Package org.apache.uima.jcas.cas

Examples of org.apache.uima.jcas.cas.FSArray

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            for ( Map.Entry<Integer,Set<UmlsConcept>> conceptEntry : conceptMap.entrySet() ) {
               final Set<UmlsConcept> conceptSet = conceptEntry.getValue();
               // Skip updating CAS if all Concepts for this type were filtered out for this span.
               if ( !conceptSet.isEmpty() ) {
                  final FSArray conceptArr = new FSArray( jcas, conceptSet.size() );
                  int arrIdx = 0;
                  for ( UmlsConcept umlsConcept : conceptSet ) {
                     conceptArr.set( arrIdx, umlsConcept );
                     arrIdx++;
                  }

                  IdentifiedAnnotation neAnnot;
                  final int conceptKey = conceptEntry.getKey();
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            for ( LookupHit lookupHit : entry.getValue() ) {
               final MetaDataHit mdh = lookupHit.getDictMetaDataHit();
               final String code = mdh.getMetaFieldValue( CODE_MF );
               validCodes.add( code );
            }
            final FSArray ocArr = createOntologyConceptArr( jcas, validCodes );
            IdentifiedAnnotation neAnnot = new MedicationMention( jcas ); // medication NEs are EventMention
            neAnnot.setTypeID( CONST.NE_TYPE_ID_DRUG );
            neAnnot.setBegin( neBegin );
            neAnnot.setEnd( neEnd );
            neAnnot.setDiscoveryTechnique( CONST.NE_DISCOVERY_TECH_DICT_LOOKUP );
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    * @param validCodes -
    * @return -
    */
   private FSArray createOntologyConceptArr( final JCas jcas, final Collection<String> validCodes ) {
      final String CODING_SCHEME = _properties.getProperty( CODING_SCHEME_PRP_KEY );
      final FSArray ocArr = new FSArray( jcas, validCodes.size() );
      int ocArrIdx = 0;
      for ( String validCode : validCodes ) {
         final OntologyConcept oc = new OntologyConcept( jcas );
         oc.setCode( validCode );
         oc.setCodingScheme( CODING_SCHEME );
         ocArr.set( ocArrIdx, oc );
         ocArrIdx++;
      }
      return ocArr;
   }
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         }
      }
      final Map<LookupHitKey, Set<LookupHit>> lookupHitMap = createLookupHitMap( lhItr );
      for ( Map.Entry<LookupHitKey, Set<LookupHit>> entry : lookupHitMap.entrySet() ) {
         final int uniqueCodeCount = countUniqueCodes( entry.getValue() );
         final FSArray ocArr = new FSArray( jcas, uniqueCodeCount );
         // iterate over the LookupHit objects and create
         // a corresponding JCas OntologyConcept object that will
         // be placed in a FSArray
         int ocArrIdx = 0;
         final Set<String> codes = new HashSet<>();
         for ( LookupHit lookupHit : entry.getValue() ) {
            final MetaDataHit mdh = lookupHit.getDictMetaDataHit();
            final String code = mdh.getMetaFieldValue( CODE_MF );
            if ( !codes.contains( code ) ) {
               // create only first entry in the array for a code
               final OntologyConcept oc = new OntologyConcept( jcas );
               oc.setCode( code );
               oc.setCodingScheme( CODING_SCHEME );
               ocArr.set( ocArrIdx, oc );
               ocArrIdx++;
               codes.add( code );
            }
         }
        
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        eventMention.setConfidence(1.0f);
        eventMention.setDiscoveryTechnique(CONST.NE_DISCOVERY_TECH_GOLD_ANNOTATION);

        // add the links between event, mention and properties
        event.setProperties(eventProperties);
        event.setMentions(new FSArray(jCas, 1));
        event.setMentions(0, eventMention);
        eventMention.setEvent(event);

        // add the annotations to the indexes
        eventProperties.addToIndexes();
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      UmlsConcept umlsConcept = new UmlsConcept(jCas);
      umlsConcept.setCui(code);
      ontologyConcept = umlsConcept;
    }
    ontologyConcept.addToIndexes();
    mention.setOntologyConceptArr(new FSArray(jCas, 1));
    mention.setOntologyConceptArr(0, ontologyConcept);

    // add entity mention to CAS
    mention.addToIndexes();
    idAnnotationMap.put(annotation.id, mention);
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        eventMention.setConfidence(1.0f);
        eventMention.setDiscoveryTechnique(CONST.NE_DISCOVERY_TECH_GOLD_ANNOTATION);

        // add the links between event, mention and properties
        event.setProperties(eventProperties);
        event.setMentions(new FSArray(jCas, 1));
        event.setMentions(0, eventMention);
        eventMention.setEvent(event);

        // add the annotations to the indexes
        eventProperties.addToIndexes();
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      UmlsConcept umlsConcept = new UmlsConcept(jCas);
      umlsConcept.setCui(code);
      ontologyConcept = umlsConcept;
    }
    ontologyConcept.addToIndexes();
    mention.setOntologyConceptArr(new FSArray(jCas, 1));
    mention.setOntologyConceptArr(0, ontologyConcept);

    // add entity mention to CAS
    mention.addToIndexes();
    idAnnotationMap.put(annotation.id, mention);
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//    FSIndexRepository fsIndexRepository = jcas.getFSIndexRepository();
//    fsIndexRepository.addFS();
//    fsIndexRepository.

    FSArray ontologyConceptArray = new FSArray(jcas, 1);
    OntologyConcept ontologyConcept = new OntologyConcept(jcas);
    String codingScheme = null;
    String code = null;
    if (conceptType.equals(ConceptType.TREATMENT))
    {
    codingScheme = "RXNORM";
    code = ConceptLookup.REVERSE_LOOKUP_TREATMENT_TUI;
    } else if (conceptType.equals(ConceptType.PROBLEM))
    {
    codingScheme = "SNOMEDCT";
    code = ConceptLookup.REVERSE_LOOKUP_PROBLEM_TUI;
    } else if (conceptType.equals(ConceptType.TEST))
    {
    codingScheme = "SNOMEDCT";
    code = ConceptLookup.REVERSE_LOOKUP_TEST_TUI;
    } else
    {
    codingScheme = null;
    code = null;
    }
    ontologyConcept.setCode(code);
    ontologyConcept.setCodingScheme(codingScheme);
   
    ontologyConceptArray.set(0,  ontologyConcept);
   
    return ontologyConceptArray;
   
  }
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      concept.setConceptText(conceptText);
      concept.setConceptType(null);

      concept.setOriginalEntityExternalId(annotation.getAddress());

      FSArray ontologyConceptArray = annotation
          .getOntologyConceptArr();

      ConceptType conceptType = ConceptLookup
          .lookupConceptType(ontologyConceptArray);
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