/**
* Convert a Tag to XML and write XML to given writer.
*
* @param tag the Tag
* @param writer the XMLStreamWriter to write to
*/
public static void marshal(Tag tag, XMLStreamWriter writer) {
try {
writer.writeCharacters("\n");
writer.writeStartElement("tag");
writer.writeAttribute("name", tag.getTagName());
writer.writeAttribute("objectIdentifier", tag.getObjectIdentifier());
writer.writeAttribute("type", "" + tag.getType());
writer.writeEndElement();
} catch (XMLStreamException e) {
throw new RuntimeException(e);
}
}
/**
* For a given FieldDescriptor, look up its 'aspect:' tags and place it in the correct map within
* placementRefsAndCollections. If categorised, remove it from the supplied miscRefs map.
*
* @param fd the FieldDecriptor (a references or collection)
* @param taggedType 'reference' or 'collection'
* @param dispRef the corresponding DisplayReference or DisplayCollection
* @param miscRefs map that contains dispRef (may be removed by this method)
* @param tagManager the tag manager
* @param sup the superuser account name
* @param placementRefsAndCollections take from the ReportObject
* @param isSuperUser if current user is superuser
*/
public static void categoriseBasedOnTags(
FieldDescriptor fd,
String taggedType,
DisplayField dispRef,
Map<String, DisplayField> miscRefs,
TagManager tagManager,
String sup,
Map<String, Map<String, DisplayField>> placementRefsAndCollections,
boolean isSuperUser) {
List<Tag> tags =
tagManager.getTags(
null,
fd.getClassDescriptor().getUnqualifiedName() + "." + fd.getName(),
taggedType,
sup);
for (Tag tag : tags) {
String tagName = tag.getTagName();
if (!isSuperUser && tagName.equals(TagNames.IM_HIDDEN)) {
// miscRefs.remove(fd.getName());
// Maybe it was added already to some placement and
// that's why it must be removed
removeField(fd.getName(), placementRefsAndCollections);
return;
}
if (AspectTagUtil.isAspectTag(tagName)) {
Map<String, DisplayField> refs = placementRefsAndCollections.get(tagName);
if (refs != null) {
refs.put(fd.getName(), dispRef);
miscRefs.remove(fd.getName());
}
} else if (tagName.equals(TagNames.IM_SUMMARY)) {
Map<String, DisplayField> summary = placementRefsAndCollections.get(TagNames.IM_SUMMARY);
if (summary != null) {
summary.put(fd.getName(), dispRef);
miscRefs.remove(fd.getName());
}
miscRefs.remove(fd.getName());
}
}
}
/** {@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;
}
/** {@inheritDoc} */
@Override
public void endElement(String uri, String localName, String qName) throws SAXException {
super.endElement(uri, localName, qName);
if ("userprofile".equals(qName)) {
Profile profile;
profile = profileHandler.getProfile();
profileManager.createProfileWithoutBags(profile);
try {
Map<String, Set<BagValue>> bagValues = profileHandler.getBagsValues();
for (StorableBag bag : profile.getAllBags().values()) {
bag.saveWithBagValues(profile.getUserId(), bagValues.get(bag.getName()));
}
} catch (ObjectStoreException ose) {
throw new SAXException(ose);
}
// Must come after the bags themselves have been stored.
try {
SharedBagManager.getInstance(profileManager);
profileHandler.getInvitationHandler().storeInvites(profile);
} catch (SQLException e) {
LOG.error("Cannot store invitations", e);
if (abortOnError) {
throw new SAXException(e);
}
}
Set<Tag> tags = profileHandler.getTags();
TagManager tagManager = new TagManagerFactory(profile.getProfileManager()).getTagManager();
for (Tag tag : tags) {
try {
tagManager.addTag(tag.getTagName(), tag.getObjectIdentifier(), tag.getType(), profile);
} catch (TagManager.TagException e) {
LOG.error("Cannot add tag: " + tag.toString(), e);
if (abortOnError) {
throw new SAXException(e);
}
} catch (RuntimeException e) {
LOG.error("Error adding tag: " + tag.toString(), e);
if (abortOnError) {
throw new SAXException(e);
}
}
}
profile.getSearchRepository().receiveEvent(new MassTaggingEvent());
profileHandler = null;
long totalTime = System.currentTimeMillis() - startTime;
LOG.info("Finished profile: " + profile.getUsername() + " took " + totalTime + "ms.");
}
if ("userprofiles".equals(qName)) {
if (!sharedBagsByUsers.isEmpty()) {
SharedBagManager sharedBagManager = SharedBagManager.getInstance(profileManager);
String bagName, dateCreated;
for (String user : sharedBagsByUsers.keySet()) {
List<Map<String, String>> sharedBags = sharedBagsByUsers.get(user);
if (!sharedBags.isEmpty()) {
for (Map<String, String> sharedBag : sharedBags) {
bagName = sharedBag.get("name");
dateCreated = sharedBag.get("dateCreated");
sharedBagManager.shareBagWithUser(bagName, dateCreated, user);
}
}
}
}
}
if (profileHandler != null) {
profileHandler.endElement(uri, localName, qName);
}
if (trackHandler != null) {
trackHandler.endElement(uri, localName, qName);
}
}