/** 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;
}
// Process the request
private String processRequest(HttpServletRequest request, HttpServletResponse response) {
HttpSession session = request.getSession();
String userIDs = (String) session.getAttribute("user.id");
userIDs = (userIDs != null && userIDs.compareTo(" ") > 0) ? userIDs : "0";
long userID = Long.parseLong(userIDs);
String command = request.getParameter("command");
String template = request.getParameter("template");
String pageHash = request.getParameter("pagehash");
String pageTitle = request.getParameter("pagetitle");
String pageDescription = request.getParameter("pagedescription");
String outLine = "";
String nextScript = request.getParameter("nextscript");
OutputStream toClient;
boolean success = false;
// System.out.println("userid=" + userID + ", id=" + id + ", command=" + command);
command = (command != null && command.compareTo(" ") > 0) ? command : "form";
nextScript = (nextScript != null && nextScript.compareTo(" ") > 0) ? nextScript : "simple1.jsp";
// inputstring = (inputstring != null && inputstring.compareTo(" ") > 0) ? inputstring : "";
DbConn myConn = null;
try {
Context initCtx = new InitialContext();
// String csiSchema = (String) initCtx.lookup("java:comp/env/csi-schema-path");
// String acronym = (String) initCtx.lookup("java:comp/env/SystemAcronym");
myConn = new DbConn();
String csiSchema = myConn.getSchemaPath();
if (userID != 0) {
if (command.equals("add")) {
outLine = "";
} else if (command.equals("update")) {
outLine = "";
} else if (command.equals("updatepage")) {
UHash uPage = new UHash(pageHash, myConn);
// System.out.println("Got Here 1");
if (template.equals("simple1")) {
TextItem title = new TextItem(uPage.get("title"), myConn);
title.setText(pageTitle);
title.save(myConn);
TextItem description = new TextItem(uPage.get("description"), myConn);
description.setText(pageDescription);
description.save(myConn);
} else if (template.equals("simple2")) {
}
} else if (command.equals("test")) {
outLine = "test";
}
success = true;
}
} catch (IllegalArgumentException e) {
outLine = outLine + "IllegalArgumentException caught: " + e.getMessage();
ALog.logActivity(userID, "csi", 0, pageHash + " error: '" + outLine + "'");
// log(outLine);
} catch (NullPointerException e) {
outLine = outLine + "NullPointerException caught: " + e.getMessage();
ALog.logActivity(userID, "csi", 0, pageHash + " error: '" + outLine + "'");
// log(outLine);
}
// catch (IOException e) {
// outLine = outLine + "IOException caught: " + e.getMessage();
// ALog.logActivity(userID, "csi", 0, pageHash + " error: '" + outLine + "'");
// //log(outLine);
// }
catch (Exception e) {
outLine = outLine + "Exception caught: " + e.getMessage();
ALog.logActivity(userID, "csi", 0, pageHash + " error: '" + outLine + "'");
// log(outLine);
} finally {
try {
generateResponse(outLine, command, nextScript, success, response);
} catch (Exception i) {
}
myConn.release();
// log("Test log message\n");
}
return outLine;
}
// Process the request
private String processRequest(HttpServletRequest request, HttpServletResponse response) {
String command = request.getParameter("command");
String id = request.getParameter("id");
String description = request.getParameter("description");
String status = request.getParameter("rstatus");
status = (status != null && status.compareTo(" ") > 0) ? status : null;
String outLine = "";
// String nextScript = "home.jsp";
String nextScript = request.getParameter("nextscript");
OutputStream toClient;
HttpSession session = request.getSession();
boolean success = false;
String userIDs = (String) session.getAttribute("user.id");
long userID = Long.parseLong(userIDs);
command = (command != null && command.compareTo(" ") > 0) ? command : "form";
nextScript = (nextScript != null && nextScript.compareTo(" ") > 0) ? nextScript : "roles.jsp";
// inputstring = (inputstring != null && inputstring.compareTo(" ") > 0) ? inputstring : "";
DbConn myConn = null;
try {
Context initCtx = new InitialContext();
// String csiSchema = (String) initCtx.lookup("java:comp/env/csi-schema-path");
String acronym = (String) initCtx.lookup("java:comp/env/SystemAcronym");
myConn = new DbConn();
String csiSchema = myConn.getSchemaPath();
if (command.equals("add")) {
Role item = new Role();
item.setDescription(description);
item.setStatus(status);
getPermissions(request, item);
getPositions(request, item);
item.add(myConn, userID);
GlobalMembership.refresh(myConn);
success = true;
outLine = "";
} else if (command.equals("update")) {
Role item = new Role(myConn, Long.parseLong(id));
item.setDescription(description);
item.setStatus(status);
getPermissions(request, item);
getPositions(request, item);
item.save(myConn, userID);
GlobalMembership.refresh(myConn);
success = true;
outLine = "";
} else if (command.equals("drop")) {
Role item = new Role(myConn, Long.parseLong(id));
item.drop(myConn, userID);
success = true;
outLine = "Role " + item.getDescription() + " Removed";
} else if (command.equals("test")) {
outLine = "test";
}
} catch (IllegalArgumentException e) {
outLine = outLine + "IllegalArgumentException caught: " + e.getMessage();
ALog.logActivity(userID, "csi", 0, "Role error: '" + outLine + "'");
// log(outLine);
} catch (NullPointerException e) {
outLine = outLine + "NullPointerException caught: " + e.getMessage();
ALog.logActivity(userID, "csi", 0, "Role error: '" + outLine + "'");
// log(outLine);
}
// catch (IOException e) {
// outLine = outLine + "IOException caught: " + e.getMessage();
// ALog.logActivity(userID, "csi", 0, "Role error: '" + outLine + "'");
// //log(outLine);
// }
catch (Exception e) {
outLine = outLine + "Exception caught: " + e.getMessage();
ALog.logActivity(userID, "csi", 0, "Role error: '" + outLine + "'");
// log(outLine);
} finally {
try {
generateResponse(outLine, command, nextScript, success, response);
} catch (Exception i) {
}
myConn.release();
// log("Test log message\n");
}
return outLine;
}