Examples of org.apache.uima.util.CasCopier

org.apache.uima.util.CasCopier
Utility class for doing deep copies of FeatureStructures from one CAS to another. To handle cases where the source CAS has multiple references to the same FS, you can create one instance of CasCopier and use it to copy multiple FeatureStructures. The CasCopier will remember previously copied FeatureStructures, so if you later copy another FS that has a reference to a previously copied FS, it will not duplicate the multiply-referenced FS.


    Set<Annotation> indexedFs = new HashSet<Annotation>();
    AnnotationIndex<Annotation> annotationIndex = fromJcas.getAnnotationIndex();
    TypeSystem typeSystem = fromJcas.getTypeSystem();
    Type docType = typeSystem.getType(UIMAConstants.TYPE_DOCUMENT);
    CasCopier casCopier = new CasCopier(fromJcas.getCas(), modview.getCas());
    for (Annotation annotation : annotationIndex) {
      // TODO be careful here, because some people inherit from DocumentAnnotation
      if (typeSystem.subsumes(docType, annotation.getType())) {
        continue;
      }
      Annotation clone = (Annotation) casCopier.copyFs(annotation);
      // change the view/sofa of the new annotation...
      // see: http://osdir.com/ml/apache.uima.general/2007-09/msg00107.html
      clone.setFeatureValue(modview.getTypeSystem()
              .getFeatureByFullName(CAS.FEATURE_FULL_NAME_SOFA), modview.getSofa());
      final int mappedBegin = map[clone.getBegin()];

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  // caution: testCas gets reset fist!
  public void resetAndFillTestCAS(CAS testCas, TextRulerTarget target) {
    testCas.reset();
    CAS docCas = getCAS();


    CasCopier cc = new CasCopier(docCas, testCas);
    testCas.setDocumentText(docCas.getDocumentText());


    // copy all annotations except the target-annotations:
    TypeSystem ts = docCas.getTypeSystem();


    List<Type> slotTypes = new ArrayList<Type>();


    for (String s : target.getSlotTypeNames())
      slotTypes.add(ts.getType(s));


    if (target.isBoundary()) {
      // add the base types (without START and END markers) also !
      for (String s : target.slotNames)
        slotTypes.add(ts.getType(s));
    }


    for (AnnotationFS fs : docCas.getAnnotationIndex()) {
      if (!slotTypes.contains(fs.getType())
              && !fs.getType().equals(docCas.getDocumentAnnotation().getType())) {
        FeatureStructure copyFs = cc.copyFs(fs);
        testCas.addFsToIndexes(copyFs);
      }
    }
  }

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    CAS inView = cas.getView(inputView);
    if(outView == null) {
      outView = getContext().getEmptyCas(CAS.class);
    }
    outView.reset();
    CasCopier cc = new CasCopier(inView, outView, true);
    cc.copyCasView(inView, outputView, true);
    try {
      writeXmi(outView, file);
    } catch (Exception e) {
      throw new AnalysisEngineProcessException(e);
    }

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    Set<Annotation> indexedFs = new HashSet<Annotation>();
    AnnotationIndex<Annotation> annotationIndex = fromJcas.getAnnotationIndex();
    TypeSystem typeSystem = fromJcas.getTypeSystem();
    Type docType = typeSystem.getType(UIMAConstants.TYPE_DOCUMENT);
    CasCopier casCopier = new CasCopier(fromJcas.getCas(), modview.getCas());
    for (Annotation annotation : annotationIndex) {
      // TODO be careful here, because some people inherit from DocumentAnnotation
      if (typeSystem.subsumes(docType, annotation.getType())) {
        continue;
      }
      Annotation clone = (Annotation) casCopier.copyFs(annotation);
      // change the view/sofa of the new annotation...
      // see: http://osdir.com/ml/apache.uima.general/2007-09/msg00107.html
      clone.setFeatureValue(modview.getTypeSystem()
              .getFeatureByFullName(CAS.FEATURE_FULL_NAME_SOFA), modview.getSofa());
      final int mappedBegin = map[clone.getBegin()];

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    Set<Annotation> indexedFs = new HashSet<Annotation>();
    AnnotationIndex<Annotation> annotationIndex = fromJcas.getAnnotationIndex();


    TypeSystem typeSystem = fromJcas.getTypeSystem();
    Type docType = typeSystem.getType(UIMAConstants.TYPE_DOCUMENT);
    CasCopier casCopier = new CasCopier(fromJcas.getCas(), modview.getCas());
    for (Annotation annotation : annotationIndex) {
      if (typeSystem.subsumes(docType, annotation.getType())) {
        continue;
      }
      Annotation clone = (Annotation) casCopier.copyFs(annotation);
      // change the view/sofa of the new annotation...
      // see: http://osdir.com/ml/apache.uima.general/2007-09/msg00107.html
      clone.setFeatureValue(modview.getTypeSystem()
              .getFeatureByFullName(CAS.FEATURE_FULL_NAME_SOFA), modview.getSofa());
      final int mappedBegin = map[clone.getBegin()];

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      // copy gold EntityMentions and Modifiers to the system view
      List<IdentifiedAnnotation> goldMentions = new ArrayList<IdentifiedAnnotation>();
      goldMentions.addAll(JCasUtil.select(goldView, EntityMention.class));
      goldMentions.addAll(JCasUtil.select(goldView, Modifier.class));
      CasCopier copier = new CasCopier(goldView.getCas(), systemView.getCas());
      for (IdentifiedAnnotation goldMention : goldMentions) {
        Annotation copy = (Annotation) copier.copyFs(goldMention);
        Feature sofaFeature = copy.getType().getFeatureByBaseName("sofa");
        copy.setFeatureValue(sofaFeature, systemView.getSofa());
        copy.addToIndexes();
      }
    }

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      // copy cTAKES EntityMentions and Modifiers to gold view
      List<IdentifiedAnnotation> cTakesMentions = new ArrayList<IdentifiedAnnotation>();
      cTakesMentions.addAll(JCasUtil.select(systemView, EntityMention.class));
      cTakesMentions.addAll(JCasUtil.select(systemView, Modifier.class));
      CasCopier copier = new CasCopier(systemView.getCas(), goldView.getCas());
      for (IdentifiedAnnotation cTakesMention : cTakesMentions) {
        Annotation copy = (Annotation) copier.copyFs(cTakesMention);
        Feature sofaFeature = copy.getType().getFeatureByBaseName("sofa");
        copy.setFeatureValue(sofaFeature, goldView.getSofa());
        copy.addToIndexes();
      }

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          if (annotation.getClass().equals(annotationClass)) {
            annotation.removeFromIndexes();
          }
        }
      }
      CasCopier copier = new CasCopier(goldView.getCas(), systemView.getCas());
      Feature sofaFeature = jCas.getTypeSystem().getFeatureByFullName(CAS.FEATURE_FULL_NAME_SOFA);
      for (Class<? extends TOP> annotationClass : this.annotationClasses) {
        for (TOP annotation : JCasUtil.select(goldView, annotationClass)) {
          TOP copy = (TOP) copier.copyFs(annotation);
          if (copy instanceof Annotation) {
            copy.setFeatureValue(sofaFeature, systemView.getSofa());
          }
          copy.addToIndexes(systemView);
        }

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      List<List<String>> componentOutcomes = new ArrayList<>();
      for(Class<?> component : components){
        JCas componentView;
        try {
          componentView = jCas.getView(component.getSimpleName());
          CasCopier casCopy = new CasCopier(jCas.getCas(), componentView.getCas());
          org.apache.uima.cas.Feature sofaFeature = jCas.getTypeSystem().getFeatureByFullName(CAS.FEATURE_FULL_NAME_SOFA);
          for(BaseToken token: tokens){
            BaseToken fs = (BaseToken) casCopy.copyFs(token);
            fs.setFeatureValue(sofaFeature, componentView.getSofa());
            fs.addToIndexes(componentView);
          }
          List<BaseToken> viewTokens = JCasUtil.selectCovered(componentView, BaseToken.class, sentence.getBegin(), sentence.getEnd());
          List<TimeMention> times = JCasUtil.selectCovered(componentView, TimeMention.class, sentence);

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      // copy gold EntityMentions and Modifiers to the system view
      List<IdentifiedAnnotation> goldMentions = new ArrayList<IdentifiedAnnotation>();
      goldMentions.addAll(JCasUtil.select(goldView, EntityMention.class));
      goldMentions.addAll(JCasUtil.select(goldView, Modifier.class));
      CasCopier copier = new CasCopier(goldView.getCas(), systemView.getCas());
      for (IdentifiedAnnotation goldMention : goldMentions)
      {
        Annotation copy = (Annotation) copier.copyFs(goldMention);
        Feature sofaFeature = copy.getType().getFeatureByBaseName("sofa");
        copy.setFeatureValue(sofaFeature, systemView.getSofa());
        copy.addToIndexes();
      }
    }

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