/** 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());
}