/**
* Returns the ID of ONE of the groups the user is a member of. If the user is an administrator,
* the ID of the "administrators" group is returned. If the user is not a member of any group, 0
* is returned
*
* @param user
* @return
* @throws SQLException
*/
public static int getOneGroupId(User user) throws SQLException {
Groups groups = Groups.getInstance();
// If the user is an administrator return the ID of the administrators group
if (groups.isMember(user.getResearcher().getID(), "administrators"))
return groups.getGroupID("administrators");
// Otherwise get a list of groups that this user is a member of. Returns the
// ID of the first group.
List<String> groupMemberships = groups.getUserGroups(user.getResearcher().getID());
if (groupMemberships != null && groupMemberships.size() > 0)
return groups.getGroupID(groupMemberships.get(0));
// If the user is not a member of any group return 0
return 0;
}
public static List<Integer> getAllGroupIds(User user) throws SQLException {
Groups groups = Groups.getInstance();
List<Integer> groupIds = new ArrayList<Integer>();
// Get a list of groups that this user is a member of.
List<String> groupMemberships = groups.getUserGroups(user.getResearcher().getID());
if (groupMemberships != null && groupMemberships.size() > 0)
groupIds.add(groups.getGroupID(groupMemberships.get(0)));
return groupIds;
}
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 {
// 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");
}
// Restrict access to researchers who are members of a group
Groups groupMan = Groups.getInstance();
if (!groupMan.isInAGroup(user.getResearcher().getID())) {
ActionErrors errors = new ActionErrors();
errors.add("access", new ActionMessage("error.access.invalidgroup"));
saveErrors(request, errors);
return mapping.findForward("standardHome");
}
UploadMSDataForm newForm = new UploadMSDataForm();
if (groupMan.isMember(user.getResearcher().getID(), "administrators")) {
newForm.setPipeline(Pipeline.TPP);
newForm.setDataServer("local");
} else if (groupMan.isMember(user.getResearcher().getID(), "MacCoss")) {
newForm.setPipeline(Pipeline.MACOSS);
newForm.setDataServer("local");
} else {
newForm.setPipeline(Pipeline.TPP);
newForm.setDataServer("local");
}
try {
int projectID = Integer.parseInt(request.getParameter("projectID"));
newForm.setProjectID(projectID);
} catch (Exception e) {
newForm.setProjectID(0);
}
request.setAttribute("uploadMSDataForm", newForm);
// get a list of projects on which this researcher is listed
List<ProjectLite> projects =
ProjectLiteDAO.instance().getResearcherWritableProjects(user.getResearcher().getID());
Collections.sort(
projects,
new Comparator<ProjectLite>() {
@Override
public int compare(ProjectLite o1, ProjectLite o2) {
return Integer.valueOf(o2.getId()).compareTo(o1.getId());
}
});
request.getSession().setAttribute("researcherProjects", projects);
// get a list of instruments available
List<MsInstrument> instruments = DAOFactory.instance().getInstrumentDAO().loadAllInstruments();
request.getSession().setAttribute("instrumentList", instruments);
// Kick it to the view page
return mapping.findForward("Success");
}
public ActionForward execute(
ActionMapping mapping,
ActionForm form,
HttpServletRequest request,
HttpServletResponse response)
throws Exception {
// 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");
}
// Restrict access to yrc members
Groups groupMan = Groups.getInstance();
if (!groupMan.isInAGroup(user.getResearcher().getID())) {
ActionErrors errors = new ActionErrors();
errors.add("access", new ActionMessage("error.access.invalidgroup"));
saveErrors(request, errors);
return mapping.findForward("Failure");
}
try {
Job job = MSJobFactory.getInstance().getJob(Integer.parseInt(request.getParameter("id")));
if (job == null) {
ActionErrors errors = new ActionErrors();
errors.add(
"general",
new ActionMessage(
"error.general.errorMessage",
"No job found with ID " + request.getParameter("id")));
saveErrors(request, errors);
return mapping.findForward("Failure");
}
request.setAttribute("job", job);
if (job instanceof MSJob) {
int speciesId = ((MSJob) job).getTargetSpecies();
Species species = Species.getInstance(speciesId);
request.setAttribute("species", species);
request.setAttribute("experimentUploadJob", true);
} else if (job instanceof MsAnalysisUploadJob) {
request.setAttribute("analysisUploadJob", true);
} else if (job instanceof PercolatorJob) {
request.setAttribute("percolatorJob", true);
}
} catch (Exception e) {
log.error("Error loading job with ID: " + request.getParameter("id"), e);
ActionErrors errors = new ActionErrors();
errors.add(
"general",
new ActionMessage(
"error.general.errorMessage",
"Error reading job with ID: "
+ request.getParameter("id")
+ ". Error was: "
+ e.getMessage()));
saveErrors(request, errors);
return mapping.findForward("Failure");
}
return mapping.findForward("Success");
}
public ActionForward execute(
ActionMapping mapping,
ActionForm form,
HttpServletRequest request,
HttpServletResponse response)
throws Exception {
// 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");
}
// we need a projectID so that we can restrict access to researchers on a project
int projectId = 0;
try {
projectId = Integer.parseInt(request.getParameter("projectId"));
} catch (NumberFormatException e) {
projectId = 0;
}
if (projectId == 0) {
ActionErrors errors = new ActionErrors();
errors.add(
"payment", new ActionMessage("error.payment.invalidid", "Invalid projectID in request"));
saveErrors(request, errors);
return mapping.findForward("standardHome");
}
// user should be an admin OR a researcher on the project
Project project = ProjectFactory.getProject(projectId);
if (!project.checkAccess(user.getResearcher())) {
ActionErrors errors = new ActionErrors();
errors.add(
"payment",
new ActionMessage(
"error.payment.invalidaccess",
"User does not have access to view details of the payment method."));
saveErrors(request, errors);
ActionForward fwd = mapping.findForward("Failure");
ActionForward newFwd =
new ActionForward(fwd.getPath() + "?ID=" + projectId, fwd.getRedirect());
return newFwd;
}
// we need a paymentMethodId
int paymentMethodId = 0;
try {
paymentMethodId = Integer.parseInt(request.getParameter("paymentMethodId"));
} catch (NumberFormatException e) {
paymentMethodId = 0;
}
if (paymentMethodId == 0) {
ActionErrors errors = new ActionErrors();
errors.add(
"payment",
new ActionMessage("error.payment.invalidid", "Invalid paymentMethodID in request"));
saveErrors(request, errors);
ActionForward fwd = mapping.findForward("Failure");
ActionForward newFwd =
new ActionForward(fwd.getPath() + "?ID=" + projectId, fwd.getRedirect());
return newFwd;
}
try {
PaymentMethod paymentMethod =
PaymentMethodDAO.getInstance().getPaymentMethod(paymentMethodId);
request.setAttribute("paymentMethod", paymentMethod);
request.setAttribute("projectId", projectId);
} catch (Exception e) {
ActionErrors errors = new ActionErrors();
errors.add("payment", new ActionMessage("error.payment.load", "ERROR: " + e.getMessage()));
saveErrors(request, errors);
log.error("Error loading payment method for ID: " + paymentMethodId, e);
ActionForward fwd = mapping.findForward("Failure");
ActionForward newFwd =
new ActionForward(fwd.getPath() + "?ID=" + projectId, fwd.getRedirect());
return newFwd;
}
return mapping.findForward("Success");
}