Example #1
0
  @Override
  protected void generateAnnotations(JCas jcas)
      throws AnalysisEngineProcessException, FeaturePathException {
    // CAS is necessary to retrieve values
    CAS currCAS = jcas.getCas();

    for (String path : paths) {

      // Separate Typename and featurepath
      String[] segments = path.split("/", 2);
      String typeName = segments[0];

      // Try to get the type from the typesystem of the CAS
      Type t = currCAS.getTypeSystem().getType(typeName);
      if (t == null) {
        throw new IllegalStateException("Type [" + typeName + "] not found in type system");
      }

      // get an fpi object and initialize it
      // initialize the FeaturePathInfo with the corresponding part
      initializeFeaturePathInfoFrom(fp, segments);

      // get the annotations
      AnnotationIndex<?> idx = currCAS.getAnnotationIndex(t);
      FSIterator<?> iterator = idx.iterator();

      while (iterator.hasNext()) {
        AnnotationFS fs = (AnnotationFS) iterator.next();

        try {
          if (this.filterFeaturePath != null) {
            // check annotation filter condition
            if (this.filterFeaturePathInfo.match(fs, this.filterCondition)) {
              createStemAnnotation(jcas, fs);
            }
          } else { // no annotation filter specified
            createStemAnnotation(jcas, fs);
          }
        } catch (AnalysisEngineProcessException e) {
          // TODO Auto-generated catch block
          throw new IllegalStateException("error occured while creating a stem annotation", e);
        }
      }
    }
  }
Example #2
0
  /**
   * Removes all annotations of type removeAnnotationType which are contained by annotations of type
   * containerAnnotationType.
   *
   * @param cas
   * @param containerAnnotationType
   * @param removeAnnotationType
   */
  public static void removeAnnotations(
      CAS cas, AnnotationFS containerAnnotation, Type removeAnnotationType) {

    FSIndex<AnnotationFS> allRemoveAnnotations = cas.getAnnotationIndex(removeAnnotationType);

    ContainingConstraint containingConstraint = new ContainingConstraint(containerAnnotation);

    Iterator<AnnotationFS> containingTokens =
        cas.createFilteredIterator(allRemoveAnnotations.iterator(), containingConstraint);

    Collection<AnnotationFS> removeAnnotations = new LinkedList<AnnotationFS>();

    while (containingTokens.hasNext()) {
      removeAnnotations.add(containingTokens.next());
    }

    for (Iterator<AnnotationFS> it = removeAnnotations.iterator(); it.hasNext(); ) {
      cas.removeFsFromIndexes(it.next());
    }
  }
  @Test
  public void testExpandOffsets() throws Exception {
    String html = "<Parent>\n";
    html += "<Child1>Some content</Child1>\n";
    html += "<Child2 attribute=“someValue” />\n";
    html += "<Child3>More content.</Child3>\n";
    html += "</Parent>\n";

    URL urlA = HtmlAnnotator.class.getClassLoader().getResource("HtmlAnnotator.xml");
    if (urlA == null) {
      urlA =
          HtmlAnnotator.class
              .getClassLoader()
              .getResource("org/apache/uima/ruta/engine/HtmlAnnotator.xml");
    }

    URL urlC = HtmlAnnotator.class.getClassLoader().getResource("HtmlConverter.xml");
    if (urlC == null) {
      urlC =
          HtmlAnnotator.class
              .getClassLoader()
              .getResource("org/apache/uima/ruta/engine/HtmlConverter.xml");
    }

    XMLInputSource inA = new XMLInputSource(urlA);
    ResourceSpecifier specifierA = UIMAFramework.getXMLParser().parseResourceSpecifier(inA);
    AnalysisEngine aeA = UIMAFramework.produceAnalysisEngine(specifierA);
    aeA.setConfigParameterValue(HtmlAnnotator.PARAM_ONLY_CONTENT, false);
    aeA.reconfigure();

    XMLInputSource inC = new XMLInputSource(urlC);
    ResourceSpecifier specifierC = UIMAFramework.getXMLParser().parseResourceSpecifier(inC);
    AnalysisEngine aeC = UIMAFramework.produceAnalysisEngine(specifierC);
    aeC.setConfigParameterValue(HtmlConverter.PARAM_SKIP_WHITESPACES, false);
    aeC.setConfigParameterValue(HtmlConverter.PARAM_PROCESS_ALL, true);
    aeC.setConfigParameterValue(HtmlConverter.PARAM_EXPAND_OFFSETS, true);
    aeC.reconfigure();

    CAS cas = aeA.newCAS();
    Type tagType = cas.getTypeSystem().getType(HtmlAnnotator.NAMESPACE + "TAG");
    Feature expandedFeature = tagType.getFeatureByBaseName("expandedOffsets");
    AnnotationIndex<AnnotationFS> ai = null;
    FSIterator<AnnotationFS> iterator = null;

    cas.setDocumentText(html);
    aeA.process(cas);
    aeC.process(cas);

    CAS plainTextCas = cas.getView(HtmlConverter.DEFAULT_MODIFIED_VIEW);

    assertEquals("Some contentMore content.", plainTextCas.getDocumentText());

    ai = plainTextCas.getAnnotationIndex(tagType);
    iterator = ai.iterator();
    assertEquals(4, ai.size());
    AnnotationFS next = null;
    next = iterator.next();
    assertEquals(false, next.getBooleanValue(expandedFeature));
    assertEquals("Some contentMore content.", next.getCoveredText());
    next = iterator.next();
    assertEquals(false, next.getBooleanValue(expandedFeature));
    assertEquals("Some content", next.getCoveredText());
    next = iterator.next();
    boolean b1 = next.getBooleanValue(expandedFeature);
    assertEquals("More content.", next.getCoveredText());
    next = iterator.next();
    boolean b2 = next.getBooleanValue(expandedFeature);
    assertEquals("More content.", next.getCoveredText());
    // for one of these two annotation (with same offsets) the feature must be set to true
    assertEquals(true, b1 || b2);

    cas.release();
  }
  @Test
  public void test() throws Exception {
    String html = "<Parent>\n";
    html += "<Child1>Some content</Child1>\n";
    html += "<Child2 attribute=“someValue” />\n";
    html += "<Child3>More content.</Child3>\n";
    html += "</Parent>\n";

    URL urlA = HtmlAnnotator.class.getClassLoader().getResource("HtmlAnnotator.xml");
    if (urlA == null) {
      urlA =
          HtmlAnnotator.class
              .getClassLoader()
              .getResource("org/apache/uima/ruta/engine/HtmlAnnotator.xml");
    }

    URL urlC = HtmlAnnotator.class.getClassLoader().getResource("HtmlConverter.xml");
    if (urlC == null) {
      urlC =
          HtmlAnnotator.class
              .getClassLoader()
              .getResource("org/apache/uima/ruta/engine/HtmlConverter.xml");
    }

    XMLInputSource inA = new XMLInputSource(urlA);
    ResourceSpecifier specifierA = UIMAFramework.getXMLParser().parseResourceSpecifier(inA);
    AnalysisEngine aeA = UIMAFramework.produceAnalysisEngine(specifierA);
    aeA.setConfigParameterValue(HtmlAnnotator.PARAM_ONLY_CONTENT, false);
    aeA.reconfigure();

    XMLInputSource inC = new XMLInputSource(urlC);
    ResourceSpecifier specifierC = UIMAFramework.getXMLParser().parseResourceSpecifier(inC);
    AnalysisEngine aeC = UIMAFramework.produceAnalysisEngine(specifierC);
    aeC.setConfigParameterValue(HtmlConverter.PARAM_SKIP_WHITESPACES, false);
    aeC.setConfigParameterValue(HtmlConverter.PARAM_PROCESS_ALL, true);
    aeC.setConfigParameterValue(
        HtmlConverter.PARAM_GAP_INDUCING_TAGS, new String[] {"child1", "child2", "child3"});
    aeC.setConfigParameterValue(HtmlConverter.PARAM_GAP_TEXT, "$");
    aeC.reconfigure();

    CAS cas = aeA.newCAS();
    Type tagType = cas.getTypeSystem().getType(HtmlAnnotator.NAMESPACE + "TAG");
    AnnotationIndex<AnnotationFS> ai = null;
    FSIterator<AnnotationFS> iterator = null;

    cas.setDocumentText(html);
    aeA.process(cas);
    aeC.process(cas);

    CAS plainTextCas = cas.getView(HtmlConverter.DEFAULT_MODIFIED_VIEW);

    assertEquals("$Some content$$More content.", plainTextCas.getDocumentText());

    ai = plainTextCas.getAnnotationIndex(tagType);
    iterator = ai.iterator();
    assertEquals(4, ai.size());
    assertEquals("$Some content$$More content.", iterator.next().getCoveredText());
    assertEquals("$Some content", iterator.next().getCoveredText());
    assertEquals("$", iterator.next().getCoveredText());
    assertEquals("$More content.", iterator.next().getCoveredText());

    cas.release();
  }
  /** Copied and modified from {@link org.apache.uima.util.CasToInlineXml} */
  private static String toXML(CAS cas, AnnotationsToElements converter) throws SAXException {
    ByteArrayOutputStream byteArrayOutputStream = new ByteArrayOutputStream();
    XMLSerializer sax2xml = new XMLSerializer(byteArrayOutputStream, false);

    // get document text
    String docText = cas.getDocumentText();
    char[] docCharArray = docText.toCharArray();

    // get iterator over annotations sorted by increasing start position and
    // decreasing end position
    FSIterator<AnnotationFS> iterator = cas.getAnnotationIndex().iterator();

    // This is basically a recursive algorithm that has had the recursion
    // removed through the use of an explicit Stack. We iterate over the
    // annotations, and if an annotation contains other annotations, we
    // push the parent annotation on the stack, process the children, and
    // then come back to the parent later.
    List<AnnotationFS> stack = new ArrayList<AnnotationFS>();
    int pos = 0;

    ContentHandler handler = sax2xml.getContentHandler();
    handler.startDocument();
    // write the start tag
    converter.startRootElement(handler);
    // now use null is a placeholder for this artificial Document annotation
    AnnotationFS curAnnot = null;

    while (iterator.isValid()) {
      AnnotationFS nextAnnot = iterator.get();

      if (curAnnot == null || nextAnnot.getBegin() < curAnnot.getEnd()) {
        // nextAnnot's start point is within the span of curAnnot
        if (curAnnot == null || nextAnnot.getEnd() <= curAnnot.getEnd()) // crossover span check
        {
          // nextAnnot is contained within curAnnot

          // write text between current pos and beginning of nextAnnot
          try {
            handler.characters(docCharArray, pos, nextAnnot.getBegin() - pos);
            pos = nextAnnot.getBegin();
            converter.startAnnotationElement(nextAnnot, handler);

            // push parent annotation on stack
            stack.add(curAnnot);
            // move on to next annotation
            curAnnot = nextAnnot;
          } catch (StringIndexOutOfBoundsException e) {
            System.err.println(
                "Invalid annotation range: "
                    + nextAnnot.getBegin()
                    + ","
                    + nextAnnot.getEnd()
                    + " in document of length "
                    + docText.length());
          }
        }
        iterator.moveToNext();
      } else {
        // nextAnnot begins after curAnnot ends
        // write text between current pos and end of curAnnot
        try {
          handler.characters(docCharArray, pos, curAnnot.getEnd() - pos);
          pos = curAnnot.getEnd();
        } catch (StringIndexOutOfBoundsException e) {
          System.err.println(
              "Invalid annotation range: "
                  + curAnnot.getBegin()
                  + ","
                  + curAnnot.getEnd()
                  + " in document of length "
                  + docText.length());
        }
        converter.endAnnotationElement(curAnnot, handler);

        // pop next containing annotation off stack
        curAnnot = stack.remove(stack.size() - 1);
      }
    }

    // finished writing all start tags, now finish up
    if (curAnnot != null) {
      try {
        handler.characters(docCharArray, pos, curAnnot.getEnd() - pos);
        pos = curAnnot.getEnd();
      } catch (StringIndexOutOfBoundsException e) {
        System.err.println(
            "Invalid annotation range: "
                + curAnnot.getBegin()
                + ","
                + curAnnot.getEnd()
                + "in document of length "
                + docText.length());
      }
      converter.endAnnotationElement(curAnnot, handler);

      while (!stack.isEmpty()) {
        curAnnot = stack.remove(stack.size() - 1); // pop
        if (curAnnot == null) {
          break;
        }
        try {
          handler.characters(docCharArray, pos, curAnnot.getEnd() - pos);
          pos = curAnnot.getEnd();
        } catch (StringIndexOutOfBoundsException e) {
          System.err.println(
              "Invalid annotation range: "
                  + curAnnot.getBegin()
                  + ","
                  + curAnnot.getEnd()
                  + "in document of length "
                  + docText.length());
        }
        converter.endAnnotationElement(curAnnot, handler);
      }
    }

    if (pos < docCharArray.length) {
      handler.characters(docCharArray, pos, docCharArray.length - pos);
    }
    converter.endRootElement(handler);
    handler.endDocument();

    // return XML string
    return new String(byteArrayOutputStream.toByteArray());
  }