public ActionForward setup(
ActionMapping mapping,
ActionForm form,
HttpServletRequest request,
HttpServletResponse response)
throws Exception {
GpIntegrationForm gpForm = (GpIntegrationForm) form;
/*setup the defined Disease query names and the list of samples selected from a Resultset*/
ClinicalGroupRetriever clinicalGroupRetriever =
new ClinicalGroupRetriever(request.getSession());
gpForm.setExistingGroupsList(clinicalGroupRetriever.getClinicalGroupsCollection());
UserListBeanHelper listHelper = new UserListBeanHelper(request.getSession());
// fetch the users gene groups populate the dropdown
List<String> names = (List<String>) listHelper.getGenericListNames(ListType.Gene);
List<LabelValueBean> gsNameList = new ArrayList<LabelValueBean>();
for (String listName : names) {
gsNameList.add(new LabelValueBean(listName, listName));
}
gpForm.setGeneSetNameList(gsNameList);
return mapping.findForward("success");
}
private ISPYGPIntegrationQueryDTO createGPIntegrationQueryDTO(
GpIntegrationForm gpQueryForm, HttpSession session) {
ISPYGPIntegrationQueryDTO gpQueryDTO =
(ISPYGPIntegrationQueryDTO)
ApplicationFactory.newQueryDTO(QueryType.PROBESET_CLONEID_QUERY_FOR_HOA);
gpQueryDTO.setQueryName(gpQueryForm.getAnalysisResultName());
HashMap<String, UserList> patientLists = new HashMap<String, UserList>();
HashMap<String, Set<TimepointType>> timepointLists = new HashMap<String, Set<TimepointType>>();
UserListBeanHelper listHelper = new UserListBeanHelper(session);
String groupTimepoint = null;
String groupName = null;
String timePointName = null;
if (gpQueryForm.getSelectedGroups() != null && gpQueryForm.getSelectedGroups().length > 0) {
for (int i = 0; i < gpQueryForm.getSelectedGroups().length; i++) {
groupTimepoint = gpQueryForm.getSelectedGroups()[i];
int index = groupTimepoint.lastIndexOf("---");
groupName = groupTimepoint.substring(0, index);
timePointName = groupTimepoint.substring(index + 3);
UserList userList = listHelper.getUserList(groupName);
patientLists.put(groupTimepoint, userList);
String[] times = timePointName.split("-");
String fixedTimepointString = null;
Set<TimepointType> set = new HashSet<TimepointType>();
for (String time : times) {
TimepointType fixedTimepointBase; // timepoint for both queryDTOs
fixedTimepointString = EnumHelper.getEnumTypeName(time, TimepointType.values());
if (fixedTimepointString != null) {
fixedTimepointBase = TimepointType.valueOf(fixedTimepointString);
set.add(fixedTimepointBase);
}
}
timepointLists.put(groupTimepoint, set);
}
}
gpQueryDTO.setPatientLists(patientLists);
gpQueryDTO.setTimepointLists(timepointLists);
// UserListBeanHelper listHelper = new UserListBeanHelper(session);
if (gpQueryForm.getGeneSetName() != null
&& (!gpQueryForm.getGeneSetName().equals("")
&& !gpQueryForm.getGeneSetName().equals("none"))) {
geneIdentifierDECollection = listHelper.getGeneDEforList(gpQueryForm.getGeneSetName());
if (geneIdentifierDECollection != null && !geneIdentifierDECollection.isEmpty()) {
logger.debug("geneIdentifierDECollection was found");
gpQueryDTO.setGeneIdentifierDEs(geneIdentifierDECollection);
gpQueryDTO.setReportersName(gpQueryForm.getGeneSetName());
} else {
logger.debug("geneIdentifierDECollection could not be found");
}
}
// Create arrayPlatfrom DEs
if (gpQueryForm.getArrayPlatform() != "" || gpQueryForm.getArrayPlatform().length() != 0) {
ArrayPlatformDE arrayPlatformDE = new ArrayPlatformDE(gpQueryForm.getArrayPlatform());
gpQueryDTO.setArrayPlatformDE(arrayPlatformDE);
}
return gpQueryDTO;
}
/**
* Method submittal
*
* @param ActionMapping mapping
* @param ActionForm form
* @param HttpServletRequest request
* @param HttpServletResponse response
* @return ActionForward
* @throws Exception
*/
public ActionForward submit(
ActionMapping mapping,
ActionForm form,
HttpServletRequest request,
HttpServletResponse response)
throws Exception {
GpIntegrationForm gpForm = (GpIntegrationForm) form;
String sessionId = request.getSession().getId();
HttpSession session = request.getSession();
ISPYGPIntegrationQueryDTO ispyGPIntegrationQueryDTO =
createGPIntegrationQueryDTO(gpForm, session);
// to filter id with time points
ISPYFindingsFactory findingFactory = new ISPYFindingsFactory();
try {
findingFactory.createGPIntegrationSampleIds(ispyGPIntegrationQueryDTO, sessionId);
} catch (FrameworkException fwe) {
logger.error(fwe.getMessage());
fwe.printStackTrace();
}
SampleGroup[] sampleGroups = ispyGPIntegrationQueryDTO.getSampleGroups();
// Now let's check id overlapping problem.
if (isIdOverlap(sampleGroups)) {
ActionErrors errors = new ActionErrors();
errors.add(
"selectedGroups1",
new ActionMessage("gov.nih.nci.nautilus.ui.struts.form.groups.intersect.error"));
this.saveErrors(request, errors);
return setup(mapping, form, request, response);
}
List<List<String>> allStringList = new ArrayList<List<String>>();
List<String> fileNameList = new ArrayList<String>();
List<String> idStringList = new ArrayList<String>();
List<String> reportIdStringList = new ArrayList<String>();
String gpModule = System.getProperty("gov.nih.nci.caintegrator.gp.modulename");
String analysisResultName =
(gpForm.getAnalysisResultName() != null && !gpForm.getAnalysisResultName().equals(""))
? (String) gpForm.getAnalysisResultName()
: "unnamed_task";
// for sample Id file
for (SampleGroup sampleGroup : sampleGroups) {
idStringList.add(getIdsAsDelimitedString(sampleGroup, "\t"));
}
allStringList.add(idStringList);
fileNameList.add("labIdsFile");
// for reporter id file
ReporterGroup reporterGroup = ispyGPIntegrationQueryDTO.getReporterGroup();
if (reporterGroup != null && reporterGroup.size() > 0) {
reportIdStringList.add(getIdsAsDelimitedString(reporterGroup, "\t"));
allStringList.add(reportIdStringList);
fileNameList.add("reproterIdsFile");
} else {
reportIdStringList.add("reporter=NONE");
allStringList.add(reportIdStringList);
fileNameList.add("reproterIdsFile");
}
// For class file
// makeClassFile(classStringList, sampleGroups);
// allStringList.add(classStringList);
// fileNameList.add("ispyClassFile");
// Now let's write them to files
List<String> filePathList = new ArrayList<String>();
writeGPFile(filePathList, allStringList, fileNameList);
// Now get the R-binary file name:
String r_fileName = null;
String a_fileName = null;
if (ispyGPIntegrationQueryDTO.getArrayPlatformDE().getValueObjectAsArrayPlatformType()
== ArrayPlatformType.AGILENT) {
r_fileName = System.getProperty("gov.nih.nci.ispyportal.agilent_data_matrix");
a_fileName = System.getProperty("gov.nih.nci.ispyportal.agilent_data_annotation");
} else {
r_fileName = System.getProperty("gov.nih.nci.ispyportal.cdna_data_matrix");
a_fileName = System.getProperty("gov.nih.nci.ispyportal.cdna_data_annotation");
}
// *** RUN TASK ON THE GP SERVER
String tid = "209";
String gpserverURL =
System.getProperty("gov.nih.nci.caintegrator.gp.server") != null
? (String) System.getProperty("gov.nih.nci.caintegrator.gp.server")
: "localhost:8080"; // default to localhost
try {
String ispyUser = (String) session.getAttribute("name");
String publicUser = System.getProperty("gov.nih.nci.caintegrator.gp.publicuser.name");
String password = System.getProperty("gov.nih.nci.caintegrator.gp.publicuser.password");
// Check to see the user is already created otherwise create one.
GPServer gpServer = null;
if (ispyUser.equals(publicUser)) {
String gpUser = (String) session.getAttribute(GenePatternPublicUserPool.PUBLIC_USER_NAME);
if (gpUser == null) {
PublicUserPool pool = GenePatternPublicUserPool.getInstance();
gpUser = pool.borrowPublicUser();
session.setAttribute(GenePatternPublicUserPool.PUBLIC_USER_NAME, gpUser);
session.setAttribute(GenePatternPublicUserPool.PUBLIC_USER_POOL, pool);
}
ispyUser = gpUser;
}
String encryptKey = System.getProperty("gov.nih.nci.caintegrator.gp.desencrypter.key");
String urlString = EncryptionUtil.encrypt(ispyUser + gpPoolString, encryptKey);
urlString = URLEncoder.encode(urlString, "UTF-8");
String ticketString = gpserverURL + "gp?ticket=" + urlString;
logger.debug(ticketString);
URL url;
try {
url = new java.net.URL(ticketString);
URLConnection conn = url.openConnection();
final int size = conn.getContentLength();
logger.debug(Integer.toString(size));
} catch (Exception e) {
logger.error(e.getMessage());
}
gpServer = new GPServer(gpserverURL, ispyUser, password);
// GPServer gpServer = new GPServer(gpserverURL, gpuname, password);
Parameter[] par = new Parameter[filePathList.size() + 3 + 3];
int currpos = 1;
for (int i = 0; i < filePathList.size(); i++) {
par[i] = new Parameter("input.filename" + currpos++, filePathList.get(i));
}
par[--currpos] = new Parameter("project.name", "ispy");
// r_fileName = "'/usr/local/genepattern/resources/DataMatrix_ISPY_306cDNA_17May07.Rda'";
par[++currpos] = new Parameter("array.filename", r_fileName);
par[++currpos] = new Parameter("annotation.filename", a_fileName);
par[++currpos] = new Parameter("analysis.name", analysisResultName);
// always just 2
par[++currpos] = new Parameter("output.cls.file", analysisResultName + ".cls");
par[++currpos] = new Parameter("output.gct.file", analysisResultName + ".gct");
// JobResult preprocess = gpServer.runAnalysis(gpModule, par);
int nowait = gpServer.runAnalysisNoWait(gpModule, par);
tid = String.valueOf(nowait);
request.setAttribute("jobId", tid);
request.setAttribute("gpStatus", "running");
session.setAttribute("genePatternServer", gpServer);
request.setAttribute("genePatternURL", ticketString);
request.getSession().setAttribute("gptid", tid);
request.getSession().setAttribute("gpUserId", ispyUser);
request.getSession().setAttribute("ticketString", ticketString);
GPTask gpTask = new GPTask(tid, analysisResultName, FindingStatus.Running);
PresentationTierCache _cacheManager = ApplicationFactory.getPresentationTierCache();
_cacheManager.addNonPersistableToSessionCache(
request.getSession().getId(), "latestGpTask", (Serializable) gpTask);
} catch (Exception e) {
StringWriter sw = new StringWriter();
PrintWriter pw = new PrintWriter(sw);
e.printStackTrace(pw);
logger.error(sw.toString());
logger.error(gpModule + " failed...." + e.getMessage());
throw new Exception(e.getMessage());
}
return mapping.findForward("viewJob");
}