Package org.apache.uima.cas

Examples of org.apache.uima.cas.Type

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    xmlReader.setContentHandler(deserHandler);
    xmlReader.parse(new InputSource(serCasStream));
    serCasStream.close();

    // check that array refs are not null
    Type entityType = cas.getTypeSystem().getType("org.apache.uima.testTypeSystem.Entity");
    Feature classesFeat = entityType.getFeatureByBaseName("classes");
    Iterator iter = cas.getIndexRepository().getIndex("testEntityIndex").iterator();
    assertTrue(iter.hasNext());
    while (iter.hasNext()) {
      FeatureStructure fs = (FeatureStructure) iter.next();
      StringArrayFS arrayFS = (StringArrayFS) fs.getFeatureValue(classesFeat);
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    xmlReader = parser.getXMLReader();
    xmlReader.setContentHandler(deserHandler2);
    xmlReader.parse(new InputSource(new StringReader(xml)));

    // check that array refs are not null
    Type entityType = cas2.getTypeSystem().getType("org.apache.uima.testTypeSystem.Entity");
    Feature classesFeat = entityType.getFeatureByBaseName("classes");
    Iterator iter = cas2.getIndexRepository().getIndex("testEntityIndex").iterator();
    assertTrue(iter.hasNext());
    while (iter.hasNext()) {
      FeatureStructure fs = (FeatureStructure) iter.next();
      StringArrayFS arrayFS = (StringArrayFS) fs.getFeatureValue(classesFeat);
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      //System.out.println("Heap size: " + heapSize + ", buffer size: " + bufSize);      
      Assert.assertTrue(bufSize < CASImpl.DEFAULT_RESET_HEAP_SIZE);
      assertTrue(heapSize <= bufSize);
     
      //create enough annotations to exceed the DEFAULT_RESET_HEAP_SIZE
      Type annotType = cas.getTypeSystem().getType(CAS.TYPE_NAME_ANNOTATION);
      for (int i = 0; i < 2000000; i++) {
        cas.createAnnotation(annotType, i, i);
      }
     
      heapSize = ((CASImpl) cas).getHeap().getCurrentTempSize();
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    //add to type system an annotation type that has an FSList feature
    TypeDescription testAnnotTypeDesc = typeSystem.addType("org.apache.uima.testTypeSystem.TestAnnotation", "", "uima.tcas.Annotation");
    testAnnotTypeDesc.addFeature("listFeat", "", "uima.cas.FSList");
    //populate a CAS with such an list
    CAS cas = CasCreationUtils.createCas(typeSystem, null, null);
    Type testAnnotType = cas.getTypeSystem().getType("org.apache.uima.testTypeSystem.TestAnnotation");
    Type orgType = cas.getTypeSystem().getType(
      "org.apache.uima.testTypeSystem.Organization");
    AnnotationFS orgAnnot1 = cas.createAnnotation(orgType, 0, 10);
    cas.addFsToIndexes(orgAnnot1);
    AnnotationFS orgAnnot2 = cas.createAnnotation(orgType, 10, 20);
    cas.addFsToIndexes(orgAnnot2);
    AnnotationFS testAnnot = cas.createAnnotation(testAnnotType, 0, 20);
    cas.addFsToIndexes(testAnnot);
    Type nonEmptyFsListType = cas.getTypeSystem().getType(CAS.TYPE_NAME_NON_EMPTY_FS_LIST);
    Type emptyFsListType = cas.getTypeSystem().getType(CAS.TYPE_NAME_EMPTY_FS_LIST);
    Feature headFeat = nonEmptyFsListType.getFeatureByBaseName("head");
    Feature tailFeat = nonEmptyFsListType.getFeatureByBaseName("tail");
    FeatureStructure emptyNode = cas.createFS(emptyFsListType);
    FeatureStructure secondNode = cas.createFS(nonEmptyFsListType);
    secondNode.setFeatureValue(headFeat, orgAnnot2);
    secondNode.setFeatureValue(tailFeat, emptyNode);
    FeatureStructure firstNode = cas.createFS(nonEmptyFsListType);
    firstNode.setFeatureValue(headFeat, orgAnnot1);
    firstNode.setFeatureValue(tailFeat, secondNode);
   
    Feature listFeat = testAnnotType.getFeatureByBaseName("listFeat");
    testAnnot.setFeatureValue(listFeat, firstNode);
   
    //serialize to XMI
    String xmiStr = serialize(cas, null);
    System.out.println(xmiStr);
   
    //deserialize into a CAS that's missing the Organization type
    File partialTypeSystemFile = JUnitExtension.getFile("ExampleCas/partialTestTypeSystem.xml");
    TypeSystemDescription partialTypeSystem = UIMAFramework.getXMLParser().parseTypeSystemDescription(
            new XMLInputSource(partialTypeSystemFile));
    testAnnotTypeDesc = partialTypeSystem.addType("org.apache.uima.testTypeSystem.TestAnnotation", "", "uima.tcas.Annotation");
    testAnnotTypeDesc.addFeature("listFeat", "", "uima.cas.FSList");
    CAS partialTsCas = CasCreationUtils.createCas(partialTypeSystem, null, null);
    XmiSerializationSharedData sharedData = new XmiSerializationSharedData();
    deserialize(xmiStr, partialTsCas, sharedData, true, -1);
   
    //check out of type system data
    Type testAnnotType2 = partialTsCas.getTypeSystem().getType("org.apache.uima.testTypeSystem.TestAnnotation");
    FeatureStructure testAnnot2 = partialTsCas.getAnnotationIndex(testAnnotType2).iterator().get();
    Feature listFeat2 = testAnnotType2.getFeatureByBaseName("listFeat");
    FeatureStructure listFs = testAnnot2.getFeatureValue(listFeat2);
    List ootsElems = sharedData.getOutOfTypeSystemElements();
    assertEquals(2, ootsElems.size());
    OotsElementData oed = sharedData.getOutOfTypeSystemFeatures(listFs.hashCode());
    XmlAttribute attr = (XmlAttribute)oed.attributes.get(0);
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    XmiCasDeserializer.deserialize(bais, cas, lenient, sharedData, mergePoint);
    bais.close();
  } 
 
  private AnnotationFS createPersonAnnot(CAS cas, int begin, int end) {
    Type personType = cas.getTypeSystem().getType("org.apache.uima.testTypeSystem.Person");
    AnnotationFS person = cas.createAnnotation(personType, begin, end);
    cas.addFsToIndexes(person);
    return person;
  }
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      return;
    }
    if (this.addr == 0) {
      return;
    }
    Type type = getType();
    CASImpl cas = this.fSTreeModel.getCas();
    if (this.fSTreeModel.getCas().isArrayType(type)) {
      int arrayLength = cas.ll_getArraySize((int) this.addr);
      if (arrayLength > 20) {
        arrayLength = 20;
      }
      FSNode node = null;
      int arrayPos = cas.getArrayStartAddress((int) this.addr);
      int nodeClass1;
      if (cas.isIntArrayType(type)) {
        nodeClass1 = FSNode.INT_FS;
      } else if (cas.isFloatArrayType(type)) {
        nodeClass1 = FSNode.FLOAT_FS;
      } else if (cas.isStringArrayType(type)) {
        nodeClass1 = FSNode.STRING_FS;
      } else if (cas.isByteArrayType(type)) {
        nodeClass1 = FSNode.BYTE_FS;
      } else if (cas.isBooleanArrayType(type)) {
        nodeClass1 = FSNode.BOOL_FS;
      } else if (cas.isShortArrayType(type)) {
        nodeClass1 = FSNode.SHORT_FS;
      } else if (cas.isLongArrayType(type)) {
        nodeClass1 = FSNode.LONG_FS;
      } else if (cas.isDoubleArrayType(type)) {
        nodeClass1 = FSNode.DOUBLE_FS;
      } else {
        nodeClass1 = FSNode.STD_FS;
      }
      ArrayList arrayNodes = new ArrayList(arrayLength);
      if (nodeClass1 == INT_FS || nodeClass1 == FLOAT_FS || nodeClass1 == STRING_FS
              || nodeClass1 == STD_FS) {
        for (int i = 0; i < arrayLength; i++) {
          node = new FSNode(this.fSTreeModel, nodeClass1, cas.getHeapValue(arrayPos), i);
          arrayNodes.add(node);
          ++arrayPos;
        }
      } else if (nodeClass1 == BYTE_FS) {
        for (int i = 0; i < arrayLength; i++) {
          node = new FSNode(this.fSTreeModel, nodeClass1, cas.ll_getByteArrayValue((int) this.addr,
                  i), i);
          arrayNodes.add(node);
          ++arrayPos;
        }
      } else if (nodeClass1 == SHORT_FS) {
        for (int i = 0; i < arrayLength; i++) {
          node = new FSNode(this.fSTreeModel, nodeClass1, cas.ll_getShortArrayValue(
                  (int) this.addr, i), i);
          arrayNodes.add(node);
          ++arrayPos;
        }
      } else if (nodeClass1 == BOOL_FS) {
        for (int i = 0; i < arrayLength; i++) {
          int temp = cas.ll_getBooleanArrayValue((int) this.addr, i) ? 1 : 0;
          node = new FSNode(this.fSTreeModel, nodeClass1, temp, i);
          arrayNodes.add(node);
          ++arrayPos;
        }
      } else if (nodeClass1 == LONG_FS) {
        for (int i = 0; i < arrayLength; i++) {
          long temp = cas.ll_getLongArrayValue((int) this.addr, i);
          node = new FSNode(this.fSTreeModel, nodeClass1, temp, i);
          arrayNodes.add(node);
          ++arrayPos;
        }
      } else if (nodeClass1 == DOUBLE_FS) {
        for (int i = 0; i < arrayLength; i++) {
          double temp = cas.ll_getDoubleArrayValue((int) this.addr, i);
          node = new FSNode(this.fSTreeModel, nodeClass1, CASImpl.double2long(temp), i);
          arrayNodes.add(node);
          ++arrayPos;
        }
      }
      this.children = FSTreeModel.createArrayChildren(0, arrayLength, arrayNodes, this.fSTreeModel);
    } else {
      this.children = new ArrayList();
      List feats = type.getFeatures();
      for (int i = 0; i < feats.size(); i++) {
        FeatureImpl feat1 = (FeatureImpl) feats.get(i);
        long featAddr = cas.getHeapValue((int) this.addr + cas.getFeatureOffset(feat1.getCode()));
        if (cas.isDoubleType(feat1.getRange()) || cas.isLongType(feat1.getRange())) {
          featAddr = cas.ll_getLongValue((int) featAddr);
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    array.set(0, null);
    assertTrue(array.get(0) == null);
  }

  public void testArraysOfArrays() {
    Type annotationType = this.ts.getType(CAS.TYPE_NAME_ANNOTATION);
    AnnotationFS annot = this.cas.createAnnotation(annotationType, 0, 5);
    IntArrayFS intArray = this.cas.createIntArrayFS(3);
    intArray.set(0, 1);
    intArray.set(1, 2);
    intArray.set(2, -10);
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    assertEquals(cas.getAnnotationIndex().size(), cas2.getAnnotationIndex().size());
    assertEquals(cas.getDocumentText(), cas2.getDocumentText());
    CasComparer.assertEquals(cas,cas2);

    // check that array refs are not null
    Type entityType = cas2.getTypeSystem().getType("org.apache.uima.testTypeSystem.Entity");
    Feature classesFeat = entityType.getFeatureByBaseName("classes");
    Iterator iter = cas2.getIndexRepository().getIndex("testEntityIndex").iterator();
    assertTrue(iter.hasNext());
    while (iter.hasNext()) {
      FeatureStructure fs = (FeatureStructure) iter.next();
      StringArrayFS arrayFS = (StringArrayFS) fs.getFeatureValue(classesFeat);
      assertNotNull(arrayFS);
      for (int i = 0; i < arrayFS.size(); i++) {
        assertNotNull(arrayFS.get(i));
      }
    }
    Type annotArrayTestType = cas2.getTypeSystem().getType("org.apache.uima.testTypeSystem.AnnotationArrayTest");
    Feature annotArrayFeat = annotArrayTestType.getFeatureByBaseName("arrayOfAnnotations");
    Iterator iter2 = cas2.getAnnotationIndex(annotArrayTestType).iterator();
    assertTrue(iter2.hasNext());
    while (iter2.hasNext()) {
      FeatureStructure fs = (FeatureStructure) iter2.next();
      ArrayFS arrayFS = (ArrayFS) fs.getFeatureValue(annotArrayFeat);
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      ContentHandler deserHandler2 = deser2.getXmiCasHandler(cas2);
      xmlReader.setContentHandler(deserHandler2);
      xmlReader.parse(new InputSource(new StringReader(xml)));

      // check that types have been filtered out
      Type orgType = cas2.getTypeSystem().getType("org.apache.uima.testTypeSystem.Organization");
      assertNotNull(orgType);
      assertTrue(cas2.getAnnotationIndex(orgType).size() == 0);
      assertTrue(cas.getAnnotationIndex(orgType).size() > 0);

      // but that some types are still there
      Type personType = cas2.getTypeSystem().getType("org.apache.uima.testTypeSystem.Person");
      FSIndex personIndex = cas2.getAnnotationIndex(personType);
      assertTrue(personIndex.size() > 0);

      // check that mentionType has been filtered out (set to null)
      FeatureStructure somePlace = personIndex.iterator().get();
      Feature mentionTypeFeat = personType.getFeatureByBaseName("mentionType");
      assertNotNull(mentionTypeFeat);
      assertNull(somePlace.getStringValue(mentionTypeFeat));
    } catch (Exception e) {
      JUnitExtension.handleException(e);
    }
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    XMLReader xmlReader = parser.getXMLReader();
    xmlReader.setContentHandler(deserHandler2);
    xmlReader.parse(new InputSource(new StringReader(xml)));

    //test that index is correctly populated
    Type intArrayType = cas2.getTypeSystem().getType(CAS.TYPE_NAME_INTEGER_ARRAY);
    Iterator iter = cas2.getIndexRepository().getAllIndexedFS(intArrayType);
    assertTrue(iter.hasNext());
    IntArrayFS intArrayFS2 = (IntArrayFS)iter.next();
    assertFalse(iter.hasNext());
    assertEquals(5, intArrayFS2.size());
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