/** * 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); } }