@Override
protected void postInit() {
profile = getPermission().getProfile();
BagManager bagManager = im.getBagManager();
lists = bagManager.getBags(profile);
knownBags = lists.keySet();
}
@Override
protected void postInit() {
profile = getPermission().getProfile();
BagManager bagManager = im.getBagManager();
lists = bagManager.getBags(profile);
knownBags.addAll(lists.keySet());
output.setHeaderAttributes(getHeaderAttributes());
}
private Set<String> getTagsForSingleList(String name, Profile profile) {
BagManager bagManager = im.getBagManager();
Map<String, InterMineBag> lists = bagManager.getBags(profile);
InterMineBag list = lists.get(name);
if (list == null) {
throw new ResourceNotFoundException("You do not have access to a list called " + name);
}
List<Tag> tags = bagManager.getTagsForBag(list, profile);
@SuppressWarnings("unchecked")
Collection<String> tagNames = collect(tags, invokerTransformer("getTagName"));
return new HashSet<String>(tagNames);
}
/**
* Fill a map with intermine bags from the names in a parameter.
*
* @param map The map to fill.
* @param param The parameter to read names from.
*/
protected void populateListMap(Map<String, InterMineBag> map, String param) {
String[] paramValues = request.getParameterValues(param);
if (paramValues != null) {
for (String value : paramValues) {
String[] names = StringUtils.split(value, LIST_SEPARATOR);
for (String name : names) {
InterMineBag list = bagManager.getBag(profile, name);
map.put(name, list);
}
}
}
}
/**
* Get the Objectstore Query to run to generate the list.
*
* @param pq The pathquery to generate the query from.
* @param profile The profile to search for bags.
* @return A query.
*/
protected Query getQuery(PathQuery pq, Profile profile) {
Query ret;
try {
ret =
MainHelper.makeQuery(
pq,
bagManager.getBags(profile),
new HashMap<String, QuerySelectable>(),
im.getBagQueryRunner(),
new HashMap<String, BagQueryResult>());
} catch (ObjectStoreException e) {
throw new InternalErrorException(e);
}
return ret;
}
/** @return a name for the new list * */
protected String produceName() {
// Give the user a default name if none is provided.
String nameParam = request.getParameter(NAME_PARAMETER);
nameParam = StringUtils.isBlank(nameParam) ? request.getParameter(ALT_NAME_PARAM) : nameParam;
String name;
if (StringUtils.isBlank(nameParam)) {
nameParam = DEFAULT_LIST_NAME;
name = nameParam;
Set<String> listNames = bagManager.getBags(profile).keySet();
int counter = 2;
while (listNames.contains(name)) {
name = nameParam + "_" + counter;
counter++;
}
} else {
name = nameParam;
}
return name;
}
private void unshareBag(HttpSession session, Profile profile, InterMineBag bag) {
InterMineAPI api = SessionMethods.getInterMineAPI(session);
BagManager bm = api.getBagManager();
bm.unshareBagWithUser(bag, profile);
}
private void combine(ActionForm form, HttpServletRequest request, String opText) {
HttpSession session = request.getSession();
final InterMineAPI im = SessionMethods.getInterMineAPI(session);
Profile profile = SessionMethods.getProfile(session);
ModifyBagForm mbf = (ModifyBagForm) form;
BagManager bagManager = im.getBagManager();
Map<String, InterMineBag> allBags = bagManager.getBags(profile);
String[] selectedBagNames = mbf.getSelectedBags();
Collection<InterMineBag> selectedBags = getSelectedBags(allBags, selectedBagNames);
String newBagName = NameUtil.validateName(allBags.keySet(), mbf.getNewBagName());
int newBagSize = 0;
try {
if (opText.equals(BagOperations.UNION)) {
newBagSize = BagOperations.union(selectedBags, newBagName, profile, im.getClassKeys());
} else if (opText.equals(BagOperations.INTERSECT)) {
newBagSize = BagOperations.intersect(selectedBags, newBagName, profile, im.getClassKeys());
} else if (opText.equals(BagOperations.SUBTRACT)) {
newBagSize = BagOperations.subtract(selectedBags, newBagName, profile, im.getClassKeys());
}
} catch (IncompatibleTypesException e) {
SessionMethods.recordError(
"You can only perform operations on lists of the same type."
+ " Lists "
+ StringUtil.prettyList(Arrays.asList(selectedBagNames))
+ " do not match.",
session);
return;
} catch (ObjectStoreException e) {
LOG.error(e);
ActionMessage actionMessage = new ActionMessage("An error occurred while saving the list");
recordError(actionMessage, request);
return;
}
if (newBagSize > 0) {
SessionMethods.recordMessage(
"Created list \""
+ newBagName
+ "\" as "
+ opText
+ " of "
+ StringUtil.prettyList(Arrays.asList(selectedBagNames))
+ ".",
session);
// track the list creation
im.getTrackerDelegate()
.trackListCreation(
BagOperations.getCommonBagType(selectedBags),
newBagSize,
ListBuildMode.OPERATION,
profile,
session.getId());
} else {
SessionMethods.recordError(
opText
+ " operation on lists "
+ StringUtil.prettyList(Arrays.asList(selectedBagNames))
+ " produced no results.",
session);
}
}
private void copy(ActionForm form, HttpServletRequest request) throws ObjectStoreException {
HttpSession session = request.getSession();
final InterMineAPI im = SessionMethods.getInterMineAPI(session);
Profile profile = SessionMethods.getProfile(session);
ModifyBagForm frm = (ModifyBagForm) form;
String[] selectedBagNames = frm.getSelectedBags();
BagManager bagManager = im.getBagManager();
Map<String, InterMineBag> allBags = bagManager.getBags(profile);
String newNameTextBox = getNewNameTextBox(request, frm.getNewBagName());
if (selectedBagNames.length == 1) {
String selectedBagName = selectedBagNames[0];
InterMineBag origBag = allBags.get(selectedBagName);
if (origBag == null) {
recordError(new ActionMessage("errors.bag.notfound"), request);
return;
}
String newBagName = "";
if (newNameTextBox != null) {
newBagName = NameUtil.validateName(allBags.keySet(), newNameTextBox);
if (newBagName.isEmpty()) {
recordError(new ActionMessage("bag.createdlists.notvalidname", newNameTextBox), request);
return;
}
}
if (newNameTextBox == null) {
newBagName = NameUtil.generateNewName(allBags.keySet(), selectedBagName);
}
if (createBag(origBag, newBagName, profile)) {
recordMessage(new ActionMessage("bag.createdlists", newBagName), request);
// track the list creation
im.getTrackerDelegate()
.trackListCreation(
origBag.getType(),
origBag.getSize(),
ListBuildMode.OPERATION,
profile,
session.getId());
}
} else {
if (newNameTextBox != null) {
recordError(new ActionMessage("errors.bag.namecannotbespecified"), request);
return;
}
String msg = "";
for (int i = 0; i < selectedBagNames.length; i++) {
String selectedBagName = selectedBagNames[i];
InterMineBag origBag = allBags.get(selectedBagName);
if (origBag == null) {
recordError(new ActionMessage("errors.bag.notfound"), request);
return;
}
String newBagName = NameUtil.generateNewName(allBags.keySet(), selectedBagName);
if (createBag(origBag, newBagName, profile)) {
msg += newBagName + ", ";
}
}
if (msg.length() > 2) {
msg = msg.substring(0, msg.length() - 2);
}
if (msg.length() > 0) {
recordMessage(new ActionMessage("bag.createdlists", msg), request);
}
}
}
/**
* Forward to the correct method based on the button pressed
*
* @param mapping The ActionMapping used to select this instance
* @param form The optional ActionForm bean for this request (if any)
* @param request The HTTP request we are processing
* @param response The HTTP response we are creating
* @return an ActionForward object defining where control goes next
* @exception Exception if the application business logic throws an exception
*/
@Override
public ActionForward execute(
ActionMapping mapping,
ActionForm form,
HttpServletRequest request,
HttpServletResponse response)
throws Exception {
HttpSession session = request.getSession();
final InterMineAPI im = SessionMethods.getInterMineAPI(session);
Profile profile = SessionMethods.getProfile(session);
Model model = im.getModel();
ModifyBagDetailsForm mbdf = (ModifyBagDetailsForm) form;
BagManager bagManager = im.getBagManager();
InterMineBag imBag = bagManager.getBag(profile, mbdf.getBagName());
String bagIdentifier = "bag." + imBag.getName();
if (request.getParameter("removeFromBag") != null) {
PagedTable pc = SessionMethods.getResultsTable(session, bagIdentifier);
String msg = "";
if (pc.isAllRowsSelected()) {
// TODO these messages need to be moved to properties file
msg = "You can't remove all items from your list. Try deleting your list instead.";
} else {
int removed = pc.removeSelectedFromBag(imBag, session);
msg = "You have removed " + removed + " items from your list.";
}
SessionMethods.recordMessage(msg, session);
// return new ForwardParameters(mapping.findForward("bagDetails"))
// .addParameter("bagName", mbdf.getBagName()).forward();
// pass an extra parameter telling the JSP to open up the results table
return new ForwardParameters(mapping.findForward("bagDetails"))
.addParameter("bagName", mbdf.getBagName())
.addParameter("table", "open")
.forward();
} else if (request.getParameter("addToBag") != null) {
InterMineBag newBag = bagManager.getBag(profile, mbdf.getExistingBagName());
String msg = "";
if (newBag.getType().equals(imBag.getType())) {
PagedTable pc = SessionMethods.getResultsTable(session, bagIdentifier);
int oldSize = newBag.size();
pc.addSelectedToBag(newBag);
int newSize = newBag.size();
int added = newSize - oldSize;
msg =
"You have added "
+ added
+ " items from list <strong>"
+ imBag.getName()
+ "</strong> to list <strong>"
+ newBag.getName()
+ "</strong>";
} else {
msg = "You can only add objects to other lists of the same type";
}
SessionMethods.recordMessage(msg, session);
// orthologues form
} else if (request.getParameter("convertToThing") != null) {
BagQueryConfig bagQueryConfig = im.getBagQueryConfig();
Set<AdditionalConverter> additionalConverters =
bagQueryConfig.getAdditionalConverters(imBag.getType());
if (additionalConverters != null && !additionalConverters.isEmpty()) {
for (AdditionalConverter additionalConverter : additionalConverters) {
BagConverter bagConverter =
PortalHelper.getBagConverter(
im, SessionMethods.getWebConfig(request), additionalConverter.getClassName());
List<Integer> converted =
bagConverter.getConvertedObjectIds(
profile, imBag.getType(), imBag.getContentsAsIds(), mbdf.getExtraFieldValue());
if (converted.size() == 1) {
return goToReport(mapping, converted.get(0).toString());
}
String bagName =
NameUtil.generateNewName(
profile.getSavedBags().keySet(),
mbdf.getExtraFieldValue() + " orthologues of " + imBag.getName());
InterMineBag newBag = profile.createBag(bagName, imBag.getType(), "", im.getClassKeys());
return createBagAndGoToBagDetails(mapping, newBag, converted);
}
}
// "use in bag" link
} else if (request.getParameter("useBag") != null) {
PagedTable pc = SessionMethods.getResultsTable(session, bagIdentifier);
PathQuery pathQuery = pc.getWebTable().getPathQuery().clone();
SessionMethods.setQuery(session, pathQuery);
session.setAttribute("path", imBag.getType());
session.setAttribute("prefix", imBag.getType());
String msg = "You can now create a query using your list " + imBag.getName();
SessionMethods.recordMessage(msg, session);
return mapping.findForward("query");
// convert links
} else if (request.getParameter("convert") != null && request.getParameter("bagName") != null) {
String type2 = request.getParameter("convert");
TemplateManager templateManager = im.getTemplateManager();
PathQuery q =
BagConversionHelper.getConvertedObjects(
session,
templateManager.getConversionTemplates(),
TypeUtil.instantiate(model.getPackageName() + "." + imBag.getType()),
TypeUtil.instantiate(model.getPackageName() + "." + type2),
imBag);
q.setTitle(type2 + "s from list '" + imBag.getName() + "'");
SessionMethods.loadQuery(q, session, response);
String qid = SessionMethods.startQueryWithTimeout(request, false, q);
Thread.sleep(200); // slight pause in the hope of avoiding holding page
final String trail = "|bag." + imBag.getName();
return new ForwardParameters(mapping.findForward("waiting"))
.addParameter("trail", trail)
.addParameter("qid", qid)
.forward();
}
return new ForwardParameters(mapping.findForward("bagDetails"))
.addParameter("bagName", mbdf.getBagName())
.forward();
}