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;
}
/**
* Processes requests for both HTTP <code>GET</code> and <code>POST</code> methods.
*
* @param request servlet request
* @param response servlet response
* @throws ServletException if a servlet-specific error occurs
* @throws IOException if an I/O error occurs
*/
protected void processRequest(HttpServletRequest request, HttpServletResponse response)
throws ServletException, IOException {
XDebug xdebug = new XDebug(request);
request.setAttribute(QueryBuilder.XDEBUG_OBJECT, xdebug);
try {
if (validate(request)) {
setGeneticProfiles(request);
}
if (request.getAttribute(ERROR) != null) {
forwardToErrorPage(request, response, (String) request.getAttribute(ERROR), xdebug);
} else {
RequestDispatcher dispatcher =
getServletContext().getRequestDispatcher("/WEB-INF/jsp/dashboard/dashboard.jsp");
dispatcher.forward(request, response);
}
} catch (DaoException e) {
xdebug.logMsg(this, "Got Database Exception: " + e.getMessage());
forwardToErrorPage(
request, response, "An error occurred while trying to connect to the database.", xdebug);
}
}