Exemplo n.º 1
0
  /**
   * Save a single object to an existing bag.
   *
   * @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
   */
  @Override
  public ActionForward execute(
      ActionMapping mapping,
      ActionForm form,
      HttpServletRequest request,
      HttpServletResponse response) {
    int id = Integer.parseInt(request.getParameter("object"));
    HttpSession session = request.getSession();

    final InterMineAPI im = SessionMethods.getInterMineAPI(request.getSession());

    Profile profile = SessionMethods.getProfile(session);
    String bagName = request.getParameter("bag");

    InterMineBag existingBag = profile.getSavedBags().get(bagName);
    if (existingBag != null) {
      // TODO add a warning when object already in bag ??
      try {
        InterMineObject o = im.getObjectStore().getObjectById(id);
        existingBag.addIdToBag(id, DynamicUtil.getFriendlyName(o.getClass()));
        recordMessage(new ActionMessage("bag.addedToBag", existingBag.getName()), request);
      } catch (IncompatibleTypesException e) {
        recordError(new ActionMessage("bag.typesDontMatch"), request);
      } catch (ObjectStoreException e) {
        recordError(new ActionMessage("bag.error"), request, e);
      }
    } else {
      recordError(new ActionMessage("bag.noSuchBag"), request);
    }
    return mapping.findForward("report");
  }
  private void doMatches(Map<String, Object> ret, BagQueryResult bqr) {

    for (Entry<Integer, List> pair : bqr.getMatches().entrySet()) {
      Map<String, Object> resultItem;
      InterMineObject imo;
      try {
        imo = im.getObjectStore().getObjectById(pair.getKey());
      } catch (ObjectStoreException e) {
        throw new IllegalStateException("Could not retrieve object reported as match", e);
      }
      String idKey = String.valueOf(imo.getId());
      if (ret.containsKey(idKey)) {
        resultItem = (Map<String, Object>) ret.get(idKey);
      } else {
        resultItem = new HashMap<String, Object>();
        resultItem.put("identifiers", new HashMap<String, Object>());
      }
      if (!resultItem.containsKey("summary")) {
        resultItem.put("summary", getObjectDetails(imo));
      }
      Map<String, Object> identifiers = (Map<String, Object>) resultItem.get("identifiers");
      for (Object o : pair.getValue()) {
        String ident = (String) o;
        if (!identifiers.containsKey(ident)) {
          identifiers.put(ident, new HashSet<String>());
        }
        Set<String> categories = (Set<String>) identifiers.get(ident);
        categories.add("MATCH");
      }
      String className = DynamicUtil.getSimpleClassName(imo.getClass());
      resultItem.put("type", className.replaceAll("^.*\\.", ""));
      ret.put(idKey, resultItem);
    }
  }
Exemplo n.º 3
0
  /** {@inheritDoc} */
  public ActionForward execute(
      @SuppressWarnings("unused") ActionMapping mapping,
      @SuppressWarnings("unused") ActionForm form,
      HttpServletRequest request,
      HttpServletResponse response)
      throws Exception {
    String type = request.getParameter("type");
    if (type == null) {
      type = "webapp";
    }

    if ("webapp".equals(type)) {
      response.getOutputStream().print("OK");
    } else if ("query".equals(type)) {
      final InterMineAPI im = SessionMethods.getInterMineAPI(request.getSession());
      ObjectStore os = im.getObjectStore();
      Query q = new Query();
      QueryClass c = new QueryClass(InterMineObject.class);
      q.addFrom(c);
      q.addToSelect(c);
      // Add a unique value to the select to avoid caching the query
      QueryValue token = new QueryValue(System.currentTimeMillis());
      q.addToSelect(token);
      Results r = os.execute(q, 1, false, false, false);
      if (r.get(0) != null) {
        response.getOutputStream().print("OK");
      } else {
        response.getOutputStream().print("NO RESULTS");
      }
    }
    return null;
  }
Exemplo n.º 4
0
  /** {@inheritDoc} */
  @Override
  public ActionForward execute(
      @SuppressWarnings("unused") ActionMapping mapping,
      @SuppressWarnings("unused") ActionForm form,
      HttpServletRequest request,
      HttpServletResponse response)
      throws Exception {
    HttpSession session = request.getSession();
    final InterMineAPI im = SessionMethods.getInterMineAPI(session);
    ObjectStore os = im.getObjectStore();
    WebConfig webConfig = SessionMethods.getWebConfig(request);
    Integer objectId = new Integer(request.getParameter("object"));
    String fieldName = request.getParameter("field");
    String fileType = request.getParameter("type");
    InterMineObject object = os.getObjectById(objectId);

    FieldExporter fieldExporter = null;

    Set classes = DynamicUtil.decomposeClass(object.getClass());

    Iterator classIter = classes.iterator();

    while (classIter.hasNext()) {
      Class c = (Class) classIter.next();

      Type thisTypeConfig = webConfig.getTypes().get(c.getName());

      FieldConfig fc = thisTypeConfig.getFieldConfigMap().get(fieldName);

      if (fc != null) {
        String fieldExporterClassName = fc.getFieldExporter();
        if (fieldExporterClassName != null) {
          fieldExporter = (FieldExporter) Class.forName(fieldExporterClassName).newInstance();
          break;
        }
      }
    }

    if (fieldExporter == null) {
      Object fieldValue = object.getFieldValue(fieldName);
      if (fileType == null || fileType.length() == 0) {
        response.setContentType("text/plain; charset=UTF-8");
        response.setHeader("Content-Disposition ", "inline; filename=" + fieldName + ".txt");
      } else {
        response.setContentType("text/" + fileType);
        response.setHeader(
            "Content-Disposition ", "inline; filename=" + fieldName + "." + fileType);
      }
      PrintStream out = new PrintStream(response.getOutputStream());
      if (fieldValue instanceof ClobAccess) {
        ((ClobAccess) fieldValue).drainToPrintStream(out);
      } else {
        out.print(fieldValue);
      }
      out.flush();
    } else {
      fieldExporter.exportField(object, fieldName, os, response);
    }
    return null;
  }
Exemplo n.º 5
0
 /**
  * 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;
 }
Exemplo n.º 6
0
  private InterMineObject getRequestedObject(InterMineAPI im, HttpServletRequest request) {

    String idString = request.getParameter("id");
    Integer id = new Integer(Integer.parseInt(idString));
    ObjectStore os = im.getObjectStore();
    InterMineObject requestedObject = null;
    try {
      requestedObject = os.getObjectById(id);
    } catch (ObjectStoreException e) {
      Log.warn("Accessed report page with id: " + id + " but failed to find object.", e);
    }
    return requestedObject;
  }
  private void doDuplicates(final Map<String, Object> ret, BagQueryResult bqr, String key) {
    Map<String, Map<String, List>> issues = bqr.getIssues().get(key);
    if (issues == null) {
      return;
    }
    for (Map<String, List> issueSet : issues.values()) {
      for (Entry<String, List> identToObjects : issueSet.entrySet()) {
        String ident = identToObjects.getKey();
        for (Object o : identToObjects.getValue()) {
          InterMineObject imo;
          Map<String, Object> resultItem;
          if (o instanceof Integer) {
            try {
              imo = im.getObjectStore().getObjectById((Integer) o);
            } catch (ObjectStoreException e) {
              throw new IllegalStateException("Could not retrieve object reported as match", e);
            }
          } else if (o instanceof ConvertedObjectPair) {
            imo = ((ConvertedObjectPair) o).getNewObject();
          } else {
            imo = (InterMineObject) o;
          }
          String idKey = String.valueOf(imo.getId());
          if (ret.containsKey(idKey)) {
            resultItem = (Map<String, Object>) ret.get(idKey);
          } else {
            resultItem = new HashMap<String, Object>();
            resultItem.put("identifiers", new HashMap<String, Object>());
          }
          if (!resultItem.containsKey("summary")) {
            resultItem.put("summary", getObjectDetails(imo));
          }
          Map<String, Object> identifiers = (Map<String, Object>) resultItem.get("identifiers");

          if (!identifiers.containsKey(ident)) {
            identifiers.put(ident, new HashSet<String>());
          }
          Set<String> categories = (Set<String>) identifiers.get(ident);
          categories.add(key);
          String className = DynamicUtil.getSimpleClassName(imo.getClass());
          resultItem.put("type", className.replaceAll("^.*\\.", ""));
          ret.put(idKey, resultItem);
        }
      }
    }
  }
Exemplo n.º 8
0
  private static void runSpanValidationQuery(InterMineAPI im) {

    // a Map contains orgName and its chrInfo accordingly
    // e.g. <D.Melanogaster, (D.Melanogaster, X, 5000)...>
    chrInfoMap = new HashMap<String, List<ChromosomeInfo>>();

    try {
      Query q = new Query();

      QueryClass qcOrg = new QueryClass(Organism.class);
      QueryClass qcChr = new QueryClass(Chromosome.class);

      // Result columns
      QueryField qfOrgName = new QueryField(qcOrg, "shortName");
      QueryField qfChrPID = new QueryField(qcChr, "primaryIdentifier");
      QueryField qfChrLength = new QueryField(qcChr, "length");

      // As in SQL SELECT ?,?,?
      q.addToSelect(qfOrgName);
      q.addToSelect(qfChrPID);
      q.addToSelect(qfChrLength);

      // As in SQL FROM ?,?
      q.addFrom(qcChr);
      q.addFrom(qcOrg);

      // As in SQL WHERE ?
      QueryObjectReference organism = new QueryObjectReference(qcChr, "organism");
      ContainsConstraint ccOrg = new ContainsConstraint(organism, ConstraintOp.CONTAINS, qcOrg);
      q.setConstraint(ccOrg);

      Results results = im.getObjectStore().execute(q);

      // a List contains all the chrInfo (organism, chrPID, length)
      List<ChromosomeInfo> chrInfoList = new ArrayList<ChromosomeInfo>();
      // a Set contains all the orgName
      Set<String> orgSet = new HashSet<String>();

      // Handle results
      for (Iterator<?> iter = results.iterator(); iter.hasNext(); ) {
        ResultsRow<?> row = (ResultsRow<?>) iter.next();

        String org = (String) row.get(0);
        String chrPID = (String) row.get(1);
        Integer chrLength = (Integer) row.get(2);

        // Add orgName to HashSet to filter out duplication
        orgSet.add(org);

        if (chrLength != null) {
          ChromosomeInfo chrInfo = new ChromosomeInfo();
          chrInfo.setOrgName(org);
          chrInfo.setChrPID(chrPID);
          chrInfo.setChrLength(chrLength);

          // Add ChromosomeInfo to Arraylist
          chrInfoList.add(chrInfo);
        }
      }

      // Iterate orgSet and chrInfoList to put data in chrInfoMap which has the key as the
      // orgName and value as a ArrayList containing a list of chrInfo which has the same
      // orgName
      for (String o : orgSet) {

        // a List to store chrInfo for the same organism
        List<ChromosomeInfo> chrInfoSubList = new ArrayList<ChromosomeInfo>();

        for (ChromosomeInfo chrInfo : chrInfoList) {
          if (o.equals(chrInfo.getOrgName())) {
            chrInfoSubList.add(chrInfo);
            chrInfoMap.put(o, chrInfoSubList);
          }
        }
      }

    } catch (Exception e) {
      e.printStackTrace();
    }
  }
Exemplo n.º 9
0
  /** The method to run all the queries. */
  @SuppressWarnings("rawtypes")
  private void queryExecutor() {

    // Use spanOverlapFullResultMap to store the data in the session
    @SuppressWarnings("unchecked")
    Map<String, Map<GenomicRegion, List<SpanQueryResultRow>>> spanOverlapFullResultMap =
        (Map<String, Map<GenomicRegion, List<SpanQueryResultRow>>>)
            request.getSession().getAttribute("spanOverlapFullResultMap");

    if (spanOverlapFullResultMap == null) {
      spanOverlapFullResultMap =
          new HashMap<String, Map<GenomicRegion, List<SpanQueryResultRow>>>();
    }

    Map<GenomicRegion, List<SpanQueryResultRow>> spanOverlapResultDisplayMap =
        Collections.synchronizedMap(new LinkedHashMap<GenomicRegion, List<SpanQueryResultRow>>());

    // GBrowse track
    @SuppressWarnings("unchecked")
    Map<String, Map<GenomicRegion, LinkedHashMap<String, LinkedHashSet<GBrowseTrackInfo>>>>
        gbrowseFullTrackMap =
            (HashMap<
                    String,
                    Map<GenomicRegion, LinkedHashMap<String, LinkedHashSet<GBrowseTrackInfo>>>>)
                request.getSession().getAttribute("gbrowseFullTrackMap");

    if (gbrowseFullTrackMap == null) {
      gbrowseFullTrackMap =
          new HashMap<
              String, Map<GenomicRegion, LinkedHashMap<String, LinkedHashSet<GBrowseTrackInfo>>>>();
    }

    Map<GenomicRegion, LinkedHashMap<String, LinkedHashSet<GBrowseTrackInfo>>> gbrowseTrackMap =
        Collections.synchronizedMap(
            new LinkedHashMap<
                GenomicRegion, LinkedHashMap<String, LinkedHashSet<GBrowseTrackInfo>>>());

    if (!spanOverlapFullResultMap.containsKey(spanUUIDString)) {
      spanOverlapFullResultMap.put(spanUUIDString, spanOverlapResultDisplayMap);
      request.getSession().setAttribute("spanOverlapFullResultMap", spanOverlapFullResultMap);

      gbrowseFullTrackMap.put(spanUUIDString, gbrowseTrackMap);
      request.getSession().setAttribute("gbrowseFullTrackMap", gbrowseFullTrackMap);

      try {
        Query q;
        for (GenomicRegion aSpan : spanList) {
          q = new Query();
          q.setDistinct(true);

          String chrPID = aSpan.getChr();
          Integer start = aSpan.getStart();
          Integer end = aSpan.getEnd();

          /*
          >>>>> TEST CODE <<<<<
          LOG.info("OrgName: " + orgName);
          LOG.info("chrPID: " + chrPID);
          LOG.info("start: " + start);
          LOG.info("end: " + end);
          LOG.info("FeatureTypes: " + ftKeys);
          LOG.info("Submissions: " + subKeys);
          >>>>> TEST CODE <<<<<
          */

          // DB tables
          QueryClass qcOrg = new QueryClass(Organism.class);
          QueryClass qcChr = new QueryClass(Chromosome.class);
          QueryClass qcFeature = new QueryClass(SequenceFeature.class);
          QueryClass qcLoc = new QueryClass(Location.class);
          QueryClass qcSubmission = new QueryClass(Submission.class);

          QueryField qfOrgName = new QueryField(qcOrg, "shortName");
          QueryField qfChrPID = new QueryField(qcChr, "primaryIdentifier");
          QueryField qfFeaturePID = new QueryField(qcFeature, "primaryIdentifier");
          QueryField qfFeatureId = new QueryField(qcFeature, "id");
          QueryField qfFeatureClass = new QueryField(qcFeature, "class");
          QueryField qfSubmissionTitle = new QueryField(qcSubmission, "title");
          QueryField qfSubmissionDCCid = new QueryField(qcSubmission, "DCCid");
          QueryField qfChr = new QueryField(qcChr, "primaryIdentifier");
          QueryField qfLocStart = new QueryField(qcLoc, "start");
          QueryField qfLocEnd = new QueryField(qcLoc, "end");

          q.addToSelect(qfFeatureId);
          q.addToSelect(qfFeaturePID);
          q.addToSelect(qfFeatureClass);
          q.addToSelect(qfChr);
          q.addToSelect(qfLocStart);
          q.addToSelect(qfLocEnd);
          q.addToSelect(qfSubmissionDCCid);
          q.addToSelect(qfSubmissionTitle);

          q.addFrom(qcChr);
          q.addFrom(qcOrg);
          q.addFrom(qcFeature);
          q.addFrom(qcLoc);
          q.addFrom(qcSubmission);

          q.addToOrderBy(qfLocStart, "ascending");

          ConstraintSet constraints = new ConstraintSet(ConstraintOp.AND);

          q.setConstraint(constraints);

          // SequenceFeature.organism = Organism
          QueryObjectReference organism = new QueryObjectReference(qcFeature, "organism");
          ContainsConstraint ccOrg = new ContainsConstraint(organism, ConstraintOp.CONTAINS, qcOrg);
          constraints.addConstraint(ccOrg);

          // Organism.name = orgName
          SimpleConstraint scOrg =
              new SimpleConstraint(qfOrgName, ConstraintOp.EQUALS, new QueryValue(orgName));
          constraints.addConstraint(scOrg);

          // Location.feature = SequenceFeature
          QueryObjectReference locSubject = new QueryObjectReference(qcLoc, "feature");
          ContainsConstraint ccLocSubject =
              new ContainsConstraint(locSubject, ConstraintOp.CONTAINS, qcFeature);
          constraints.addConstraint(ccLocSubject);

          // Location.locatedOn = Chromosome
          QueryObjectReference locObject = new QueryObjectReference(qcLoc, "locatedOn");
          ContainsConstraint ccLocObject =
              new ContainsConstraint(locObject, ConstraintOp.CONTAINS, qcChr);
          constraints.addConstraint(ccLocObject);

          // Chromosome.primaryIdentifier = chrPID
          SimpleConstraint scChr =
              new SimpleConstraint(qfChrPID, ConstraintOp.EQUALS, new QueryValue(chrPID));
          constraints.addConstraint(scChr);

          // SequenceFeature.submissions = Submission
          QueryCollectionReference submission =
              new QueryCollectionReference(qcFeature, "submissions");
          ContainsConstraint ccSubmission =
              new ContainsConstraint(submission, ConstraintOp.CONTAINS, qcSubmission);
          constraints.addConstraint(ccSubmission);

          // SequenceFeature.class in a list
          constraints.addConstraint(new BagConstraint(qfFeatureClass, ConstraintOp.IN, ftKeys));
          // Submission.CCDid in a list
          constraints.addConstraint(new BagConstraint(qfSubmissionDCCid, ConstraintOp.IN, subKeys));

          OverlapRange overlapInput =
              new OverlapRange(new QueryValue(start), new QueryValue(end), locObject);
          OverlapRange overlapFeature =
              new OverlapRange(
                  new QueryField(qcLoc, "start"), new QueryField(qcLoc, "end"), locObject);
          OverlapConstraint oc =
              new OverlapConstraint(overlapInput, ConstraintOp.OVERLAPS, overlapFeature);
          constraints.addConstraint(oc);

          Results results = im.getObjectStore().execute(q);

          /*
          >>>>> TEST CODE <<<<<
          LOG.info("Query: " + q.toString());
          LOG.info("Result Size: " + results.size());
          LOG.info("Result >>>>> " + results);
          >>>>> TEST CODE <<<<<
          */

          List<SpanQueryResultRow> spanResults = new ArrayList<SpanQueryResultRow>();
          if (results == null || results.isEmpty()) {
            spanOverlapResultDisplayMap.put(aSpan, null);
            gbrowseTrackMap.put(aSpan, null);
          } else {
            for (Iterator<?> iter = results.iterator(); iter.hasNext(); ) {
              ResultsRow<?> row = (ResultsRow<?>) iter.next();

              SpanQueryResultRow aRow = new SpanQueryResultRow();
              aRow.setFeatureId((Integer) row.get(0));
              aRow.setFeaturePID((String) row.get(1));
              aRow.setFeatureClass(((Class) row.get(2)).getSimpleName());
              aRow.setChr((String) row.get(3));
              aRow.setStart((Integer) row.get(4));
              aRow.setEnd((Integer) row.get(5));
              aRow.setSubDCCid((String) row.get(6));
              aRow.setSubTitle((String) row.get(7));

              spanResults.add(aRow);
            }
            spanOverlapResultDisplayMap.put(aSpan, spanResults);
            gbrowseTrackMap.put(aSpan, getSubGbrowseTrack(spanResults)); // Gbrowse
          }
        }

      } catch (Exception e) {
        e.printStackTrace();
      }
    }
  }
  /** {@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(".", " &gt; ");
        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;
  }
  @Override
  public void display(HttpServletRequest request, ReportObject reportObject) {

    // get the gene/protein in question from the request
    InterMineObject object = reportObject.getObject();

    // API connection
    HttpSession session = request.getSession();
    final InterMineAPI im = SessionMethods.getInterMineAPI(session);
    Model model = im.getModel();
    PathQuery query = new PathQuery(model);

    // cast me Gene
    Gene gene = (Gene) object;
    Object genePrimaryIDObj = gene.getPrimaryIdentifier();
    if (genePrimaryIDObj != null) {
      // fetch the expression
      String genePrimaryID = String.valueOf(genePrimaryIDObj);
      query = geneExpressionAtlasQuery(genePrimaryID, query);

      // execute the query
      Profile profile = SessionMethods.getProfile(session);
      PathQueryExecutor executor = im.getPathQueryExecutor(profile);
      ExportResultsIterator values = executor.execute(query);

      // convert to a map
      GeneExpressionAtlasDiseasesExpressions geae =
          new GeneExpressionAtlasDiseasesExpressions(values);

      // attach to results
      request.setAttribute("expressions", geae);
      request.setAttribute("url", "http://www.ebi.ac.uk/gxa/experiment/E-MTAB-62/" + genePrimaryID);
      request.setAttribute("defaultPValue", "1e-4");
      request.setAttribute("defaultTValue", "4");

      // get the corresponding collection
      for (FieldDescriptor fd : reportObject.getClassDescriptor().getAllFieldDescriptors()) {
        if ("atlasExpression".equals(fd.getName()) && fd.isCollection()) {
          // fetch the collection
          Collection<?> collection = null;
          try {
            collection = (Collection<?>) reportObject.getObject().getFieldValue("atlasExpression");
          } catch (IllegalAccessException e) {
            e.printStackTrace();
          }

          List<Class<?>> lc =
              PathQueryResultHelper.queryForTypesInCollection(
                  reportObject.getObject(), "atlasExpression", im.getObjectStore());

          // create an InlineResultsTable
          InlineResultsTable t =
              new InlineResultsTable(
                  collection,
                  fd.getClassDescriptor().getModel(),
                  SessionMethods.getWebConfig(request),
                  im.getClassKeys(),
                  collection.size(),
                  false,
                  lc);

          request.setAttribute("collection", t);
          break;
        }
      }
    }
  }
Exemplo n.º 12
0
  /** {@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;
  }