/**
     * Set the feature types for this request. Immediately parses the class names to
     * ClassDescriptors and fails as soon as possible.
     *
     * @param featureTypes A collection of feature type names.
     * @throws BadRequestException if the feature types are not mappable to classes, and if those
     *     classes are not Sequence Features.
     */
    public void setFeatureTypes(Collection<String> featureTypes) {
      this.featureTypes = new HashSet<String>(featureTypes);
      this.featureCds = new HashSet<ClassDescriptor>();

      Set<String> badTypes = new HashSet<String>();
      Model model = api.getModel();
      ClassDescriptor sfCd = model.getClassDescriptorByName(sequenceFeature);
      for (String f : this.featureTypes) {
        ClassDescriptor cld = model.getClassDescriptorByName(f);
        if (cld == null) {
          badTypes.add(f);
        } else {
          try {
            if (!sequenceFeature.equals(f)
                && !sfCd.getUnqualifiedName().equals(f)
                && !ClassDescriptor.findSuperClassNames(model, f).contains(sequenceFeature)) {
              throw new BadRequestException(f + " is not a " + sequenceFeature);
            }
          } catch (MetaDataException e) {
            // This should never happen.
            throw new ServiceException(e);
          }
          featureCds.add(cld);
          for (ClassDescriptor subCld : model.getAllSubs(cld)) {
            featureCds.add(subCld);
          }
        }
      }
      if (!badTypes.isEmpty()) {
        throw new BadRequestException(
            "The following feature types are not " + "valid feature class names: " + badTypes);
      }
    }
Exemple #2
0
 /**
  * Make a feature track of the form (for a feature of the type <code>ClassName</code>):
  *
  * <pre>
  * {
  *   "type": "JBrowse/View/Track/CanvasFeatures",
  *   "storeClass": "JBrowse/Store/SeqFeature/REST",
  *   "category": "Features",
  *   "key": "Class Name",
  *   "label": "ClassName",
  *   "baseUrl": "http://www.foo.com/foomine/service/jbrowse/1234",
  *   "autocomplete": "all",
  *   "region_feature_densities": true,
  *   "query": { "type": "ClassName" }
  * }
  * </pre>
  *
  * @param feature The type of feature to build a track for.
  * @return A representation of the track configuration.
  */
 private Map<String, Object> featureTrack(ClassDescriptor feature) {
   Map<String, Object> ret = new HashMap<String, Object>();
   ret.put("type", "JBrowse/View/Track/CanvasFeatures");
   ret.put("storeClass", "JBrowse/Store/SeqFeature/REST");
   ret.put("category", featureCat);
   ret.put("key", WebUtil.formatClass(feature, config)); // In JBrowse "key" means human-readable.
   ret.put(
       "label",
       dataset + "-" + feature.getUnqualifiedName()); // and "label" means machine-readable.
   ret.put("baseUrl", getBaseUrl() + domain);
   Map<String, Object> query = new HashMap<String, Object>();
   query.put("type", feature.getUnqualifiedName());
   ret.put("query", query);
   ret.put("autocomplete", "all");
   ret.put("region_feature_densities", true);
   return ret;
 }
 private static List<String> getAttributeView(ClassDescriptor cld) {
   List<String> view = new ArrayList<String>();
   String basePath = cld.getUnqualifiedName() + ".";
   for (AttributeDescriptor att : cld.getAllAttributeDescriptors()) {
     if (!"id".equals(att.getName())) {
       view.add(basePath + att.getName());
     }
   }
   return view;
 }
 private Map<String, Object> getObjectDetails(InterMineObject imo) {
   WebConfig webConfig = InterMineContext.getWebConfig();
   Model m = im.getModel();
   Map<String, Object> objectDetails = new HashMap<String, Object>();
   String className = DynamicUtil.getSimpleClassName(imo.getClass());
   ClassDescriptor cd = m.getClassDescriptorByName(className);
   for (FieldConfig fc : FieldConfigHelper.getClassFieldConfigs(webConfig, cd)) {
     try {
       Path p = new Path(m, cd.getUnqualifiedName() + "." + fc.getFieldExpr());
       if (p.endIsAttribute() && fc.getShowInSummary()) {
         objectDetails.put(
             p.getNoConstraintsString().replaceAll("^[^.]*\\.", ""), PathUtil.resolvePath(p, imo));
       }
     } catch (PathException e) {
       LOG.error(e);
     }
   }
   return objectDetails;
 }
 /**
  * Get the view as configured in the webconfig. Guarantees to return a non-empty non-null list.
  *
  * @param type The type we are trying to get a view for.
  * @param model The data model
  * @param webConfig The web-configuration.
  * @param fieldConfigs
  * @return The list of paths that we can use to construct a query.
  * @throws UnconfiguredException if the class has not configured view.
  */
 private static List<String> getConfiguredView(ClassDescriptor cld, WebConfig webConfig)
     throws UnconfiguredException {
   Collection<String> view = new LinkedHashSet<String>(); // Preserve order and uniqueness.
   Model m = cld.getModel();
   for (FieldConfig fieldConfig : resultConfigs(webConfig, cld)) {
     try {
       Path p = new Path(m, cld.getUnqualifiedName() + "." + fieldConfig.getFieldExpr());
       // add subpaths of references and roots, attrs themselves, ignore collections.
       if (p.isRootPath() || p.endIsReference()) {
         view.addAll(getSubview(webConfig, m, p));
       } else if (p.endIsAttribute()) {
         view.add(p.getNoConstraintsString());
       }
     } catch (PathException e) {
       LOG.error("Invalid path configured in webconfig for class: " + cld);
     }
   }
   if (view.isEmpty()) {
     throw new UnconfiguredException();
   }
   return new ArrayList<String>(view);
 }
  /** {@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;
  }