/**
* Returns all NEW projects submitted to this YRC member's group(s)
*
* @param researcherID The researcher ID of the YRC member
* @return A list of new projects (within the last 30 days) for this member's groups, null if this
* is not a YRC member
*/
public static List<Project> getNewProjectsForYRCMember(Researcher r) throws SQLException {
int researcherID = r.getID();
Groups gm = Groups.getInstance();
// return null if they're not in a YRC group
if (!gm.isInAGroup(researcherID)) return null;
ProjectsSearcher ps = new ProjectsSearcher();
// ps.setResearcher(r);
// Set the start date of the search to 1 month ago
Calendar cal = GregorianCalendar.getInstance();
cal.add(Calendar.MONTH, -1);
ps.setStartDate(cal.getTime());
// Set the groups to search
List groups = gm.getGroups();
Iterator iter = groups.iterator();
while (iter.hasNext()) {
String group = (String) (iter.next());
if (gm.isMember(researcherID, group)) {
ps.addGroup(group);
}
}
List<Project> projects = ps.search();
return projects;
}
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;
}
/**
* 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 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");
}