/** * Constructor with necessary objects to generate an ObjectStore query from a PathQuery and * execute it. * * @param im intermine API * @param profile the user executing the query - for access to saved lists */ public WebResultsExecutor(InterMineAPI im, Profile profile) { os = im.getObjectStore(); bagQueryRunner = im.getBagQueryRunner(); this.profile = profile; this.im = im; bagManager = im.getBagManager(); this.summaryBatchSize = Constants.BATCH_SIZE; }
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); } } }
/** {@inheritDoc} */ @Override public ActionForward execute( ComponentContext context, ActionMapping mapping, ActionForm form, HttpServletRequest request, HttpServletResponse response) throws Exception { boolean canExportAsBED = false; HttpSession session = request.getSession(); final InterMineAPI im = SessionMethods.getInterMineAPI(session); Model model = im.getModel(); PathQuery query = new PathQuery(model); // org and dbkey for galaxy use Set<String> orgSet = new HashSet<String>(); Set<String> genomeBuildSet = new HashSet<String>(); // Build GenomicRegion pathquery, the request is from GenomicRegionSearch "export to Galaxy" if (request.getParameter("featureIds") != null) { String featureIds = request.getParameter("featureIds").trim(); String orgName = request.getParameter("orgName"); if (orgName != null && !"".equals(orgName)) { orgSet.add(orgName); } // Refer to GenomicRegionSearchService.getExportFeaturesQuery method String path = "SequenceFeature"; query.addView(path + ".primaryIdentifier"); query.addView(path + ".chromosomeLocation.locatedOn.primaryIdentifier"); query.addView(path + ".chromosomeLocation.start"); query.addView(path + ".chromosomeLocation.end"); query.addView(path + ".organism.name"); // use ids or pids String[] idsInStr = featureIds.split(","); Set<Integer> ids = new HashSet<Integer>(); boolean isIds = true; for (String id : idsInStr) { id = id.trim(); if (!Pattern.matches("^\\d+$", id)) { isIds = false; break; } ids.add(Integer.valueOf(id)); } if (isIds) { query.addConstraint(Constraints.inIds(path, ids)); } else { if (featureIds.contains("'")) { featureIds = featureIds.replaceAll("'", "\\\\'"); } query.addConstraint(Constraints.lookup(path, featureIds, null)); } canExportAsBED = true; } else { // request from normal result table String tableName = request.getParameter("table"); request.setAttribute("table", tableName); PagedTable pt = SessionMethods.getResultsTable(session, tableName); // Null check to page table, maybe session timeout? if (pt == null) { LOG.error("Page table is NULL..."); return null; } // Check if can export as BED TableHttpExporter tableExporter = new BEDHttpExporter(); try { canExportAsBED = tableExporter.canExport(pt); } catch (Exception e) { canExportAsBED = false; LOG.error("Caught an error running canExport() for: BEDHttpExporter. " + e); e.printStackTrace(); } LinkedHashMap<Path, Integer> exportClassPathsMap = getExportClassPaths(pt); List<Path> exportClassPaths = new ArrayList<Path>(exportClassPathsMap.keySet()); Map<String, String> pathMap = new LinkedHashMap<String, String>(); for (Path path : exportClassPaths) { String pathString = path.toStringNoConstraints(); String displayPath = pathString.replace(".", " > "); pathMap.put(pathString, displayPath); } Map<String, Integer> pathIndexMap = new LinkedHashMap<String, Integer>(); for (int index = 0; index < exportClassPaths.size(); index++) { String pathString = exportClassPaths.get(index).toStringNoConstraints(); Integer idx = exportClassPathsMap.get(exportClassPaths.get(index)); pathIndexMap.put(pathString, idx); } request.setAttribute("exportClassPaths", pathMap); request.setAttribute("pathIndexMap", pathIndexMap); // Support export public and private lists to Galaxy query = pt.getWebTable().getPathQuery(); ObjectStore os = im.getObjectStore(); Map<PathConstraint, String> constrains = query.getConstraints(); for (PathConstraint constraint : constrains.keySet()) { if (constraint instanceof PathConstraintBag) { String bagName = ((PathConstraintBag) constraint).getBag(); InterMineBag imBag = im.getBagManager().getBag(SessionMethods.getProfile(session), bagName); // find the classKeys Set<String> classKeySet = new LinkedHashSet<String>(); for (Integer id : imBag.getContentsAsIds()) { String classKey = pt.findClassKeyValue(im.getClassKeys(), os.getObjectById(id)); classKeySet.add(classKey); } String path = ((PathConstraintBag) constraint).getPath(); // replace constraint in the pathquery PathConstraintLookup newConstraint = new PathConstraintLookup( path, classKeySet.toString().substring(1, classKeySet.toString().length() - 1), null); query.replaceConstraint(constraint, newConstraint); } } orgSet = SequenceFeatureExportUtil.getOrganisms(query, session); } if (query instanceof TemplateQuery) { TemplateQuery templateQuery = (TemplateQuery) query; Map<PathConstraint, SwitchOffAbility> constraintSwitchOffAbilityMap = templateQuery.getConstraintSwitchOffAbility(); for (Map.Entry<PathConstraint, SwitchOffAbility> entry : constraintSwitchOffAbilityMap.entrySet()) { if (entry.getValue().compareTo(SwitchOffAbility.OFF) == 0) { templateQuery.removeConstraint(entry.getKey()); } } } String queryXML = PathQueryBinding.marshal(query, "", model.getName(), PathQuery.USERPROFILE_VERSION); // String encodedQueryXML = URLEncoder.encode(queryXML, "UTF-8"); String tableViewURL = new URLGenerator(request).getPermanentBaseURL() + "/service/query/results"; request.setAttribute("tableURL", tableViewURL); request.setAttribute("queryXML", queryXML); request.setAttribute("size", 1000000); // If can export as BED request.setAttribute("canExportAsBED", canExportAsBED); if (canExportAsBED) { String bedURL = new URLGenerator(request).getPermanentBaseURL() + "/service/query/results/bed"; request.setAttribute("bedURL", bedURL); genomeBuildSet = (Set<String>) OrganismGenomeBuildLookup.getGenomeBuildByOrgansimCollection(orgSet); String org = (orgSet.size() < 1) ? "Organism information not available" : StringUtil.join(orgSet, ","); // possible scenario: [null, ce3, null], should remove all null element and then join genomeBuildSet.removeAll(Collections.singleton(null)); String dbkey = (genomeBuildSet.size() < 1) ? "Genome Build information not available" : StringUtil.join(genomeBuildSet, ","); request.setAttribute("org", org); request.setAttribute("dbkey", dbkey); } // PathMap Map<String, String> pathsMap = new LinkedHashMap<String, String>(); List<String> views = query.getView(); for (String view : views) { String title = query.getGeneratedPathDescription(view); title = WebUtil.formatColumnName(title); pathsMap.put(view, title); } request.setAttribute("pathsMap", pathsMap); return null; }
/** * Constructor. * * @param im The intermine settings bundle */ public QueryToListService(InterMineAPI im) { super(im); bagManager = im.getBagManager(); }
/** * 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; }