public void oncreate() {

    if (Gate.getPluginsHome() != null) {
      System.out.println(Gate.getPluginsHome());
    } else {
      Gate.setPluginsHome(new File("C:/Program Files/GATE_Developer_8.0/plugins"));
    }
  }
 /** Constructor, setting the home directory. */
 public TestLearningAPI(String arg0) throws GateException, MalformedURLException {
   super(arg0);
   if (!initialized) {
     Gate.init();
     learningHome = new File(new File(Gate.getGateHome(), "plugins"), "Learning");
     Gate.getCreoleRegister().addDirectory(learningHome.toURI().toURL());
     initialized = true;
   }
 }
Exemple #3
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  @Override
  public void setUp() throws MalformedURLException, IOException, GateException {
    if (!Gate.isInitialised()) {
      Gate.init();
    }

    File baseDir = new File(Gate.getPluginsHome(), "Tagger_Measurements");

    parser =
        new MeasurementsParser(
            (new File(baseDir, "resources/units.dat")).toURI().toURL(),
            new File(baseDir, "resources/common_words.txt").toURI().toURL());
  }
Exemple #4
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  public static void main(String[] args) throws Exception {

    /*Set to your Gate installation home*/
    XMLConfiguration config = new XMLConfiguration("config/madaap.xml");
    Gate.setGateHome(new File(config.getString("gate.home")));

    Gate.init();

    Gate.getCreoleRegister()
        .registerDirectories(
            new File(Gate.getPluginsHome(), ANNIEConstants.PLUGIN_DIR).toURI().toURL());

    /*Set the path to \Plugins\Tools directory*/
    Gate.getCreoleRegister()
        .registerDirectories(
            new File(config.getString("gate.home") + "\\plugins\\Tools").toURI().toURL());

    /*Declare queue to receive URL from various collectors*/
    BlockingQueue<URL> queue = new LinkedBlockingQueue<URL>();

    /*Start extractor, initialization will run the thread*/
    Extractor e = new Extractor(queue);

    /*Timer to schedule collector tasks at regular intervals*/
    Timer timer = new Timer();

    /*Collect URL from /input/url.txt*/
    TimerTask manualFeederTask = new ManualFeeder(queue);
    long manualFeederTime =
        Long.parseLong(config.getString("timer.ManualFeederInterval"))
            * ONE_HOUR; // Unit of ManualFeederTime: hour
    timer.scheduleAtFixedRate(manualFeederTask, 0, manualFeederTime);

    /*Collect URL from twitter feed*/

    TimerTask twitterTask = new Twitter(queue);
    long twitterTime =
        Long.parseLong(config.getString("timer.TwitterInterval"))
            * ONE_MIN; // Unit of twitterTime: minutes
    timer.scheduleAtFixedRate(twitterTask, 0, twitterTime);

    /*Check all URL if they are active or not*/
    TimerTask checkerTask = new Checker();
    long checkerTime =
        Long.parseLong(config.getString("timer.CheckerInterval"))
            * ONE_HOUR; // Unit of CheckerTime: hour
    timer.scheduleAtFixedRate(checkerTask, 0, checkerTime);
  }
Exemple #5
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  @Override
  public void setIndexDefinition(IndexDefinition definition) {
    if (definition != null) {
      this.getFeatures().put(GateConstants.CORPUS_INDEX_DEFINITION_FEATURE_KEY, definition);

      String className = definition.getIrEngineClassName();
      try {
        // Class aClass = Class.forName(className);
        Class<?> aClass = Class.forName(className, true, Gate.getClassLoader());
        IREngine engine = (IREngine) aClass.newInstance();
        this.indexManager = engine.getIndexmanager();
        this.indexManager.setIndexDefinition(definition);
        this.indexManager.setCorpus(this);
      } catch (Exception e) {
        e.printStackTrace(Err.getPrintWriter());
      }
      // switch (definition.getIndexType()) {
      // case GateConstants.IR_LUCENE_INVFILE:
      // this.indexManager = new LuceneIndexManager();
      // this.indexManager.setIndexDefinition(definition);
      // this.indexManager.setCorpus(this);
      // break;
      // }
      this.addedDocs = new Vector<Document>();
      this.removedDocIDs = new Vector<String>();
      this.changedDocs = new Vector<Document>();
    }
  }
  /** This method is called when the SAX parser encounts the beginning of the XML document. */
  @Override
  public void startDocument() throws org.xml.sax.SAXException {
    // init of variables in the parent
    super.startDocument();

    /**
     * We will attempt to add namespace feature info to each namespaced element only if three
     * parameters are set in the global or local config file: ADD_NAMESPACE_FEATURES: boolean flag
     * ELEMENT_NAMESPACE_URI: feature name to use to hold namespace uri ELEMENT_NAMESPACE_PREFIX:
     * feature name to use to hold namespace prefix
     */
    OptionsMap configData = Gate.getUserConfig();

    boolean addNSFeature =
        Boolean.parseBoolean((String) configData.get(GateConstants.ADD_NAMESPACE_FEATURES));
    namespaceURIFeature = (String) configData.get(GateConstants.ELEMENT_NAMESPACE_URI);
    namespacePrefixFeature = (String) configData.get(GateConstants.ELEMENT_NAMESPACE_PREFIX);

    deserializeNamespaceInfo =
        (addNSFeature
            && namespacePrefixFeature != null
            && !namespacePrefixFeature.isEmpty()
            && namespaceURIFeature != null
            && !namespaceURIFeature.isEmpty());
  }
Exemple #7
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  @Override
  public URL getResource(String name) {
    URL result = null;

    result = super.getResource(name);
    if (result != null) return result;

    if (getParent() == null) {
      result = Gate.getClassLoader().findResource(name);
      if (result != null) return result;
    }

    Set<GateClassLoader> children;
    synchronized (childClassLoaders) {
      children = new LinkedHashSet<GateClassLoader>(childClassLoaders.values());
    }

    for (GateClassLoader cl : children) {
      if (!cl.isIsolated()) {
        result = cl.getResource(name);
        if (result != null) return result;
      }
    }

    return null;
  }
  public void setConf(Configuration conf) {
    config = conf;

    if (applicationDescriptorPath == null)
      throw new RuntimeException("GATE application path is null");

    // create one instance of the GATE application
    // need to avoid concurrent access to the application
    try {

      if (inited == false) {
        File gateHome = new File(applicationDescriptorPath.getFile()).getParentFile();
        LOG.info("Setting GATE_HOME as " + gateHome);
        File pluginsHome = new File(gateHome, "plugins");
        // the config files are in the job archive - not in the GATE
        // application
        // zip
        // File siteConfigFile = new File(conf
        // .getResource("site-gate.xml").getFile());
        // File userConfig = new File(conf.getResource("user-gate.xml")
        // .getFile());
        Gate.runInSandbox(true);
        Gate.setGateHome(gateHome);
        Gate.setPluginsHome(pluginsHome);
        // Gate.setSiteConfigFile(siteConfigFile);
        // Gate.setUserConfigFile(userConfig);
        // the builtInCreoleDir files
        // are stored in the same place as the config ones
        // Gate.setBuiltinCreoleDir(conf.getResource("creole.xml"));
        Gate.init();
        inited = true;
      }

      corpus = Factory.newCorpus("DummyCorpus");

      this.GATEapplication =
          (CorpusController) PersistenceManager.loadObjectFromUrl(applicationDescriptorPath);

      // load the annotation and feature filters from the configuration
      this.filters = GATEAnnotationFilters.getFilters(config);

    } catch (Exception e) {
      LOG.error("Encountered error while initialising GATE", e);
      throw new RuntimeException(e);
    }
  }
Exemple #9
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 protected void initLocalData() {
   docTableModel = new DocumentTableModel();
   try {
     documentsLoadedCount = Gate.getCreoleRegister().getAllInstances("gate.Document").size();
   } catch (GateException exception) {
     exception.printStackTrace();
   }
 }
  public JSONObject persian_sentiment(String text) throws Exception {

    oncreate();

    File PersianGapp = new File("C:/Users/mohammad/Desktop/New folder/Gate/application.xgapp");
    // initialise GATE - this must be done before calling any GATE APIs
    Gate.init();

    // load the saved application

    CorpusController application =
        (CorpusController) PersistenceManager.loadObjectFromFile(PersianGapp);

    // Create a Corpus to use.  We recycle the same Corpus object for each
    // iteration.  The string parameter to newCorpus() is simply the
    // GATE-internal name to use for the corpus.  It has no particular
    // significance.
    Corpus corpus = Factory.newCorpus("BatchProcessApp Corpus");
    application.setCorpus(corpus);

    // process the files one by one

    // load the document (using the specified encoding if one was given)

    Document doc = Factory.newDocument(text);

    // put the document in the corpus
    corpus.add(doc);

    // run the application
    application.execute();

    String featureName = "Doc_sentiment";
    FeatureMap features = doc.getFeatures();
    // remove the document from the corpus again
    corpus.clear();

    // doc.getFeatures().
    // Release the document, as it is no longer needed
    Factory.deleteResource(doc);

    LinkedHashMap originalContent = (LinkedHashMap) features.get(featureName);

    String obj = (String) originalContent.get("sentiment");
    // BigDecimal pos =(BigDecimal) originalContent.get("positive");
    // BigDecimal neg =(BigDecimal) originalContent.get("negative");
    // System.out.println(obj);
    // create Json for response to user
    JSONObject obj1 = new JSONObject();
    obj1.put("sentiment", obj);
    /*obj1.put("positive",pos);
    //obj1.put("negative",neg);
    System.out.print("----------");
    System.out.print(obj1);
    System.out.print("----------");*/
    // application.cleanup();
    return obj1;
  }
  /**
   * Initialise the ANNIE system. This creates a "corpus pipeline" application that can be used to
   * run sets of documents through the extraction system.
   */
  public void initAnnie() throws GateException, IOException {
    Out.prln("Initialising ANNIE...");

    // load the ANNIE application from the saved state in plugins/ANNIE
    File pluginsHome = Gate.getPluginsHome();
    File anniePlugin = new File(pluginsHome, "ANNIE");
    File annieGapp = new File(anniePlugin, "ANNIE_with_defaults.gapp");
    annieController = (CorpusController) PersistenceManager.loadObjectFromFile(annieGapp);

    Out.prln("...ANNIE loaded");
  } // initAnnie()
Exemple #12
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 /**
  * Every LR that is a CreoleListener (and other Listeners too) must override this method and make
  * sure it removes itself from the objects which it has been listening to. Otherwise, the object
  * will not be released from memory (memory leak!).
  */
 @Override
 public void cleanup() {
   if (DEBUG) Out.prln("serial corpus cleanup called");
   if (corpusListeners != null) corpusListeners = null;
   if (documents != null) documents.clear();
   docDataList.clear();
   Gate.getCreoleRegister().removeCreoleListener(this);
   if (this.dataStore != null) {
     this.dataStore.removeDatastoreListener(this);
   }
 }
Exemple #13
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 public static void main(String[] args) {
   try {
     Gate.init();
     TestHashGazetteer testGaz = new TestHashGazetteer("");
     testGaz.setUp();
     testGaz.testHashGazetteer();
     testGaz.tearDown();
   } catch (Exception e) {
     e.printStackTrace();
   }
 } // main
Exemple #14
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 public void actionPerformed(ActionEvent e) {
   List<Resource> loadedDocuments;
   try {
     // get all the documents loaded in the system
     loadedDocuments = Gate.getCreoleRegister().getAllInstances("gate.Document");
   } catch (GateException ge) {
     // gate.Document is not registered in creole.xml....what is!?
     throw new GateRuntimeException(
         "gate.Document is not registered in the creole register!\n"
             + "Something must be terribly wrong...take a vacation!");
   }
   Vector<String> docNames = new Vector<String>();
   for (Resource loadedDocument : new ArrayList<Resource>(loadedDocuments)) {
     if (corpus.contains(loadedDocument)) {
       loadedDocuments.remove(loadedDocument);
     } else {
       docNames.add(loadedDocument.getName());
     }
   }
   JList docList = new JList(docNames);
   docList.getSelectionModel().setSelectionInterval(0, docNames.size() - 1);
   docList.setCellRenderer(renderer);
   final JOptionPane optionPane =
       new JOptionPane(
           new JScrollPane(docList), JOptionPane.QUESTION_MESSAGE, JOptionPane.OK_CANCEL_OPTION);
   final JDialog dialog =
       optionPane.createDialog(CorpusEditor.this, "Add document(s) to this corpus");
   docList.addMouseListener(
       new MouseAdapter() {
         public void mouseClicked(MouseEvent e) {
           if (e.getClickCount() == 2) {
             optionPane.setValue(JOptionPane.OK_OPTION);
             dialog.dispose();
           }
         }
       });
   dialog.setVisible(true);
   if (optionPane.getValue().equals(JOptionPane.OK_OPTION)) {
     int[] selectedIndices = docList.getSelectedIndices();
     for (int selectedIndice : selectedIndices) {
       corpus.add((Document) loadedDocuments.get(selectedIndice));
     }
   }
   changeMessage();
 }
 public RuleBaseViewer() {
   super();
   String pluginPath = "";
   try {
     File pluginDir = new File(Gate.getGateHome().toString() + "/plugins/Semano/");
     pluginPath = pluginDir.getAbsoluteFile().toURI().toURL().toString();
     if (pluginPath != null) {
       pluginPath = pluginPath.substring(5, pluginPath.length());
       System.out.println("plugin directory: " + pluginPath);
     }
     editURL = new File(pluginPath + "pencil.gif").toURI().toURL();
     deleteURL = new File(pluginPath + "delete.gif").toURI().toURL();
     System.out.println("loading icons from " + editURL.toString());
   } catch (MalformedURLException e) {
     // this should never be reached!
     System.err.println("icons not found!");
   }
 }
Exemple #16
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  /**
   * Constructor to create a SerialCorpus from a transient one. This is called by adopt() to store
   * the transient corpus and re-route the methods calls to it, until the corpus is sync-ed on disk.
   * After that, the transientCorpus will always be null, so the new functionality will be used
   * instead.
   */
  protected SerialCorpusImpl(Corpus tCorpus) {
    // copy the corpus name and features from the one in memory
    this.setName(tCorpus.getName());
    this.setFeatures(tCorpus.getFeatures());

    docDataList = new ArrayList<DocumentData>();
    // now cache the names of all docs for future use
    List<String> docNames = tCorpus.getDocumentNames();
    for (int i = 0; i < docNames.size(); i++) {
      Document doc = tCorpus.get(i);
      docDataList.add(new DocumentData(docNames.get(i), null, doc.getClass().getName()));
    }

    // copy all the documents from the transient corpus
    documents = new ArrayList<Document>();
    documents.addAll(tCorpus);

    // make sure we fire events when docs are added/removed/etc
    Gate.getCreoleRegister().addCreoleListener(this);
  }
Exemple #17
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  /**
   * Populates this Persistence with the data that needs to be stored from the original source
   * object.
   */
  @Override
  public void extractDataFromSource(Object source) throws PersistenceException {
    if (!(source instanceof ProcessingResource)) {
      throw new UnsupportedOperationException(
          getClass().getName()
              + " can only be used for "
              + ProcessingResource.class.getName()
              + " objects!\n"
              + source.getClass().getName()
              + " is not a "
              + ProcessingResource.class.getName());
    }

    super.extractDataFromSource(source);
    Resource res = (Resource) source;

    ResourceData rData = Gate.getCreoleRegister().get(res.getClass().getName());
    if (rData == null)
      throw new PersistenceException("Could not find CREOLE data for " + res.getClass().getName());

    // now get the runtime params
    ParameterList params = rData.getParameterList();
    try {
      // get the values for the init time parameters
      runtimeParams = Factory.newFeatureMap();
      // this is a list of lists
      Iterator<List<Parameter>> parDisjIter = params.getRuntimeParameters().iterator();
      while (parDisjIter.hasNext()) {
        Iterator<Parameter> parIter = parDisjIter.next().iterator();
        while (parIter.hasNext()) {
          Parameter parameter = parIter.next();
          String parName = parameter.getName();
          Object parValue = res.getParameterValue(parName);
          ((FeatureMap) runtimeParams).put(parName, parValue);
        }
      }
      runtimeParams = PersistenceManager.getPersistentRepresentation(runtimeParams);
    } catch (ResourceInstantiationException rie) {
      throw new PersistenceException(rie);
    }
  }
Exemple #18
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  public void setTransientSource(Object source) {
    if (!(source instanceof Corpus)) return;

    // the following initialisation is only valid when we're
    // constructing
    // this object from a transient one. If it has already been stored
    // in
    // a datastore, then the initialisation is done in readObject()
    // since
    // this method is the one called by serialisation, when objects
    // are restored.
    if (this.dataStore != null && this.lrPersistentId != null) return;

    Corpus tCorpus = (Corpus) source;

    // copy the corpus name and features from the one in memory
    this.setName(tCorpus.getName());
    this.setFeatures(tCorpus.getFeatures());

    docDataList = new ArrayList<DocumentData>();
    // now cache the names of all docs for future use
    List<String> docNames = tCorpus.getDocumentNames();
    for (int i = 0; i < docNames.size(); i++) {
      Document aDoc = tCorpus.get(i);
      docDataList.add(new DocumentData(docNames.get(i), null, aDoc.getClass().getName()));
    }

    // copy all the documents from the transient corpus
    documents = new ArrayList<Document>();
    documents.addAll(tCorpus);

    this.addedDocs = new Vector<Document>();
    this.removedDocIDs = new Vector<String>();
    this.changedDocs = new Vector<Document>();

    // make sure we fire events when docs are added/removed/etc
    Gate.getCreoleRegister().addCreoleListener(this);
  }
Exemple #19
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  /**
   * readObject - calls the default readObject() and then initialises the transient data
   *
   * @serialData Read serializable fields. No optional data read.
   */
  private void readObject(ObjectInputStream s) throws IOException, ClassNotFoundException {
    s.defaultReadObject();
    documents = new ArrayList<Document>(docDataList.size());
    for (int i = 0; i < docDataList.size(); i++) documents.add(null);
    corpusListeners = new Vector<CorpusListener>();
    // finally set the creole listeners if the LR is like that
    Gate.getCreoleRegister().addCreoleListener(this);
    if (this.dataStore != null) this.dataStore.addDatastoreListener(this);

    // if indexed construct the manager.
    /*IndexDefinition definition = (IndexDefinition)this.getFeatures().get(
            GateConstants.CORPUS_INDEX_DEFINITION_FEATURE_KEY);
    if(definition != null) {
      String className = definition.getIrEngineClassName();
      try {
        // Class aClass = Class.forName(className);
        Class<?> aClass = Class.forName(className, true, Gate.getClassLoader());
        IREngine engine = (IREngine)aClass.newInstance();
        this.indexManager = engine.getIndexmanager();
        this.indexManager.setIndexDefinition(definition);
        this.indexManager.setCorpus(this);
      }
      catch(Exception e) {
        e.printStackTrace(Err.getPrintWriter());
      }
      // switch (definition.getIndexType()) {
      // case GateConstants.IR_LUCENE_INVFILE:
      // this.indexManager = new LuceneIndexManager();
      // this.indexManager.setIndexDefinition(definition);
      // this.indexManager.setCorpus(this);
      // break;
      // }
      this.addedDocs = new Vector<Document>();
      this.removedDocIDs = new Vector<String>();
      this.changedDocs = new Vector<Document>();
    }*/
  } // readObject
Exemple #20
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  /**
   * @param args
   * @throws Exception
   */
  public static void main(String[] args) throws Exception {
    /* Parse command line arguments */
    Getopt g = new Getopt("gateExtractor", args, "i:r:te");
    g.setOpterr(false);

    String inputPath = "";
    String outputPath = "";

    boolean train = false;
    boolean eval = false;
    boolean run = false;

    int c;
    String arg;
    while ((c = g.getopt()) != -1) {
      switch (c) {
        case 'i':
          arg = g.getOptarg();
          if (arg == null || arg.isEmpty()) {
            usage("Please provide an input path");
          }
          inputPath = arg;
          break;
        case 'r':
          run = true;
          arg = g.getOptarg();
          if (arg == null || arg.isEmpty()) {
            usage("Please provide an output path");
          }
          outputPath = arg;
          break;
        case 't':
          train = true;
          break;
        case 'e':
          eval = true;
          break;
        case '?':
        default:
          usage(null);
      }
    }

    if (args.length == 0 || (!run && !train && !eval)) {
      usage("Nothing to do.");
    }

    if (inputPath == null || inputPath.isEmpty()) {
      usage("Please provide an input path");
    }

    if (run && (outputPath == null || outputPath.isEmpty())) {
      usage("Please provide an output directory!");
    }

    if (train && eval) {
      usage("Only one mode allowed at a time");
    }

    if (train && run) {
      usage("Only one mode allowed at a time");
    }

    if (eval && run) {
      usage("Only one mode allowed at a time");
    }

    /* Initialize GATE */
    String location =
        new File(Main.class.getProtectionDomain().getCodeSource().getLocation().getPath())
            .getParent();
    String resourcesFolder = location + "/resources";
    Gate.setGateHome(new File(resourcesFolder));

    /* Create ml-config.xml with threads */

    createConfig(resourcesFolder + File.separator);
    Gate.init();

    /* Load Corpus */
    log.info("Loading Corpus ... ");
    Corpus corpus = Factory.newCorpus("Training Corpus");
    File directory = new File(inputPath);
    URL url = directory.toURI().toURL();
    corpus.populate(url, null, null, true);
    log.info("Done loading Corpus!");

    Pipeline pipeline = null;

    /* Do Tagging */
    pipeline = new Tagger();
    pipeline.run(corpus, resourcesFolder);

    /* Train */
    if (train) {
      pipeline = new Trainer();
      pipeline.run(corpus, resourcesFolder);
    }

    /* Apply learned rules */
    if (run) {
      pipeline = new Extractor();
      pipeline.run(corpus, resourcesFolder);

      ExecutorService executorService = Executors.newFixedThreadPool(20);
      for (int i = 0; i < corpus.size(); i++) {
        executorService.execute(new OutputGenerator(outputPath, corpus.get(i)));
      }
      executorService.shutdown();
      executorService.awaitTermination(Long.MAX_VALUE, TimeUnit.DAYS);
    }

    /* Evaluate results */
    if (eval) {
      pipeline = new Evaluator();
      pipeline.run(corpus, resourcesFolder);
    }

    /* Clean up */
    Factory.deleteResource(corpus);
    outputFile_mlConfigThreads.delete();
  }
  @Override
  public Resource init() throws ResourceInstantiationException {
    gracefulExit = false;

    if (configFileURL == null) {
      gracefulExit = true;
      gate.util.Err.println("No configuration file provided!");
    }

    if (japeURL == null) {
      gracefulExit = true;
      gate.util.Err.println("No JAPE grammar file provided!");
    }

    // create the init params for the JAPE transducer
    FeatureMap params = Factory.newFeatureMap();
    params.put(Transducer.TRANSD_GRAMMAR_URL_PARAMETER_NAME, japeURL);
    // Code borrowed from Mark Greenwood's Measurements PR
    if (japeTransducer == null) {
      // if this is the first time we are running init then actually create a
      // new transducer as we don't already have one
      FeatureMap hidden = Factory.newFeatureMap();
      Gate.setHiddenAttribute(hidden, true);
      japeTransducer =
          (Transducer) Factory.createResource("gate.creole.Transducer", params, hidden);
    } else {
      // we are being run through a call to reInit so simply re-init the
      // underlying JAPE transducer
      japeTransducer.setParameterValues(params);
      japeTransducer.reInit();
    }

    ConfigReader config = new ConfigReader(configFileURL);
    gracefulExit = config.config();

    try {
      HashMap<String, String> options = config.getOptions();

      patternMap = new HashMap<String, Pattern>();
      addSuffixPattern("disease_suffix", options);
      addWordPattern("disease_abbrevs", options);
      addWordPattern("disease_sense", options);
      addWordExtraPattern("disease_sense_context", options);
      addPossessiveWordPattern("disease_named_syndrome", options);
      addWordExtraPattern("disease_generic_context", options);
      addWordExtraPattern("disease_anatomy_context", options);
      addSuffixPluralPattern("procedure_suffix", options);
      addWordPluralPattern("procedure_key", options);
      addWordExtraPattern("procedure_anatomy_context", options);
      addWordPluralPattern("symptom_key", options);
      addWordPattern("test_key", options);

      addSuffixPattern("anatomy_suffix_adjective", options);
      addSuffixPattern("anatomy_suffix", options);
      addPrefixPattern("anatomy_prefix", options);
      addWordPattern("anatomy_position", options);
      addWordPluralPattern("anatomy_space_region_junction", options);
      addWordPattern("anatomy_part_adjective", options);
      addWordPattern("anatomy_latin_noun", options);
      addWordPattern("anatomy_muscle", options);
      addWordPluralPattern("anatomy_part", options);
      addWordPluralPattern("anatomy_fluid", options);

    } catch (NullPointerException ne) {
      gracefulExit = true;
      gate.util.Err.println(
          "Missing or unset configuration options. Please check configuration file.");
    }

    return this;
  } // end init()
  /**
   * Run from the command-line, with a list of URLs as argument.
   *
   * <p><B>NOTE:</B><br>
   * This code will run with all the documents in memory - if you want to unload each from memory
   * after use, add code to store the corpus in a DataStore.
   */
  public static void main(String args[]) throws GateException, IOException {
    // initialise the GATE library
    Out.prln("Initialising GATE...");
    Gate.init();
    Out.prln("...GATE initialised");

    // initialise ANNIE (this may take several minutes)
    StandAloneAnnie annie = new StandAloneAnnie();
    annie.initAnnie();

    // create a GATE corpus and add a document for each command-line
    // argument
    Corpus corpus = Factory.newCorpus("StandAloneAnnie corpus");
    for (int i = 0; i < args.length; i++) {
      URL u = new URL(args[i]);
      FeatureMap params = Factory.newFeatureMap();
      params.put("sourceUrl", u);
      params.put("preserveOriginalContent", new Boolean(true));
      params.put("collectRepositioningInfo", new Boolean(true));
      Out.prln("Creating doc for " + u);
      Document doc = (Document) Factory.createResource("gate.corpora.DocumentImpl", params);
      corpus.add(doc);
    } // for each of args

    // tell the pipeline about the corpus and run it
    annie.setCorpus(corpus);
    annie.execute();

    // for each document, get an XML document with the
    // person and location names added
    Iterator iter = corpus.iterator();
    int count = 0;
    String startTagPart_1 = "<span GateID=\"";
    String startTagPart_2 = "\" title=\"";
    String startTagPart_3 = "\" style=\"background:Red;\">";
    String endTag = "</span>";

    while (iter.hasNext()) {
      Document doc = (Document) iter.next();
      AnnotationSet defaultAnnotSet = doc.getAnnotations();
      Set annotTypesRequired = new HashSet();
      annotTypesRequired.add("Person");
      annotTypesRequired.add("Location");
      Set<Annotation> peopleAndPlaces =
          new HashSet<Annotation>(defaultAnnotSet.get(annotTypesRequired));

      FeatureMap features = doc.getFeatures();
      String originalContent =
          (String) features.get(GateConstants.ORIGINAL_DOCUMENT_CONTENT_FEATURE_NAME);
      RepositioningInfo info =
          (RepositioningInfo) features.get(GateConstants.DOCUMENT_REPOSITIONING_INFO_FEATURE_NAME);

      ++count;
      File file = new File("StANNIE_" + count + ".HTML");
      Out.prln("File name: '" + file.getAbsolutePath() + "'");
      if (originalContent != null && info != null) {
        Out.prln("OrigContent and reposInfo existing. Generate file...");

        Iterator it = peopleAndPlaces.iterator();
        Annotation currAnnot;
        SortedAnnotationList sortedAnnotations = new SortedAnnotationList();

        while (it.hasNext()) {
          currAnnot = (Annotation) it.next();
          sortedAnnotations.addSortedExclusive(currAnnot);
        } // while

        StringBuffer editableContent = new StringBuffer(originalContent);
        long insertPositionEnd;
        long insertPositionStart;
        // insert anotation tags backward
        Out.prln("Unsorted annotations count: " + peopleAndPlaces.size());
        Out.prln("Sorted annotations count: " + sortedAnnotations.size());
        for (int i = sortedAnnotations.size() - 1; i >= 0; --i) {
          currAnnot = (Annotation) sortedAnnotations.get(i);
          insertPositionStart = currAnnot.getStartNode().getOffset().longValue();
          insertPositionStart = info.getOriginalPos(insertPositionStart);
          insertPositionEnd = currAnnot.getEndNode().getOffset().longValue();
          insertPositionEnd = info.getOriginalPos(insertPositionEnd, true);
          if (insertPositionEnd != -1 && insertPositionStart != -1) {
            editableContent.insert((int) insertPositionEnd, endTag);
            editableContent.insert((int) insertPositionStart, startTagPart_3);
            editableContent.insert((int) insertPositionStart, currAnnot.getType());
            editableContent.insert((int) insertPositionStart, startTagPart_2);
            editableContent.insert((int) insertPositionStart, currAnnot.getId().toString());
            editableContent.insert((int) insertPositionStart, startTagPart_1);
          } // if
        } // for

        FileWriter writer = new FileWriter(file);
        writer.write(editableContent.toString());
        writer.close();
      } // if - should generate
      else if (originalContent != null) {
        Out.prln("OrigContent existing. Generate file...");

        Iterator it = peopleAndPlaces.iterator();
        Annotation currAnnot;
        SortedAnnotationList sortedAnnotations = new SortedAnnotationList();

        while (it.hasNext()) {
          currAnnot = (Annotation) it.next();
          sortedAnnotations.addSortedExclusive(currAnnot);
        } // while

        StringBuffer editableContent = new StringBuffer(originalContent);
        long insertPositionEnd;
        long insertPositionStart;
        // insert anotation tags backward
        Out.prln("Unsorted annotations count: " + peopleAndPlaces.size());
        Out.prln("Sorted annotations count: " + sortedAnnotations.size());
        for (int i = sortedAnnotations.size() - 1; i >= 0; --i) {
          currAnnot = (Annotation) sortedAnnotations.get(i);
          insertPositionStart = currAnnot.getStartNode().getOffset().longValue();
          insertPositionEnd = currAnnot.getEndNode().getOffset().longValue();
          if (insertPositionEnd != -1 && insertPositionStart != -1) {
            editableContent.insert((int) insertPositionEnd, endTag);
            editableContent.insert((int) insertPositionStart, startTagPart_3);
            editableContent.insert((int) insertPositionStart, currAnnot.getType());
            editableContent.insert((int) insertPositionStart, startTagPart_2);
            editableContent.insert((int) insertPositionStart, currAnnot.getId().toString());
            editableContent.insert((int) insertPositionStart, startTagPart_1);
          } // if
        } // for

        FileWriter writer = new FileWriter(file);
        writer.write(editableContent.toString());
        writer.close();
      } else {
        Out.prln("Content : " + originalContent);
        Out.prln("Repositioning: " + info);
      }

      String xmlDocument = doc.toXml(peopleAndPlaces, false);
      String fileName = new String("StANNIE_toXML_" + count + ".HTML");
      FileWriter writer = new FileWriter(fileName);
      writer.write(xmlDocument);
      writer.close();
    } // for each doc
  } // main
 /** Releases all resources and listeners */
 public void cleanup() {
   Gate.getCreoleRegister().removeCreoleListener(this);
   // remove the annotationSetListener as well
 }
  public static void main(String[] args) throws Exception {

    int num_threads = Integer.parseInt(args[0]);
    int chunk_size = 100000;
    int total_lines_read = 0;
    if (args.length > 4) chunk_size = Integer.parseInt(args[4]);
    // initialise GATE - this must be done before calling any GATE APIs
    Gate.init();

    CorpusController application =
        (CorpusController)
            PersistenceManager.loadObjectFromFile(new File("TJInfoExtractor/application.xgapp"));

    List<CorpusController> applicationList = new ArrayList<CorpusController>();
    for (int i = 0; i < num_threads; ++i)
      applicationList.add((CorpusController) Factory.duplicate(application));

    String outfile = "Out.csv";
    if (args.length > 2) outfile = args[2];
    PrintWriter writer = new PrintWriter(outfile, "UTF-8");
    writer.println(
        "Perspective_1st,Perspective_3rd,Name,Age,Cost,Height_ft,Height_in,Weight,Cup,Chest,Waist,Hip,Ethnicity,SkinColor,EyeColor,HairColor,Restriction_Type,Restriction_Ethnicity,Restriction_Age,PhoneNumber,AreaCode_State,AreaCode_Cities,Email,Url,Media");

    outfile = "Out.txt";
    if (args.length > 3) outfile = args[3];
    PrintWriter writer2 = new PrintWriter(outfile, "UTF-8");

    // load the document
    System.out.println("Reading document " + args[1] + "...");
    BufferedReader br = new BufferedReader(new FileReader(args[1]));
    Boolean done = false;

    while (!done) {
      List<String> FileLines = new ArrayList<String>();
      // Create container for results
      List<String> AnnotationResults = new ArrayList<String>();
      List<String> AnnotationText = new ArrayList<String>();

      int LinesRead = 0;
      String fileline;
      // read the file
      while (true) {
        if (LinesRead >= chunk_size) break;
        if ((fileline = br.readLine()) == null) {
          done = true;
          break;
        }
        FileLines.add(fileline);
        LinesRead++;
        total_lines_read++;
      }

      // launch threads to process each chunk
      int step = (int) Math.ceil(((double) FileLines.size()) / ((double) num_threads));
      List<ExtractorThread> pool = new ArrayList<ExtractorThread>();
      for (int i = 0; i < num_threads; ++i) {
        pool.add(
            new ExtractorThread(
                FileLines.subList(i * step, Math.min((i + 1) * step, FileLines.size())),
                applicationList.get(i),
                i));
      }
      for (int i = 0; i < num_threads; ++i) {
        pool.get(i).t.join();
        if (pool.get(i).results != null) AnnotationResults.addAll(pool.get(i).results);
        if (pool.get(i).text != null) AnnotationText.addAll(pool.get(i).text);
      }

      for (String l : AnnotationResults) writer.println(l);
      for (String l : AnnotationText) writer2.println(l);
      System.out.println("Processed " + total_lines_read + " lines...");
    }

    br.close();
    writer.close();
    writer2.close();
    System.out.println("All done");
  }
  /**
   * The main entry point. First we parse the command line options (see usage() method for details),
   * then we take all remaining command line parameters to be file names to process. Each file is
   * loaded, processed using the application and the results written to the output file
   * (inputFile.out.xml).
   */
  public static void main(String[] args) throws Exception {
    parseCommandLine(args);

    // initialise GATE - this must be done before calling any GATE APIs
    Gate.init();

    // load the saved application
    CorpusController application =
        (CorpusController) PersistenceManager.loadObjectFromFile(gappFile);

    // Create a Corpus to use.  We recycle the same Corpus object for each
    // iteration.  The string parameter to newCorpus() is simply the
    // GATE-internal name to use for the corpus.  It has no particular
    // significance.

    ArrayList<String> files = getFilesFromDir(inputDir);
    gate.Corpus corpus = createCorpus(files);
    // Corpus corpus = Factory.newCorpus("BatchProcessApp Corpus");
    application.setCorpus(corpus);

    System.out.println("Processing " + files.size() + " files");

    // process the files one by one
    for (int i = 0; i < files.size(); i++) {

      // load the document (using the specified encoding if one was given)
      File docFile = new File(files.get(i));
      System.out.print("Processing document " + docFile + " (" + i + ") ...");
      Document doc = Factory.newDocument(docFile.toURL(), encoding);

      // put the document in the corpus
      corpus.add(doc);

      // run the application
      application.execute();

      // remove the document from the corpus again
      corpus.clear();

      String docXMLString = null;
      // if we want to just write out specific annotation types, we must
      // extract the annotations into a Set
      if (annotTypesToWrite != null) {
        // Create a temporary Set to hold the annotations we wish to write out
        Set annotationsToWrite = new HashSet();

        // we only extract annotations from the default (unnamed) AnnotationSet
        // in this example
        AnnotationSet defaultAnnots = doc.getAnnotations("Output");
        Iterator annotTypesIt = annotTypesToWrite.iterator();
        while (annotTypesIt.hasNext()) {
          // extract all the annotations of each requested type and add them to
          // the temporary set
          AnnotationSet annotsOfThisType = defaultAnnots.get((String) annotTypesIt.next());
          if (annotsOfThisType != null) {
            annotationsToWrite.addAll(annotsOfThisType);
          }
        }

        // create the XML string using these annotations
        docXMLString = doc.toXml(annotationsToWrite, true);
      }
      // otherwise, just write out the whole document as GateXML
      else {
        docXMLString = doc.toXml();
      }

      // Release the document, as it is no longer needed
      Factory.deleteResource(doc);

      // output the XML to <inputFile>.out.xml
      System.out.println("Writing file " + docFile.getName());
      String outputFileName = docFile.getName() + ".out.xml";
      // File outputFile = new File(docFile.getParentFile(), outputFileName);
      File outputFile = new File(new File(outputDir).getAbsolutePath(), outputFileName);

      // Write output files using the same encoding as the original
      FileOutputStream fos = new FileOutputStream(outputFile);
      BufferedOutputStream bos = new BufferedOutputStream(fos);
      OutputStreamWriter out;
      if (encoding == null) {
        out = new OutputStreamWriter(bos);
      } else {
        out = new OutputStreamWriter(bos, encoding);
      }

      out.write(docXMLString);

      out.close();
      System.out.println("done");
    } // for each file

    System.out.println("All done");
  } // void main(String[] args)
Exemple #26
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  /** Delegate loading to the super class (loadClass has protected access there). */
  private Class<?> loadClass(
      String name, boolean resolve, boolean localOnly, Set<GateClassLoader> visited)
      throws ClassNotFoundException {

    Class<?> previous = findLoadedClass(name);

    if (previous != null) {
      if (DEBUG) System.out.println("CACHE HIT: " + name + " -- " + id);

      return previous;
    }

    if (DEBUG)
      System.out.println(
          name + " -- " + id + ": " + localOnly + "/" + isolated + "/" + getParent());

    // to ensure we don't end up looping through the same classloader
    // twice we
    // keep a track of which ones we have already visited
    visited.add(this);

    if (!this.equals(Gate.getClassLoader())) {
      try {
        // first we see if we can find the class via the system class
        // path
        Class<?> found = Gate.getClassLoader().getParent().loadClass(name);

        URL url = findResource(name.replace('.', '/') + ".class");
        if (url != null)
          log.warn(
              name
                  + " is available via both the system classpath and a plugin; the plugin classes will be ignored");

        // if we got to here then the class has been found via the
        // system
        // classpath so return it and stop looking
        return found;

      } catch (ClassNotFoundException e) {
        // this can safely be ignored
      }
    }

    try {
      // try loading and returning by looking within this classloader
      return super.loadClass(name, resolve);
    } catch (ClassNotFoundException e) {
      // this can safely be ignored
    }

    if (this.getParent() != null && this.getParent() instanceof GateClassLoader)
      visited.add((GateClassLoader) this.getParent());

    if (!localOnly) {
      // if we aren't just looking locally then...

      if (getParent() == null) {
        try {
          // if this classloader doesn't have a parent then it must be
          // disposable, but as we haven't found the class we need yet
          // we should
          // now look into the main GATE classloader
          return Gate.getClassLoader().loadClass(name, resolve, false, visited);
        } catch (ClassNotFoundException e) {
          // this can safely be ignored
        }
      }

      Set<GateClassLoader> children;
      synchronized (childClassLoaders) {
        children = new LinkedHashSet<GateClassLoader>(childClassLoaders.values());
      }

      // make sure we don't visit a classloader we've already been
      // through
      children.removeAll(visited);

      for (GateClassLoader cl : children) {
        // the class isn't to be found in either this classloader or the
        // main
        // GATE classloader so let's check all the other disposable
        // classloaders
        try {
          if (!cl.isIsolated()) return cl.loadClass(name, resolve, true, visited);
        } catch (ClassNotFoundException e) {
          // this can safely be ignored
        }
      }
    }

    // if we got to here then no matter where we have looked we have
    // been unable
    // to find the class requested so throw an exception
    throw new ClassNotFoundException(name);
  }
Exemple #27
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  /** This method is called when all characters between specific tags have been read completely */
  public void charactersAction(char[] text, int start, int length) throws SAXException {
    // correction of real offset. Didn't affect on other data.
    super.characters(text, start, length);
    // create a string object based on the reported text
    String content = new String(text, start, length);
    StringBuffer contentBuffer = new StringBuffer("");
    int tmpDocContentSize = tmpDocContent.length();
    boolean incrementStartIndex = false;
    boolean addExtraSpace = true;
    if (Gate.getUserConfig().get(GateConstants.DOCUMENT_ADD_SPACE_ON_UNPACK_FEATURE_NAME) != null) {
      addExtraSpace =
          Gate.getUserConfig()
              .getBoolean(GateConstants.DOCUMENT_ADD_SPACE_ON_UNPACK_FEATURE_NAME)
              .booleanValue();
    }
    // If the first char of the text just read "text[0]" is NOT whitespace AND
    // the last char of the tmpDocContent[SIZE-1] is NOT whitespace then
    // concatenation "tmpDocContent + content" will result into a new different
    // word... and we want to avoid that, because the tokenizer, gazetter and
    // Jape work on the raw text and concatenating tokens might be not good.
    if (tmpDocContentSize != 0
        && content.length() != 0
        && !Character.isWhitespace(content.charAt(0))
        && !Character.isWhitespace(tmpDocContent.charAt(tmpDocContentSize - 1))) {

      // If we are here it means that a concatenation between the last
      // token in the tmpDocContent and the content(which doesn't start
      // with a white space) will be performed. In order to prevent this,
      // we will add a " " space char in order to assure that the 2 tokens
      // stay apart. Howerver we will except from this rule the most known
      // internal entities like &, <, >, etc
      if (( // Testing the length against 1 makes it more likely that
          // an internal entity was called. characters() gets called for
          // each entity separately.
          (content.length() == 1)
              && (content.charAt(0) == '&'
                  || content.charAt(0) == '<'
                  || content.charAt(0) == '>'
                  || content.charAt(0) == '"'
                  || content.charAt(0) == '\''))
          || (tmpDocContent.charAt(tmpDocContentSize - 1) == '&'
              || tmpDocContent.charAt(tmpDocContentSize - 1) == '<'
              || tmpDocContent.charAt(tmpDocContentSize - 1) == '>'
              || tmpDocContent.charAt(tmpDocContentSize - 1) == '"'
              || tmpDocContent.charAt(tmpDocContentSize - 1)
                  == '\'')) { // do nothing. The content will be appended
      } else if (!addExtraSpace) {
      } else {
        // In all other cases append " "
        contentBuffer.append(" ");
        incrementStartIndex = true;
      } // End if
    } // End if

    // put the repositioning information
    if (reposInfo != null) {
      if (!(start == 0 && length == 1 && text.length <= 2)) {
        // normal piece of text
        reposInfo.addPositionInfo(
            getRealOffset(),
            content.length(),
            tmpDocContent.length() + contentBuffer.length(),
            content.length());
        if (DEBUG) {
          Out.println("Info: " + getRealOffset() + ", " + content.length());
          Out.println("Start: " + start + " len" + length);
        } // DEBUG
      } else {
        // unicode char or &xxx; coding
        // Reported from the parser offset is 0
        // The real offset should be found in the ampCodingInfo structure.

        long lastPosition = 0;
        RepositioningInfo.PositionInfo pi;

        if (reposInfo.size() > 0) {
          pi = reposInfo.get(reposInfo.size() - 1);
          lastPosition = pi.getOriginalPosition();
        } // if

        for (int i = 0; i < ampCodingInfo.size(); ++i) {
          pi = ampCodingInfo.get(i);
          if (pi.getOriginalPosition() > lastPosition) {
            // found
            reposInfo.addPositionInfo(
                pi.getOriginalPosition(),
                pi.getOriginalLength(),
                tmpDocContent.length() + contentBuffer.length(),
                content.length());
            break;
          } // if
        } // for
      } // if
    } // if

    // update the document content
    contentBuffer.append(content);
    // calculate the End index for all the elements of the stack
    // the expression is : End index = Current doc length + text length
    Long end = new Long(tmpDocContent.length() + contentBuffer.length());

    CustomObject obj = null;
    // Iterate through stack to modify the End index of the existing elements

    Iterator<CustomObject> anIterator = stack.iterator();
    while (anIterator.hasNext()) {
      // get the object and move to the next one
      obj = anIterator.next();
      if (incrementStartIndex && obj.getStart().equals(obj.getEnd())) {
        obj.setStart(new Long(obj.getStart().longValue() + 1));
      } // End if
      // sets its End index
      obj.setEnd(end);
    } // End while

    tmpDocContent.append(contentBuffer.toString());
  } // characters();
Exemple #28
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  protected void initListeners() {

    // mouse double-click to open the document
    // context menu to get the actions for the selection
    docTable.addMouseListener(
        new MouseAdapter() {
          public void mouseClicked(MouseEvent e) {
            processMouseEvent(e);
          }

          public void mousePressed(MouseEvent e) {
            if (e.isPopupTrigger()) {
              processMouseEvent(e);
            }
          }

          public void mouseReleased(MouseEvent e) {
            if (e.isPopupTrigger()) {
              processMouseEvent(e);
            }
          }

          private void processMouseEvent(MouseEvent e) {
            int row = docTable.rowAtPoint(e.getPoint());
            if (row == -1) {
              return;
            }

            if (e.isPopupTrigger()) {
              // context menu
              if (!docTable.isRowSelected(row)) {
                // if right click outside the selection then reset selection
                docTable.getSelectionModel().setSelectionInterval(row, row);
              }
              JPopupMenu popup = new XJPopupMenu();
              popup.add(openDocumentsAction);
              popup.add(removeDocumentsAction);
              popup.show(docTable, e.getPoint().x, e.getPoint().y);

            } else if (e.getID() == MouseEvent.MOUSE_CLICKED && e.getClickCount() == 2) {
              // open document on double-click
              openDocumentsAction.actionPerformed(null);
            }
          }
        });

    // Enter key opens the selected documents
    docTable.addKeyListener(
        new KeyAdapter() {
          public void keyPressed(KeyEvent e) {
            if (e.getKeyCode() == KeyEvent.VK_ENTER) {
              openDocumentsAction.actionPerformed(null);
            }
          }
        });

    docTable
        .getSelectionModel()
        .addListSelectionListener(
            new ListSelectionListener() {
              public void valueChanged(ListSelectionEvent e) {
                // enable/disable buttons according to the selection
                removeDocumentsAction.setEnabled(docTable.getSelectedRowCount() > 0);
                openDocumentsAction.setEnabled(docTable.getSelectedRowCount() > 0);
                moveUpAction.setEnabled(
                    docTable.getSelectedRowCount() > 0 && !docTable.isRowSelected(0));
                moveDownAction.setEnabled(
                    docTable.getSelectedRowCount() > 0
                        && !docTable.isRowSelected(docTable.getRowCount() - 1));
              }
            });

    Gate.getCreoleRegister()
        .addCreoleListener(
            new CreoleListener() {
              public void resourceLoaded(CreoleEvent e) {
                if (e.getResource() instanceof Document) {
                  documentsLoadedCount++;
                  changeMessage();
                }
              }

              public void resourceUnloaded(CreoleEvent e) {
                if (e.getResource() instanceof Document) {
                  documentsLoadedCount--;
                  changeMessage();
                }
              }

              public void datastoreOpened(CreoleEvent e) {
                /* do nothing */
              }

              public void datastoreCreated(CreoleEvent e) {
                /* do nothing */
              }

              public void datastoreClosed(CreoleEvent e) {
                /* do nothing */
              }

              public void resourceRenamed(Resource resource, String oldName, String newName) {
                /* do nothing */
              }
            });
  }
Exemple #29
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  /**
   * Loads any custom operators and annotation accessors into the ConstraintFactory.
   *
   * @throws ResourceInstantiationException
   */
  protected void initCustomConstraints() throws ResourceInstantiationException {
    // Load operators
    if (operators != null) {
      for (String opName : operators) {
        Class<? extends ConstraintPredicate> clazz = null;
        try {
          clazz =
              Class.forName(opName, true, Gate.getClassLoader())
                  .asSubclass(ConstraintPredicate.class);
        } catch (ClassNotFoundException e) {
          // if couldn't find it that way, try with current thread class loader
          try {
            clazz =
                Class.forName(opName, true, Thread.currentThread().getContextClassLoader())
                    .asSubclass(ConstraintPredicate.class);
          } catch (ClassNotFoundException e1) {
            throw new ResourceInstantiationException(
                "Cannot load class for operator: " + opName, e1);
          }
        } catch (ClassCastException cce) {
          throw new ResourceInstantiationException(
              "Operator class '" + opName + "' must implement ConstraintPredicate");
        }

        // instantiate an instance of the class so can get the operator string
        try {
          ConstraintPredicate predicate = clazz.newInstance();
          String opSymbol = predicate.getOperator();
          // now store it in ConstraintFactory
          Factory.getConstraintFactory().addOperator(opSymbol, clazz);
        } catch (Exception e) {
          throw new ResourceInstantiationException(
              "Cannot instantiate class for operator: " + opName, e);
        }
      }
    }

    // Load annotationAccessors
    if (annotationAccessors != null) {
      for (String accessorName : annotationAccessors) {
        Class<? extends AnnotationAccessor> clazz = null;
        try {
          clazz =
              Class.forName(accessorName, true, Gate.getClassLoader())
                  .asSubclass(AnnotationAccessor.class);
        } catch (ClassNotFoundException e) {
          // if couldn't find it that way, try with current thread class loader
          try {
            clazz =
                Class.forName(accessorName, true, Thread.currentThread().getContextClassLoader())
                    .asSubclass(AnnotationAccessor.class);
          } catch (ClassNotFoundException e1) {
            throw new ResourceInstantiationException(
                "Cannot load class for accessor: " + accessorName, e1);
          }
        } catch (ClassCastException cce) {
          throw new ResourceInstantiationException(
              "Operator class '" + accessorName + "' must implement AnnotationAccessor");
        }

        // instantiate an instance of the class so can get the meta-property name string
        try {
          AnnotationAccessor aa = clazz.newInstance();
          String accSymbol = (String) aa.getKey();
          // now store it in ConstraintFactory
          Factory.getConstraintFactory().addMetaProperty(accSymbol, clazz);
        } catch (Exception e) {
          throw new ResourceInstantiationException(
              "Cannot instantiate class for accessor: " + accessorName, e);
        }
      }
    }
  }
 public GateAnalyzer(String appPath) throws Exception {
   Gate.init();
   controller =
       (SerialAnalyserController) PersistenceManager.loadObjectFromFile(new File(appPath));
 }