org.apache.uima.jcas.JCas#getView

Source File: BmeowTypeAnnotator.java From ambiverse-nlu with Apache License 2.0

6 votes

@Override
public void process(JCas jCas) throws AnalysisEngineProcessException {
	BmeowTypeDictionary dict = null;
	try {
		if (gold) {
			JCas goldView = jCas.getView("gold");
			dict = constructBmeowTypeDictionaryFromGoldStandard(goldView);
		} else {
			dict = constructBmeowTypeDictionaryFromAida(jCas);
		}
		Collection<Token> tokens = JCasUtil.select(jCas, Token.class);

		for(Token token : tokens){
			annotateBmeowType(jCas, dict, token);
		}
	} catch (EntityLinkingDataAccessException | CASException e) {
		throw new AnalysisEngineProcessException(e);
	}
}

Source File: TestMistAnalysisEngine.java From ctakes-docker with Apache License 2.0

6 votes

public static void main(String[] args) throws Exception {

//        TypeSystemDescription tsd = TypeSystemDescriptionFactory.createTypeSystemDescriptionFromPath("../desc/TypeSystem.xml");
        JCas jcas = JCasFactory.createJCas();
        jcas.setDocumentText("Patient is a 30-year-old man named Leroy Butler from Green Bay, WI.");
        AnalysisEngineDescription aed = AnalysisEngineFactory.createEngineDescription(MistAnalysisEngine.class,
                MistAnalysisEngine.PARAM_MODEL_PATH,
                "SHARP/model/model");
        SimplePipeline.runPipeline(jcas, aed);
        for(Annotation annot : JCasUtil.select(jcas, Annotation.class)){
            System.out.println("Found annotation: " + annot.getCoveredText());
        }
        JCas deidView = jcas.getView(MistAnalysisEngine.DEID_VIEW_NAME);
        System.out.println("Deidentified version:");
        System.out.println(deidView.getDocumentText());
    }

Source File: I2b2JdbcWriter.java From ctakes-docker with Apache License 2.0

6 votes

/**
 * {@inheritDoc}
 * Like process for AEs
 */
@Override
protected void writeJCasInformation( final JCas jcas, 
                                     final String instance,
                                     final int encounterNum,
                                     final long patientNum, final String providerId,
                                     final Timestamp startDate ) throws SQLException {
 
   JCas deidView = null;
   try {
 	  deidView = jcas.getView("DeidView");
   } catch(CASException e) {
 	  throw new RuntimeException(e);
   }

   logger.log(Level.INFO,"view = " + deidView.getViewName());
   writeConceptRows( deidView, instance, Long.toString(patientNum), Integer.toString(encounterNum), providerId );

}

Source File: I2b2ReadyFileWriter.java From ctakes-docker with Apache License 2.0

6 votes

@Override
   public void process( final JCas jcas ) throws AnalysisEngineProcessException {

      final String patient = Long.toString( SourceMetadataUtil.getPatientNum( jcas ) );
      final SourceData sourceData = SourceMetadataUtil.getSourceData( jcas );
      final String encounter = sourceData==null?"null":sourceData.getSourceEncounterId();
      final String providerId = sourceData==null?"null":SourceMetadataUtil.getProviderId( sourceData );
      // source date not used ???
//      final String sourceDate = sourceData.getSourceOriginalDate();
      JCas deidView = null;
      try{
        deidView = jcas.getView(DEID_VIEW);
      }catch(CASException e){
        throw new AnalysisEngineProcessException(e);
      }
      final Collection<String> conceptLines = createConceptLines( deidView, patient, encounter, providerId );

      final File outputFile = new File( _outputRootDir, encounter );
      saveAnnotations( outputFile, conceptLines );

   }

Source File: EvaluationAnnotator.java From bluima with Apache License 2.0

6 votes

@SuppressWarnings({ "unchecked", "rawtypes" })
@Override
public void process(JCas jCas) throws AnalysisEngineProcessException {

    JCas goldView, systemView;
    try {
        goldView = jCas.getView(VIEW_GOLD);
        systemView = jCas.getView(VIEW_SYSTEM);
    } catch (CASException e) {
        throw new AnalysisEngineProcessException(e);
    }

    Collection goldAnnot = select(goldView, goldAnnotation);
    Collection systAnnot = select(systemView, systemAnnotation);
    if (verbose)
        System.out
                .println("comparing #gold:" + goldAnnot.size() + " #sys:"
                        + systAnnot.size() + " [pmid "
                        + getHeaderDocId(jCas) + "]");

    String log = evaluator.add(goldAnnot, systAnnot, "");
    if (verbose)
        System.out.println(log);
    // System.out.println(evaluator.compare());
}

Source File: CooccurrencesEvaluationAnnotator.java From bluima with Apache License 2.0

6 votes

@SuppressWarnings({ "unchecked", "rawtypes" })
@Override
public void process(JCas jCas) throws AnalysisEngineProcessException {
    String pmId = BlueCasUtil.getHeaderDocId(jCas);
    print("pmId " + pmId);

    JCas goldView, systemView;
    try {
        goldView = jCas.getView(VIEW_GOLD);
        systemView = jCas.getView(VIEW_SYSTEM);
    } catch (CASException e) {
        throw new AnalysisEngineProcessException(e);
    }

    Collection goldAnnot = select(goldView, Cooccurrence.class);
    Collection systAnnot = select(systemView, Cooccurrence.class);
    print("comparing #gold:" + goldAnnot.size() + " #sys:"
            + systAnnot.size());

    print(/* "pmId:"+pmId + "\t" + */evaluator.add(goldAnnot, systAnnot,
            pmId));
}

Source File: Annotator2.java From uima-uimafit with Apache License 2.0

6 votes

@Override
public void process(JCas jCas) throws AnalysisEngineProcessException {
  try {
    JCas sortedView = ViewCreatorAnnotator.createViewSafely(jCas, ViewNames.SORTED_VIEW);
    jCas = jCas.getView(CAS.NAME_DEFAULT_SOFA);
    String initialText = jCas.getDocumentText();
    char[] chars = initialText.toCharArray();
    Arrays.sort(chars);
    String sortedText = new String(chars).trim();
    sortedView.setDocumentText(sortedText);

    sortedView = ViewCreatorAnnotator.createViewSafely(jCas, ViewNames.SORTED_PARENTHESES_VIEW);
    JCas parenthesesView = jCas.getView(ViewNames.PARENTHESES_VIEW);
    String parenthesesText = parenthesesView.getDocumentText();
    chars = parenthesesText.toCharArray();
    Arrays.sort(chars);
    sortedText = new String(chars).trim();
    sortedView.setDocumentText(sortedText);

  } catch (CASException e) {
    throw new AnalysisEngineProcessException(e);
  }

}

Source File: SentenceAndTokenCopier.java From uima-uimafit with Apache License 2.0

6 votes

@Override
public void process(JCas jCas) throws AnalysisEngineProcessException {
  try {
    JCas view1 = jCas.getView(VIEW1);
    JCas view2 = jCas.getView(VIEW2);

    for (Token token1 : select(view1, Token.class)) {
      new Token(view2, token1.getBegin(), token1.getEnd()).addToIndexes();
    }

    for (Sentence sentence1 : select(view1, Sentence.class)) {
      new Sentence(view2, sentence1.getBegin(), sentence1.getEnd()).addToIndexes();
    }
  } catch (CASException ce) {
    throw new AnalysisEngineProcessException(ce);
  }
}

Source File: JcasSofaTest.java From uima-uimaj with Apache License 2.0

6 votes

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);      
  }      
}

Source File: CopyAnnotationsAnnotator2Test.java From bluima with Apache License 2.0

5 votes

@Test
public void test() throws Exception {

    AnalysisEngineDescription copyAnnots = createEngineDescription(
            CopyAnnotationsAnnotator2.class, //
            TO_VIEW, "blah",//
            PARAM_ANNOTATION_CLASS, Protein.class.getName(),//
            DELETE_FROM, true);

    JCas jCas = getTestCas();
    assertEquals("has a DocumentAnnotation at first", 1,
            select(jCas, Annotation.class).size());

    Protein p = new Protein(jCas, 5, 10);
    p.addToIndexes();
    runPipeline(jCas, copyAnnots);
    assertTrue("no more Protein in initial view",
            !exists(jCas, Protein.class));

    JCas newView = jCas.getView("blah");
    Collection<Protein> pNew = select(newView, Protein.class);
    assertEquals("copied to new view", 1, pNew.size());
    assertTrue(haveSameBeginEnd(p, pNew.iterator().next()));

    // copy it back
    AnalysisEngineDescription copyAnnotsBack = createEngineDescription(
            CopyAnnotationsAnnotator2.class, //
            FROM_VIEW, "blah",//
            TO_VIEW, BlueUima.VIEW_SYSTEM,//
            PARAM_ANNOTATION_CLASS, Protein.class.getName(),//
            DELETE_FROM, true);
    runPipeline(jCas, copyAnnotsBack);

    assertTrue(!exists(newView, Protein.class));
    Collection<Protein> pBack = select(jCas, Protein.class);
    assertEquals("copied to protein", 1, pBack.size());
    assertTrue(haveSameBeginEnd(p, pBack.iterator().next()));
}

Source File: ViewTextCopierAnnotator.java From uima-uimafit with Apache License 2.0

5 votes

@Override
public void process(final JCas jCas) throws AnalysisEngineProcessException {
  try {
    final JCas sourceView = jCas.getView(sourceViewName);
    JCas destinationView;
    try {
      destinationView = jCas.getView(destinationViewName);
    } catch (CASRuntimeException ce) {
      destinationView = jCas.createView(destinationViewName);
    }
    destinationView.setDocumentText(sourceView.getDocumentText());
  } catch (CASException e) {
    throw new AnalysisEngineProcessException(e);
  }
}

Source File: Annotator1.java From uima-uimafit with Apache License 2.0

5 votes

@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);
  }

}

Source File: Annotator3.java From uima-uimafit with Apache License 2.0

5 votes

@Override
public void process(JCas jCas) throws AnalysisEngineProcessException {
  try {
    jCas = jCas.getView(CAS.NAME_DEFAULT_SOFA);
    String text = jCas.getDocumentText();
    String reverseText = reverse(text);
    JCas reverseView = ViewCreatorAnnotator.createViewSafely(jCas, ViewNames.REVERSE_VIEW);
    reverseView.setDocumentText(reverseText);
  } catch (CASException e) {
    throw new AnalysisEngineProcessException(e);
  }
}

Source File: ViewCreatorAnnotatorTest.java From uima-uimafit with Apache License 2.0

5 votes

@Override
public void process(JCas jCas) throws AnalysisEngineProcessException {
  JCas view;
  try {
    view = jCas.getView(CAS.NAME_DEFAULT_SOFA);
  } catch (CASException e) {
    throw new AnalysisEngineProcessException(e);
  }

  view.setDocumentText("some text");
  Token token = new Token(view, 0, 4);
  token.addToIndexes();
}

Source File: Evaluator.java From uima-uimafit with Apache License 2.0

5 votes

@Override
public void process(JCas jCas) throws AnalysisEngineProcessException {
  try {
    JCas goldView = jCas.getView(GOLD_VIEW);
    JCas systemView = jCas.getView(SYSTEM_VIEW);

    for (Sentence goldSentence : select(goldView, Sentence.class)) {
      List<Token> goldTokens = selectCovered(goldView, Token.class, goldSentence);
      List<Token> systemTokens = selectCovered(systemView, Token.class, goldSentence);
      if (goldTokens.size() == systemTokens.size()) {
        for (int i = 0; i < goldTokens.size(); i++) {
          String goldPos = goldTokens.get(i).getPos();
          String systemPos = systemTokens.get(i).getPos();
          if (goldPos.equals(systemPos)) {
            totalCorrect++;
          } else {
            totalWrong++;
          }
        }
      } else {
        throw new RuntimeException(
                "number of tokens in gold view differs from number of tokens in system view");
      }
    }
  } catch (CASException ce) {
    throw new AnalysisEngineProcessException(ce);
  }

}

Java Code Examples for org.apache.uima.jcas.JCas#getView()