public ActionForward execute(
ActionMapping mapping,
ActionForm form,
HttpServletRequest request,
HttpServletResponse response)
throws Exception {
// The protein we're viewing
int proteinID;
// User making this request
User user = UserUtils.getUser(request);
if (user == null) {
ActionErrors errors = new ActionErrors();
errors.add("username", new ActionMessage("error.login.notloggedin"));
saveErrors(request, errors);
return mapping.findForward("authenticate");
}
NRProtein protein = null;
try {
String strID = request.getParameter("id");
if (strID == null || strID.equals("")) {
ActionErrors errors = new ActionErrors();
errors.add("protein", new ActionMessage("error.protein.invalidid"));
saveErrors(request, errors);
return mapping.findForward("Failure");
}
proteinID = Integer.parseInt(strID);
// Load our protein
NRProteinFactory nrpf = NRProteinFactory.getInstance();
protein = (NRProtein) (nrpf.getProtein(proteinID));
// Abundance information. Only for yeast
// Ghaemmaghami, et al., Nature 425, 737-741 (2003)
if (protein.getSpecies().getId() == TaxonomyUtils.SACCHAROMYCES_CEREVISIAE) {
List<YeastOrfAbundance> abundances =
ProteinAbundanceDao.getInstance().getAbundance(protein.getId());
if (abundances == null || abundances.size() == 0)
request.setAttribute("proteinAbundance", "NOT AVAILABLE");
else {
if (abundances.size() == 1) {
request.setAttribute("proteinAbundance", abundances.get(0).getAbundanceString());
} else {
String aString = "";
for (YeastOrfAbundance a : abundances) {
aString += ", " + a.getAbundanceAndOrfNameString();
}
aString = aString.substring(1);
request.setAttribute("proteinAbundance", aString);
}
}
}
} catch (NumberFormatException nfe) {
ActionErrors errors = new ActionErrors();
errors.add("protein", new ActionMessage("error.project.invalidid"));
saveErrors(request, errors);
return mapping.findForward("Failure");
} catch (Exception e) {
ActionErrors errors = new ActionErrors();
errors.add("username", new ActionMessage("error.project.projectnotfound"));
saveErrors(request, errors);
return mapping.findForward("Failure");
}
Map goterms = protein.getGOAll();
if (((Collection) goterms.get("P")).size() > 0)
request.setAttribute("processes", goterms.get("P"));
if (((Collection) goterms.get("C")).size() > 0)
request.setAttribute("components", goterms.get("C"));
if (((Collection) goterms.get("F")).size() > 0)
request.setAttribute("functions", goterms.get("F"));
// clean up
goterms = null;
YatesRunSearcher yrs = new YatesRunSearcher();
yrs.setProtein(protein);
Collection runs = yrs.search();
// Make sure only runs belonging to projects this user has access to are listed.
if (runs != null && runs.size() > 0) {
Iterator iter = runs.iterator();
while (iter.hasNext()) {
YatesRun yr = (YatesRun) (iter.next());
if (!yr.getProject().checkReadAccess(user.getResearcher())) iter.remove();
}
request.setAttribute("yatesdata", runs);
}
// Get the protein inference runs where this protein was listed
// This is a bit convoluted
// First get all the users' projects (projects the user has read access to)
ProjectsSearcher projSearcher = new ProjectsSearcher();
projSearcher.setResearcher(user.getResearcher());
List<Project> projects = projSearcher.search();
// List<Project> projects = user.getProjects();
List<Integer> pinferIds = new ArrayList<Integer>();
for (Project project : projects) {
List<Integer> experimentIds =
ProjectExperimentDAO.instance().getExperimentIdsForProject(project.getID());
for (int experimentId : experimentIds) {
List<ProteinferJob> piJobs =
ProteinInferJobSearcher.getInstance().getProteinferJobsForMsExperiment(experimentId);
for (ProteinferJob job : piJobs) {
pinferIds.add(job.getPinferId());
}
}
}
// We now have the protein inference runs for this user.
// Find out which one of then has the protein of interest.
List<ProteinferRun> piRuns = new ArrayList<ProteinferRun>(pinferIds.size());
ProteinferRunDAO piRunDao = ProteinferDAOFactory.instance().getProteinferRunDao();
ProteinferProteinDAO protDao = ProteinferDAOFactory.instance().getProteinferProteinDao();
ArrayList<Integer> nrseqIds = new ArrayList<Integer>(1);
nrseqIds.add(proteinID);
for (int pinferId : pinferIds) {
if (protDao.getProteinIdsForNrseqIds(pinferId, nrseqIds).size() > 0) {
ProteinferRun piRun = piRunDao.loadProteinferRun(pinferId);
piRuns.add(piRun);
}
}
request.setAttribute("piRuns", piRuns);
// Set this project in the request, as a bean to be displayed on the view
request.setAttribute("protein", protein);
return mapping.findForward("Success");
}
public ActionForward execute(
ActionMapping mapping,
ActionForm form,
HttpServletRequest request,
HttpServletResponse response)
throws Exception {
log.info("Got request for GO Slim analysis for ProtenProphet protein inference");
// form for filtering and display options
ProteinProphetFilterForm filterForm = (ProteinProphetFilterForm) form;
// get the protein inference id
int pinferId = filterForm.getPinferId();
long s = System.currentTimeMillis();
// Get the peptide definition; We don't get peptide definition from ProteinProphet params so
// just
// use a dummy one.
PeptideDefinition peptideDef = new PeptideDefinition();
peptideDef.setUseCharge(true);
peptideDef.setUseMods(true);
// filtering criteria from the request
ProteinProphetFilterCriteria filterCriteria_request = filterForm.getFilterCriteria(peptideDef);
// protein Ids
List<Integer> proteinIds = null;
ProteinInferSessionManager sessionManager = ProteinInferSessionManager.getInstance();
// Check if we already have information in the session
ProteinProphetFilterCriteria filterCriteria_session =
sessionManager.getFilterCriteriaForProteinProphet(request, pinferId);
proteinIds = sessionManager.getStoredProteinIds(request, pinferId);
// If we don't have a filtering criteria in the session return an error
if (filterCriteria_session == null || proteinIds == null) {
log.info("NO information in session for: " + pinferId);
// redirect to the /viewProteinInferenceResult action if this different from the
// protein inference ID stored in the session
log.error("Stale ProteinProphet ID: " + pinferId);
response.setContentType("text/html");
response.getWriter().write("STALE_ID");
return null;
} else {
log.info("Found information in session for: " + pinferId);
System.out.println("stored protein ids: " + proteinIds.size());
// we will use the sorting column and sorting order from the filter criteria in the session.
filterCriteria_request.setSortBy(filterCriteria_session.getSortBy());
filterCriteria_request.setSortOrder(filterCriteria_session.getSortOrder());
boolean match = matchFilterCriteria(filterCriteria_session, filterCriteria_request);
// if the filtering criteria has changed we need to filter the results again
if (!match) {
log.info("Filtering criteria has changed");
proteinIds = ProteinProphetResultsLoader.getProteinIds(pinferId, filterCriteria_request);
}
}
long e = System.currentTimeMillis();
log.info(
"Got filtered nrseq protein ids for GO Slim analysis in: "
+ TimeUtils.timeElapsedMinutes(s, e)
+ " minutes");
request.setAttribute("pinferId", pinferId);
request.setAttribute("goAspect", filterForm.getGoAspect());
request.setAttribute("goSlimTermId", filterForm.getGoSlimTermId());
if (filterForm.isGetGoSlimTree()) {
// We have the protein inference protein IDs; Get the corresponding nrseq protein IDs
List<Integer> nrseqIds = new ArrayList<Integer>(proteinIds.size());
ProteinferDAOFactory factory = ProteinferDAOFactory.instance();
ProteinferProteinDAO protDao = factory.getProteinferProteinDao();
for (int proteinId : proteinIds) {
ProteinferProtein protein = protDao.loadProtein(proteinId);
nrseqIds.add(protein.getNrseqProteinId());
}
request.setAttribute("nrseqProteinIds", nrseqIds);
return mapping.findForward("GoTree");
} else {
// We have the protein inference protein IDs; Get the corresponding nrseq protein IDs and
// protein group IDs
List<GOAnalysisProtein> goAnalysisProteins =
new ArrayList<GOAnalysisProtein>(proteinIds.size());
ProteinferDAOFactory factory = ProteinferDAOFactory.instance();
ProteinProphetProteinDAO protDao = factory.getProteinProphetProteinDao();
for (int proteinId : proteinIds) {
ProteinProphetProtein protein = protDao.loadProtein(proteinId);
goAnalysisProteins.add(
new GOAnalysisProtein(protein.getNrseqProteinId(), protein.getGroupId()));
}
request.setAttribute("goSlimProteins", goAnalysisProteins);
request.setAttribute(
"doGroupAnalysis", true); // default is to get GO information at the group level
return mapping.findForward("Success");
}
}