Package org.apache.uima.jcas

Examples of org.apache.uima.jcas.JCas

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      e.printStackTrace();
    }
  }

  private void mapAnnotations(JCas fromJcas, int[] map, String toView) throws CASException {
    JCas modview = fromJcas.getView(toView);

    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()];
      final int mappedEnd = map[clone.getEnd()];
      if (mappedBegin < mappedEnd) {
        if (mappedEnd > fromJcas.getCas().getDocumentAnnotation().getEnd()) {
          getContext().getLogger().log(Level.WARNING, "illegal annotation offset mapping");
        } else {
          int max = modview.getCas().getDocumentAnnotation().getEnd();
          if (mappedBegin < max && mappedEnd <= max && mappedBegin >= 0 && mappedEnd > 0) {
            clone.setBegin(mappedBegin);
            clone.setEnd(mappedEnd);
            // TODO handle nested annotation features
            modview.addFsToIndexes(clone);
            indexedFs.add(clone);
          } else {
            getContext().getLogger().log(Level.WARNING, "illegal annotation offset mapping");
          }
        }
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      String value = each.getKey().getStringValue(parent, matchedAnnotation, stream);
      map.put(value, each.getValue());
    }

    TypeSystem typeSystem = stream.getCas().getTypeSystem();
    JCas jcas = stream.getJCas();
    List<?> featuresList = structure.getType().getFeatures();
    for (int i = 0; i < featuresList.size(); i++) {
      Feature targetFeature = (Feature) featuresList.get(i);
      String name = targetFeature.getName();
      String shortFName = name.substring(name.indexOf(":") + 1, name.length());
      Object valueObject = map.get(shortFName);
      Type range = targetFeature.getRange();
      if (valueObject != null) {
        if (valueObject instanceof TypeExpression
                && range.getName().equals(UIMAConstants.TYPE_STRING)) {
          TypeExpression type = (TypeExpression) valueObject;
          List<AnnotationFS> annotationsInWindow = stream.getAnnotationsInWindow(matchedAnnotation,
                  type.getType(parent));
          if (annotationsInWindow != null && !annotationsInWindow.isEmpty()) {
            AnnotationFS annotation = annotationsInWindow.get(0);
            structure.setStringValue(targetFeature, annotation.getCoveredText());
          }
        } else if (valueObject instanceof IStringExpression
                && range.getName().equals(UIMAConstants.TYPE_STRING)) {
          structure.setStringValue(targetFeature, ((IStringExpression) valueObject).getStringValue(
                  parent, matchedAnnotation, stream));

        } else if (valueObject instanceof INumberExpression) {
          if (range.getName().equals(UIMAConstants.TYPE_INTEGER)) {
            structure.setIntValue(targetFeature, ((INumberExpression) valueObject).getIntegerValue(
                    parent, matchedAnnotation, stream));
          } else if (range.getName().equals(UIMAConstants.TYPE_DOUBLE)) {
            structure.setDoubleValue(targetFeature, ((INumberExpression) valueObject)
                    .getDoubleValue(parent, matchedAnnotation, stream));
          } else if (range.getName().equals(UIMAConstants.TYPE_FLOAT)) {
            structure.setFloatValue(targetFeature, ((INumberExpression) valueObject).getFloatValue(
                    parent, matchedAnnotation, stream));
          } else if (range.getName().equals(UIMAConstants.TYPE_BYTE)) {
            structure.setByteValue(targetFeature, (byte) ((INumberExpression) valueObject)
                    .getIntegerValue(parent, matchedAnnotation, stream));
          } else if (range.getName().equals(UIMAConstants.TYPE_SHORT)) {
            structure.setShortValue(targetFeature, (short) ((INumberExpression) valueObject)
                    .getIntegerValue(parent, matchedAnnotation, stream));
          } else if (range.getName().equals(UIMAConstants.TYPE_LONG)) {
            structure.setLongValue(targetFeature, (long) ((INumberExpression) valueObject)
                    .getIntegerValue(parent, matchedAnnotation, stream));
          }
        } else if (valueObject instanceof IBooleanExpression
                && range.getName().equals(UIMAConstants.TYPE_BOOLEAN)) {
          structure.setBooleanValue(targetFeature, ((IBooleanExpression) valueObject)
                  .getBooleanValue(parent, matchedAnnotation, stream));
        } else if (valueObject instanceof TypeExpression) {
          TypeExpression type = (TypeExpression) valueObject;
          List<AnnotationFS> annotationsInWindow = stream.getAnnotationsInWindow(matchedAnnotation,
                  type.getType(parent));
          if (typeSystem.subsumes(jcas.getCasType(FSArray.type), range)) {
            structure
                    .setFeatureValue(targetFeature, UIMAUtils.toFSArray(jcas, annotationsInWindow));
          } else if (typeSystem.subsumes(range, type.getType(parent))
                  && !annotationsInWindow.isEmpty()) {
            AnnotationFS annotation = annotationsInWindow.get(0);
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    try {
      String viewName = cas.getViewName();
      if (viewName == null) {
        cas = cas.getView(CAS.NAME_DEFAULT_SOFA);
      }
      JCas modifiedView = null;
      Iterator<?> viewIterator = cas.getViewIterator();
      while (viewIterator.hasNext()) {
        JCas each = (JCas) viewIterator.next();
        if (each.getViewName().equals(modifiedViewName)) {
          modifiedView = each;
          break;
        }
      }
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      e.printStackTrace();
    }
  }

  private void mapAnnotations(JCas fromJcas, int[] map, String toView) throws CASException {
    JCas modview = fromJcas.getView(toView);

    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()];
      final int mappedEnd = map[clone.getEnd()];
      if (mappedBegin < mappedEnd) {
        if (mappedEnd > fromJcas.getCas().getDocumentAnnotation().getEnd()) {
          getContext().getLogger().log(Level.WARNING, "illegal annotation offset mapping");
        } else {
          int max = modview.getCas().getDocumentAnnotation().getEnd();
          if (mappedBegin < max && mappedEnd <= max && mappedBegin >= 0 && mappedEnd > 0) {
            clone.setBegin(mappedBegin);
            clone.setEnd(mappedEnd);
            // TODO handle nested annotation features
            modview.addFsToIndexes(clone);
            indexedFs.add(clone);
          } else {
            getContext().getLogger().log(Level.WARNING, "illegal annotation offset mapping");
          }
        }
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  private final Pattern markupPattern = Pattern
          .compile("</?\\w+((\\s+\\w+(\\s*=\\s*(?:\".*?\"|'.*?'|[^'\">\\s]+))?)+\\s*|\\s*)/?>");

  public Type seed(String text, CAS cas) {
    Type result = null;
    JCas jCas = null;
    int size = 0;
    try {
      jCas = cas.getJCas();
      size = jCas.getAnnotationIndex(TokenSeed.type).size();
      result = jCas.getTypeSystem().getType(seedType);
    } catch (CASException e1) {
    }
    // do not apply seeding if there are already annotations of this seed type
    if (jCas == null || size != 0 || text == null) {
      return result;
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    keep = (String) aContext.getConfigParameterValue(KEEP);
  }

  @Override
  public void process(JCas jcaz) throws AnalysisEngineProcessException {
    JCas jcas;
    try {
      if (inputViewName != null) {
        jcas = jcaz.getView(inputViewName);
      } else {
        jcas = jcaz;
      }
    } catch (CASException e1) {
      throw new AnalysisEngineProcessException(e1.getCause());
    }
    // init:
    String documentText = jcas.getDocumentText();
    map = new int[documentText.length() + 1];
    JCas modview = null;
    try {
      // check if view already exists:
      Iterator<JCas> viewIterator = jcas.getViewIterator();
      while (viewIterator.hasNext()) {
        JCas jCas2 = (JCas) viewIterator.next();
        if (jCas2.getViewName().equals(outputViewName)) {
          modview = jCas2;
          getContext().getLogger().log(Level.WARNING,
                  "view with name \"" + outputViewName + "\" already exists.");
        }
      }
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  /**
   * @see org.apache.uima.collection.CollectionReader#getNext(org.apache.uima.cas.CAS)
   */
  public void getNext(CAS aCAS) throws IOException, CollectionException {
    JCas jcas;
    try {
      jcas = aCAS.getJCas();
    } catch (CASException e) {
      throw new CollectionException(e);
    }

    // open input stream to file
    File file = (File) mFiles.get(mCurrentIndex++);
    String text = FileUtils.file2String(file, mEncoding);
      // put document in CAS
    jcas.setDocumentText(text);

    // set language if it was explicitly specified as a configuration parameter
    if (mLanguage != null) {
      ((DocumentAnnotation) jcas.getDocumentAnnotationFs()).setLanguage(mLanguage);
    }

    // Also store location of source document in CAS. This information is critical
    // if CAS Consumers will need to know where the original document contents are located.
    // For example, the Semantic Search CAS Indexer writes this information into the
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   *           if there is an error in processing the Resource
   *
   * @see org.apache.uima.collection.base_cpm.CasObjectProcessor#processCas(org.apache.uima.cas.CAS)
   */
  public void processCas(CAS aCAS) throws ResourceProcessException {
    JCas jcas;
    try {
      jcas = aCAS.getJCas();
    } catch (CASException e) {
      throw new ResourceProcessException(e);
    }

    // retreive the filename of the input file from the CAS
    FSIterator it = jcas.getAnnotationIndex(SourceDocumentInformation.type).iterator();
    File outFile = null;
    if (it.hasNext()) {
      SourceDocumentInformation fileLoc = (SourceDocumentInformation) it.next();
      File inFile;
      try {
        inFile = new File(new URL(fileLoc.getUri()).getPath());
        String outFileName = inFile.getName();
        if (fileLoc.getOffsetInSource() > 0) {
          outFileName += fileLoc.getOffsetInSource();
        }
        outFile = new File(mOutputDir, outFileName);
      } catch (MalformedURLException e1) {
        // invalid URL, use default processing below
      }
    }
    if (outFile == null) {
      outFile = new File(mOutputDir, "doc" + mDocNum++);
    }
    // serialize XCAS and write to output file
    try {
      writeXCas(jcas.getCas(), outFile);
    } catch (IOException e) {
      throw new ResourceProcessException(e);
    } catch (SAXException e) {
      throw new ResourceProcessException(e);
    }
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   * @see org.apache.uima.collection.base_cpm.CasObjectProcessor#processCas(org.apache.uima.cas.CAS)
   */
  public void processCas(CAS aCAS) throws ResourceProcessException {
    String modelFileName = null;

    JCas jcas;
    try {
      jcas = aCAS.getJCas();
    } catch (CASException e) {
      throw new ResourceProcessException(e);
    }

    // retreive the filename of the input file from the CAS
    FSIterator it = jcas.getAnnotationIndex(SourceDocumentInformation.type).iterator();
    File outFile = null;
    if (it.hasNext()) {
      SourceDocumentInformation fileLoc = (SourceDocumentInformation) it.next();
      File inFile;
      try {
        inFile = new File(new URL(fileLoc.getUri()).getPath());
        String outFileName = inFile.getName();
        if (fileLoc.getOffsetInSource() > 0) {
          outFileName += ("_" + fileLoc.getOffsetInSource());
        }
        outFileName += ".xmi";
        outFile = new File(mOutputDir, outFileName);
        modelFileName = mOutputDir.getAbsolutePath() + "/" + inFile.getName() + ".ecore";
      } catch (MalformedURLException e1) {
        // invalid URL, use default processing below
      }
    }
    if (outFile == null) {
      outFile = new File(mOutputDir, "doc" + mDocNum++ + ".xmi");    
    }
    // serialize XCAS and write to output file
    try {
      writeXmi(jcas.getCas(), outFile, modelFileName);
    } catch (IOException e) {
      throw new ResourceProcessException(e);
    } catch (SAXException e) {
      throw new ResourceProcessException(e);
    }
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   * @see org.apache.uima.collection.base_cpm.CasObjectProcessor#processCas(org.apache.uima.cas.CAS)
   */
  public void processCas(CAS aCAS) throws ResourceProcessException {
    String modelFileName = null;

    JCas jcas;
    try {
      jcas = aCAS.getJCas();
    } catch (CASException e) {
      throw new ResourceProcessException(e);
    }

    // retreive the filename of the input file from the CAS
    FSIterator it = jcas.getAnnotationIndex(SourceDocumentInformation.type).iterator();
    File outFile = null;
    if (it.hasNext()) {
      SourceDocumentInformation fileLoc = (SourceDocumentInformation) it.next();
      File inFile;
      try {
        inFile = new File(new URL(fileLoc.getUri()).getPath());
        String outFileName = inFile.getName();
        if (fileLoc.getOffsetInSource() > 0) {
          outFileName += ("_" + fileLoc.getOffsetInSource());
        }
        outFileName += ".xmi";
        outFile = new File(mOutputDir, outFileName);
        modelFileName = mOutputDir.getAbsolutePath() + "/" + inFile.getName() + ".ecore";
      } catch (MalformedURLException e1) {
        // invalid URL, use default processing below
      }
    }
    if (outFile == null) {
      outFile = new File(mOutputDir, "doc" + mDocNum++);
    }
    // serialize XCAS and write to output file
    try {
      writeXmi(jcas.getCas(), outFile, modelFileName);
    } catch (IOException e) {
      throw new ResourceProcessException(e);
    } catch (SAXException e) {
      throw new ResourceProcessException(e);
    }
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