Examples of AggregateBuilder

org.apache.uima.fit.factory.AggregateBuilder

This builder makes it easier to create an aggregate analysis engine. A typical use-case would involve initializing this builder with your preferred type system and type priorities (the latter may be null). This is followed by adding analysis engine descriptions one at a time until done. This makes it easy to have runtime decisions determine how the aggregate engine should be built. Finally, one of the create methods are called and an AnalysisEngine or AnalysisEngineDescription is returned.

This is an example taken from our test cases:

 import static org.apache.uima.fit.factory.AnalysisEngineFactory.createPrimitiveDescription; AggregateBuilder builder = new AggregateBuilder(); builder.add(createPrimitiveDescription(Annotator1.class, typeSystemDescription), ViewNames.PARENTHESES_VIEW, "A"); builder.add(createPrimitiveDescription(Annotator2.class, typeSystemDescription), ViewNames.SORTED_VIEW, "B", ViewNames.SORTED_PARENTHESES_VIEW, "C", ViewNames.PARENTHESES_VIEW, "A"); builder.add(createPrimitiveDescription(Annotator3.class, typeSystemDescription), ViewNames.INITIAL_VIEW, "B"); AnalysisEngine aggregateEngine = builder.createAggregate();

org.uimafit.factory.AggregateBuilder

Examples of org.uimafit.factory.AggregateBuilder

    writeDesc(options.descDir, "DegreeOfRelationExtractorAnnotator", degreeOfRelationExtractorDesc);
    AnalysisEngineDescription emPairRelationExtractorDesc = trainRelationExtractor(modelsDirEMPair, trainFiles, EntityMentionPairRelationExtractorAnnotator.class, dataWriterClass, emPairParams);
    writeDesc(options.descDir, "EntityMentionPairRelationExtractorAnnotator", emPairRelationExtractorDesc);


    // create the aggregate description
    AggregateBuilder builder = new AggregateBuilder();
    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(modifierExtractorDesc);
    builder.add(degreeOfRelationExtractorDesc);
    builder.add(emPairRelationExtractorDesc);
    AnalysisEngineDescription aggregateDescription = builder.createAggregateDescription();
    
    // write out the XML version of the aggregate description
    writeDesc(options.descDir, "RelationExtractorAggregate", aggregateDescription);
  }

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Examples of org.uimafit.factory.AggregateBuilder


  @Override
  protected void train(CollectionReader collectionReader, File directory) throws Exception {
    //    if(this.baseline) return;
    if(this.skipTrain) return;
    AggregateBuilder aggregateBuilder = this.getPreprocessorAggregateBuilder();
    aggregateBuilder.add(CopyFromGold.getDescription(EventMention.class, TimeMention.class, BinaryTextRelation.class));
    aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(RemoveCrossSentenceRelations.class));
    if(!this.useGoldAttributes){
      aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(RemoveGoldAttributes.class));
    }
    if (this.useClosure) {
      aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(AddClosure.class));//aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(AddTransitiveContainsRelations.class));
//      aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(AddContain2Overlap.class));
      //      aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(AddTransitiveBeforeAndOnRelations.class));
    }
//    aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(RemoveNonContainsRelations.class));
    aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(AddFlippedOverlap.class));//add flipped overlap instances to training data
    
    aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(RemoveEventEventRelations.class));
    aggregateBuilder.add(EventTimeRelationAnnotator.createDataWriterDescription(
        //                LIBSVMStringOutcomeDataWriter.class,
        TKSVMlightStringOutcomeDataWriter.class,
        //        TKLIBSVMStringOutcomeDataWriter.class,
        //        SVMlightStringOutcomeDataWriter.class,        
        directory,
        params.probabilityOfKeepingANegativeExample));
    SimplePipeline.runPipeline(collectionReader, aggregateBuilder.createAggregate());
    String[] optArray;


    if(this.kernelParams == null){
      ArrayList<String> svmOptions = new ArrayList<String>();
      svmOptions.add("-c"); svmOptions.add(""+params.svmCost);        // svm cost

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Examples of org.uimafit.factory.AggregateBuilder

  }


  @Override
  protected AnnotationStatistics<String> test(CollectionReader collectionReader, File directory)
      throws Exception {
    AggregateBuilder aggregateBuilder = this.getPreprocessorAggregateBuilder();
    aggregateBuilder.add(CopyFromGold.getDescription(EventMention.class, TimeMention.class));
    
    aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(
        RemoveCrossSentenceRelations.class,
        RemoveCrossSentenceRelations.PARAM_SENTENCE_VIEW,
        CAS.NAME_DEFAULT_SOFA,
        RemoveCrossSentenceRelations.PARAM_RELATION_VIEW,
        GOLD_VIEW_NAME));
    if (this.useClosure) {
      aggregateBuilder.add(
          AnalysisEngineFactory.createPrimitiveDescription(AddClosure.class),//AnalysisEngineFactory.createPrimitiveDescription(AddTransitiveContainsRelations.class),
          CAS.NAME_DEFAULT_SOFA,
          GOLD_VIEW_NAME);
          
//      aggregateBuilder.add(
//          AnalysisEngineFactory.createPrimitiveDescription(AddContain2Overlap.class),
//          CAS.NAME_DEFAULT_SOFA,
//          GOLD_VIEW_NAME);
      //      aggregateBuilder.add(
      //          AnalysisEngineFactory.createPrimitiveDescription(AddTransitiveBeforeAndOnRelations.class),
      //          CAS.NAME_DEFAULT_SOFA,
      //          GOLD_VIEW_NAME);
    }
    
//    aggregateBuilder.add(
//        AnalysisEngineFactory.createPrimitiveDescription(RemoveNonContainsRelations.class,
//            RemoveNonContainsRelations.PARAM_RELATION_VIEW,
//            GOLD_VIEW_NAME));
    aggregateBuilder.add(
        AnalysisEngineFactory.createPrimitiveDescription(RemoveEventEventRelations.class),
        CAS.NAME_DEFAULT_SOFA,
        GOLD_VIEW_NAME);


    aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(RemoveRelations.class));
    aggregateBuilder.add(this.baseline ? RecallBaselineEventTimeRelationAnnotator.createAnnotatorDescription(directory) :
      EventTimeRelationAnnotator.createAnnotatorDescription(directory));
    if(this.i2b2Output != null){
      aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(WriteI2B2XML.class, WriteI2B2XML.PARAM_OUTPUT_DIR, this.i2b2Output), "TimexView", CAS.NAME_DEFAULT_SOFA);
    }
    if (this.useClosure) {//add closure for system output
      aggregateBuilder.add(
          AnalysisEngineFactory.createPrimitiveDescription(AddClosure.class),//AnalysisEngineFactory.createPrimitiveDescription(AddTransitiveContainsRelations.class),
          GOLD_VIEW_NAME,
          CAS.NAME_DEFAULT_SOFA
          );
    }
    Function<BinaryTextRelation, ?> getSpan = new Function<BinaryTextRelation, HashableArguments>() {
      public HashableArguments apply(BinaryTextRelation relation) {
        return new HashableArguments(relation);
      }
    };
    Function<BinaryTextRelation, String> getOutcome = AnnotationStatistics.annotationToFeatureValue("category");


    AnnotationStatistics<String> stats = new AnnotationStatistics<String>();
    JCasIterable jcasIter =new JCasIterable(collectionReader, aggregateBuilder.createAggregate());
    JCas jCas = null;
    while(jcasIter.hasNext()) {
      jCas = jcasIter.next();
      JCas goldView = jCas.getView(GOLD_VIEW_NAME);
      JCas systemView = jCas.getView(CAS.NAME_DEFAULT_SOFA);

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Examples of org.uimafit.factory.AggregateBuilder

    }
  }


  @Override
  protected void train(CollectionReader collectionReader, File directory) throws Exception {
    AggregateBuilder aggregateBuilder = this.getPreprocessorAggregateBuilder();
    aggregateBuilder.add(CopyFromGold.getDescription(EventMention.class));
    aggregateBuilder.add(CopyFromGold.getDescription(EventProperties.class));
    SimplePipeline.runPipeline(collectionReader, aggregateBuilder.createAggregate());
  }

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Examples of org.uimafit.factory.AggregateBuilder


  @Override
  protected Map<String, AnnotationStatistics<String>> test(
      CollectionReader collectionReader,
      File directory) throws Exception {
    AggregateBuilder aggregateBuilder = this.getPreprocessorAggregateBuilder();
    aggregateBuilder.add(CopyFromGold.getDescription(EventMention.class));
    aggregateBuilder.add(CopyFromGold.getDescription(TimeMention.class));
    aggregateBuilder.add(SentenceAnnotator.getDescription());
    aggregateBuilder.add(TokenAnnotator.getDescription());
    aggregateBuilder.add(PosTaggerAnnotator.getDescription());
    aggregateBuilder.add(DefaultSnowballStemmer.getDescription("English"));
    aggregateBuilder.add(ParserAnnotator.getDescription());
    aggregateBuilder.add(EventToClearTKEventAnnotator.getAnnotatorDescription());//for every cTakes eventMention, create a cleartk event
    aggregateBuilder.add(ClearTKDocumentCreationTimeAnnotator.getAnnotatorDescription());//for every jCAS create an empty DCT, and add it to index
    aggregateBuilder.add(EventTenseAnnotator.FACTORY.getAnnotatorDescription("/org/cleartk/timeml/event/eventtenseannotator/model.jar"));
    aggregateBuilder.add(EventAspectAnnotator.FACTORY.getAnnotatorDescription("/org/cleartk/timeml/event/eventaspectannotator/model.jar"));
    aggregateBuilder.add(EventClassAnnotator.FACTORY.getAnnotatorDescription("/org/cleartk/timeml/event/eventclassannotator/model.jar"));
    aggregateBuilder.add(EventPolarityAnnotator.FACTORY.getAnnotatorDescription("/org/cleartk/timeml/event/eventpolarityannotator/model.jar"));
    aggregateBuilder.add(EventModalityAnnotator.FACTORY.getAnnotatorDescription("/org/cleartk/timeml/event/eventmodalityannotator/model.jar"));
    aggregateBuilder.add(TemporalLinkEventToDocumentCreationTimeAnnotator.FACTORY.getAnnotatorDescription("/org/cleartk/timeml/tlink/temporallinkeventtodocumentcreationtimeannotator/model.jar"));
    aggregateBuilder.add(ClearTKDocTimeRelAnnotator.getAnnotatorDescription());// for every tlink, check if it cover and event, add the tlink type to the event's docTimeRel attribute


    Function<EventMention, ?> eventMentionToSpan = AnnotationStatistics.annotationToSpan();
    Map<String, Function<EventMention, String>> propertyGetters;
    propertyGetters = new HashMap<String, Function<EventMention, String>>();
    for (String name : PROPERTY_NAMES) {
      propertyGetters.put(name, getPropertyGetter(name));
    }


    Map<String, AnnotationStatistics<String>> statsMap = new HashMap<String, AnnotationStatistics<String>>();
    statsMap.put(DOC_TIME_REL, new AnnotationStatistics<String>());
    for (JCas jCas : new JCasIterable(collectionReader, aggregateBuilder.createAggregate())) {
      JCas goldView = jCas.getView(GOLD_VIEW_NAME);
      JCas systemView = jCas.getView(CAS.NAME_DEFAULT_SOFA);
      String text = goldView.getDocumentText();
      for (Segment segment : JCasUtil.select(jCas, Segment.class)) {
        if (!THYMEData.SEGMENTS_TO_SKIP.contains(segment.getId())) {

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Examples of org.uimafit.factory.AggregateBuilder


  protected abstract void trainAndPackage(File directory) throws Exception;


  @Override
  protected void train(CollectionReader collectionReader, File directory) throws Exception {
    AggregateBuilder aggregateBuilder = this.getPreprocessorAggregateBuilder();
    aggregateBuilder.add(CopyFromGold.getDescription(this.annotationClass));
    aggregateBuilder.add(this.getDataWriterDescription(directory), "TimexView", CAS.NAME_DEFAULT_SOFA);
    SimplePipeline.runPipeline(collectionReader, aggregateBuilder.createAggregate());
    this.trainAndPackage(directory);
  }

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Examples of org.uimafit.factory.AggregateBuilder

  protected abstract Collection<? extends Annotation> getSystemAnnotations(JCas jCas, Segment segment);


  @Override
  protected AnnotationStatistics<String> test(CollectionReader collectionReader, File directory)
      throws Exception {
    AggregateBuilder aggregateBuilder = this.getPreprocessorAggregateBuilder();
    aggregateBuilder.add(this.getAnnotatorDescription(directory), "TimexView", CAS.NAME_DEFAULT_SOFA);
    if(this.i2b2Output != null){
      aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(WriteI2B2XML.class, WriteI2B2XML.PARAM_OUTPUT_DIR, this.i2b2Output), "TimexView", CAS.NAME_DEFAULT_SOFA);
    }
    AnnotationStatistics<String> stats = new AnnotationStatistics<String>();
    Ordering<Annotation> bySpans = Ordering.<Integer> natural().lexicographical().onResultOf(
        new Function<Annotation, List<Integer>>() {
          @Override
          public List<Integer> apply(Annotation annotation) {
            return Arrays.asList(annotation.getBegin(), annotation.getEnd());
          }
        });
    for (JCas jCas : new JCasIterable(collectionReader, aggregateBuilder.createAggregate())) {
      JCas goldView = jCas.getView(GOLD_VIEW_NAME);
      JCas systemView = jCas.getView(CAS.NAME_DEFAULT_SOFA);
      for (Segment segment : JCasUtil.select(jCas, Segment.class)) {
        if (!THYMEData.SEGMENTS_TO_SKIP.contains(segment.getId())) {
          Collection<? extends Annotation> goldAnnotations = this.getGoldAnnotations(goldView, segment);

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Examples of org.uimafit.factory.AggregateBuilder

    
    JCasIterable[] casIters = new JCasIterable[nFolds];
    for (int fold = 0; fold < nFolds; ++fold) {
      List<Integer> xfoldTrain = selectTrainItems(allTrain, nFolds, fold);
      List<Integer> xfoldTest = selectTestItems(allTrain, nFolds, fold);
      AggregateBuilder aggregateBuilder = this.getPreprocessorAggregateBuilder();
      File modelDirectory = getModelDirectory(new File("target/eval/time-spans/fold_"+fold));
      for (Class<? extends JCasAnnotator_ImplBase> annotatorClass : annotatorClasses) {
        EvaluationOfTimeSpans evaluation = new EvaluationOfTimeSpans(
            new File("target/eval/time-spans/" ),
            this.rawTextDirectory,
            this.xmlDirectory,
            this.xmlFormat,
            this.xmiDirectory,
            this.treebankDirectory,
            1,
            0,
            annotatorClass,
            false,
            annotatorTrainingArguments.get(annotatorClass));
        evaluation.prepareXMIsFor(allTrain);
        String name = String.format("%s.errors", annotatorClass.getSimpleName());
        evaluation.setLogging(Level.FINE, new File("target/eval", name));


        // train on 4 of the folds of the training data:
        evaluation.train(evaluation.getCollectionReader(xfoldTrain), modelDirectory);
        if(fold == 0){
          // train the main model as well:
          evaluation.train(evaluation.getCollectionReader(allTrain), directory);
        }
        
      }
      casIters[fold] = new JCasIterable(getCollectionReader(xfoldTest), aggregateBuilder.createAggregate());
    }
    // run meta data-writer for this fold:
    AggregateBuilder writerBuilder = new AggregateBuilder();
    writerBuilder.add(CopyFromGold.getDescription(TimeMention.class));
    writerBuilder.add(this.getDataWriterDescription(directory));
    AnalysisEngine writer = writerBuilder.createAggregate();
    for(JCasIterable casIter : casIters){
      for(JCas jcas : casIter){
        SimplePipeline.runPipeline(jcas, writer);
      }
    }

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Examples of org.uimafit.factory.AggregateBuilder

    assertTrue(tokens.get(29).getCanonicalForm() == null);
    
  }
  
  public static AnalysisEngineDescription getPrerequisitePipeline() throws ResourceInitializationException{
    AggregateBuilder builder = new AggregateBuilder();
    builder.add(SimpleSegmentAnnotator.createAnnotatorDescription());
    builder.add(SentenceDetector.createAnnotatorDescription());
    builder.add(TokenizerAnnotatorPTB.createAnnotatorDescription());
    return builder.createAggregateDescription();
  }

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Examples of org.uimafit.factory.AggregateBuilder

    builder.add(TokenizerAnnotatorPTB.createAnnotatorDescription());
    return builder.createAggregateDescription();
  }
  
  public static AnalysisEngineDescription getDefaultPipeline() throws ResourceInitializationException, URISyntaxException{
    AggregateBuilder builder = new AggregateBuilder();
    builder.add(getPrerequisitePipeline());
    builder.add(LvgAnnotator.createAnnotatorDescription());
    return builder.createAggregateDescription();
  }

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