/** 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;
}
private String getShortcutScript(HashMap<String, String> usedButtonShortCuts) {
StringBuffer shortcuts = new StringBuffer();
shortcuts.append(" function buttonListShorcuts() {\n");
Iterator<String> ik = usedButtonShortCuts.keySet().iterator();
Iterator<String> iv = usedButtonShortCuts.values().iterator();
while (ik.hasNext() && iv.hasNext()) {
shortcuts
.append(" keyArray[keyArray.length] = new keyArrayItem(\"")
.append(ik.next())
.append("\", \"")
.append(iv.next())
.append("\", null, \"altKey\", false, \"onkeydown\");\n");
}
shortcuts.append(" return true;\n}");
return shortcuts.toString();
}
public LDAPolicy(String[] serverAddresses) {
super(serverAddresses);
numberOfServers = serverAddresses.length;
serverRequests = new int[numberOfServers];
// System.out.println("Loading input data from "+localPath);
servletNameToClusterIds =
(HashMap<String, Integer>)
DataReader.loadSerializedObject(localPath + "servletNameToClusterId.serialized");
methodHashCodesToClusterIds =
(HashMap<Integer, Integer>)
DataReader.loadSerializedObject(localPath + "hashCodesToClusterIds.serialized");
if (servletNameToClusterIds != null && methodHashCodesToClusterIds != null) {
for (String s : servletNameToClusterIds.keySet()) {
// System.out.println("Servlet["+s+"] in
// cluster["+methodHashCodesToClusterIds.get(s.hashCode())+"]");
}
} else {
throw new Error(
"Could not load properly the load balancing input data. Terminating application");
}
}