org.apache.uima.cas.CAS Java Examples

public static CAS readWebAnnoTSV(String aPath, TypeSystemDescription aType)
    throws UIMAException, IOException
{
    CollectionReader reader = createReader(WebannoTsv2Reader.class,
            WebannoTsv2Reader.PARAM_SOURCE_LOCATION, "src/test/resources/" + aPath);
    CAS cas;
    if (aType != null) {
        TypeSystemDescription builtInTypes = TypeSystemDescriptionFactory
                .createTypeSystemDescription();
        List<TypeSystemDescription> allTypes = new ArrayList<>();
        allTypes.add(builtInTypes);
        allTypes.add(aType);
        cas = JCasFactory.createJCas(CasCreationUtils.mergeTypeSystems(allTypes)).getCas();
    }
    else {
        cas = JCasFactory.createJCas().getCas();
    }

    reader.getNext(cas);

    return cas;
}
 

private void actionAnnotate(AjaxRequestTarget aTarget)
{
    try {
        // When updating an annotation in the sidebar, we must not force a
        // re-focus after rendering
        getRequestCycle().setMetaData(IsSidebarAction.INSTANCE, true);
        
        // Load the boiler-plate
        CAS cas = jcasProvider.get();
        FeatureStructure fs = selectFsByAddr(cas, getModelObject().getId());
        AnnotationLayer layer = annotationService.findLayer(project.getObject(), fs);
        TypeAdapter adapter = annotationService.getAdapter(layer);

        // Update the features of the selected annotation from the values presently in
        // the feature editors
        writeFeatureEditorModelsToCas(adapter, cas);
        
        // persist changes
        annotationPage.writeEditorCas(cas);
    }
    catch (Exception e) {
        handleException(DocumentMetadataAnnotationDetailPanel.this, aTarget, e);
    }
}
 

public static TypeSystemDescription createMultiLinkWithRoleTestTypeSytem(String... aFeatures)
    throws Exception
{
    List<TypeSystemDescription> typeSystems = new ArrayList<>();

    TypeSystemDescription tsd = new TypeSystemDescription_impl();

    // Link type
    TypeDescription linkTD = tsd.addType(LINK_TYPE, "", CAS.TYPE_NAME_TOP);
    linkTD.addFeature("role", "", CAS.TYPE_NAME_STRING);
    linkTD.addFeature("target", "", Token.class.getName());

    // Link host
    TypeDescription hostTD = tsd.addType(HOST_TYPE, "", CAS.TYPE_NAME_ANNOTATION);
    hostTD.addFeature("links", "", CAS.TYPE_NAME_FS_ARRAY, linkTD.getName(), false);
    for (String feature : aFeatures) {
        hostTD.addFeature(feature, "", CAS.TYPE_NAME_STRING);
    }

    typeSystems.add(tsd);
    typeSystems.add(TypeSystemDescriptionFactory.createTypeSystemDescription());

    return CasCreationUtils.mergeTypeSystems(typeSystems);
}
 

private void reinitTypeSystem(TypeSystemImpl tsa) {
  annotationType = tsa.getType(CAS.TYPE_NAME_ANNOTATION);

  // new primitive types
  exampleType = tsa.refreshType(exampleType);

  floatFeature = tsa.refreshFeature(floatFeature);
  stringFeature = tsa.refreshFeature(stringFeature);
  booleanFeature = tsa.refreshFeature(booleanFeature);
  byteFeature = tsa.refreshFeature(byteFeature);
  shortFeature = tsa.refreshFeature(shortFeature);
  longFeature = tsa.refreshFeature(longFeature);
  doubleFeature = tsa.refreshFeature(doubleFeature);

  intArrayFeature = tsa.refreshFeature(intArrayFeature);
  floatArrayFeature = tsa.refreshFeature(floatArrayFeature);
  stringArrayFeature = tsa.refreshFeature(stringArrayFeature);
  booleanArrayFeature = tsa.refreshFeature(booleanArrayFeature);
  byteArrayFeature = tsa.refreshFeature(byteArrayFeature);
  shortArrayFeature = tsa.refreshFeature(shortArrayFeature);
  longArrayFeature = tsa.refreshFeature(longArrayFeature);
  doubleArrayFeature = tsa.refreshFeature(doubleArrayFeature);
}
 

/**
 * Register the given CAS for a special purpose into the session.
 * 
 * @param aSpecialPurpose
 *            the unique purpose identifier - unique with respect to the current session.
 * @param aMode
 *            the access mode.
 * @param aCas
 *            the CAS itself.
 * @return the managed CAS state.
 */
public SessionManagedCas add(String aSpecialPurpose, CasAccessMode aMode, CAS aCas)
{
    Validate.notNull(aSpecialPurpose, "The purpose cannot be null");
    Validate.notNull(aMode, "The access mode cannot be null");
    Validate.notNull(aCas, "The CAS cannot be null");

    SessionManagedCas managedCas = new SessionManagedCas(SPECIAL_PURPOSE, aSpecialPurpose,
            aMode, aCas);

    Map<String, SessionManagedCas> casByUser = managedCases
            .computeIfAbsent(SPECIAL_PURPOSE, key -> new LinkedHashMap<>());
    casByUser.put(aSpecialPurpose, managedCas);
    
    LOGGER.trace("CAS storage session [{}]: added {}", hashCode(), managedCas);
    
    return managedCas;
}
 

@Override
public CAS getEditorCas()
    throws IOException
{
    AnnotatorState state = CurationPage.this.getModelObject();
    
    if (state.getDocument() == null) {
        throw new IllegalStateException("Please open a document first!");
    }

    // If we have a timestamp, then use it to detect if there was a concurrent access
    verifyAndUpdateDocumentTimestamp(state, curationDocumentService
            .getCurationCasTimestamp(state.getDocument()));

    return curationDocumentService.readCurationCas(state.getDocument());
}
 

@Test
public void singleEmptyCasTest()
    throws Exception
{
    String text = "";
    
    CAS user1Cas = JCasFactory.createJCas().getCas();
    user1Cas.setDocumentText(text);
    
    Map<String, List<CAS>> casByUser = new LinkedHashMap<>();
    casByUser.put("user1", asList(user1Cas));

    List<SpanDiffAdapter> diffAdapters = asList(new SpanDiffAdapter(Token.class.getName()));

    DiffResult result = doDiff(diffAdapters, LINK_TARGET_AS_LABEL, casByUser).toResult();
    
    // result.print(System.out);
    
    assertEquals(0, result.size());
    assertEquals(0, result.getDifferingConfigurationSets().size());
}
 

private String actionGetDocument(CAS aCas)
{
    StopWatch timer = new StopWatch();
    timer.start();
    
    GetDocumentResponse response = new GetDocumentResponse();
    String json;
    if (getModelObject().getProject() != null) {
        render(response, aCas);
        json = toJson(response);
        lastRenderedJson = json;
    }
    else {
        json = toJson(response);
    }
    
    timer.stop();
    metrics.renderComplete(RenderType.FULL, timer.getTime(), json, null);
    
    return json;
}
 

/**
 * @see junit.framework.TestCase#setUp()
 */
public void setUp() throws Exception {
  super.setUp();
  casMgr = initCAS();
  cas = (CASImpl)casMgr;

  TypeSystem ts = cas.getTypeSystem();
  wordType = ts.getType(WORD_TYPE);
  // assert(wordType != null);
  separatorType = ts.getType(SEP_TYPE);
  eosType = ts.getType(EOS_TYPE);
  tokenType = ts.getType(TOKEN_TYPE);
  tokenTypeFeature = ts.getFeatureByFullName(TOKEN_TYPE_FEAT_Q);
  startFeature = ts.getFeatureByFullName(CAS.FEATURE_FULL_NAME_BEGIN);
  endFeature = ts.getFeatureByFullName(CAS.FEATURE_FULL_NAME_END);
  sentenceType = ts.getType(SENT_TYPE);
}
 

private void createChunkLayer(Project aProject)
    throws IOException
{
    AnnotationLayer chunkLayer = new AnnotationLayer(Chunk.class.getName(), "Chunk", SPAN_TYPE,
            aProject, true, TOKENS, NO_OVERLAP);
    annotationSchemaService.createLayer(chunkLayer);

    AnnotationFeature chunkValueFeature = new AnnotationFeature();
    chunkValueFeature.setDescription("Chunk tag");
    chunkValueFeature.setName("chunkValue");
    chunkValueFeature.setType(CAS.TYPE_NAME_STRING);
    chunkValueFeature.setProject(aProject);
    chunkValueFeature.setUiName("Tag");
    chunkValueFeature.setLayer(chunkLayer);
    annotationSchemaService.createFeature(chunkValueFeature);
}
 

@Test
public void thatIncrementalPosEvaluationWorks() throws Exception
{
    IncrementalSplitter splitStrategy = new IncrementalSplitter(0.8, 250, 10);
    OpenNlpPosRecommender sut = new OpenNlpPosRecommender(recommender, traits);
    List<CAS> casList = loadAllData();

    int i = 0;
    while (splitStrategy.hasNext() && i < 3) {
        splitStrategy.next();
        
        double score = sut.evaluate(casList, splitStrategy).computeF1Score();

        assertThat(score).isStrictlyBetween(0.0, 1.0);
        
        i++;
    }
}
 

public static void renderTokens(CAS aCas, GetDocumentResponse aResponse, AnnotatorState aState)
{
    int winBegin = aState.getWindowBeginOffset();
    int winEnd = aState.getWindowEndOffset();
    Type tokenType = CasUtil.getType(aCas, Token.class);

    List<AnnotationFS> tokens = selectCovered(aCas, tokenType, winBegin, winEnd);
    for (AnnotationFS fs : tokens) {
        // attach type such as POS adds non-existing token element for ellipsis annotation
        if (fs.getBegin() == fs.getEnd()) {
            continue;
        }
        
        split(aResponse.getSentenceOffsets(), fs.getCoveredText(), fs.getBegin() - winBegin,
                fs.getEnd() - winBegin)                    
                .forEach(range -> {
                    aResponse.addToken(range.getBegin(), range.getEnd());
                    if (DEBUG) {
                        aResponse.addEntity(new Entity(new VID(fs), "Token",
                                new Offsets(range.getBegin(), range.getEnd()),
                                fs.getCoveredText(), "#d9d9d9",
                                "[" + fs.getBegin() + "-" + fs.getEnd() + "]"));
                    }
                });
    }
}
 

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();
   deserialize(xmiStr3, newCas, null, false, -1);
   CasComparer.assertEquals(originalCas, newCas);    
}
 

@Override
public boolean accepts(AnnotationLayer aLayer, AnnotationFeature aFeature)
{
    if (aLayer == null || aFeature == null) {
        return false;
    }
    
    return (asList(SINGLE_TOKEN, TOKENS).contains(aLayer.getAnchoringMode()))
            && !aLayer.isCrossSentence() && SPAN_TYPE.equals(aLayer.getType())
            && (CAS.TYPE_NAME_STRING.equals(aFeature.getType()) || aFeature.isVirtualFeature());
}
 

public boolean hasNext() throws AnalysisEngineProcessException {
  CAS outputCas = getEmptyCAS();
  try {
    Assert.assertTrue(((TypeSystemImpl)mInputCAS.getTypeSystem()).getLargestTypeCode() ==
      ((TypeSystemImpl)outputCas.getTypeSystem()).getLargestTypeCode());
    Assert.assertTrue(mInputCAS.getTypeSystem() == outputCas.getTypeSystem());
  }
  finally {
    outputCas.release();
  }
  return false;
}
 

@Override
public List<Pair<LogMessage, AnnotationFS>> validate(CAS aCas)
{
    List<Pair<LogMessage, AnnotationFS>> messages = new ArrayList<>();
    for (SpanLayerBehavior behavior : behaviors) {
        long startTime = currentTimeMillis();
        messages.addAll(behavior.onValidate(this, aCas));
        log.trace("Validation for [{}] on [{}] took {}ms", behavior.getClass().getSimpleName(),
                getLayer().getUiName(), currentTimeMillis() - startTime);
    }
    return messages;
}
 

private AnnotationFS createNEAnno(CAS aCas, String aValue, int aBegin, int aEnd)
{
    Type type = aCas.getTypeSystem().getType(NamedEntity.class.getTypeName());
    AnnotationFS clickedFs = aCas.createAnnotation(type, aBegin, aEnd);
    Feature value = type.getFeatureByBaseName("value");
    clickedFs.setStringValue(value, aValue);
    aCas.addFsToIndexes(clickedFs);
    return clickedFs;
}
 

@Test
public void testOK()
    throws Exception
{
    TypeSystemDescription tsd = UIMAFramework.getResourceSpecifierFactory()
            .createTypeSystemDescription();
    
    String refTypeName = "RefType";
    
    TypeDescription refTypeDesc = tsd.addType(refTypeName, null, CAS.TYPE_NAME_ANNOTATION);
    refTypeDesc.addFeature("ref", null, CAS.TYPE_NAME_ANNOTATION);
    
    CAS cas = CasCreationUtils.createCas(tsd, null, null);
    
    Type refType = cas.getTypeSystem().getType(refTypeName);
    
    // A regular index annotation
    AnnotationFS anno1 = cas.createAnnotation(cas.getAnnotationType(), 0, 1);
    cas.addFsToIndexes(anno1);

    // An indexed annotation but reachable through an indexe one (below)
    AnnotationFS anno2 = cas.createAnnotation(cas.getAnnotationType(), 0, 1);
    cas.addFsToIndexes(anno2);

    // An indexed annotation that references the non-indexed annotation above
    AnnotationFS anno3 = cas.createAnnotation(refType, 0, 1);
    anno3.setFeatureValue(refType.getFeatureByBaseName("ref"), anno2);
    cas.addFsToIndexes(anno3);
    
    List<LogMessage> messages = new ArrayList<>();
    CasDoctor cd = new CasDoctor(AllFeatureStructuresIndexedCheck.class);
    // A project is not required for this check
    boolean result = cd.analyze(null, cas, messages);
    
    messages.forEach(System.out::println);
    
    assertTrue(result);
}
 

public static Map<String, List<CAS>> loadWebAnnoTSV(TypeSystemDescription aTypes,
        String... aPaths)
    throws UIMAException, IOException
{
    Map<String, List<CAS>> casByUser = new LinkedHashMap<>();
    int n = 1;
    for (String path : aPaths) {
        CAS cas = readWebAnnoTSV(path, aTypes);
        casByUser.put("user" + n, asList(cas));
        n++;
    }
    return casByUser;
}
 

@Override
public CAS createOrReadInitialCas(SourceDocument aDocument, CasUpgradeMode aUpgradeMode,
        CasAccessMode aAccessMode)
    throws IOException
{
    return createOrReadInitialCas(aDocument, aUpgradeMode, aAccessMode, null);
}
 

@Override
public void process(JCas jCas) throws AnalysisEngineProcessException {
  try {
    JCas parentheticalView = ViewCreatorAnnotator.createViewSafely(jCas,
            ViewNames.PARENTHESES_VIEW);
    jCas = jCas.getView(CAS.NAME_DEFAULT_SOFA);
    String initialText = jCas.getDocumentText();
    String parentheticalText = initialText.replaceAll("[aeiou]+", "($0)");
    parentheticalView.setDocumentText(parentheticalText);
  } catch (CASException e) {
    throw new AnalysisEngineProcessException(e);
  }

}
 

public UimaTokenizer(String tokens, UimaResource resource, boolean checkForLabel) {

        this.checkForLabel = checkForLabel;
        this.tokens = new ArrayList<>();
        try {
            CAS cas = resource.process(tokens);

            Collection<Token> tokenList = JCasUtil.select(cas.getJCas(), Token.class);

            for (Token t : tokenList) {

                if (!checkForLabel || valid(t.getCoveredText()))
                    if (t.getLemma() != null)
                        this.tokens.add(t.getLemma());
                    else if (t.getStem() != null)
                        this.tokens.add(t.getStem());
                    else
                        this.tokens.add(t.getCoveredText());
            }


            resource.release(cas);


        } catch (Exception e) {
            log.error("",e);
            throw new RuntimeException(e);
        }

    }
 

public static Optional<String> getSourceDocumentName(CAS aCas)
{
    try {
        FeatureStructure fs = CasUtil.selectSingle(aCas, getType(aCas, CASMetadata.class));
        return Optional.ofNullable(FSUtil.getFeature(fs, "sourceDocumentName", String.class));
    }
    catch (IllegalArgumentException e) {
        return Optional.empty();
    }
}
 

public static void writeSerializedCas(CAS aCas, File aFile)
    throws IOException
{
    FileUtils.forceMkdir(aFile.getParentFile());

    try (ObjectOutputStream os = new ObjectOutputStream(new FileOutputStream(aFile))) {
        CASCompleteSerializer serializer = serializeCASComplete((CASImpl) aCas);
        os.writeObject(serializer);
    }
}
 

private static List<AnnotationFS> getCandidateAnnotations(CAS aTargetCas, AnnotationFS aSource)
{
    return selectCovered(aTargetCas, aSource.getType(), aSource.getBegin(), aSource.getEnd())
            .stream()
            .filter(fs -> isEquivalentAnnotation(fs, aSource))
            .collect(Collectors.toList());
}
 

public static Map<String, List<CAS>> load(String... aPaths)
    throws UIMAException, IOException
{
    Map<String, List<CAS>> casByUser = new LinkedHashMap<>();
    int n = 1;
    for (String path : aPaths) {
        CAS cas = read(path);
        casByUser.put("user" + n, asList(cas));
        n++;
    }
    return casByUser;
}
 

/**
 * @see org.apache.uima.collection.CollectionReader#getNext(org.apache.uima.cas.CAS)
 */
public void getNext(CAS aCAS) throws IOException, CollectionException {
  File currentFile = (File) mFiles.get(mCurrentIndex++);
  try (InputStream inputStream = new FileInputStream(currentFile)) {
    XmiCasDeserializer.deserialize(inputStream, aCAS, !mFailOnUnknownType);
  } catch (SAXException e) {
    throw new CollectionException(e);
  }
}
 

/**
 * To test non-normal case, change Eclipse run config by adding the jvm arg:
 *   -Duima.allow_duplicate_add_to_indexes
 * @throws CASException
 */
public void testDupFsIndex() throws CASException {
  cas.setSofaDataString("something", "text"); // otherwise triggers failure in addFsToIndex - no sofa ref
  JCas jcas = cas.getJCas();
  Annotation a = new Annotation(jcas, 0, 4);
  cas.addFsToIndexes(a);
  cas.addFsToIndexes(a);
  cas.addFsToIndexes(a);
  int expected = /*FSIndexRepositoryImpl.IS_ALLOW_DUP_ADD_2_INDEXES ? 4 :*/ 2;
  assertEquals(expected, cas.getIndexRepository().getIndex(CASTestSetup.ANNOT_SORT_INDEX).size());
  assertEquals(expected, cas.getIndexRepository().getIndex(CASTestSetup.ANNOT_BAG_INDEX).size());
  assertEquals(expected, cas.getIndexRepository().getIndex(CAS.STD_ANNOTATION_INDEX).size());
}
 

private static void assertCorrectlyLoaded(CAS cas, boolean leniently) throws Exception {
    // Check if all the annotations are there (mind the file contains FSes that are NOT annotations!)
    Assert.assertEquals(
            leniently ? SIMPLE_CAS_DEFAULT_INDEX_SIZE_LENIENT : SIMPLE_CAS_DEFAULT_INDEX_SIZE,
            cas.getAnnotationIndex().size());
    
    // Count ALL FSes now, including the ones that are not annotations!
    List<String> expectedTypes = new ArrayList<>(asList(
            "org.apache.uima.testTypeSystem.Entity", 
            "org.apache.uima.testTypeSystem.Organization", 
            "org.apache.uima.testTypeSystem.Owner", 
            "org.apache.uima.testTypeSystem.Person", 
            "uima.tcas.DocumentAnnotation"));
    
    if (leniently) {
      // This type was renamed to "org.apache.uima.testTypeSystem.OwnerRenamed"
      expectedTypes.remove("org.apache.uima.testTypeSystem.Owner");
    }
    
    List<String> fsTypes = new ArrayList<>();
//    FSIterator<FeatureStructure> fsi = cas.getIndexRepository()
//            .getAllIndexedFS(cas.getTypeSystem().getTopType());
    Collection<TOP> s = cas.getIndexedFSs();
    Iterator<TOP> fsi = s.iterator();
    int fsCount = 0;
    while (fsi.hasNext()) {
      TOP fs = (TOP) fsi.next();
      String typeName = fs.getType().getName();
      if (!fsTypes.contains(typeName)) {
        fsTypes.add(typeName);
      }
      fsCount++;
    }
    Collections.sort(fsTypes);
    
    Assert.assertEquals(
            leniently ? SIMPLE_CAS_ALL_INDEXED_SIZE_LENIENT : SIMPLE_CAS_ALL_INDEXED_SIZE, fsCount);
    
    Assert.assertEquals(expectedTypes, fsTypes);
  }
 

/**
 * Retrieves annotation editor adapters.
 *
 * @param adapter the adapter
 * @return an adapter or null
 */
@Override
public Object getAdapter(@SuppressWarnings("rawtypes") Class adapter) {

  if (IContentOutlinePage.class.equals(adapter) && getDocument() != null) {
    return mOutlinePage;
  }
  else if (CAS.class.equals(adapter) && getDocument() != null) {
    return getDocument().getCAS();
  }
  else {
    return super.getAdapter(adapter);
  }

}