Package org.uimafit.factory

Examples of org.uimafit.factory.AggregateBuilder

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    return fileList;
  }

  public void execute() throws UIMAException, IOException, URISyntaxException
  {
    AggregateBuilder builder = new AggregateBuilder();
   
    TypeSystemDescription typeSystemDescription = TypeSystemDescriptionFactory.createTypeSystemDescriptionFromPath();
   
    CollectionReader reader =
        CollectionReaderFactory.createCollectionReader(
          XMIReader.class,
          typeSystemDescription,
          XMIReader.PARAM_FILES,
          inputFiles);
   
      AnalysisEngineDescription documentIdPrinter =
          AnalysisEngineFactory.createPrimitiveDescription(DocumentIdPrinterAnalysisEngine.class);
      builder.add(documentIdPrinter);
   
      String generalSectionRegexFileUri =
        "org/mitre/medfacts/zoner/section_regex.xml";
      //URI generalSectionRegexFileUri =
      //  this.getClass().getClassLoader().getResource("org/mitre/medfacts/zoner/section_regex.xml").toURI();
//      ExternalResourceDescription generalSectionRegexDescription = ExternalResourceFactory.createExternalResourceDescription(
//          SectionRegexConfigurationResource.class, new File(generalSectionRegexFileUri));
      AnalysisEngineDescription zonerAnnotator =
          AnalysisEngineFactory.createPrimitiveDescription(ZoneAnnotator.class,
              ZoneAnnotator.PARAM_SECTION_REGEX_FILE_URI,
              generalSectionRegexFileUri
              );
      builder.add(zonerAnnotator);

      String mayoSectionRegexFileUri =
          "org/mitre/medfacts/zoner/mayo_sections.xml";
//      URI mayoSectionRegexFileUri =
//          this.getClass().getClassLoader().getResource("org/mitre/medfacts/zoner/mayo_sections.xml").toURI();
//        ExternalResourceDescription mayoSectionRegexDescription = ExternalResourceFactory.createExternalResourceDescription(
//            SectionRegexConfigurationResource.class, new File(mayoSectionRegexFileUri));
      AnalysisEngineDescription mayoZonerAnnotator =
          AnalysisEngineFactory.createPrimitiveDescription(ZoneAnnotator.class,
              ZoneAnnotator.PARAM_SECTION_REGEX_FILE_URI,
              mayoSectionRegexFileUri
              );
      builder.add(mayoZonerAnnotator);

      AnalysisEngineDescription xWriter = AnalysisEngineFactory.createPrimitiveDescription(
          XWriter.class,
          typeSystemDescription,
          XWriter.PARAM_OUTPUT_DIRECTORY_NAME,
          outputDirectory.toString(),
          XWriter.PARAM_FILE_NAMER_CLASS_NAME,
          CtakesFileNamer.class.getName()
          );
     
      builder.add(xWriter);

    logger.info("BEFORE RUNNING PIPELINE...");
    SimplePipeline.runPipeline(reader,  builder.createAggregateDescription());
    logger.info("AFTER RUNNING PIPELINE...COMPLETED");
  }
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        this.getClass().getSimpleName(),
        this.relationClass.getSimpleName(),
        directory.getName());
    System.err.println(this.parameterSettings);

    AggregateBuilder builder = new AggregateBuilder();
    // remove cTAKES entity mentions and modifiers in the system view and copy
    // in the gold relations
    builder.add(AnalysisEngineFactory.createPrimitiveDescription(RemoveCTakesMentionsAndCopyGoldRelations.class));
    // add the relation extractor, configured for training mode
    AnalysisEngineDescription classifierAnnotator =
        AnalysisEngineFactory.createPrimitiveDescription(
            this.classifierAnnotatorClass,
            this.parameterSettings.configurationParameters);
    ConfigurationParameterFactory.addConfigurationParameters(
        classifierAnnotator,
        DefaultDataWriterFactory.PARAM_DATA_WRITER_CLASS_NAME,
        this.parameterSettings.dataWriterClass,
        DirectoryDataWriterFactory.PARAM_OUTPUT_DIRECTORY,
        directory.getPath());
    builder.add(classifierAnnotator);

    // run the data-writing pipeline
    SimplePipeline.runPipeline(collectionReader, builder.createAggregateDescription());

    // train the classifier and package it into a .jar file
    JarClassifierBuilder.trainAndPackage(directory, this.parameterSettings.trainingArguments);
  }
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  }

  @Override
  protected AnnotationStatistics<String> test(CollectionReader collectionReader, File directory)
      throws Exception {
    AggregateBuilder builder = new AggregateBuilder();
    if (this.testOnCTakes) {
      // add the modifier extractor
      File file = new File("desc/analysis_engine/ModifierExtractorAnnotator.xml");
      XMLInputSource source = new XMLInputSource(file);
      builder.add(UIMAFramework.getXMLParser().parseAnalysisEngineDescription(source));
      // remove extraneous entity mentions
      builder.add(AnalysisEngineFactory.createPrimitiveDescription(RemoveSmallerEventMentions.class));
    } else {
      // replace cTAKES entity mentions and modifiers in the system view with
      // the gold annotations
      builder.add(AnalysisEngineFactory.createPrimitiveDescription(ReplaceCTakesMentionsWithGoldMentions.class));
    }
    // add the relation extractor, configured for classification mode
    AnalysisEngineDescription classifierAnnotator =
        AnalysisEngineFactory.createPrimitiveDescription(
            this.classifierAnnotatorClass,
            this.parameterSettings.configurationParameters);
    ConfigurationParameterFactory.addConfigurationParameters(
        classifierAnnotator,
        GenericJarClassifierFactory.PARAM_CLASSIFIER_JAR_PATH,
        JarClassifierBuilder.getModelJarFile(directory));
    builder.add(classifierAnnotator);

    // statistics will be based on the "category" feature of the
    // BinaryTextRelations
    AnnotationStatistics<String> stats = new AnnotationStatistics<String>();
    Function<BinaryTextRelation, HashableArguments> getSpan =
        new Function<BinaryTextRelation, HashableArguments>() {
          @Override
          public HashableArguments apply(BinaryTextRelation relation) {
            return new HashableArguments(relation);
          }
        };
    Function<BinaryTextRelation, String> getOutcome =
        AnnotationStatistics.annotationToFeatureValue("category");

    // calculate statistics, iterating over the results of the classifier
    AnalysisEngine engine = builder.createAggregate();
    for (JCas jCas : new JCasIterable(collectionReader, engine)) {

      // get the gold view
      JCas goldView;
      try {
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  public void createTrainDescriptor() throws Exception
  {
    File trainDirectory = new File("/tmp/assertion_data/train");
    File directory = trainDirectory;
    AggregateBuilder builder = new AggregateBuilder();

////
    AnalysisEngineDescription goldCopierIdentifiedAnnotsAnnotator = AnalysisEngineFactory.createPrimitiveDescription(ReferenceIdentifiedAnnotationsSystemToGoldCopier.class);
    builder.add(goldCopierIdentifiedAnnotsAnnotator);
   
    AnalysisEngineDescription goldCopierSupportingAnnotsAnnotator = AnalysisEngineFactory.createPrimitiveDescription(ReferenceSupportingAnnotationsSystemToGoldCopier.class);
    builder.add(goldCopierSupportingAnnotsAnnotator);
   
    AnalysisEngineDescription assertionAttributeClearerAnnotator = AnalysisEngineFactory.createPrimitiveDescription(ReferenceAnnotationsSystemAssertionClearer.class);
    builder.add(assertionAttributeClearerAnnotator);
   
    String generalSectionRegexFileUri =
        "org/mitre/medfacts/zoner/section_regex.xml";
    AnalysisEngineDescription zonerAnnotator =
        AnalysisEngineFactory.createPrimitiveDescription(ZoneAnnotator.class,
            ZoneAnnotator.PARAM_SECTION_REGEX_FILE_URI,
            generalSectionRegexFileUri
            );
    builder.add(zonerAnnotator);

    String mayoSectionRegexFileUri =
        "org/mitre/medfacts/uima/mayo_sections.xml";
    AnalysisEngineDescription mayoZonerAnnotator =
        AnalysisEngineFactory.createPrimitiveDescription(ZoneAnnotator.class,
            ZoneAnnotator.PARAM_SECTION_REGEX_FILE_URI,
            mayoSectionRegexFileUri
            );
    builder.add(mayoZonerAnnotator);
   
   
    AnalysisEngineDescription polarityAnnotator = AnalysisEngineFactory.createPrimitiveDescription(PolarityCleartkAnalysisEngine.class); //,  this.additionalParamemters);
    ConfigurationParameterFactory.addConfigurationParameters(
        polarityAnnotator,
        AssertionCleartkAnalysisEngine.PARAM_GOLD_VIEW_NAME,
        AssertionEvaluation.GOLD_VIEW_NAME,
        CleartkAnnotator.PARAM_DATA_WRITER_FACTORY_CLASS_NAME,
        this.dataWriterFactoryClass.getName(),
        DirectoryDataWriterFactory.PARAM_OUTPUT_DIRECTORY,
        new File(directory, "polarity").getPath()
        );
    builder.add(polarityAnnotator);

    AnalysisEngineDescription conditionalAnnotator = AnalysisEngineFactory.createPrimitiveDescription(ConditionalCleartkAnalysisEngine.class); //,  this.additionalParamemters);
    ConfigurationParameterFactory.addConfigurationParameters(
        conditionalAnnotator,
        AssertionCleartkAnalysisEngine.PARAM_GOLD_VIEW_NAME,
        AssertionEvaluation.GOLD_VIEW_NAME,
        CleartkAnnotator.PARAM_DATA_WRITER_FACTORY_CLASS_NAME,
        this.dataWriterFactoryClass.getName(),
        DirectoryDataWriterFactory.PARAM_OUTPUT_DIRECTORY,
        new File(directory, "conditional").getPath()
        );
    builder.add(conditionalAnnotator);

    AnalysisEngineDescription uncertaintyAnnotator = AnalysisEngineFactory.createPrimitiveDescription(UncertaintyCleartkAnalysisEngine.class); //,  this.additionalParamemters);
    ConfigurationParameterFactory.addConfigurationParameters(
        uncertaintyAnnotator,
        AssertionCleartkAnalysisEngine.PARAM_GOLD_VIEW_NAME,
        AssertionEvaluation.GOLD_VIEW_NAME,
        CleartkAnnotator.PARAM_DATA_WRITER_FACTORY_CLASS_NAME,
        this.dataWriterFactoryClass.getName(),
        DirectoryDataWriterFactory.PARAM_OUTPUT_DIRECTORY,
        new File(directory, "uncertainty").getPath()
        );
    builder.add(uncertaintyAnnotator);

    AnalysisEngineDescription subjectAnnotator = AnalysisEngineFactory.createPrimitiveDescription(SubjectCleartkAnalysisEngine.class); //,  this.additionalParamemters);
    ConfigurationParameterFactory.addConfigurationParameters(
        subjectAnnotator,
        AssertionCleartkAnalysisEngine.PARAM_GOLD_VIEW_NAME,
        AssertionEvaluation.GOLD_VIEW_NAME,
        CleartkAnnotator.PARAM_DATA_WRITER_FACTORY_CLASS_NAME,
        this.dataWriterFactoryClass.getName(),
        DirectoryDataWriterFactory.PARAM_OUTPUT_DIRECTORY,
        new File(directory, "subject").getPath()
        );
    builder.add(subjectAnnotator);

    AnalysisEngineDescription genericAnnotator = AnalysisEngineFactory.createPrimitiveDescription(GenericCleartkAnalysisEngine.class); //,  this.additionalParamemters);
    ConfigurationParameterFactory.addConfigurationParameters(
        genericAnnotator,
        AssertionCleartkAnalysisEngine.PARAM_GOLD_VIEW_NAME,
        AssertionEvaluation.GOLD_VIEW_NAME,
        CleartkAnnotator.PARAM_DATA_WRITER_FACTORY_CLASS_NAME,
        this.dataWriterFactoryClass.getName(),
        DirectoryDataWriterFactory.PARAM_OUTPUT_DIRECTORY,
        new File(directory, "generic").getPath()
        );
    builder.add(genericAnnotator);
   
////
   
    FileOutputStream outputStream = new FileOutputStream("desc/analysis_engine/assertion_train.xml");
   
    AnalysisEngineDescription description = builder.createAggregateDescription();
   
    description.toXML(outputStream);
  }
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  public void createTestDescriptor() throws Exception
  {
    File testDirectory = new File("/tmp/assertion_data/test");
    File directory = testDirectory;
    File testOutputDirectory = new File("/tmp/assertion_data/test_output");
    AggregateBuilder builder = new AggregateBuilder();

////
    AnalysisEngineDescription goldCopierAnnotator = AnalysisEngineFactory.createPrimitiveDescription(ReferenceIdentifiedAnnotationsSystemToGoldCopier.class);
    builder.add(goldCopierAnnotator);
   
    AnalysisEngineDescription assertionAttributeClearerAnnotator = AnalysisEngineFactory.createPrimitiveDescription(ReferenceAnnotationsSystemAssertionClearer.class);
    builder.add(assertionAttributeClearerAnnotator);
   
    String generalSectionRegexFileUri =
      "org/mitre/medfacts/zoner/section_regex.xml";
    AnalysisEngineDescription zonerAnnotator =
        AnalysisEngineFactory.createPrimitiveDescription(ZoneAnnotator.class,
            ZoneAnnotator.PARAM_SECTION_REGEX_FILE_URI,
            generalSectionRegexFileUri
            );
    builder.add(zonerAnnotator);

    String mayoSectionRegexFileUri =
      "org/mitre/medfacts/uima/mayo_sections.xml";
    AnalysisEngineDescription mayoZonerAnnotator =
        AnalysisEngineFactory.createPrimitiveDescription(ZoneAnnotator.class,
            ZoneAnnotator.PARAM_SECTION_REGEX_FILE_URI,
            mayoSectionRegexFileUri
            );
    builder.add(mayoZonerAnnotator);
   
    AnalysisEngineDescription polarityAnnotator = AnalysisEngineFactory.createPrimitiveDescription(PolarityCleartkAnalysisEngine.class); //,  this.additionalParamemters);
    ConfigurationParameterFactory.addConfigurationParameters(
        polarityAnnotator,
        AssertionCleartkAnalysisEngine.PARAM_GOLD_VIEW_NAME,
        AssertionEvaluation.GOLD_VIEW_NAME,
        GenericJarClassifierFactory.PARAM_CLASSIFIER_JAR_PATH,
        new File(new File(directory, "polarity"), "model.jar").getPath()
        );
    builder.add(polarityAnnotator);

    AnalysisEngineDescription conditionalAnnotator = AnalysisEngineFactory.createPrimitiveDescription(ConditionalCleartkAnalysisEngine.class); //,  this.additionalParamemters);
    ConfigurationParameterFactory.addConfigurationParameters(
        conditionalAnnotator,
        AssertionCleartkAnalysisEngine.PARAM_GOLD_VIEW_NAME,
        AssertionEvaluation.GOLD_VIEW_NAME,
        GenericJarClassifierFactory.PARAM_CLASSIFIER_JAR_PATH,
        new File(new File(directory, "conditional"), "model.jar").getPath()
        );
    builder.add(conditionalAnnotator);
 
    AnalysisEngineDescription uncertaintyAnnotator = AnalysisEngineFactory.createPrimitiveDescription(UncertaintyCleartkAnalysisEngine.class); //,  this.additionalParamemters);
    ConfigurationParameterFactory.addConfigurationParameters(
        uncertaintyAnnotator,
        AssertionCleartkAnalysisEngine.PARAM_GOLD_VIEW_NAME,
        AssertionEvaluation.GOLD_VIEW_NAME,
        GenericJarClassifierFactory.PARAM_CLASSIFIER_JAR_PATH,
        new File(new File(directory, "uncertainty"), "model.jar").getPath()
        );
    builder.add(uncertaintyAnnotator);

    AnalysisEngineDescription subjectAnnotator = AnalysisEngineFactory.createPrimitiveDescription(SubjectCleartkAnalysisEngine.class); //,  this.additionalParamemters);
    ConfigurationParameterFactory.addConfigurationParameters(
        subjectAnnotator,
        AssertionCleartkAnalysisEngine.PARAM_GOLD_VIEW_NAME,
        AssertionEvaluation.GOLD_VIEW_NAME,
        GenericJarClassifierFactory.PARAM_CLASSIFIER_JAR_PATH,
        new File(new File(directory, "subject"), "model.jar").getPath()
        );
    builder.add(subjectAnnotator);

    AnalysisEngineDescription genericAnnotator = AnalysisEngineFactory.createPrimitiveDescription(GenericCleartkAnalysisEngine.class); //,  this.additionalParamemters);
    ConfigurationParameterFactory.addConfigurationParameters(
        genericAnnotator,
        AssertionCleartkAnalysisEngine.PARAM_GOLD_VIEW_NAME,
        AssertionEvaluation.GOLD_VIEW_NAME,
        GenericJarClassifierFactory.PARAM_CLASSIFIER_JAR_PATH,
        new File(new File(directory, "generic"), "model.jar").getPath()
        );
    builder.add(genericAnnotator);

    AnalysisEngineDescription xwriter =
    AnalysisEngineFactory.createPrimitiveDescription(
          XWriter.class,
          AssertionComponents.CTAKES_CTS_TYPE_SYSTEM_DESCRIPTION,
          XWriter.PARAM_OUTPUT_DIRECTORY_NAME,
          testOutputDirectory,
          XWriter.PARAM_XML_SCHEME_NAME,
          XWriter.XMI);
    builder.add(xwriter);
////
   
    FileOutputStream outputStream = new FileOutputStream("desc/analysis_engine/assertion_test.xml");
   
    AnalysisEngineDescription description = builder.createAggregateDescription();
   
    description.toXML(outputStream);
  }
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        decodingInputDirectory,
        XReader.PARAM_XML_SCHEME,
        XReader.XMI);
   
   
    AggregateBuilder trainingBuilder = new AggregateBuilder();
   
    AnalysisEngineDescription goldCopierAnnotator = AnalysisEngineFactory.createPrimitiveDescription(ReferenceIdentifiedAnnotationsSystemToGoldCopier.class);
    trainingBuilder.add(goldCopierAnnotator);
   
    AnalysisEngineDescription assertionAttributeClearerAnnotator = AnalysisEngineFactory.createPrimitiveDescription(ReferenceAnnotationsSystemAssertionClearer.class);
    trainingBuilder.add(assertionAttributeClearerAnnotator);
   
    Class<? extends DataWriterFactory<String>> dataWriterFactoryClass = DefaultMaxentDataWriterFactory.class;
    AnalysisEngineDescription trainingAssertionAnnotator =
        AnalysisEngineFactory.createPrimitiveDescription(
            AssertionCleartkAnalysisEngine.class,
            AssertionComponents.CTAKES_CTS_TYPE_SYSTEM_DESCRIPTION
            );
    ConfigurationParameterFactory.addConfigurationParameters(
        trainingAssertionAnnotator,
        AssertionCleartkAnalysisEngine.PARAM_GOLD_VIEW_NAME,
        AssertionEvaluation.GOLD_VIEW_NAME,
        CleartkAnnotator.PARAM_DATA_WRITER_FACTORY_CLASS_NAME,
        dataWriterFactoryClass.getName(),
        DirectoryDataWriterFactory.PARAM_OUTPUT_DIRECTORY,
        modelOutputDirectory
        );
    trainingBuilder.add(trainingAssertionAnnotator);
   
   
   
//    CollectionReader collectionReader = XReader.getCollectionReader(
//        trainingDataDirectory);
//    collectionReader.setConfigParameterValue(XReader.PARAM_XML_SCHEME, XReader.XMI);
//    collectionReader.reconfigure();

    logger.info("starting feature generation...");
    SimplePipeline.runPipeline(
        trainingCollectionReader,
//        FilesCollectionReader.getCollectionReaderWithView(
//            "src/test/resources/data/treebank/11597317.tree",
//            TreebankConstants.TREEBANK_VIEW)
//        ,
//        TreebankGoldAnnotator.getDescriptionPOSTagsOnly(),
//        DefaultSnowballStemmer.getDescription("English"),
//        dataWriter);
        trainingBuilder.createAggregateDescription());
    logger.info("finished feature generation.");

    String[] args;
    if (trainingArgs != null && trainingArgs.length > 0) {
      args = new String[trainingArgs.length + 1];
      args[0] = modelOutputDirectory;
      System.arraycopy(trainingArgs, 0, args, 1, trainingArgs.length);
    } else {
      args = new String[] { modelOutputDirectory };
    }

    HideOutput hider = new HideOutput();
    logger.info("starting training...");
    org.cleartk.classifier.jar.Train.main(args);
    logger.info("finished training.");
    hider.restoreOutput();

    AggregateBuilder decodingBuilder = new AggregateBuilder();
   
    //AnalysisEngineDescription goldCopierAnnotator = AnalysisEngineFactory.createPrimitiveDescription(ReferenceIdentifiedAnnotationsSystemToGoldCopier.class);
    decodingBuilder.add(goldCopierAnnotator);
   
    //AnalysisEngineDescription assertionAttributeClearerAnnotator = AnalysisEngineFactory.createPrimitiveDescription(ReferenceAnnotationsSystemAssertionClearer.class);
    decodingBuilder.add(assertionAttributeClearerAnnotator);
   
    AnalysisEngineDescription decodingAssertionAnnotator =
      AnalysisEngineFactory.createPrimitiveDescription(
        AssertionCleartkAnalysisEngine.class,
        AssertionComponents.CTAKES_CTS_TYPE_SYSTEM_DESCRIPTION
        );
    ConfigurationParameterFactory.addConfigurationParameters(
        decodingAssertionAnnotator,
        AssertionCleartkAnalysisEngine.PARAM_GOLD_VIEW_NAME,
        AssertionEvaluation.GOLD_VIEW_NAME,
        GenericJarClassifierFactory.PARAM_CLASSIFIER_JAR_PATH,
        new File(modelOutputDirectory, "model.jar").getPath()
        );
    decodingBuilder.add(decodingAssertionAnnotator);
   
    //SimplePipeline.runPipeline(collectionReader,  builder.createAggregateDescription());
    AnalysisEngineDescription decodingAggregateDescription = decodingBuilder.createAggregateDescription();
   
   
   
//    AnalysisEngineDescription taggerDescription = AnalysisEngineFactory.createPrimitiveDescription(
//        AssertionCleartkAnalysisEngine.class,
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  public void execute() throws UIMAException, IOException
  {
    logger.info("starting");

    AggregateBuilder builder = new AggregateBuilder();
   
    TypeSystemDescription typeSystemDescription = TypeSystemDescriptionFactory.createTypeSystemDescription();
    String filename = "/work/medfacts/sharp/data/2013-01-11_cue_phrase_feature_test/ON03FP00037D00207__merged.txt.xmi";
   
    JCas jcas = JCasFactory.createJCas(filename, typeSystemDescription);
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      files.addAll(getTestTextFiles(options.getBatchesDirectory()));
      CollectionReader reader = UriCollectionReader.getCollectionReaderFromFiles(files);

      // load the text from the URI, run the preprocessor, then run the
      // Knowtator XML reader
      AggregateBuilder builder = new AggregateBuilder();
      builder.add(UriToDocumentTextAnnotator.getDescription());
      File preprocessDescFile = new File("desc/analysis_engine/RelationExtractorPreprocessor.xml");
      XMLParser parser = UIMAFramework.getXMLParser();
      XMLInputSource source = new XMLInputSource(preprocessDescFile);
      builder.add(parser.parseAnalysisEngineDescription(source));
      builder.add(AnalysisEngineFactory.createPrimitiveDescription(
          ViewCreatorAnnotator.class,
          ViewCreatorAnnotator.PARAM_VIEW_NAME,
          GOLD_VIEW_NAME));
      builder.add(AnalysisEngineFactory.createPrimitiveDescription(CopyDocumentTextToGoldView.class));
      builder.add(
          AnalysisEngineFactory.createPrimitiveDescription(DocumentIDAnnotator.class),
          CAS.NAME_DEFAULT_SOFA,
          GOLD_VIEW_NAME);
      builder.add(
          AnalysisEngineFactory.createPrimitiveDescription(SHARPKnowtatorXMLReader.class),
          CAS.NAME_DEFAULT_SOFA,
          GOLD_VIEW_NAME);

      // write out an XMI for each file
      for (JCas jCas : new JCasIterable(reader, builder.createAggregate())) {
        JCas goldView = jCas.getView(GOLD_VIEW_NAME);
        String documentID = DocumentIDAnnotationUtil.getDocumentID(goldView);
        if (documentID == null) {
          throw new IllegalArgumentException("No documentID for CAS:\n" + jCas);
        }
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  public void execute() throws UIMAException, IOException
  {
    logger.info("starting");

    AggregateBuilder builder = new AggregateBuilder();
   
    TypeSystemDescription typeSystemDescription = TypeSystemDescriptionFactory.createTypeSystemDescription();
    String filename = "/work/medfacts/sharp/data/2013-01-11_cue_phrase_feature_test/ON03FP00037D00207__merged.txt.xmi";
   
    JCas jcas = JCasFactory.createJCas(filename, typeSystemDescription);
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   */
  public static void main(String[] args) throws UIMAException, IOException {
    TypeSystemDescription types = TypeSystemDescriptionFactory.createTypeSystemDescription();
   
//    AnalysisEngine ae = AnalysisEngineFactory.createAnalysisEngineFromPath("desc/analysis_engine/AggregateParsingProcessor.xml");
    AggregateBuilder builder = new AggregateBuilder();
    builder.add(AnalysisEngineFactory.createPrimitiveDescription(SimpleSegmentAnnotator.class));
      builder.add(AnalysisEngineFactory.createPrimitiveDescription(
              SentenceDetector.class,
              SentenceDetector.SD_MODEL_FILE_PARAM,
              "org/apache/ctakes/core/sentdetect/sd-med-model.zip"));
    builder.add(AnalysisEngineFactory.createPrimitiveDescription(TokenizerAnnotatorPTB.class));
    builder.add(AnalysisEngineFactory.createPrimitiveDescription(ConstituencyParser.class));
   
    AnalysisEngine ae = builder.createAggregate();
   
    Scanner scanner = new Scanner(System.in);
    while(scanner.hasNextLine()){
      JCas jcas = JCasFactory.createJCas(types);
      jcas.setDocumentText(scanner.nextLine());
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