Examples of org.apache.uima.cas.FSIndex

org.apache.uima.cas.FSIndex
Feature structure index access interface.
Notice that each feature structure index uses its own ordering relation that will usually be different from index to index. In particular, equality with respect to the index ordering will in general not imply object identity for the feature structures.
We currently support three different kinds of indexes: sorted, set and bag indexes. The default index is a sorted index. In a sorted index, all FSs that are committed are entered, even if they are duplicates of already existing FSs. The index is sorted in the sense that iterators will output FSs in sorted order according to the comparator for that index. The order of FSs that are equal wrt the comparator is arbitrary but fixed. That is, if you iterate over the same index several times, you will see the same relative order of FSs every time. We also guarantee that reverse iterators will produce exactly the reverse sequence of forward iteration.
A set index will contain no duplicates of the same type, where a duplicate is defined by the indexing comparator. That is, if you commit two feature structures of the same type that are equal wrt the indexing comparator, only the first one will be entered into the index. Note that you can still have duplicates wrt the indexing order if they are of a different type. A set index is not guaranteed to be sorted.
A bag index finally simply stores everything, without any guaranteed order. Our current implementation works such that for any two FSs of the same type, they will be returned in the order in which they are committed (FIFO style). Note that any operation like find() or FSIterator.moveTo() will not produce useful results on bag indexes, since bag indexes do not honor comparators. Only use a bag index if you want very fast adding and will have to iterate over the whole index anyway.

        cas1.getIndexRepository().addFS(anAnnot2);
        AnnotationFS anAnnot3 = cas1.createAnnotation(cas1.getAnnotationType(), 8, 13);
        cas1.getIndexRepository().addFS(anAnnot3);
        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);

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    mCategoryFeature = mCategoryType.getFeatureByBaseName(categoryFeatureName);
  }
  
  public void processCas(CAS cas) throws ResourceProcessException {
    
    FSIndex categoryIndex = cas.getAnnotationIndex(mCategoryType);
    
    if (categoryIndex.size() > 0) {
      AnnotationFS categoryAnnotation  = 
          (AnnotationFS) categoryIndex.iterator().next();
      
      // add to event collection
      
      DocumentSample sample = new DocumentSample(
        categoryAnnotation.getStringValue(mCategoryFeature),

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      // Test that the annotations are in separate index spaces, and that Sofas are indexed
      JFSIndexRepository indexes = jcas.getJFSIndexRepository();
      // FSIndex sofaIndex = indexes.getIndex(CAS.SOFA_INDEX_NAME);
      indexes = engJcas.getJFSIndexRepository();
      FSIndex engIndex = indexes.getAnnotationIndex(Annotation.type);
      indexes = gerJcas.getJFSIndexRepository();
      FSIndex gerIndex = indexes.getAnnotationIndex(Annotation.type);
      indexes = frJcas.getJFSIndexRepository();
      FSIndex frIndex = indexes.getAnnotationIndex(Annotation.type);
      FSIterator sofaIter = jcas.getSofaIterator();
      int numSofas = 0;
      while (sofaIter.isValid()) {
        numSofas++;
        sofaIter.moveToNext();
      }
      // assertTrue(sofaIndex.size() == 3); // 3 sofas
      assertTrue(numSofas == 3);
      assertTrue(engIndex.size() == 5); // 4 annots plus documentAnnotation
      assertTrue(gerIndex.size() == 5); // 4 annots plus documentAnnotation
      assertTrue(frIndex.size() == 5); // 4 annots plus documentAnnotation


      // Test that the annotations are of the correct types
      FSIterator engIt = engIndex.iterator();
      FSIterator gerIt = gerIndex.iterator();
      FSIterator frIt = frIndex.iterator();
      Annotation engAnnot = (Annotation) engIt.get();
      Annotation gerAnnot = (Annotation) gerIt.get();
      Annotation frAnnot = (Annotation) frIt.get();
      assertTrue((CAS.TYPE_NAME_DOCUMENT_ANNOTATION).equals(engAnnot.getType().getName()));
      assertTrue((CAS.TYPE_NAME_DOCUMENT_ANNOTATION).equals(gerAnnot.getType().getName()));

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      Assert.assertEquals("EnumType", et.getName());
      Assert.assertEquals(et, f2.getRange());


      // indexes
      FSIndexRepository irep = cas.getIndexRepository();
      FSIndex ind = irep.getIndex("Index1");
      Assert.assertNotNull(ind);
      Assert.assertEquals("Type1", ind.getType().getName());
      Assert.assertEquals(FSIndex.SORTED_INDEX, ind.getIndexingStrategy());


      FeatureStructure fs1 = cas.createFS(t1);
      fs1.setIntValue(f1, 0);
      FeatureStructure fs2 = cas.createFS(t1);
      fs2.setIntValue(f1, 1);
      Assert.assertTrue(ind.compare(fs1, fs2) < 0);


      FSIndex ind2 = irep.getIndex("Index2");
      Assert.assertNotNull(ind2);
      Assert.assertEquals("Type2", ind2.getType().getName());
      Assert.assertEquals(FSIndex.SET_INDEX, ind2.getIndexingStrategy());


      FeatureStructure fs3 = cas.createFS(t2);
      fs3.setStringValue(f2, "One");
      FeatureStructure fs4 = cas.createFS(t2);
      fs4.setStringValue(f2, "Two");
      Assert.assertTrue(ind2.compare(fs3, fs4) > 0);


      FSIndex ind3 = irep.getIndex("Index3");
      Assert.assertNotNull(ind3);
      Assert.assertEquals("uima.tcas.Annotation", ind3.getType().getName());
      Assert.assertEquals(FSIndex.SORTED_INDEX, ind3.getIndexingStrategy());


      AnnotationFS fs5 = cas.createAnnotation(t1, 0, 0);
      AnnotationFS fs6 = cas.createAnnotation(t2, 0, 0);
      AnnotationFS fs7 = cas.createAnnotation(t1, 0, 0);
      Assert.assertTrue(ind3.compare(fs5, fs6) < 0);
      Assert.assertTrue(ind3.compare(fs6, fs7) > 0);


      // only way to check if allowed values is correct is to try to set an
      // invalid value?
      CASRuntimeException ex = null;
      try {

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      }
      return;
    }
    // Attempt to find a non-set index first.
    // If none found, then use the an arbitrary set index if any.
    FSIndex setIndex = null;
    final Iterator<String> iter = getLabels();
    while (iter.hasNext()) {
      final String label = iter.next();
      final FSIndex index = getIndex(label);
      // Ignore auto-indexes at this stage, they're handled above.
      if (index.getIndexingStrategy() == FSIndex.DEFAULT_BAG_INDEX) {
        continue;
      }
      if (this.typeSystem.subsumes(index.getType(), type)) {
        if (index.getIndexingStrategy() != FSIndex.SET_INDEX) {
          iteratorList.add(getIndex(label, type).iterator());
          // Done, found non-set index.
          return;
        }
        setIndex = getIndex(label, type);

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    if (this.cas != null && useCAS) {
      FSIndexRepository ir = this.cas.getIndexRepository();
      Iterator<String> it = ir.getLabels();
      while (it.hasNext()) {
        String label = it.next();
        FSIndex index1 = ir.getIndex(label);
        IndexTreeNode nodeObj = new IndexTreeNode(label, index1.getType(), index1.size());
        DefaultMutableTreeNode node = new DefaultMutableTreeNode(nodeObj);
        root.add(node);
        node.add(createTypeTree(index1.getType(), this.cas.getTypeSystem(), label, ir));
      }
    }
    DefaultTreeModel model = (DefaultTreeModel) this.indexTree.getModel();
    // 1.3 workaround
    TreeModelListener[] listeners = org.apache.uima.tools.cvd.tsview.MainFrame

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      // Test that the annotations are in separate index spaces, and that Sofas are indexed
      JFSIndexRepository indexes = jcas.getJFSIndexRepository();
      // FSIndex sofaIndex = indexes.getIndex(CAS.SOFA_INDEX_NAME);
      indexes = engJcas.getJFSIndexRepository();
      FSIndex engIndex = indexes.getAnnotationIndex(Annotation.type);
      indexes = gerJcas.getJFSIndexRepository();
      FSIndex gerIndex = indexes.getAnnotationIndex(Annotation.type);
      indexes = frJcas.getJFSIndexRepository();
      FSIndex frIndex = indexes.getAnnotationIndex(Annotation.type);
      FSIterator sofaIter = jcas.getSofaIterator();
      int numSofas = 0;
      while (sofaIter.isValid()) {
        numSofas++;
        sofaIter.moveToNext();
      }
      // assertTrue(sofaIndex.size() == 3); // 3 sofas
      assertTrue(numSofas == 3);
      assertTrue(engIndex.size() == 5); // 4 annots plus documentAnnotation
      assertTrue(gerIndex.size() == 5); // 4 annots plus documentAnnotation
      assertTrue(frIndex.size() == 5); // 4 annots plus documentAnnotation


      // Test that the annotations are of the correct types
      FSIterator engIt = engIndex.iterator();
      FSIterator gerIt = gerIndex.iterator();
      FSIterator frIt = frIndex.iterator();
      Annotation engAnnot = (Annotation) engIt.get();
      Annotation gerAnnot = (Annotation) gerIt.get();
      Annotation frAnnot = (Annotation) frIt.get();
      assertTrue((CAS.TYPE_NAME_DOCUMENT_ANNOTATION).equals(engAnnot.getType().getName()));
      assertTrue((CAS.TYPE_NAME_DOCUMENT_ANNOTATION).equals(gerAnnot.getType().getName()));

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    // print out annotations of the Source SofA
    CAS englishView = cas.getView("SourceDocument");
    Assert.assertNotNull(englishView);
    Assert.assertEquals("this beer is good", englishView.getDocumentText());
    FSIndex anIndex = englishView.getAnnotationIndex();
    FSIterator anIter = anIndex.iterator();
    Assert.assertEquals("this beer is good", ((AnnotationFS) anIter.next()).getCoveredText());
    Assert.assertEquals("this", ((AnnotationFS) anIter.next()).getCoveredText());
    if ("this".equals(((AnnotationFS) anIter.get()).getCoveredText()))
      anIter.moveToNext(); // because sometimes the test case runs 2 copies of the TransAnnotator
    Assert.assertEquals("beer", ((AnnotationFS) anIter.next()).getCoveredText());
    if ("beer".equals(((AnnotationFS) anIter.get()).getCoveredText()))
      anIter.moveToNext();
    Assert.assertEquals("is", ((AnnotationFS) anIter.next()).getCoveredText());
    if ("is".equals(((AnnotationFS) anIter.get()).getCoveredText()))
      anIter.moveToNext();
    Assert.assertEquals("good", ((AnnotationFS) anIter.next()).getCoveredText());
    if (anIter.isValid() && "good".equals(((AnnotationFS) anIter.get()).getCoveredText()))
      anIter.moveToNext();
    Assert.assertFalse(anIter.hasNext());


    // print out annotations of the transalation SofA
    // System.out.println("\n----------------\n");
    CAS germanView = cas.getView("TranslatedDocument");
    Assert.assertNotNull(germanView);
    Assert.assertEquals("das bier ist gut", germanView.getDocumentText());
    Type cross = cas.getTypeSystem().getType("sofa.test.CrossAnnotation");
    Feature other = cross.getFeatureByBaseName("otherAnnotation");
    anIndex = germanView.getAnnotationIndex(cross);
    anIter = anIndex.iterator();
    AnnotationFS annot = (AnnotationFS) anIter.next();
    Assert.assertEquals("das", annot.getCoveredText());
    AnnotationFS crossAnnot = (AnnotationFS) annot.getFeatureValue(other);
    Assert.assertEquals("this", crossAnnot.getCoveredText());
    annot = (AnnotationFS) anIter.next();

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    if (this.cas != null && useCAS) {
      FSIndexRepository ir = this.cas.getIndexRepository();
      Iterator<String> it = ir.getLabels();
      while (it.hasNext()) {
        String label = it.next();
        FSIndex index1 = ir.getIndex(label);
        IndexTreeNode nodeObj = new IndexTreeNode(label, index1.getType(), index1.size());
        DefaultMutableTreeNode node = new DefaultMutableTreeNode(nodeObj);
        root.add(node);
        node.add(createTypeTree(index1.getType(), this.cas.getTypeSystem(), label, ir));
      }
    }
    DefaultTreeModel model = (DefaultTreeModel) this.indexTree.getModel();
    // 1.3 workaround
    TreeModelListener[] listeners = org.apache.uima.tools.cvd.tsview.MainFrame

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  public void processCas(CAS cas) throws ResourceProcessException {
    Assert.assertNotNull(cas);
    Assert.assertEquals("das bier ist gut", cas.getDocumentText());
    Type cross = cas.getTypeSystem().getType("sofa.test.CrossAnnotation");
    Feature other = cross.getFeatureByBaseName("otherAnnotation");
    FSIndex anIndex = cas.getAnnotationIndex(cross);
    FSIterator anIter = anIndex.iterator();
    AnnotationFS annot = (AnnotationFS) anIter.next();
    Assert.assertEquals("das", annot.getCoveredText());
    AnnotationFS crossAnnot = (AnnotationFS) annot.getFeatureValue(other);
    Assert.assertEquals("this", crossAnnot.getCoveredText());
    annot = (AnnotationFS) anIter.next();

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