Java Code Examples for org.apache.uima.cas.impl.Serialization#deserializeCASComplete()

public SCAS copy() throws UIMAException, IOException, ClassNotFoundException {
    JCas jcas = JCasFactory.createJCas();
    ByteArrayOutputStream buffer = new ByteArrayOutputStream();
    ObjectOutputStream docOS = new ObjectOutputStream(buffer);
    CASCompleteSerializer serializerOut = Serialization.serializeCASComplete(this.getJCas().getCasImpl());
    docOS.writeObject(serializerOut);
    docOS.close();
    ObjectInputStream is = new ObjectInputStream(new ByteArrayInputStream(buffer.toByteArray()));
    CASCompleteSerializer serializerIn = (CASCompleteSerializer)is.readObject();
    Serialization.deserializeCASComplete(serializerIn, jcas.getCasImpl());
    return new SCAS(jcas.getCas());
}
 

/**
 * Analyzes a given document by a CasObjectProcessor. When completed this method returns a
 * VinciFrame containing XCAS translated into a set of Vinci subFrames. Each subframe containing
 * one annotation with all its attributes.
 *
 * @param aRequestFrame          request frame
 * @return VinciFrame containing XCAS translated into a set of Vinci subframes.
 * @throws ServiceException the service exception
 */
private Transportable analyze(AFrame aRequestFrame) throws ServiceException {
  CAS cas = null;
  try {
    // get CAS object from pool
    cas = mCasPool.getCas(0);

    // deserialize into CAS object
    byte[] casBytes = aRequestFrame.fgetTrueBinary("BinaryCAS");
    CASCompleteSerializer serializer = (CASCompleteSerializer) SerializationUtils
            .deserialize(casBytes);
    Serialization.deserializeCASComplete(serializer, (CASMgr) cas);

    long annotStartTime = System.currentTimeMillis();
    // invoke Analysis Engine
    mAE.processCas(cas);
    int annotationTime = (int) (System.currentTimeMillis() - annotStartTime);
    if (debug) {
      System.out.println("Annotation took: " + annotationTime + "ms");
    }

    // serialize CAS
    AFrame responseFrame = new AFrame();
    CASSerializer responseSerializer = Serialization.serializeCAS(cas);
    byte[] responseCasBytes = SerializationUtils.serialize(responseSerializer);
    responseFrame.fsetTrueBinary("BinaryCAS", responseCasBytes);
    // also add annotation time
    responseFrame.fset(Constants.ANNOTATION_TIME, annotationTime);

    // UIMAFramework.getLogger().log("CAS ACount::" +
    // cas.getAnnotationIndex().size());
    int totalAnnots = 0;
    SofaFS sofa;
    FSIterator sItr = cas.getSofaIterator();
    while (sItr.isValid()) {
      sofa = (SofaFS) sItr.get();
      totalAnnots += cas.getView(sofa).getAnnotationIndex().size();
      sItr.moveToNext();
    }
    UIMAFramework.getLogger().log(Level.FINE, "CAS Annotation Count::" + totalAnnots);

    return responseFrame;
  } catch (Throwable ex) {
    UIMAFramework.getLogger().log(Level.SEVERE, "", ex);
    throw new ServiceException("Unexpected exception in analyze(): " + ex);
  } finally {
    // release CAS back to pool
    if (cas != null) {
      mCasPool.releaseCas(cas);
    }
  }
}
 

/**
 * Called when the applet is initialized.
 */
@Override
public void init() {
  try {
    // get applet parameter - URL from which to get the CAS
    String casURL = getParameter("CasUrl");

    // open URL connection to get the serialized CAS
    URLConnection con = new URL(casURL).openConnection();

    con.setDoInput(true);
    con.setDoOutput(true);
    con.setUseCaches(false);
    con.setDefaultUseCaches(false);
    con.setRequestProperty("Content-Type", "application/octet-stream");
    // con.connect();

    InputStream in = con.getInputStream();
    ByteArrayOutputStream byteStream = new ByteArrayOutputStream();
    byte[] buf = new byte[2048];
    int bytesRead = in.read(buf);
    while (bytesRead > 0) {
      byteStream.write(buf, 0, bytesRead);
      bytesRead = in.read(buf);
    }
    byte[] bytes = byteStream.toByteArray();
    in.close();
    byteStream.close();
    System.out.println("Got " + bytes.length + " bytes.");

    // deserialize CAS
    CASMgr casMgr = CASFactory.createCAS();
    CASCompleteSerializer serializer = (CASCompleteSerializer) SerializationUtils
            .deserialize(bytes);
    Serialization.deserializeCASComplete(serializer, casMgr);

    // create tree viewer component and add to this applet
    mTreeViewer = new CasTreeViewer(casMgr.getCAS().getView(CAS.NAME_DEFAULT_SOFA));
    getContentPane().add(mTreeViewer);

    // add a listener that detects resize events
    addComponentListener(new MyComponentListener());

    // set initial size of tree viewer panel
    resizeTreeViewer();

  } catch (Exception e) {
    e.printStackTrace();
  }

}
 

/**
 * Called when the applet is initialized.
 */
@Override
public void init() {
  try {
    // get applet parameter - URL from which to get the CAS
    String casURL = getParameter("CasUrl");

    // open URL connection to get the serialized CAS
    URLConnection con = new URL(casURL).openConnection();

    con.setDoInput(true);
    con.setDoOutput(true);
    con.setUseCaches(false);
    con.setDefaultUseCaches(false);
    con.setRequestProperty("Content-Type", "application/octet-stream");
    // con.connect();

    InputStream in = con.getInputStream();
    ByteArrayOutputStream byteStream = new ByteArrayOutputStream();
    byte[] buf = new byte[2048];
    int bytesRead = in.read(buf);
    while (bytesRead > 0) {
      byteStream.write(buf, 0, bytesRead);
      bytesRead = in.read(buf);
    }
    byte[] bytes = byteStream.toByteArray();
    in.close();
    byteStream.close();
    System.out.println("Got " + bytes.length + " bytes.");

    // deserialize CAS
    CASMgr casMgr = CASFactory.createCAS();
    CASCompleteSerializer serializer = (CASCompleteSerializer) SerializationUtils
            .deserialize(bytes);
    Serialization.deserializeCASComplete(serializer, casMgr);

    // get 2nd applet parameter - right-to-left text orientation
    boolean rightToLeft = false;
    String rightToLeftParam = getParameter("RightToLeftTextOrientation");
    if (rightToLeftParam != null && rightToLeftParam.equalsIgnoreCase("true")) {
      rightToLeft = true;
    }

    // create viewer component and add to this applet
    mViewer = new CasAnnotationViewer();
    // NOTE: it seems to be important to add the viewer to the frame
    // before calling setCAS. If we do it the other way around
    // we seem to frequently cause the browser to hang.
    getContentPane().add(mViewer);

    mViewer.setCAS(casMgr.getCAS().getView(CAS.NAME_DEFAULT_SOFA));
    mViewer.setRightToLeftTextOrientation(rightToLeft);

    // add a listener that detects resize events
    addComponentListener(new MyComponentListener());

    // set initial size of tree viewer panel
    resizeTreeViewer();

  } catch (Exception e) {
    e.printStackTrace();
  }

}
 

/**
 * Test driver.
 */
public void testMain() throws Exception {

  for (int i = 0; i < 10; i++) {
    cas.getIndexRepository().addFS(cas.createAnnotation(annotationType, i * 2, (i * 2) + 1));
    cas.getIndexRepository().addFS(cas.createAnnotation(sentenceType, i * 2, (i * 2) + 1));
    cas.getIndexRepository().addFS(cas.createAnnotation(tokenType, i * 2, (i * 2) + 1));
    cas.getIndexRepository().addFS(cas.createAnnotation(tokenType, i * 2, (i * 2) + 1));
    cas.getIndexRepository().addFS(cas.createAnnotation(tokenType, i * 2, (i * 2) + 1));
  }
  for (int i = 19; i >= 10; i--) {
    cas.getIndexRepository().addFS(cas.createAnnotation(annotationType, i * 2, (i * 2) + 1));
    cas.getIndexRepository().addFS(cas.createAnnotation(sentenceType, i * 2, (i * 2) + 1));
    cas.getIndexRepository().addFS(cas.createAnnotation(tokenType, i * 2, (i * 2) + 1));
    cas.getIndexRepository().addFS(cas.createAnnotation(tokenType, i * 2, (i * 2) + 1));
    cas.getIndexRepository().addFS(cas.createAnnotation(tokenType, i * 2, (i * 2) + 1));
  }

  AnnotationFS searchAnnot = cas.createAnnotation(annotationType, 0, 1);
  assertTrue(cas.getAnnotationIndex().find(searchAnnot) != null);
  assertTrue(cas.getIndexRepository().getIndex(ANNOT_SET_INDEX).find(searchAnnot) != null);
  // find() does not produce useful results on bag indexes, since the comparator
  // is not defined.
  // assertTrue(cas.getIndexRepository().getIndex(ANNOT_BAG_INDEX).find(searchAnnot) != null);

  searchAnnot.setIntValue(endFeature, 4);
  assertTrue(cas.getAnnotationIndex().find(searchAnnot) == null);
  assertTrue(cas.getIndexRepository().getIndex(ANNOT_SET_INDEX).find(searchAnnot) == null);
  assertTrue(cas.getIndexRepository().getIndex(ANNOT_BAG_INDEX).find(searchAnnot) == null);

  final int ordSize = cas.getAnnotationIndex().size();
  final int setSize = cas.getIndexRepository().getIndex(ANNOT_SET_INDEX).size();
  final int bagSize = cas.getIndexRepository().getIndex(ANNOT_BAG_INDEX).size();
  // System.out.println("Before serialization\n");
  // System.out.println("Size of ordered index: " + ordSize);
  // System.out.println("Size of set index: " + setSize);
  // System.out.println("Size of bag index: " + bagSize);

  CASCompleteSerializer cs;
  cs = Serialization.serializeCASComplete(casMgr);
  // casMgr = CASFactory.createCAS();
  CASMgr realCasMgr = CASFactory.createCAS();  // creates base view, but no ts, so no ir
  ((CASImpl) realCasMgr).commitTypeSystem();   // also makes index repo (which will be replaced), but doesn't init the built-in indexes
  Serialization.deserializeCASComplete(cs, realCasMgr);
  cas = ((CASImpl) realCasMgr).getCurrentView();
  casMgr = (CASMgr) cas;

  // System.out.println("After serialization\n");
  FSIndex<? extends FeatureStructure> index = cas.getAnnotationIndex();
  assertTrue(index != null);
  assertTrue(index.getIndexingStrategy() == FSIndex.SORTED_INDEX);
  // System.out.println("Size of ordered index: " + index.size());
  assertTrue(index.size() == ordSize);

  index = cas.getIndexRepository().getIndex(ANNOT_BAG_INDEX);
  assertTrue(index != null);
  assertTrue(index.getIndexingStrategy() == FSIndex.BAG_INDEX);
  // System.out.println("Size of bag index: " + index.size());
  assertTrue(index.size() == bagSize);

  index = cas.getIndexRepository().getIndex(ANNOT_SET_INDEX);
  assertTrue(index != null);
  assertTrue(index.getIndexingStrategy() == FSIndex.SET_INDEX);
  // System.out.println("Size of set index: " + index.size());
  // System.out.println("Should be: " + setSize);
  assertTrue(index.size() == setSize);

}
 

/**
 * Unmarshalls the CAS data in this <code>ServiceDataCargo</code> into an existing
 * <code>CAS</code> instance. The data in the exsiting CAS will be replaced by the CAS data in
 * this object.
 * 
 * @param aCas the CAS to unmarshal into
 * @param aReplaceCasTypeSystem if true, assumes serialized data contains the type system
 * @throws CASException passthru
 */
 public void unmarshalCas(CAS aCas, boolean aReplaceCasTypeSystem) throws CASException {
  CASMgr casMgr = (CASMgr) aCas;
  if (aReplaceCasTypeSystem) {
    Serialization.deserializeCASComplete(mCasSer, casMgr);
  } else {
    Serialization.createCAS(casMgr, mCasSer.getCASSerializer());
  }
}