Examples of org.apache.uima.cas.FeatureStructure

org.apache.uima.cas.FeatureStructure
Interface for feature structures.
Note that object identity is not meaningful for feature structures. You may ask the CAS for the same feature structure two times in a row, and get different object references. Use {@link #equals equals()} instead.

      AnnotationFS anAnnot4 = cas1.createAnnotation(cas1.getAnnotationType(), 15, 30);
      cas1.getIndexRepository().addFS(anAnnot4);
      FSIndex tIndex = cas1.getAnnotationIndex();
      assertTrue(tIndex.size() == 5); //doc annot plus 4 annots
      
      FeatureStructure entityFS = cas1.createFS(entityType);
      cas1.getIndexRepository().addFS(entityFS);
      
      StringArrayFS strArrayFS = cas1.createStringArrayFS(5);
      strArrayFS.set(0, "class1");
      entityFS.setFeatureValue(classesFeat, strArrayFS);
      
      //create listFS and set the link feature
      FeatureStructure emptyNode = cas1.createFS(emptyFsListType);
      FeatureStructure secondNode = cas1.createFS(nonEmptyFsListType);
      secondNode.setFeatureValue(headFeat, anAnnot2);
      secondNode.setFeatureValue(tailFeat, emptyNode);
      FeatureStructure firstNode = cas1.createFS(nonEmptyFsListType);
      firstNode.setFeatureValue(headFeat, anAnnot1);
      firstNode.setFeatureValue(tailFeat, secondNode);
      entityFS.setFeatureValue(linksFeat, firstNode);
      
      // create a view w/o setting document text
      CAS view1 = cas1.createView("View1");
      
      // create another view 
      CAS preexistingView = cas1.createView("preexistingView");
      String preexistingViewText = "John Smith blah blah blah";
      preexistingView.setDocumentText(preexistingViewText);
      AnnotationFS person1Annot = createPersonAnnot(preexistingView, 0, 10);
      person1Annot.setStringValue(componentIdFeat, "deltacas1");
      AnnotationFS person2Annot = createPersonAnnot(preexistingView, 0, 5);
      AnnotationFS orgAnnot = preexistingView.createAnnotation(orgType, 16, 24);
      preexistingView.addFsToIndexes(orgAnnot);
      
      AnnotationFS ownerAnnot = preexistingView.createAnnotation(ownerType, 0, 24);
      preexistingView.addFsToIndexes(ownerAnnot);
      FeatureStructure relArgs = cas1.createFS(relArgsType);
      relArgs.setFeatureValue(domainFeat, person1Annot);
      ownerAnnot.setFeatureValue(argsFeat, relArgs);
      
      //serialize complete  
      XmiSerializationSharedData sharedData = new XmiSerializationSharedData();
      String xml = serialize(cas1, sharedData);
      int maxOutgoingXmiId = sharedData.getMaxXmiId();
      //System.out.println("CAS1 " + xml);
      //System.out.println("MaxOutgoingXmiId " + maxOutgoingXmiId);
   
      //deserialize into cas2
      XmiSerializationSharedData sharedData2 = new XmiSerializationSharedData();      
      this.deserialize(xml, cas2, sharedData2, true, -1);
      CasComparer.assertEquals(cas1, cas2);
 
      //=======================================================================
      //create Marker, add/modify fs and serialize in delta xmi format.
      Marker marker = cas2.createMarker();
      FSIndex cas2tIndex = cas2.getAnnotationIndex();
      CAS cas2preexistingView = cas2.getView("preexistingView");
      FSIndex cas2personIndex = cas2preexistingView.getAnnotationIndex(personType);
      FSIndex cas2orgIndex = cas2preexistingView.getAnnotationIndex(orgType);
      FSIndex cas2ownerIndex = cas2preexistingView.getAnnotationIndex(ownerType);
      
      // create an annotation and add to index
      AnnotationFS cas2anAnnot5 = cas2.createAnnotation(cas2.getAnnotationType(), 6, 8);
      cas2.getIndexRepository().addFS(cas2anAnnot5);
      assertTrue(cas2tIndex.size() == 6); // prev annots and this new one
     
      // set document text of View1
      CAS cas2view1 = cas2.getView("View1");
      cas2view1.setDocumentText("This is the View1 document.");
      //create an annotation in View1
      AnnotationFS cas2view1Annot = cas2view1.createAnnotation(cas2.getAnnotationType(), 1, 5);
      cas2view1.getIndexRepository().addFS(cas2view1Annot);
      FSIndex cas2view1Index = cas2view1.getAnnotationIndex();
      assertTrue(cas2view1Index.size() == 2); //document annot and this annot
      
      //modify an existing annotation
      Iterator<FeatureStructure> tIndexIter = cas2tIndex.iterator();
      AnnotationFS docAnnot = (AnnotationFS) tIndexIter.next(); //doc annot
      AnnotationFS modAnnot1 = (AnnotationFS) tIndexIter.next();
      AnnotationFS delAnnot = (AnnotationFS)  tIndexIter.next();
      
      //modify language feature
      Feature languageF = cas2.getDocumentAnnotation().getType().getFeatureByBaseName(CAS.FEATURE_BASE_NAME_LANGUAGE);
      docAnnot.setStringValue(languageF, "en");
      
      //index update - reindex
      cas2.getIndexRepository().removeFS(modAnnot1);
      Feature endF = cas2.getAnnotationType().getFeatureByBaseName(CAS.FEATURE_BASE_NAME_END);
      modAnnot1.setIntValue(endF, 4);
      cas2.getIndexRepository().addFS(modAnnot1);
      //index update - remove annotation from index 
      cas2.getIndexRepository().removeFS(delAnnot);
      
      //modify FS - string feature and FS feature.
      Iterator<FeatureStructure> personIter = cas2personIndex.iterator();     
      AnnotationFS cas2person1 = (AnnotationFS) personIter.next();
      AnnotationFS cas2person2 = (AnnotationFS) personIter.next();
      
      cas2person1.setFloatValue(confidenceFeat, (float) 99.99);
      cas2person1.setStringValue(mentionTypeFeat, "FULLNAME");
      
      cas2person2.setStringValue(componentIdFeat, "delataCas2");
      cas2person2.setStringValue(mentionTypeFeat, "FIRSTNAME");
      
      Iterator<FeatureStructure> orgIter = cas2orgIndex.iterator();
      AnnotationFS cas2orgAnnot = (AnnotationFS) orgIter.next();
      cas2orgAnnot.setStringValue(mentionTypeFeat, "ORGNAME");
      
      //modify FS feature
      Iterator<FeatureStructure> ownerIter = cas2ownerIndex.iterator();
      AnnotationFS cas2ownerAnnot = (AnnotationFS) ownerIter.next();
      FeatureStructure cas2relArgs = cas2ownerAnnot.getFeatureValue(argsFeat);
      cas2relArgs.setFeatureValue(rangeFeat, cas2orgAnnot);
      
    //Test modification of a nonshared multivalued feature.
      //This should serialize the encompassing FS.
      Iterator<FeatureStructure> iter = cas2.getIndexRepository().getIndex("testEntityIndex").iterator();
      FeatureStructure cas2EntityFS = (FeatureStructure) iter.next();
      StringArrayFS cas2strarrayFS = (StringArrayFS) cas2EntityFS.getFeatureValue(classesFeat);
      cas2strarrayFS.set(1, "class2");
      cas2strarrayFS.set(2, "class3");
      cas2strarrayFS.set(3, "class4");
      cas2strarrayFS.set(4, "class5");
      
      //add to FSList 
      FeatureStructure cas2linksFS = cas2EntityFS.getFeatureValue(linksFeat);
      FeatureStructure cas2secondNode = cas2linksFS.getFeatureValue(tailFeat);
      FeatureStructure cas2emptyNode = cas2secondNode.getFeatureValue(tailFeat);
      FeatureStructure cas2thirdNode = cas2.createFS(nonEmptyFsListType);
      cas2thirdNode.setFeatureValue(headFeat, cas2anAnnot5);
      cas2thirdNode.setFeatureValue(tailFeat, cas2emptyNode);
      cas2secondNode.setFeatureValue(tailFeat, cas2thirdNode);
      
//      // Test that the new access method returns an array containing just the right marker
      // removed per https://issues.apache.org/jira/browse/UIMA-2478
//      List<Marker> mkrs = cas2.getMarkers();

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        AnnotationFS anAnnot4 = cas1.createAnnotation(cas1.getAnnotationType(), 15, 30);
        cas1.getIndexRepository().addFS(anAnnot4);
        FSIndex tIndex = cas1.getAnnotationIndex();
        assertTrue(tIndex.size() == 5); //doc annot plus 4 annots
        
        FeatureStructure entityFS = cas1.createFS(entityType);
        cas1.getIndexRepository().addFS(entityFS);
        
        StringArrayFS strArrayFS = cas1.createStringArrayFS(5);
        strArrayFS.set(0, "class1");
        entityFS.setFeatureValue(classesFeat, strArrayFS);
        
        //create listFS and set the link feature
        FeatureStructure emptyNode = cas1.createFS(emptyFsListType);
        FeatureStructure secondNode = cas1.createFS(nonEmptyFsListType);
        secondNode.setFeatureValue(headFeat, anAnnot2);
        secondNode.setFeatureValue(tailFeat, emptyNode);
        FeatureStructure firstNode = cas1.createFS(nonEmptyFsListType);
        firstNode.setFeatureValue(headFeat, anAnnot1);
        firstNode.setFeatureValue(tailFeat, secondNode);
        entityFS.setFeatureValue(linksFeat, firstNode);
        
        // create a view w/o setting document text
        CAS view1 = cas1.createView("View1");
         
        //serialize complete  
        XmiSerializationSharedData sharedData = new XmiSerializationSharedData();
        String xml = serialize(cas1, sharedData);
        int maxOutgoingXmiId = sharedData.getMaxXmiId();
        //System.out.println("CAS1 " + xml);
        //System.out.println("MaxOutgoingXmiId " + maxOutgoingXmiId);
     
        //deserialize into cas2
        XmiSerializationSharedData sharedData2 = new XmiSerializationSharedData();      
        this.deserialize(xml, cas2, sharedData2, true, -1);
        CasComparer.assertEquals(cas1, cas2);
   
        //=======================================================================
        //create Marker, add/modify fs and serialize in delta xmi format.
        Marker marker = cas2.createMarker();
        FSIndex cas2tIndex = cas2.getAnnotationIndex();
        
        // create an annotation and add to index
        AnnotationFS cas2anAnnot5 = cas2.createAnnotation(cas2.getAnnotationType(), 6, 8);
        cas2.getIndexRepository().addFS(cas2anAnnot5);
        assertTrue(cas2tIndex.size() == 6); // prev annots and this new one
        // create an annotation and add to index
        AnnotationFS cas2anAnnot6 = cas2.createAnnotation(cas2.getAnnotationType(), 6, 8);
        cas2.getIndexRepository().addFS(cas2anAnnot6);
        assertTrue(cas2tIndex.size() == 7); // prev annots and twonew one
        
        //add to FSList 
        Iterator<FeatureStructure> iter = cas2.getIndexRepository().getIndex("testEntityIndex").iterator();
        FeatureStructure cas2EntityFS = iter.next();
        FeatureStructure cas2linksFS = cas2EntityFS.getFeatureValue(linksFeat);
        FeatureStructure cas2secondNode = cas2linksFS.getFeatureValue(tailFeat);
        FeatureStructure cas2emptyNode = cas2secondNode.getFeatureValue(tailFeat);
        FeatureStructure cas2thirdNode = cas2.createFS(nonEmptyFsListType);
        FeatureStructure cas2fourthNode = cas2.createFS(nonEmptyFsListType);
        
        cas2secondNode.setFeatureValue(tailFeat, cas2thirdNode);
        cas2thirdNode.setFeatureValue(headFeat, cas2anAnnot5);
        cas2thirdNode.setFeatureValue(tailFeat, cas2fourthNode);
        cas2fourthNode.setFeatureValue(headFeat, cas2anAnnot6);
        cas2fourthNode.setFeatureValue(tailFeat, cas2emptyNode);
        
        // serialize cas2 in delta format 
        String deltaxml1 = serialize(cas2, sharedData2, marker);
        //System.out.println("delta cas");
        //System.out.println(deltaxml1);

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    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);

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    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);

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    remoteCas = setupCas(m);
    
    TTypeSystem mSrc = getTT(TwoTypes);
    makeFeaturesForAkof(casSrc, mSrc, Akof1);
    
    FeatureStructure otherTsFs = casSrc.createFS(mSrc.getType(Akof2));
    FeatureStructure fsOrig = lfs.get(0);
    fsOrig.setFeatureValue(mSrc.getFeature(fsOrig, "Fs"), otherTsFs);
    
    FeatureStructure ts1Fs = casSrc.createFS(mSrc.getType(Akof1));
    otherTsFs.setFeatureValue(mSrc.getFeature(otherTsFs, "Fs"), ts1Fs);
    
    if (indexed) {
      casSrc.addFsToIndexes(ts1Fs);
    }

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    remoteCas = setupCas(m);
    loadCas(casSrc, mSrc);
    ReuseInfo[] ri = serializeDeserialize(casSrc, remoteCas, null, null);
    MarkerImpl marker = (MarkerImpl) remoteCas.createMarker();
    lfs = getIndexedFSs(remoteCas, m);
    FeatureStructure fs = lfs.get(10);
    StringArrayFS sa = (StringArrayFS) maybeGetFeatureKind(fs, m, "Astring");
    sa.set(0, "change2");
    verifyDelta(marker, ri);
  }

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    remoteCas = setupCas(m);
    loadCas(casSrc, mSrc);
    ReuseInfo[] ri = serializeDeserialize(casSrc, remoteCas, null, null);
    MarkerImpl marker = (MarkerImpl) remoteCas.createMarker();
    lfs = getIndexedFSs(remoteCas, m);
    FeatureStructure fs = lfs.get(10);  /* has double array length 2 */
    DoubleArrayFS d = (DoubleArrayFS) maybeGetFeatureKind(fs, m, "Adouble");
    d.set(0, 12.34D);
    verifyDelta(marker, ri);
  }

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    ReuseInfo[] ri = serializeDeserialize(casSrc, remoteCas, null, null);
    MarkerImpl marker = (MarkerImpl) remoteCas.createMarker();
    
    lfs = getIndexedFSs(remoteCas, m); // gets FSs below the line


    FeatureStructure fs = lfs.get(10);
    ByteArrayFS sfs = (ByteArrayFS) maybeGetFeatureKind(fs, m, "Abyte");
    sfs.set(0, (byte)21);


    verifyDelta(marker, ri);
  }

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    ReuseInfo[] ri = serializeDeserialize(casSrc, remoteCas, null, null);
    MarkerImpl marker = (MarkerImpl) remoteCas.createMarker();
    
    lfs = getIndexedFSs(remoteCas, m);


    FeatureStructure fs = lfs.get(10);
    StringArrayFS sfs = (StringArrayFS) maybeGetFeatureKind(fs, m, "Astring");
    if (sfs != null) {
      sfs.set(0, "change");
    }

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    loadCas(casSrc, mSrc);
    ReuseInfo ri[] = serializeDeserialize(casSrc, remoteCas, null, null);
    MarkerImpl marker = (MarkerImpl) remoteCas.createMarker();
    
    lfs = getIndexedFSs(remoteCas, m);
    FeatureStructure fs = remoteCas.createFS(m.getType(Akof1));
    maybeSetFeature(fs, m, lfs.get(0));
    ArrayFS fsafs = remoteCas.createArrayFS(4);
    fsafs.set(1, lfs.get(1));
    fsafs.set(2, lfs.get(2));
    fsafs.set(3, lfs.get(3));

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