Examples of org.apache.uima.cas.CAS

org.apache.uima.cas.CAS
Object-oriented CAS (Common Analysis System) API.
A CAS object provides the starting point for working with the CAS. It provides access to the type system, to indexes, iterators and filters (constraints). It also lets you create new annotations and other data structures. You can create a CAS object using static methods on the class {@link org.apache.uima.util.CasCreationUtils}.
The CAS object is also the container that manages multiple Subjects of Analysis or Sofas. A Sofa represents some form of an unstructured artifact that is processed in a UIMA pipeline. The Java string called the "DocumentText" used in a UIMA text processing pipeline is an example of a Sofa. A Sofa can be analyzed independently using the standard UIMA programming model or analyzed together with other Sofas utilizing the Sofa programming model extensions.
A Sofa is implemented as a built-in CAS type uima.cas.Sofa. Use {@link org.apache.uima.cas.CAS#createSofa CAS.createSofa()} to instantiate a Sofa featurestructure. The {@link SofaFS SofaFS} class provides methods to set and get the features of aSofaFS. Although Sofas are implemented as standard feature structures, generic CAS APIs must never be used to create Sofas or set their features.
Use {@link org.apache.uima.cas.CAS#getView(String)} or{@link org.apache.uima.cas.CAS#getView(SofaFS)} to obtain a view of a particular Sofa in the CAS.This view will provide access to the Sofa data (for example the document text) as well as the index repository, which contains metadata (annotations and other feature structures) about that Sofa.
Use {@link #getTypeSystem getTypeSystem()} to access the type system. With a{@link TypeSystem TypeSystem} object, you can access the {@link Type Type} and{@link Feature Feature} objects for the CAS built-in types. Note that this interface alsoprovides constants for the names of the built-in types and features.

  public void testOutOfTypeSystemArrayElement() throws Exception {
    //add to type system an annotation type that has an FSArray feature
    TypeDescription testAnnotTypeDesc = typeSystem.addType("org.apache.uima.testTypeSystem.TestAnnotation", "", "uima.tcas.Annotation");
    testAnnotTypeDesc.addFeature("arrayFeat", "", "uima.cas.FSArray");
    //populate a CAS with such an array
    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);
    ArrayFS arrayFs = cas.createArrayFS(2);
    arrayFs.set(0, orgAnnot1);
    arrayFs.set(1, orgAnnot2);
    Feature arrayFeat = testAnnotType.getFeatureByBaseName("arrayFeat");
    testAnnot.setFeatureValue(arrayFeat, arrayFs);
    
    //serialize to XMI
    String xmiStr = serialize(cas, null);
    
    //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("arrayFeat", "", "uima.cas.FSArray");
    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 arrayFeat2 = testAnnotType2.getFeatureByBaseName("arrayFeat");
    FeatureStructure arrayFs2 = testAnnot2.getFeatureValue(arrayFeat2);
    List ootsElems = sharedData.getOutOfTypeSystemElements();
    assertEquals(2, ootsElems.size());
    List ootsArrayElems = sharedData.getOutOfTypeSystemArrayElements(arrayFs2.hashCode());
    assertEquals(2, ootsArrayElems.size());
    for (int i = 0; i < 2; i++) {
      OotsElementData oed = (OotsElementData)ootsElems.get(i);
      XmiArrayElement arel = (XmiArrayElement)ootsArrayElems.get(i);
      assertEquals(oed.xmiId, arel.xmiId);      
    }
    
    //reserialize along with out of type system data
    String xmiStr2 = serialize(partialTsCas, sharedData);
    
    //deserialize into a new CAS and compare
    CAS cas2 = CasCreationUtils.createCas(typeSystem, null, null);
    deserialize(xmiStr2, cas2, null, false, -1);
    
    CasComparer.assertEquals(cas, cas2);    
  }

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  public void testOutOfTypeSystemListElement() throws Exception {
    //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);
    assertNotNull(attr);
    assertEquals(CAS.FEATURE_BASE_NAME_HEAD, attr.name);
    assertEquals(attr.value, ((OotsElementData)ootsElems.get(0)).xmiId);
    
    //reserialize along with out of type system data
    String xmiStr2 = serialize(partialTsCas, sharedData);
    System.out.println(xmiStr2);
    
    //deserialize into a new CAS and compare
    CAS cas2 = CasCreationUtils.createCas(typeSystem, null, null);
    deserialize(xmiStr2, cas2, null, false, -1);
    
    CasComparer.assertEquals(cas, cas2);    
  }

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      ResourceSpecifier specifier = UIMAFramework.getXMLParser().parseResourceSpecifier(in);
      // Create the Text Analysis Engine.
      ae = UIMAFramework.produceAnalysisEngine(specifier, null, null);


      // Create a new CAS.
      CAS cas = ae.newCAS();
      // Set the document text on the CAS.
      cas.setDocumentText("This is a simple text to check if the configuration works");
      cas.setDocumentLanguage("en");
      // Process the sample document.
      ae.process(cas);


      return ae;
    } catch (Exception ex) {

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   * @throws Exception
   */
  public CAS performTest(String text, String language) throws Exception {
    try {
      // Create a new CAS.
      CAS cas = this.ae.newCAS();
      // Set the document text on the CAS.
      cas.setDocumentText(text);
      cas.setDocumentLanguage(language);
      // Process the sample document.
      this.ae.process(cas);


      return cas;
    } catch (Exception ex) {

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      ResourceSpecifier specifier = UIMAFramework.getXMLParser().parseResourceSpecifier(in);
      // Create the Text Analysis Engine.
      ae = UIMAFramework.produceAnalysisEngine(specifier, null, null);


      // Create a new CAS.
      CAS cas = ae.newCAS();
      // Set the document text on the CAS.
      cas.setDocumentText(text);
      cas.setDocumentLanguage(language);
      // Process the sample document.
      ae.process(cas);


      return cas;
    } catch (Exception ex) {

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    CasComparer.assertEquals(cas, cas2);    
  }
  
  public void testOutOfTypeSystemDataComplexCas() throws Exception {
    // deserialize a complex XCAS
    CAS originalCas = CasCreationUtils.createCas(typeSystem, null, indexes);
    InputStream serCasStream = new FileInputStream(JUnitExtension.getFile("ExampleCas/cas.xml"));
    XCASDeserializer.deserialize(serCasStream, originalCas);
    serCasStream.close();
    
    //serialize to XMI
    String xmiStr = serialize(originalCas, null);
    
    //deserialize into a CAS with no type system
    CAS casWithNoTs = CasCreationUtils.createCas(new TypeSystemDescription_impl(),
            new TypePriorities_impl(), new FsIndexDescription[0]);
    XmiSerializationSharedData sharedData = new XmiSerializationSharedData();
    deserialize(xmiStr, casWithNoTs, sharedData, true, -1);
        
    // now reserialize including OutOfTypeSystem data
    String xmiStr2 = serialize(casWithNoTs, sharedData);
    
    //deserialize into a new CAS that has the full type system
    CAS newCas = CasCreationUtils.createCas(typeSystem, null, indexes);
    deserialize(xmiStr2, newCas, null, false, -1);
    
    //compare
    CasComparer.assertEquals(originalCas, newCas);
    
    //Test a partial type system with a missing some missing features and
    //missing "Organization" type
    File partialTypeSystemFile = JUnitExtension.getFile("ExampleCas/partialTestTypeSystem.xml");
    TypeSystemDescription partialTypeSystem = UIMAFramework.getXMLParser().parseTypeSystemDescription(
            new XMLInputSource(partialTypeSystemFile));
    CAS partialTsCas = CasCreationUtils.createCas(partialTypeSystem, null, indexes);
    XmiSerializationSharedData sharedData2 = new XmiSerializationSharedData();
    deserialize(xmiStr, partialTsCas, sharedData2, true, -1);
        
    String xmiStr3 = serialize(partialTsCas, sharedData2);
    newCas.reset();

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    CasComparer.assertEquals(originalCas, newCas);    
 }
  
  public void testGetNumChildren() throws Exception {
    // deserialize a complex XCAS
    CAS cas = CasCreationUtils.createCas(typeSystem, null, indexes);
//    InputStream serCasStream = new FileInputStream(JUnitExtension.getFile("ExampleCas/cas.xml"));
//    XCASDeserializer.deserialize(serCasStream, cas);
//    serCasStream.close();
  InputStream serCasStream = new FileInputStream(JUnitExtension.getFile("ExampleCas/simpleCas.xmi"));
  XmiCasDeserializer.deserialize(serCasStream, cas);
  serCasStream.close();
    
    // call serializer with a ContentHandler that checks numChildren
    XmiCasSerializer xmiSer = new XmiCasSerializer(cas.getTypeSystem());
    GetNumChildrenTestHandler handler = new GetNumChildrenTestHandler(xmiSer);
    xmiSer.serialize(cas, handler);
  }

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   */
  public static CAS getCASfromXCAS(File tsFile, File xcasFile) throws Exception{
    try {
      Object tsDescriptor = UIMAFramework.getXMLParser().parse(new XMLInputSource(tsFile));
      TypeSystemDescription tsDesc = (TypeSystemDescription) tsDescriptor;
      CAS cas = CasCreationUtils.createCas(tsDesc, null, new FsIndexDescription[0]);


      SAXParser parser = SAXParserFactory.newInstance().newSAXParser();
      XCASDeserializer xcasDeserializer = new XCASDeserializer(cas.getTypeSystem());
      parser.parse(xcasFile, xcasDeserializer.getXCASHandler(cas));


      return cas;
    } catch (Exception ex) {
      JUnitExtension.handleException(ex);

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    // create Analysis Engine
    AnalysisEngine ae = UIMAFramework.produceAnalysisEngine(specifier);
    
    // create a CAS
    CAS cas = ae.newCAS();
    
    // Create a file filter depending on the format
    // to filter out all file which do not have the
    // expected file ending
    FileFilter fileFilter;

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              .getFile("CasCreationUtilsTest/AggregateTaeWithImports.xml");
      AnalysisEngineDescription desc = UIMAFramework.getXMLParser().parseAnalysisEngineDescription(
              new XMLInputSource(taeDescriptorWithImport));
      ArrayList mdList = new ArrayList();
      mdList.add(desc);
      CAS tcas = CasCreationUtils.createCas(mdList, UIMAFramework
              .getDefaultPerformanceTuningProperties(), resMgr);
      // check that imports were resolved correctly
      assertNotNull(tcas.getTypeSystem().getType("DocumentStructure"));
      assertNotNull(tcas.getTypeSystem().getType("NamedEntity"));
      assertNotNull(tcas.getTypeSystem().getType("TestType3"));
      assertNotNull(tcas.getTypeSystem().getType("Sentence"));


      assertNotNull(tcas.getIndexRepository().getIndex("TestIndex"));
      assertNotNull(tcas.getIndexRepository().getIndex("ReverseAnnotationIndex"));
      assertNotNull(tcas.getIndexRepository().getIndex("DocumentStructureIndex"));


      // Check elementType and multipleReferencesAllowed for array feature
      Feature arrayFeat = tcas.getTypeSystem().getFeatureByFullName("Paragraph:sentences");
      assertNotNull(arrayFeat);
      assertFalse(arrayFeat.isMultipleReferencesAllowed());
      Type sentenceArrayType = arrayFeat.getRange();
      assertNotNull(sentenceArrayType);
      assertTrue(sentenceArrayType.isArray());
      assertEquals(tcas.getTypeSystem().getType("Sentence"), sentenceArrayType.getComponentType());


      Feature arrayFeat2 = tcas.getTypeSystem().getFeatureByFullName(
              "Paragraph:testMultiRefAllowedFeature");
      assertNotNull(arrayFeat2);
      assertTrue(arrayFeat2.isMultipleReferencesAllowed());


      // test imports aren't resolved more than once

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