/**
   * Create a PathQuery to get results for a collection of items from an InterMineObject
   *
   * @param webConfig the WebConfig
   * @param os the production ObjectStore
   * @param object the InterMineObject
   * @param referencedClassName the collection type
   * @param field the name of the field for the collection in the InterMineObject
   * @return a PathQuery
   */
  public static PathQuery makePathQueryForCollection(
      WebConfig webConfig,
      ObjectStore os,
      InterMineObject object,
      String referencedClassName,
      String field) {

    String className = TypeUtil.unqualifiedName(DynamicUtil.getSimpleClassName(object.getClass()));
    Path path;
    try {
      path = new Path(os.getModel(), className + "." + field);
    } catch (PathException e) {
      throw new IllegalArgumentException(
          "Could not build path for \"" + className + "." + field + "\".");
    }
    List<Class<?>> types = new ArrayList<Class<?>>();
    if (path.endIsCollection()) {
      CollectionDescriptor end = (CollectionDescriptor) path.getEndFieldDescriptor();
      // Only look for types if the refClass exactly matches the path type.
      if (end.getReferencedClassName().equals(referencedClassName)) {
        types = queryForTypesInCollection(object, field, os);
      }
      if (types.isEmpty()) {
        // the collection was empty, but still generate a query with the collection type
        types.add(os.getModel().getClassDescriptorByName(referencedClassName).getType());
      }
    } else if (path.endIsReference()) {
      types.add(path.getLastClassDescriptor().getType());
    }
    return makePathQueryForCollectionForClass(webConfig, os.getModel(), object, field, types);
  }
Example #2
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;
  }
  /** {@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;
  }
Example #4
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;
  }
 public void testTranslation() throws Exception {
   ObjectStore os2 =
       new ObjectStoreTranslatingImpl(
           Model.getInstanceByName("testmodel"),
           ObjectStoreFactory.getObjectStore("os.unittest"),
           new CompanyTranslator());
   Query q = new Query();
   QueryClass qc = new QueryClass(InterMineObject.class);
   q.addToSelect(qc);
   q.addFrom(qc);
   Results res = os2.execute(q);
   assertEquals(2, res.size());
   assertEquals("CompanyA", ((Bank) ((ResultsRow) res.get(0)).get(0)).getName());
   assertEquals("CompanyB", ((Bank) ((ResultsRow) res.get(1)).get(0)).getName());
 }
Example #6
0
  /**
   * Constructor.
   *
   * @param name The name of this bag.
   * @param type The type it is meant to have.
   * @param desc A free text description of the bag.
   * @param createdAt When this list was first created.
   * @param os The production object store.
   * @param profileId The internal DB id of the profile of the user this list belongs to.
   * @param savedBagId The internal DB id of the saved bag this list represents.
   * @param osb The bag that represents the production DB level stored set of object ids.
   * @param userprofileObjectStore The user-profile object store writer.
   * @throws ObjectStoreException If a ObjectStoreBag needs to be created and there is a problem
   *     doing so.
   */
  public InvalidBag(
      String name,
      String type,
      String desc,
      Date createdAt,
      ObjectStore os,
      Integer savedBagId,
      Integer profileId,
      ObjectStoreBag osb,
      ObjectStoreWriter userprofileObjectStore)
      throws ObjectStoreException {

    this.type = TypeUtil.unqualifiedName(type);
    this.name = name;
    this.description = desc;
    this.dateCreated = createdAt;

    checkArguments(os, userprofileObjectStore);
    this.os = os;
    if (osb == null) {
      this.osb = os.createObjectStoreBag();
    } else {
      this.osb = osb;
    }
    this.uosw = userprofileObjectStore;

    this.profileId = profileId;
    this.savedBagId = savedBagId;
  }
  /**
   * Retrieve the publications to be updated
   *
   * @param os The ObjectStore to read from
   * @return a List of publications
   */
  protected List<Publication> getPublications(ObjectStore os) {
    Query q = new Query();
    QueryClass qc = new QueryClass(Publication.class);
    q.addFrom(qc);
    q.addToSelect(qc);

    ConstraintSet cs = new ConstraintSet(ConstraintOp.OR);

    SimpleConstraint scTitle =
        new SimpleConstraint(new QueryField(qc, "title"), ConstraintOp.IS_NULL);
    cs.addConstraint(scTitle);

    SimpleConstraint scYear =
        new SimpleConstraint(new QueryField(qc, "year"), ConstraintOp.IS_NULL);
    cs.addConstraint(scYear);

    SimpleConstraint scFirstAuthor =
        new SimpleConstraint(new QueryField(qc, "firstAuthor"), ConstraintOp.IS_NULL);
    cs.addConstraint(scFirstAuthor);

    q.setConstraint(cs);

    @SuppressWarnings("unchecked")
    List<Publication> retval = (List<Publication>) ((List) os.executeSingleton(q));
    return retval;
  }
Example #8
0
 /**
  * Add a contains constraint to Query (q) built with the query class and attribute given in input
  *
  * @param query The query to add a reference to.
  * @param qc The class the reference belongs to.
  * @param attribute the name of the field of the class.
  * @param attributePath Another similarly named field - I wish it had been documented!
  * @return The query class of the attributePath.
  */
 protected QueryClass addReference(
     final Query query, final QueryClass qc, String attribute, String attributePath) {
   ConstraintSet cs = (ConstraintSet) query.getConstraint();
   QueryReference qr = null;
   String type = "";
   boolean useSubClass = false;
   if (WidgetConfigUtil.isPathContainingSubClass(os.getModel(), attribute)) {
     useSubClass = true;
     type = attribute.substring(attribute.indexOf("[") + 1, attribute.indexOf("]"));
     attribute = attribute.substring(0, attribute.indexOf("["));
   }
   QueryClass qcTmp = null;
   try {
     qr = new QueryObjectReference(qc, attribute);
     if (useSubClass) {
       try {
         qcTmp = new QueryClass(Class.forName(os.getModel().getPackageName() + "." + type));
       } catch (ClassNotFoundException cnfe) {
         LOG.error("The type " + type + " doesn't exist in the model.");
       }
     } else {
       qcTmp = new QueryClass(qr.getType());
     }
   } catch (IllegalArgumentException e) {
     // Not a reference - try collection instead
     qr = new QueryCollectionReference(qc, attribute);
     if (useSubClass) {
       try {
         qcTmp = new QueryClass(Class.forName(os.getModel().getPackageName() + "." + type));
       } catch (ClassNotFoundException cnfe) {
         LOG.error("The type " + type + " doesn't exist in the model.");
       }
     } else {
       qcTmp = new QueryClass(TypeUtil.getElementType(qc.getType(), attribute));
     }
   }
   QueryClass ret;
   if (!queryClassInQuery.containsKey(attributePath)) {
     ret = qcTmp;
     query.addFrom(ret);
     cs.addConstraint(new ContainsConstraint(qr, ConstraintOp.CONTAINS, ret));
     queryClassInQuery.put(attributePath, ret);
   } else {
     ret = queryClassInQuery.get(attributePath);
   }
   return ret;
 }
  @Override
  public void execute() {
    System.out.println("Creating lucene index for keyword search...");

    ObjectStore os;
    try {
      os = getObjectStore();
    } catch (Exception e) {
      throw new BuildException(e);
    }
    if (!(os instanceof ObjectStoreInterMineImpl)) {
      // Yes, yes, this is horrific...
      throw new RuntimeException(
          "Got invalid ObjectStore - must be an " + "instance of ObjectStoreInterMineImpl!");
    }

    /*
    String configFileName = "objectstoresummary.config.properties";
    InputStream configStream = classLoader.getResourceAsStream(configFileName);
    if (configStream == null) {
        throw new RuntimeException("can't find resource: " + configFileName);
    }

    Properties properties = new Properties();
    properties.load(configStream);*/

    // read class keys to figure out what are keyFields during indexing
    InputStream is = this.getClass().getClassLoader().getResourceAsStream("class_keys.properties");
    Properties classKeyProperties = new Properties();
    try {
      classKeyProperties.load(is);
    } catch (NullPointerException e) {
      throw new BuildException("Could not find the class keys");
    } catch (IOException e) {
      throw new BuildException("Could not read the class keys", e);
    }
    Map<String, List<FieldDescriptor>> classKeys =
        ClassKeyHelper.readKeys(os.getModel(), classKeyProperties);

    // index and save
    KeywordSearch.saveIndexToDatabase(os, classKeys);
    KeywordSearch.deleteIndexDirectory();
  }
 private static Map<String, List<FieldDescriptor>> getClassKeys(ObjectStore os) {
   Properties classKeyProps = new Properties();
   try {
     InputStream inputStream =
         ProfileManagerBinding.class.getClassLoader().getResourceAsStream("class_keys.properties");
     classKeyProps.load(inputStream);
   } catch (IOException ioe) {
     throw new BuildException("class_keys.properties not found", ioe);
   }
   return ClassKeyHelper.readKeys(os.getModel(), classKeyProps);
 }
Example #11
0
 /**
  * Fix this bag by changing its type. If fixed, the DB will be corrected to store the new state,
  * and this bag will be marked as deleted.
  *
  * @param newType The new type of this list. This must be a valid type in the current model.
  * @return A valid InterMineBag.
  * @throws UnknownBagTypeException If the new type is not in the current model.
  * @throws ObjectStoreException If there is a problem saving state to the DB.
  */
 public InterMineBag amendTo(String newType) throws UnknownBagTypeException, ObjectStoreException {
   if (os.getModel().getClassDescriptorByName(newType) == null) {
     throw new UnknownBagTypeException(newType + " is not a valid class name");
   }
   fireEvent(new DeletionEvent(this));
   InvalidBag amended =
       new InvalidBag(
           name, newType, description, dateCreated, os, savedBagId, profileId, osb, uosw);
   SavedBag sb = amended.storeSavedBag();
   deleted = true;
   return new InterMineBag(os, sb.getId(), uosw);
 }
Example #12
0
 /**
  * Initialises the state of this object. This is done lazily, because it requires the use of a
  * database connection to discover the length of the clob, and that cannot be done while inside
  * the ObjectStoreWriter while it has exclusive use of the connection.
  */
 protected void init() {
   if (results == null) {
     Query q = new Query();
     q.addToSelect(clob);
     results = os.executeSingleton(q, 20, false, false, true);
     int pageCount = results.size();
     if (pageCount == 0) {
       length = 0;
     } else {
       String lastPage = (String) results.get(pageCount - 1);
       length = CLOB_PAGE_SIZE * (pageCount - 1) + lastPage.length();
     }
   }
 }
  /**
   * Search for the classes in a collection for a given InterMineObject, for example find all of the
   * sub-classes of Employee in the Department.employees collection of a given Department. If there
   * are no subclasses or the collection is empty a list with the type of the collection is
   * returned.
   *
   * @param object an InterMineObject to inspect
   * @param field the name if the collection to check
   * @param os the ObjectStore in which to execute the query
   * @return a list of classes in the collection
   */
  public static List<Class<?>> queryForTypesInCollection(
      InterMineObject object, String field, ObjectStore os) {
    List<Class<?>> typesInCollection = new ArrayList<Class<?>>();

    // if there are no subclasses there can only be one type in the collection
    Model model = os.getModel();
    ClassDescriptor startCld =
        model.getClassDescriptorByName(DynamicUtil.getSimpleClassName(object));
    CollectionDescriptor col = startCld.getCollectionDescriptorByName(field, true);
    ClassDescriptor colCld = col.getReferencedClassDescriptor();

    if (model.getAllSubs(colCld).isEmpty()) {
      // there aren't any subclasses, so no need to do a query
      typesInCollection.add(colCld.getType());
    } else {
      // there may be multiple subclasses in the collection, need to run a query
      Query query = new Query();
      QueryClass qc = new QueryClass(colCld.getType());
      query.addFrom(qc);
      query.addToSelect(new QueryField(qc, "class"));
      query.setDistinct(true);
      query.setConstraint(
          new ContainsConstraint(
              new QueryCollectionReference(object, field), ConstraintOp.CONTAINS, qc));
      for (Object o : os.executeSingleton(query)) {
        typesInCollection.add((Class<?>) o);
      }

      // Collection was empty but add collection type to be consistent with collection types
      // without subclasses.
      if (typesInCollection.isEmpty()) {
        typesInCollection.add(colCld.getType());
      }
    }
    return typesInCollection;
  }
Example #14
0
 /**
  * @param bag the intermine bag
  * @param os the object store
  * @param filter the filter
  * @param config The description of the widget.
  */
 public WidgetLdr(InterMineBag bag, ObjectStore os, String filter, WidgetConfig config) {
   this.bag = bag;
   this.os = os;
   this.filter = filter;
   try {
     startClass =
         new QueryClass(
             Class.forName(os.getModel().getPackageName() + "." + config.getStartClass()));
   } catch (ClassNotFoundException e) {
     if (config instanceof EnrichmentWidgetConfig || config instanceof GraphWidgetConfig) {
       throw new IllegalArgumentException(
           "Not found the class set in startClass for the" + " widget " + config.getId(), e);
     }
   }
 }
Example #15
0
  /**
   * Constructor callable by the ProfileManager.
   *
   * @param savedBag The saved bag retrieved from the DB.
   * @param profileId The id of the user profile.
   * @param os The production object store.
   * @param userprofileObjectStore The userprofile object store.
   * @throws ObjectStoreException If there is a problem creating an ObjectStoreBag.
   */
  protected InvalidBag(
      SavedBag savedBag,
      Integer profileId,
      ObjectStore os,
      ObjectStoreWriter userprofileObjectStore)
      throws ObjectStoreException {

    this.type = TypeUtil.unqualifiedName(savedBag.getType());
    this.name = savedBag.getName();
    this.description = savedBag.getDescription();
    this.dateCreated = savedBag.getDateCreated();

    checkArguments(os, userprofileObjectStore);
    this.os = os;
    this.osb = os.createObjectStoreBag();
    this.uosw = userprofileObjectStore;

    this.profileId = profileId;
    this.savedBagId = savedBag.getId();
  }
  /**
   * @param os object store
   * @return map of name to so term
   * @throws ObjectStoreException if something goes wrong
   */
  protected Map<String, SOTerm> populateSOTermMap(ObjectStore os) throws ObjectStoreException {
    Map<String, SOTerm> soTerms = new HashMap<String, SOTerm>();
    Query q = new Query();
    q.setDistinct(false);

    QueryClass qcSOTerm = new QueryClass(SOTerm.class);
    q.addToSelect(qcSOTerm);
    q.addFrom(qcSOTerm);
    q.addToOrderBy(qcSOTerm);

    Results res = os.execute(q);

    Iterator it = res.iterator();

    while (it.hasNext()) {
      ResultsRow<InterMineObject> rr = (ResultsRow<InterMineObject>) it.next();
      SOTerm soTerm = (SOTerm) rr.get(0);
      soTerms.put(soTerm.getName(), soTerm);
    }
    return soTerms;
  }
  /** {@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;
  }
  public void testLoad() throws Exception {

    TSVFileReaderTask tsvTask = new TSVFileReaderTask();
    tsvTask.setIgnoreDuplicates(true);
    tsvTask.setIntegrationWriterAlias("integration.unittestmulti");
    tsvTask.setSourceName("testsource");

    cleanObjects(tsvTask.getDirectDataLoader().getIntegrationWriter());

    File tempFile = File.createTempFile("TSVFileReaderTaskTest", "tmp");
    FileWriter fw = new FileWriter(tempFile);
    InputStream is = getClass().getClassLoader().getResourceAsStream("TSVFileReaderTaskTest.tsv");
    BufferedReader br = new BufferedReader(new InputStreamReader(is));

    String line = null;
    while ((line = br.readLine()) != null) {
      fw.write(line + "\n");
    }

    fw.close();

    FileSet fileSet = new FileSet();

    fileSet.setFile(tempFile);

    tsvTask.addFileSet(fileSet);

    InputStream confInputStream =
        getClass().getClassLoader().getResourceAsStream("TSVFileReaderTaskTest.properties");
    DelimitedFileConfiguration dfc = new DelimitedFileConfiguration(model, confInputStream);

    tsvTask.executeInternal(dfc, tempFile);

    // Check the results to see if we have some data...
    ObjectStore os = tsvTask.getDirectDataLoader().getIntegrationWriter().getObjectStore();

    Query q = new Query();
    QueryClass empQueryClass = new QueryClass(Employee.class);
    QueryField qf0 = new QueryField(empQueryClass, "age");
    QueryField qf1 = new QueryField(empQueryClass, "name");
    QueryField qf2 = new QueryField(empQueryClass, "fullTime");

    q.addToSelect(qf0);
    q.addToSelect(qf1);
    q.addToSelect(qf2);
    q.addFrom(empQueryClass);

    q.addToOrderBy(qf1);

    Results r = os.execute(q);

    if (r.size() != 3) {
      for (List<Object> rr : (List<List<Object>>) ((List) r)) {
        System.err.print("row: ");
        for (Object obj : rr) {
          System.err.print("{" + obj + "} ");
        }
        System.err.println();
      }
    }

    assertEquals(3, r.size());

    List expectedRow0 = Arrays.asList(new Object[] {new Integer(10), "EmployeeA1", Boolean.FALSE});
    assertEquals(expectedRow0, r.get(0));

    List expectedRow1 = Arrays.asList(new Object[] {new Integer(20), "EmployeeA2", Boolean.TRUE});
    assertEquals(expectedRow1, r.get(1));

    List expectedRow2 = Arrays.asList(new Object[] {new Integer(0), "EmployeeA3", Boolean.FALSE});
    assertEquals(expectedRow2, r.get(2));
  }
  /** {@inheritDoc} */
  public PathQuery generatePathQuery(
      ObjectStore os, InterMineBag bag, String series, String category) {

    Model model = os.getModel();
    PathQuery q = new PathQuery(model);

    Path geneSymbol = PathQuery.makePath(model, q, "Gene.symbol");
    Path genePrimary = PathQuery.makePath(model, q, "Gene.primaryIdentifier");
    Path haemAtlasSampleName =
        PathQuery.makePath(model, q, "Gene.probeSets.haemAtlasResults.sampleName");
    Path haemAtlasGroup = PathQuery.makePath(model, q, "Gene.probeSets.haemAtlasResults.group");
    Path haemAtlasAverage =
        PathQuery.makePath(model, q, "Gene.probeSets.haemAtlasResults.averageIntensity");
    Path haemAtlasSample = PathQuery.makePath(model, q, "Gene.probeSets.haemAtlasResults.sample");
    Path haemAtlasP =
        PathQuery.makePath(model, q, "Gene.probeSets.haemAtlasResults.detectionProbabilities");
    Path haemAtlasIlluId = PathQuery.makePath(model, q, "Gene.probeSets.illuId");

    List<Path> view = new ArrayList<Path>();

    view.add(geneSymbol);
    view.add(genePrimary);
    view.add(haemAtlasSampleName);
    view.add(haemAtlasGroup);
    view.add(haemAtlasAverage);
    view.add(haemAtlasSample);
    view.add(haemAtlasP);
    view.add(haemAtlasIlluId);

    q.setViewPaths(view);

    String bagType = bag.getType();
    ConstraintOp constraintOp = ConstraintOp.IN;
    String constraintValue = bag.getName();

    String label = null, id = null, code = q.getUnusedConstraintCode();
    Constraint c = new Constraint(constraintOp, constraintValue, false, label, code, id, null);
    q.addNode(bagType).getConstraints().add(c);

    constraintOp = ConstraintOp.EQUALS;
    code = q.getUnusedConstraintCode();
    PathNode categoryNode = q.addNode("Gene.probeSets.haemAtlasResults.sampleName");
    Constraint categoryConstraint =
        new Constraint(constraintOp, series, false, label, code, id, null);
    categoryNode.getConstraints().add(categoryConstraint);

    constraintOp = ConstraintOp.LESS_THAN;
    code = q.getUnusedConstraintCode();
    PathNode seriesNode = q.addNode("Gene.probeSets.haemAtlasResults.detectionProbabilities");
    Constraint seriesConstraint = new Constraint(constraintOp, 0.01, false, label, code, id, null);
    seriesNode.getConstraints().add(seriesConstraint);

    q.setConstraintLogic("A and B and C");
    q.syncLogicExpression("and");

    List<OrderBy> sortOrder = new ArrayList<OrderBy>();

    sortOrder.add(new OrderBy(geneSymbol, "asc"));
    sortOrder.add(new OrderBy(genePrimary));

    q.setSortOrder(sortOrder);

    return q;
  }
  public void testCreateSpanningLocations() throws Exception {
    Exon exon1 = (Exon) DynamicUtil.createObject(Collections.singleton(Exon.class));
    exon1.setId(new Integer(107));
    Exon exon2 = (Exon) DynamicUtil.createObject(Collections.singleton(Exon.class));
    exon2.setId(new Integer(108));
    Exon exon3 = (Exon) DynamicUtil.createObject(Collections.singleton(Exon.class));
    exon3.setId(new Integer(109));

    Location exon1OnChr = createLocation(getChromosome(), exon1, "1", 51, 100, Location.class);
    exon1OnChr.setId(new Integer(1010));
    Location exon2OnChr = createLocation(getChromosome(), exon2, "1", 201, 250, Location.class);
    exon2OnChr.setId(new Integer(1011));
    Location exon3OnChr = createLocation(getChromosome(), exon3, "1", 201, 400, Location.class);
    exon3OnChr.setId(new Integer(1012));

    Transcript trans1 =
        (Transcript) DynamicUtil.createObject(Collections.singleton(Transcript.class));
    trans1.setId(new Integer(201));

    Transcript trans2 =
        (Transcript) DynamicUtil.createObject(Collections.singleton(Transcript.class));
    trans2.setId(new Integer(202));

    Location trans2OnChr = createLocation(getChromosome(), trans2, "1", 61, 300, Location.class);

    Gene gene = (Gene) DynamicUtil.createObject(Collections.singleton(Gene.class));
    gene.setId(new Integer(301));

    exon1.setTranscripts(new HashSet<Transcript>(Arrays.asList(new Transcript[] {trans1})));
    exon2.setTranscripts(new HashSet<Transcript>(Arrays.asList(new Transcript[] {trans1})));

    // the location of exon3 should be ignored by createSpanningLocations() because trans2
    // already has a location
    exon3.setTranscripts(new HashSet<Transcript>(Arrays.asList(new Transcript[] {trans2})));

    trans1.setGene(gene);
    trans2.setGene(gene);

    Set<InterMineObject> toStore =
        new HashSet<InterMineObject>(
            Arrays.asList(
                new InterMineObject[] {
                  getChromosome(),
                  gene,
                  trans1,
                  trans2,
                  exon1,
                  exon2,
                  exon3,
                  exon1OnChr,
                  exon2OnChr,
                  trans2OnChr
                }));

    for (InterMineObject imo : toStore) {
      osw.store(imo);
    }

    CalculateLocations cl = new CalculateLocations(osw);
    cl.createSpanningLocations("Transcript", "Exon", "exons");
    cl.createSpanningLocations("Gene", "Transcript", "transcripts");

    ObjectStore os = osw.getObjectStore();
    Transcript resTrans1 = (Transcript) os.getObjectById(new Integer(201));

    Assert.assertEquals(1, resTrans1.getLocations().size());
    Location resTrans1Location = (Location) resTrans1.getLocations().iterator().next();
    Assert.assertEquals(51, resTrans1Location.getStart().intValue());
    Assert.assertEquals(250, resTrans1Location.getEnd().intValue());

    Transcript resTrans2 = (Transcript) os.getObjectById(new Integer(202));

    Assert.assertEquals(1, resTrans2.getLocations().size());
    Location resTrans2Location = (Location) resTrans2.getLocations().iterator().next();
    Assert.assertEquals(61, resTrans2Location.getStart().intValue());
    Assert.assertEquals(300, resTrans2Location.getEnd().intValue());

    Gene resGene = (Gene) os.getObjectById(new Integer(301));
    Assert.assertEquals(1, resGene.getLocations().size());
    Location resGeneLocation = (Location) resGene.getLocations().iterator().next();
    Assert.assertEquals(51, resGeneLocation.getStart().intValue());
    Assert.assertEquals(300, resGeneLocation.getEnd().intValue());
  }
Example #21
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;
  }
  /**
   * Synchronize publications with pubmed using pmid
   *
   * @throws Exception if an error occurs
   */
  public void execute() throws Exception {
    // Needed so that STAX can find it's implementation classes
    ClassLoader cl = Thread.currentThread().getContextClassLoader();

    Thread.currentThread().setContextClassLoader(getClass().getClassLoader());

    Database db = null;
    Transaction txn = null;
    try {
      if (osAlias == null) {
        throw new BuildException("osAlias attribute is not set");
      }
      if (outputFile == null) {
        throw new BuildException("outputFile attribute is not set");
      }

      // environment is transactional
      EnvironmentConfig envConfig = new EnvironmentConfig();
      envConfig.setTransactional(true);
      envConfig.setAllowCreate(true);

      Environment env = new Environment(new File(cacheDirName), envConfig);

      DatabaseConfig dbConfig = new DatabaseConfig();
      dbConfig.setTransactional(true);
      dbConfig.setAllowCreate(true);
      dbConfig.setSortedDuplicates(true);

      db = env.openDatabase(null, "publications_db", dbConfig);

      txn = env.beginTransaction(null, null);

      LOG.info("Starting EntrezPublicationsRetriever");

      Writer writer = new FileWriter(outputFile);
      ObjectStore os = ObjectStoreFactory.getObjectStore(osAlias);

      Set<Integer> idsToFetch = new HashSet<Integer>();
      itemFactory = new ItemFactory(os.getModel(), "-1_");
      writer.write(FullRenderer.getHeader() + ENDL);
      for (Iterator<Publication> iter = getPublications(os).iterator(); iter.hasNext(); ) {
        String pubMedId = iter.next().getPubMedId();
        Integer pubMedIdInteger;
        try {
          pubMedIdInteger = Integer.valueOf(pubMedId);
        } catch (NumberFormatException e) {
          // not a pubmed id
          continue;
        }

        if (seenPubMeds.contains(pubMedIdInteger)) {
          continue;
        }
        DatabaseEntry key = new DatabaseEntry(pubMedId.getBytes());
        DatabaseEntry data = new DatabaseEntry();
        if (db.get(txn, key, data, null).equals(OperationStatus.SUCCESS)) {
          try {
            ByteArrayInputStream mapInputStream = new ByteArrayInputStream(data.getData());
            ObjectInputStream deserializer = new ObjectInputStream(mapInputStream);
            Map<String, Object> pubMap = (Map) deserializer.readObject();
            writeItems(writer, mapToItems(itemFactory, pubMap));
            seenPubMeds.add(pubMedIdInteger);
          } catch (EOFException e) {
            // ignore and fetch it again
            System.err.println(
                "found in cache, but igored due to cache problem: " + pubMedIdInteger);
          }
        } else {
          idsToFetch.add(pubMedIdInteger);
        }
      }

      Iterator<Integer> idIter = idsToFetch.iterator();
      Set<Integer> thisBatch = new HashSet<Integer>();
      while (idIter.hasNext()) {
        Integer pubMedIdInteger = idIter.next();
        thisBatch.add(pubMedIdInteger);
        if (thisBatch.size() == BATCH_SIZE || !idIter.hasNext() && thisBatch.size() > 0) {
          try {
            // the server may return less publications than we ask for, so keep a Map
            Map<String, Map<String, Object>> fromServerMap = null;

            for (int i = 0; i < MAX_TRIES; i++) {
              BufferedReader br = new BufferedReader(getReader(thisBatch));
              StringBuffer buf = new StringBuffer();
              String line;
              while ((line = br.readLine()) != null) {
                buf.append(line + "\n");
              }
              fromServerMap = new HashMap<String, Map<String, Object>>();
              Throwable throwable = null;
              try {
                if (loadFullRecord) {
                  SAXParser.parse(
                      new InputSource(new StringReader(buf.toString())),
                      new FullRecordHandler(fromServerMap),
                      false);
                } else {
                  SAXParser.parse(
                      new InputSource(new StringReader(buf.toString())),
                      new SummaryRecordHandler(fromServerMap),
                      false);
                }
              } catch (Throwable e) {
                LOG.error("Couldn't parse PubMed XML", e);
                // try again or re-throw the Throwable
                throwable = e;
              }
              if (i == MAX_TRIES) {
                throw new RuntimeException(
                    "failed to parse: " + buf.toString() + " - tried " + MAX_TRIES + " times",
                    throwable);
              } else {
                if (throwable != null) {
                  // try again
                  continue;
                }
              }

              for (String id : fromServerMap.keySet()) {
                writeItems(writer, mapToItems(itemFactory, fromServerMap.get(id)));
              }
              addToDb(txn, db, fromServerMap);
              break;
            }
            thisBatch.clear();
          } finally {
            txn.commit();
            // start a new transaction incase there is an exception while parsing
            txn = env.beginTransaction(null, null);
          }
        }
      }
      writeItems(writer, authorMap.values());
      writeItems(writer, meshTerms.values());
      writer.write(FullRenderer.getFooter() + ENDL);
      writer.flush();
      writer.close();
    } catch (Throwable e) {
      throw new RuntimeException("failed to get all publications", e);
    } finally {
      txn.commit();
      db.close();
      Thread.currentThread().setContextClassLoader(cl);
    }
  }
Example #23
0
  /**
   * Read the UTRs collection of MRNA then set the fivePrimeUTR and threePrimeUTR fields with the
   * corresponding UTRs.
   *
   * @throws Exception if anything goes wrong
   */
  public void createUtrRefs() throws Exception {
    long startTime = System.currentTimeMillis();
    Query q = new Query();
    q.setDistinct(false);

    QueryClass qcMRNA = new QueryClass(model.getClassDescriptorByName("MRNA").getType());
    q.addFrom(qcMRNA);
    q.addToSelect(qcMRNA);
    q.addToOrderBy(qcMRNA);

    QueryClass qcUTR = new QueryClass(model.getClassDescriptorByName("UTR").getType());
    q.addFrom(qcUTR);
    q.addToSelect(qcUTR);
    q.addToOrderBy(qcUTR);

    QueryCollectionReference mrnaUtrsRef = new QueryCollectionReference(qcMRNA, "UTRs");
    ContainsConstraint mrnaUtrsConstraint =
        new ContainsConstraint(mrnaUtrsRef, ConstraintOp.CONTAINS, qcUTR);

    QueryObjectReference fivePrimeRef = new QueryObjectReference(qcMRNA, "fivePrimeUTR");
    ContainsConstraint fivePrimeNullConstraint =
        new ContainsConstraint(fivePrimeRef, ConstraintOp.IS_NULL);
    QueryObjectReference threePrimeRef = new QueryObjectReference(qcMRNA, "threePrimeUTR");
    ContainsConstraint threePrimeNullConstraint =
        new ContainsConstraint(threePrimeRef, ConstraintOp.IS_NULL);

    ConstraintSet cs = new ConstraintSet(ConstraintOp.AND);
    cs.addConstraint(mrnaUtrsConstraint);
    cs.addConstraint(fivePrimeNullConstraint);
    cs.addConstraint(threePrimeNullConstraint);

    q.setConstraint(cs);

    ObjectStore os = osw.getObjectStore();

    ((ObjectStoreInterMineImpl) os).precompute(q, Constants.PRECOMPUTE_CATEGORY);
    Results res = os.execute(q, 500, true, true, true);

    int count = 0;
    InterMineObject lastMRNA = null;

    InterMineObject fivePrimeUTR = null;
    InterMineObject threePrimeUTR = null;

    osw.beginTransaction();

    Class<? extends FastPathObject> fivePrimeUTRCls =
        model.getClassDescriptorByName("FivePrimeUTR").getType();

    Iterator<?> resIter = res.iterator();
    while (resIter.hasNext()) {
      ResultsRow<?> rr = (ResultsRow<?>) resIter.next();
      InterMineObject mrna = (InterMineObject) rr.get(0);
      InterMineObject utr = (InterMineObject) rr.get(1);

      if (lastMRNA != null && !mrna.getId().equals(lastMRNA.getId())) {
        // clone so we don't change the ObjectStore cache
        InterMineObject tempMRNA = PostProcessUtil.cloneInterMineObject(lastMRNA);
        if (fivePrimeUTR != null) {
          tempMRNA.setFieldValue("fivePrimeUTR", fivePrimeUTR);
          fivePrimeUTR = null;
        }
        if (threePrimeUTR != null) {
          tempMRNA.setFieldValue("threePrimeUTR", threePrimeUTR);
          threePrimeUTR = null;
        }
        osw.store(tempMRNA);
        count++;
      }

      if (DynamicUtil.isInstance(utr, fivePrimeUTRCls)) {
        fivePrimeUTR = utr;
      } else {
        threePrimeUTR = utr;
      }

      lastMRNA = mrna;
    }

    if (lastMRNA != null) {
      // clone so we don't change the ObjectStore cache
      InterMineObject tempMRNA = PostProcessUtil.cloneInterMineObject(lastMRNA);
      tempMRNA.setFieldValue("fivePrimeUTR", fivePrimeUTR);
      tempMRNA.setFieldValue("threePrimeUTR", threePrimeUTR);
      osw.store(tempMRNA);
      count++;
    }
    LOG.info(
        "Stored MRNA "
            + count
            + " times ("
            + count * 2
            + " fields set)"
            + " - took "
            + (System.currentTimeMillis() - startTime)
            + " ms.");
    osw.commitTransaction();

    // now ANALYSE tables relating to class that has been altered - may be rows added
    // to indirection tables
    if (osw instanceof ObjectStoreWriterInterMineImpl) {
      ClassDescriptor cld = model.getClassDescriptorByName("MRNA");
      DatabaseUtil.analyse(((ObjectStoreWriterInterMineImpl) osw).getDatabase(), cld, false);
    }
  }
Example #24
0
 @SuppressWarnings("unchecked")
 private Collection<E> executeCollection(Query q) {
   return (Collection) os.executeSingleton(q, batchSize, !noOptimise, !noExplain, true);
 }
  public void testSetChromosomeLocationsAndLengths() throws Exception {
    Chromosome chr1 =
        (Chromosome) DynamicUtil.createObject(Collections.singleton(Chromosome.class));
    chr1.setPrimaryIdentifier("1");
    chr1.setId(new Integer(101));
    Chromosome chr2 =
        (Chromosome) DynamicUtil.createObject(Collections.singleton(Chromosome.class));
    chr1.setPrimaryIdentifier("2");
    chr1.setId(new Integer(102));

    Exon exon1 = (Exon) DynamicUtil.createObject(Collections.singleton(Exon.class));
    exon1.setId(new Integer(107));
    exon1.setLength(new Integer(1000));
    Exon exon2 = (Exon) DynamicUtil.createObject(Collections.singleton(Exon.class));
    exon2.setId(new Integer(108));
    Exon exon3 = (Exon) DynamicUtil.createObject(Collections.singleton(Exon.class));
    exon3.setId(new Integer(109));

    // exon 2 has two chromosome locations, shouldn't get chromosome[Location] references
    Location exon1OnChr = createLocation(chr1, exon1, "1", 51, 100, Location.class);
    exon1OnChr.setId(new Integer(1010));
    Location exon2OnChr = createLocation(chr2, exon2, "1", 201, 250, Location.class);
    exon2OnChr.setId(new Integer(1011));
    Location exon2OnChrDup = createLocation(chr1, exon2, "1", 501, 550, Location.class);
    exon2OnChrDup.setId(new Integer(1012));
    Location exon3OnChr = createLocation(chr2, exon3, "1", 601, 650, Location.class);
    exon3OnChr.setId(new Integer(1013));

    Set<InterMineObject> toStore =
        new HashSet<InterMineObject>(
            Arrays.asList(
                new InterMineObject[] {
                  chr1, chr2, exon1, exon2, exon3, exon1OnChr, exon2OnChr, exon2OnChrDup, exon3OnChr
                }));

    for (InterMineObject imo : toStore) {
      osw.store(imo);
    }

    CalculateLocations cl = new CalculateLocations(osw);
    cl.setChromosomeLocationsAndLengths();

    ObjectStore os = osw.getObjectStore();
    Exon resExon1 = (Exon) os.getObjectById(new Integer(107));
    Exon resExon2 = (Exon) os.getObjectById(new Integer(108));
    Exon resExon3 = (Exon) os.getObjectById(new Integer(109));

    assertEquals(chr1.getId(), resExon1.getChromosome().getId());
    assertEquals(exon1OnChr.getId(), resExon1.getChromosomeLocation().getId());

    assertNull(resExon2.getChromosome());
    assertNull(resExon2.getChromosomeLocation());

    assertEquals(chr2.getId(), resExon3.getChromosome().getId());
    assertEquals(exon3OnChr.getId(), resExon3.getChromosomeLocation().getId());

    // exon1 has length set so should stay as 1000, exon3 should get length 50 set from location
    assertEquals(new Integer(1000), resExon1.getLength());
    assertEquals(new Integer(50), resExon3.getLength());
    // nothing done to exon2
    assertNull(resExon2.getLength());
  }