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JcasSofaTest.java

/*
 * Licensed to the Apache Software Foundation (ASF) under one
 * or more contributor license agreements.  See the NOTICE file
 * distributed with this work for additional information
 * regarding copyright ownership.  The ASF licenses this file
 * to you under the Apache License, Version 2.0 (the
 * "License"); you may not use this file except in compliance
 * with the License.  You may obtain a copy of the License at
 * 
 *   http://www.apache.org/licenses/LICENSE-2.0
 * 
 * Unless required by applicable law or agreed to in writing,
 * software distributed under the License is distributed on an
 * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY
 * KIND, either express or implied.  See the License for the
 * specific language governing permissions and limitations
 * under the License.
 */

package org.apache.uima.cas.test;

import java.io.BufferedInputStream;
import java.io.File;
import java.io.FileInputStream;
import java.io.FileOutputStream;
import java.io.IOException;
import java.io.InputStream;
import java.io.OutputStream;
import java.nio.ByteBuffer;
import java.util.Iterator;
import java.util.StringTokenizer;

import junit.framework.TestCase;

import org.apache.uima.UIMAFramework;
import org.apache.uima.cas.CAS;
import org.apache.uima.cas.FSIndex;
import org.apache.uima.cas.FSIterator;
import org.apache.uima.cas.SofaFS;
import org.apache.uima.cas.SofaID;
import org.apache.uima.cas.Type;
import org.apache.uima.cas.admin.CASFactory;
import org.apache.uima.cas.admin.CASMgr;
import org.apache.uima.cas.admin.FSIndexRepositoryMgr;
import org.apache.uima.cas.admin.TypeSystemMgr;
import org.apache.uima.cas.impl.CASImpl;
import org.apache.uima.cas.impl.CASSerializer;
import org.apache.uima.cas.impl.Serialization;
import org.apache.uima.cas.impl.XCASDeserializer;
import org.apache.uima.cas.impl.XCASSerializer;
import org.apache.uima.impl.SofaID_impl;
import org.apache.uima.jcas.JCas;
import org.apache.uima.jcas.JFSIndexRepository;
import org.apache.uima.jcas.cas.ByteArray;
import org.apache.uima.jcas.cas.DoubleArray;
import org.apache.uima.jcas.cas.FSArray;
import org.apache.uima.jcas.cas.FloatArray;
import org.apache.uima.jcas.cas.IntegerArray;
import org.apache.uima.jcas.cas.LongArray;
import org.apache.uima.jcas.cas.ShortArray;
import org.apache.uima.jcas.cas.Sofa;
import org.apache.uima.jcas.tcas.Annotation;
import org.apache.uima.resource.metadata.TypeSystemDescription;
import org.apache.uima.resource.metadata.impl.TypeSystemDescription_impl;
import org.apache.uima.test.junit_extension.JUnitExtension;
import org.apache.uima.util.CasCreationUtils;
import org.apache.uima.util.XMLInputSource;
import org.apache.uima.util.XMLSerializer;
import org.xml.sax.SAXException;


00072 public class JcasSofaTest extends TestCase {

  private CASMgr casMgr;

  private CAS cas;

  private JCas jcas;

  public JcasSofaTest(String arg) {
    super(arg);
  }

  /**
   * @see junit.framework.TestCase#setUp()
   */
00087   protected void setUp() throws Exception {
    try {
      super.setUp();
      casMgr = CASFactory.createCAS();
      CasCreationUtils.setupTypeSystem(casMgr, (TypeSystemDescription) null);
      // Create a writable type system.
      TypeSystemMgr tsa = casMgr.getTypeSystemMgr();
      // Add new types and features.
      Type annotType = tsa.getType(CAS.TYPE_NAME_ANNOTATION);
      Type crossType = tsa.addType("org.apache.uima.cas.test.CrossAnnotation", annotType);
      tsa.addFeature("otherAnnotation", crossType, annotType);
      // Commit the type system.
      ((CASImpl) casMgr).commitTypeSystem();

      // Create the Base indexes.
      casMgr.initCASIndexes();
      FSIndexRepositoryMgr irm = casMgr.getIndexRepositoryMgr();
      // init.initIndexes(irm, casMgr.getTypeSystemMgr());
      irm.commit();

      cas = casMgr.getCAS().getView(CAS.NAME_DEFAULT_SOFA);
      jcas = cas.getJCas();
    } catch (Exception e) {
      JUnitExtension.handleException(e);
    }

  }

  /**
   * Test driver.
   */
00118   public void testMain() throws Exception {
    try {

      // Create a Sofa using OLD APIs for now
      SofaID_impl id = new SofaID_impl();
      id.setSofaID("EnglishDocument");
      Sofa es = new Sofa(jcas, id, "text");
      // Initial View is #1!!!
      assertTrue(2 == es.getSofaRef());

      // Set the document text
      es.setLocalSofaData("this beer is good");

      // Test Multiple Sofas across XCAS serialization
      XCASSerializer ser = new XCASSerializer(cas.getTypeSystem());
      OutputStream outputXCAS = new FileOutputStream("Sofa.xcas");
      XMLSerializer xmlSer = new XMLSerializer(outputXCAS);
      try {
        ser.serialize(cas, xmlSer.getContentHandler());
        outputXCAS.close();
      } catch (IOException e) {
        e.printStackTrace();
      } catch (SAXException e) {
        e.printStackTrace();
      }

      // Deserialize XCAS
      cas.reset();
      InputStream inputXCAS = new FileInputStream("Sofa.xcas");
      try {
        XCASDeserializer.deserialize(inputXCAS, cas, false);
        inputXCAS.close();
      } catch (SAXException e2) {
        e2.printStackTrace();
      } catch (IOException e2) {
        e2.printStackTrace();
      }

      // Add a new Sofa
      // id.setSofaID("GermanDocument");
      // Sofa gs = new Sofa(jcas, id, "text");
      JCas gerJcas = jcas.createView("GermanDocument");
      Sofa gs = gerJcas.getSofa();
      assertTrue(3 == gs.getSofaRef());

      // Set the document text
      // gs.setLocalSofaData("das bier ist gut");
      gerJcas.setDocumentText("das bier ist gut");

      // Test multiple Sofas across binary serialization
      CASSerializer cs = Serialization.serializeNoMetaData(cas);
      cas = Serialization.createCAS(casMgr, cs);

      // Add a new Sofa
      // id.setSofaID("FrenchDocument");
      // Sofa fs = new Sofa(jcas, id, "text");
      CAS frCas = jcas.getCas().createView("FrenchDocument");
      SofaFS fs = frCas.getSofa();
      assertTrue(4 == fs.getSofaRef());

      // Open JCas views of some Sofas
      JCas engJcas = cas.getJCas(es);
      JCas frJcas = jcas.getView("FrenchDocument");

      // Set the document text after the Jcas view exists using JCas.setDocumentText method
      frJcas.setSofaDataString("cette biere est bonne", "text");

      // Create standard annotations against eng & fr and cross annotations against ger
      int engEnd = 0;
      int gerEnd = 0;
      int frEnd = 0;
      String engText = engJcas.getDocumentText();
      String gerText = gerJcas.getDocumentText();
      String frText = frJcas.getDocumentText();
      StringTokenizer est = new StringTokenizer(engText);
      StringTokenizer gst = new StringTokenizer(gerText);
      StringTokenizer fst = new StringTokenizer(frText);

      while (est.hasMoreTokens()) {
        assertTrue(gst.hasMoreTokens());
        assertTrue(fst.hasMoreTokens());

        String eTok = est.nextToken();
        int engBegin = engText.indexOf(eTok, engEnd);
        engEnd = engBegin + eTok.length();

        String gTok = gst.nextToken();
        int gerBegin = gerText.indexOf(gTok, gerEnd);
        gerEnd = gerBegin + gTok.length();

        String fTok = fst.nextToken();
        int frBegin = frText.indexOf(fTok, frEnd);
        frEnd = frBegin + fTok.length();

        Annotation engAnnot = new Annotation(engJcas, engBegin, engEnd);
        engAnnot.addToIndexes();

        Annotation frAnnot = new Annotation(frJcas, frBegin, frEnd);
        frAnnot.addToIndexes();

        CrossAnnotation gerAnnot = new CrossAnnotation(gerJcas);
        gerAnnot.setBegin(gerBegin);
        gerAnnot.setEnd(gerEnd);
        gerAnnot.setOtherAnnotation(engAnnot);
        gerAnnot.addToIndexes();
      }

      // 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()));
      assertTrue((CAS.TYPE_NAME_DOCUMENT_ANNOTATION).equals(frAnnot.getType().getName()));

      engIt.moveToNext();
      gerIt.moveToNext();
      frIt.moveToNext();
      engAnnot = (Annotation) engIt.get();
      CrossAnnotation gerCrossAnnot = (CrossAnnotation) gerIt.get();
      frAnnot = (Annotation) frIt.get();
      assertTrue((CAS.TYPE_NAME_ANNOTATION).equals(engAnnot.getType().getName()));
      assertTrue(("this").equals(engAnnot.getCoveredText()));
      assertTrue((CAS.TYPE_NAME_ANNOTATION).equals(frAnnot.getType().getName()));
      assertTrue(("cette").equals(frAnnot.getCoveredText()));
      assertTrue(("org.apache.uima.cas.test.CrossAnnotation").equals(gerCrossAnnot.getType()
              .getName()));
      assertTrue(("das").equals(gerCrossAnnot.getCoveredText()));

      // Test that the other annotation feature of cross annotations works
      Annotation crossAnnot = gerCrossAnnot.getOtherAnnotation();
      assertTrue((CAS.TYPE_NAME_ANNOTATION).equals(crossAnnot.getType().getName()));
      assertTrue(("this").equals(crossAnnot.getCoveredText()));

      // Test that annotations accessed from a reference in the base CAS work correctly
      FSArray anArray = new FSArray(jcas, 3);
      anArray.set(0, engAnnot);
      anArray.set(1, frAnnot);
      anArray.set(2, gerCrossAnnot);
      Annotation tstAnnot = (Annotation) anArray.get(0);
      assertTrue(("this").equals(tstAnnot.getCoveredText()));
      tstAnnot = (Annotation) anArray.get(1);
      assertTrue(("cette").equals(tstAnnot.getCoveredText()));
      tstAnnot = (Annotation) anArray.get(2);
      assertTrue(("das").equals(tstAnnot.getCoveredText()));
    } catch (Exception e) {
      JUnitExtension.handleException(e);
    }
  }

  /**
   * Test stream access to Sofa Data.
   * 
   * @throws Exception
   */
00297   public void testSofaDataStream() throws Exception {
    try {

      // Create Sofas
      // Create a local Sofa and set string feature
      // SofaID_impl id = new SofaID_impl();
      // id.setSofaID("StringSofaData");
      // Sofa strSofa = new Sofa(jcas, id, "text");
      // strSofa.setLocalSofaData("this beer is good");
      JCas stringView = jcas.createView("StringSofaData");
      stringView.setDocumentText("this beer is good");

      // create a int array fs
      IntegerArray intArrayFS = new IntegerArray(jcas, 5);
      intArrayFS.set(0, 1);
      intArrayFS.set(1, 2);
      intArrayFS.set(2, 3);
      intArrayFS.set(3, 4);
      intArrayFS.set(4, 5);
      // create a Sofa and set the SofaArray feature to an int array FS.
      // id = new SofaID_impl();
      // id.setSofaID("intArraySofaData");
      // SofaFS intarraySofaFS = new Sofa(jcas, id, "text");
      // intarraySofaFS.setLocalSofaData(intArrayFS);
      JCas intArrayView = jcas.createView("intArraySofaData");
      intArrayView.setSofaDataArray(intArrayFS, "integers");

      // create a float array fs
      FloatArray floatArrayFS = new FloatArray(jcas, 5);
      floatArrayFS.set(0, (float) 0.1);
      floatArrayFS.set(1, (float) 0.2);
      floatArrayFS.set(2, (float) 0.3);
      floatArrayFS.set(3, (float) 0.4);
      floatArrayFS.set(4, (float) 0.5);
      // create a sofa and set the SofaArray feature to the float array
      // id = new SofaID_impl();
      // id.setSofaID("floatArraySofaData");
      // SofaFS floatarraySofaFS = new Sofa(jcas, id, "text");
      // floatarraySofaFS.setLocalSofaData(floatArrayFS);
      JCas floatArrayView = jcas.createView("floatArraySofaData");
      floatArrayView.setSofaDataArray(floatArrayFS, "floats");

      // create a short array fs
      ShortArray shortArrayFS = new ShortArray(jcas, 5);
      shortArrayFS.set(0, (short) 128);
      shortArrayFS.set(1, (short) 127);
      shortArrayFS.set(2, (short) 126);
      shortArrayFS.set(3, (short) 125);
      shortArrayFS.set(4, (short) 124);
      // create a Sofa and set the SofaArray feature to an int array FS.
      JCas shortArrayView = jcas.createView("shortArraySofaData");
      shortArrayView.setSofaDataArray(shortArrayFS, "shorts");

      // create a byte array fs
      ByteArray byteArrayFS = new ByteArray(jcas, 5);
      byteArrayFS.set(0, (byte) 8);
      byteArrayFS.set(1, (byte) 16);
      byteArrayFS.set(2, (byte) 64);
      byteArrayFS.set(3, (byte) 128);
      byteArrayFS.set(4, (byte) 255);
      // create a Sofa and set the SofaArray feature.
      JCas byteArrayView = jcas.createView("byteArraySofaData");
      byteArrayView.setSofaDataArray(byteArrayFS, "bytes");

      // create a long array fs
      LongArray longArrayFS = new LongArray(jcas, 5);
      longArrayFS.set(0, Long.MAX_VALUE);
      longArrayFS.set(1, Long.MAX_VALUE - 1);
      longArrayFS.set(2, Long.MAX_VALUE - 2);
      longArrayFS.set(3, Long.MAX_VALUE - 3);
      longArrayFS.set(4, Long.MAX_VALUE - 4);
      // create a Sofa and set the SofaArray feature.
      JCas longArrayView = jcas.createView("longArraySofaData");
      longArrayView.setSofaDataArray(longArrayFS, "longs");

      DoubleArray doubleArrayFS = new DoubleArray(jcas, 5);
      doubleArrayFS.set(0, Double.MAX_VALUE);
      doubleArrayFS.set(1, Double.MIN_VALUE);
      doubleArrayFS.set(2, Double.parseDouble("1.5555"));
      doubleArrayFS.set(3, Double.parseDouble("99.000000005"));
      doubleArrayFS.set(4, Double.parseDouble("4.44444444444444444"));
      // create a Sofa and set the SofaArray feature.
      JCas doubleArrayView = jcas.createView("doubleArraySofaData");
      doubleArrayView.setSofaDataArray(doubleArrayFS, "doubles");

      // create remote sofa and set the SofaURI feature
      JCas remoteView = jcas.createView("remoteSofaData");
      String sofaFileName = "./Sofa.xcas";
      remoteView.setSofaDataURI("file:" + sofaFileName, "text");

      // read sofa data
      InputStream is = stringView.getSofaDataStream();
      assertTrue(is != null);
      byte[] dest = new byte[1];
      StringBuffer buf = new StringBuffer();
      while (is.read(dest) != -1) {
        buf.append((char) dest[0]);
      }
      assertTrue(buf.toString().equals("this beer is good"));

      dest = new byte[4];
      is.close();
      is = intArrayView.getSofaDataStream();
      assertTrue(is != null);
      BufferedInputStream bis = new BufferedInputStream(is);
      int i = 0;
      while (bis.read(dest) != -1) {
        assertTrue(ByteBuffer.wrap(dest).getInt() == intArrayFS.get(i++));
      }

      bis.close();
      
      is = floatArrayView.getSofaDataStream();
      assertTrue(is != null);
      bis = new BufferedInputStream(is);
      i = 0;
      while (bis.read(dest) != -1) {
        assertTrue(ByteBuffer.wrap(dest).getFloat() == floatArrayFS.get(i++));
      }

      dest = new byte[2];
      bis.close();
      is = shortArrayView.getSofaDataStream();
      assertTrue(is != null);
      bis = new BufferedInputStream(is);
      i = 0;
      while (bis.read(dest) != -1) {
        assertTrue(ByteBuffer.wrap(dest).getShort() == shortArrayFS.get(i++));
      }

      dest = new byte[1];
      bis.close();
      is = byteArrayView.getSofaDataStream();
      assertTrue(is != null);
      bis = new BufferedInputStream(is);
      i = 0;
      while (bis.read(dest) != -1) {
        assertTrue(ByteBuffer.wrap(dest).get() == byteArrayFS.get(i++));
      }

      dest = new byte[8];
      bis.close();
      is = longArrayView.getSofaDataStream();
      assertTrue(is != null);
      bis = new BufferedInputStream(is);
      i = 0;
      while (bis.read(dest) != -1) {
        assertTrue(ByteBuffer.wrap(dest).getLong() == longArrayFS.get(i++));
      }

      bis.close();
      is = doubleArrayView.getSofaDataStream();
      assertTrue(is != null);
      bis = new BufferedInputStream(is);
      i = 0;
      while (bis.read(dest) != -1) {
        assertTrue(ByteBuffer.wrap(dest).getDouble() == doubleArrayFS.get(i++));
      }

      dest = new byte[1];
      bis.close();
      is = remoteView.getSofaDataStream();
      assertTrue(is != null);
      is.close();
      
      // Delete the generated file.
      File xcasFile = new File(sofaFileName);
      if (xcasFile.exists()) {
        assertTrue(xcasFile.delete());
      }
    } catch (Exception e) {
      JUnitExtension.handleException(e);
    }
  }
  
  public void testIndexTwice() throws Exception {
    try {
      CAS newCas = CasCreationUtils.createCas(new TypeSystemDescription_impl(), null, null);
      JCas newJCas = newCas.getJCas();
      CAS view = newCas.createView("DetaggedView");
      view.getJCas();

      Annotation annot = new Annotation(newJCas);
      annot.addToIndexes();
      
      Iterator<Annotation> annotIter = newJCas.getAnnotationIndex(Annotation.type).iterator();
      Annotation annot2 = annotIter.next();
      assertEquals(annot, annot2);
      assertEquals(annot2.getSofa(), annot2.getCASImpl().getSofa());
      
      annot2.addToIndexes();
    }
    catch (Exception e) {
      JUnitExtension.handleException(e);      
    }    
  }
  
  public void testGetSofa() throws Exception {
    try {
      File typeSystemFile = JUnitExtension.getFile("ExampleCas/testTypeSystem.xml");
      TypeSystemDescription typeSystem = UIMAFramework.getXMLParser().parseTypeSystemDescription(
              new XMLInputSource(typeSystemFile));
      CAS newCas = CasCreationUtils.createCas(typeSystem, null, null);
      File xcasFile = JUnitExtension.getFile("ExampleCas/multiSofaCas.xml"); 
      XCASDeserializer.deserialize(new FileInputStream(xcasFile), newCas);
      JCas newJCas = newCas.getJCas();
      
      SofaID sofaId = new SofaID_impl("EnglishDocument");
      JCas view = newJCas.getView(newJCas.getSofa(sofaId));
    }
    catch (Exception e) {
      JUnitExtension.handleException(e);      
    }      
  }

  public static void main(String[] args) {
    junit.textui.TestRunner.run(JcasSofaTest.class);
  }

}

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