortName);
return cancerStudy;
}
/**
* Test importing of Clinical Data File.
*
* @throws DaoException Database Access Error.
* @throws IOException IO Error.
*/
@Test
@Ignore("To be fixed")
public void testImportClinicalDataSlice() 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();
List<ClinicalParameterMap> slice =
DaoClinicalData.getDataSlice(study.getInternalId(), Arrays.asList("PLATINUMSTATUS"));
assertTrue(slice.size() >= 1);
ClinicalParameterMap paramMap = slice.get(0);
assertEquals("PLATINUMSTATUS", paramMap.getName());
assertEquals("Sensitive", paramMap.getValue("TCGA-A1-A0SD"));
assertEquals("NA", paramMap.getValue("TCGA-A1-A0SE"));
assertEquals(2, paramMap.getDistinctCategories().size());
}
private void processRequestStatistics(
HttpServletRequest request, HttpServletResponse response, String type)
throws ServletException, IOException {
String cancerStudyIds = request.getParameter(QueryBuilder.CANCER_STUDY_ID);
try {
boolean includeMut = "mut".equalsIgnoreCase(type);
boolean includeCna = "cna".equalsIgnoreCase(type);
Map<String, Map<String, Object>> data = new HashMap<String, Map<String, Object>>();
// get list of cancer studies
AccessControl accessControl = getaccessControl();
List<CancerStudy> cancerStudies;
if (cancerStudyIds == null || cancerStudyIds.isEmpty()) {
cancerStudies = accessControl.getCancerStudies();
} else {
cancerStudies = new ArrayList<CancerStudy>();
for (String studyId : cancerStudyIds.split("[ ,]+")) {
CancerStudy study = DaoCancerStudy.getCancerStudyByStableId(studyId);
if (study != null && !accessControl.isAccessibleCancerStudy(studyId).isEmpty()) {
cancerStudies.add(study);
}
}
}
for (CancerStudy cancerStudy : cancerStudies) {
if (cancerStudy.getCancerStudyStableId().equalsIgnoreCase("all")) {
continue;
}
Map<String, Object> row = new HashMap<String, Object>();
data.put(cancerStudy.getCancerStudyStableId(), row);
if (!includeMut && !includeMut) {
row.put("name", cancerStudy.getName());
String pmid = cancerStudy.getPmid();
if (pmid != null) {
row.put("pmid", pmid);
}
String citation = cancerStudy.getCitation();
if (citation != null) {
row.put("citation", citation);
}
row.put(
"cases", DaoPatient.getPatientsByCancerStudyId(cancerStudy.getInternalId()).size());
}
if (includeMut) {
GeneticProfile mutProfile = cancerStudy.getMutationProfile();
if (mutProfile == null) {
row.put("mut", 0);
} else {
int mutEvents = DaoMutation.countMutationEvents(mutProfile.getGeneticProfileId());
int samplesWithMut =
DaoSampleProfile.countSamplesInProfile(mutProfile.getGeneticProfileId());
row.put("mut", 1.0 * mutEvents / samplesWithMut);
}
}
if (includeCna) {
GeneticProfile cnaProfile = cancerStudy.getCopyNumberAlterationProfile(false);
if (cnaProfile == null) {
row.put("cna", 0);
} else {
List<Integer> samples =
DaoSampleProfile.getAllSampleIdsInProfile(cnaProfile.getGeneticProfileId());
Map<Integer, Double> fracs =
DaoCopyNumberSegment.getCopyNumberActeredFraction(
samples,
cnaProfile.getCancerStudyId(),
GlobalProperties.getPatientViewGenomicOverviewCnaCutoff()[0]);
double aveFrac = 0;
for (double frac : fracs.values()) {
aveFrac += frac;
}
aveFrac /= samples.size();
row.put("cna", aveFrac);
}
}
}
response.setContentType("application/json");
PrintWriter out = response.getWriter();
try {
JSONValue.writeJSONString(data, out);
} finally {
out.close();
}
} catch (DaoException ex) {
throw new ServletException(ex);
} catch (ProtocolException ex) {
throw new ServletException(ex);
}
}
/**
* 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();
}
}