/** {@inheritDoc} */
@Override
public ActionForward execute(
ComponentContext context,
ActionMapping mapping,
ActionForm form,
HttpServletRequest request,
HttpServletResponse response)
throws Exception {
HttpSession session = request.getSession();
final InterMineAPI im = SessionMethods.getInterMineAPI(session);
InterMineBag imBag = (InterMineBag) request.getAttribute("bag");
WebConfig webConfig = SessionMethods.getWebConfig(request);
Model model = im.getModel();
TemplateManager templateManager = im.getTemplateManager();
Map<Class, ApiTemplate> conversionTypesMap =
TypeConverter.getConversionTemplates(
templateManager.getConversionTemplates(),
TypeUtil.instantiate(model.getPackageName() + "." + imBag.getType()));
ArrayList<String> conversionTypes = new ArrayList<String>();
Map<Type, Boolean> fastaMap = new HashMap<Type, Boolean>();
for (Class<?> clazz : conversionTypesMap.keySet()) {
conversionTypes.add(TypeUtil.unqualifiedName(clazz.getName()));
Type type = webConfig.getTypes().get(clazz.getName());
FieldConfig fieldConfig = type.getFieldConfigMap().get("length");
if (fieldConfig != null && fieldConfig.getDisplayer() != null) {
fastaMap.put(type, Boolean.TRUE);
} else {
fastaMap.put(type, Boolean.FALSE);
}
}
// Use custom converters
BagQueryConfig bagQueryConfig = im.getBagQueryConfig();
String bagType = imBag.getType();
Set<AdditionalConverter> additionalConverters = bagQueryConfig.getAdditionalConverters(bagType);
request.setAttribute("customConverters", additionalConverters);
request.setAttribute("conversionTypes", conversionTypes);
request.setAttribute("fastaMap", fastaMap);
return null;
}
/**
* 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();
}
/** {@inheritDoc} */
@SuppressWarnings("unused")
@Override
public ActionForward execute(
@SuppressWarnings("unused") ActionMapping mapping,
@SuppressWarnings("unused") ActionForm form,
HttpServletRequest request,
@SuppressWarnings("unused") HttpServletResponse response)
throws Exception {
long startTime = System.currentTimeMillis();
HttpSession session = request.getSession();
InterMineAPI im = SessionMethods.getInterMineAPI(session);
if (im.getBagManager().isAnyBagToUpgrade(SessionMethods.getProfile(session))) {
recordError(new ActionMessage("login.upgradeListManually"), request);
}
// fetch & set requested object
InterMineObject requestedObject = getRequestedObject(im, request);
if (requestedObject != null) {
ReportObjectFactory reportObjectFactory = SessionMethods.getReportObjects(session);
ReportObject reportObject = reportObjectFactory.get(requestedObject);
request.setAttribute("object", reportObject);
request.setAttribute("reportObject", reportObject);
request.setAttribute("requestedObject", requestedObject);
// hell starts here
TagManager tagManager = im.getTagManager();
ServletContext servletContext = session.getServletContext();
ObjectStore os = im.getObjectStore();
String superuser = im.getProfileManager().getSuperuser();
if (superuser.equals(SessionMethods.getProfile(session).getUsername())) {
request.setAttribute("SHOW_TAGS", true);
}
// place InlineLists based on TagManager, reportObject is cached while Controller is not
Map<String, List<InlineList>> placedInlineLists = new TreeMap<String, List<InlineList>>();
// traverse all unplaced (non-header) InlineLists
for (InlineList list : reportObject.getNormalInlineLists()) {
FieldDescriptor fd = list.getDescriptor();
String taggedType = getTaggedType(fd);
// assign lists to any aspects they are tagged to or put in unplaced lists
String fieldPath = fd.getClassDescriptor().getUnqualifiedName() + "." + fd.getName();
List<Tag> tags = tagManager.getTags(null, fieldPath, taggedType, superuser);
for (Tag tag : tags) {
String tagName = tag.getTagName();
if (AspectTagUtil.isAspectTag(tagName)) {
List<InlineList> listsForAspect = placedInlineLists.get(tagName);
if (listsForAspect == null) {
listsForAspect = new ArrayList<InlineList>();
placedInlineLists.put(tagName, listsForAspect);
}
listsForAspect.add(list);
} else if (tagName.equals(TagNames.IM_SUMMARY)) {
List<InlineList> summaryLists = placedInlineLists.get(tagName);
if (summaryLists == null) {
summaryLists = new ArrayList<InlineList>();
placedInlineLists.put(tagName, summaryLists);
}
summaryLists.add(list);
}
}
}
// any lists that aren't tagged will be 'unplaced'
List<InlineList> unplacedInlineLists =
new ArrayList<InlineList>(reportObject.getNormalInlineLists());
unplacedInlineLists.removeAll(placedInlineLists.values());
long now = System.currentTimeMillis();
LOG.info("TIME placed inline lists: " + (now - startTime) + "ms");
long stepTime = now;
request.setAttribute("mapOfInlineLists", placedInlineLists);
request.setAttribute("listOfUnplacedInlineLists", unplacedInlineLists);
Map<String, Map<String, DisplayField>> placementRefsAndCollections =
new TreeMap<String, Map<String, DisplayField>>();
Set<String> aspects = new LinkedHashSet<String>(SessionMethods.getCategories(servletContext));
Set<ClassDescriptor> cds =
os.getModel().getClassDescriptorsForClass(requestedObject.getClass());
for (String aspect : aspects) {
placementRefsAndCollections.put(
TagNames.IM_ASPECT_PREFIX + aspect,
new TreeMap<String, DisplayField>(String.CASE_INSENSITIVE_ORDER));
}
Map<String, DisplayField> miscRefs =
new TreeMap<String, DisplayField>(reportObject.getRefsAndCollections());
placementRefsAndCollections.put(TagNames.IM_ASPECT_MISC, miscRefs);
// summary refs and colls
Map<String, DisplayField> summaryRefsCols = new TreeMap<String, DisplayField>();
placementRefsAndCollections.put(TagNames.IM_SUMMARY, summaryRefsCols);
for (Iterator<Entry<String, DisplayField>> iter =
reportObject.getRefsAndCollections().entrySet().iterator();
iter.hasNext(); ) {
Map.Entry<String, DisplayField> entry = iter.next();
DisplayField df = entry.getValue();
if (df instanceof DisplayReference) {
categoriseBasedOnTags(
((DisplayReference) df).getDescriptor(),
"reference",
df,
miscRefs,
tagManager,
superuser,
placementRefsAndCollections,
SessionMethods.isSuperUser(session));
} else if (df instanceof DisplayCollection) {
categoriseBasedOnTags(
((DisplayCollection) df).getDescriptor(),
"collection",
df,
miscRefs,
tagManager,
superuser,
placementRefsAndCollections,
SessionMethods.isSuperUser(session));
}
}
// remove any fields overridden by displayers
removeFieldsReplacedByReportDisplayers(reportObject, placementRefsAndCollections);
request.setAttribute("placementRefsAndCollections", placementRefsAndCollections);
String type = reportObject.getType();
request.setAttribute("objectType", type);
String stableLink = PortalHelper.generatePortalLink(reportObject.getObject(), im, request);
if (stableLink != null) {
request.setAttribute("stableLink", stableLink);
}
stepTime = System.currentTimeMillis();
startTime = stepTime;
// attach only non empty categories
Set<String> allClasses = new HashSet<String>();
for (ClassDescriptor cld : cds) {
allClasses.add(cld.getUnqualifiedName());
}
TemplateManager templateManager = im.getTemplateManager();
Map<String, List<ReportDisplayer>> displayerMap = reportObject.getReportDisplayers();
stepTime = System.currentTimeMillis();
startTime = stepTime;
List<String> categories = new LinkedList<String>();
for (String aspect : aspects) {
// 1) Displayers
// 2) Inline Lists
if ((displayerMap != null && displayerMap.containsKey(aspect))
|| placedInlineLists.containsKey(aspect)) {
categories.add(aspect);
} else {
// 3) Templates
if (!templateManager.getReportPageTemplatesForAspect(aspect, allClasses).isEmpty()) {
categories.add(aspect);
} else {
// 4) References & Collections
if (placementRefsAndCollections.containsKey("im:aspect:" + aspect)
&& placementRefsAndCollections.get("im:aspect:" + aspect) != null) {
for (DisplayField df :
placementRefsAndCollections.get("im:aspect:" + aspect).values()) {
categories.add(aspect);
break;
}
}
}
}
}
if (!categories.isEmpty()) {
request.setAttribute("categories", categories);
}
now = System.currentTimeMillis();
LOG.info("TIME made list of categories: " + (now - stepTime) + "ms");
}
return null;
}