/**
* 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.ctakes.dictionary.lookup.ae;
import org.apache.ctakes.dictionary.lookup.MetaDataHit;
import org.apache.ctakes.dictionary.lookup.vo.LookupHit;
import org.apache.ctakes.typesystem.type.constants.CONST;
import org.apache.ctakes.typesystem.type.refsem.OntologyConcept;
import org.apache.ctakes.typesystem.type.textsem.AnatomicalSiteMention;
import org.apache.ctakes.typesystem.type.textsem.DiseaseDisorderMention;
import org.apache.ctakes.typesystem.type.textsem.EntityMention;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
import org.apache.ctakes.typesystem.type.textsem.LabMention;
import org.apache.ctakes.typesystem.type.textsem.MedicationMention;
import org.apache.ctakes.typesystem.type.textsem.ProcedureMention;
import org.apache.ctakes.typesystem.type.textsem.SignSymptomMention;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.jcas.JCas;
import org.apache.uima.jcas.cas.FSArray;
import java.util.*;
/**
* @author Mayo Clinic
*/
public class NamedEntityLookupConsumerImpl extends BaseLookupConsumerImpl {
private static final String CODE_MF_PRP_KEY = "codeMetaField";
private static final String CODING_SCHEME_PRP_KEY = "codingScheme";
private static final String TYPE_ID_FIELD = "typeIdField";
private final Properties _properties;
private static int iv_maxSize;
public NamedEntityLookupConsumerImpl( final UimaContext aCtx, final Properties props, final int maxListSize ) {
// TODO property validation could be done here
_properties = props;
iv_maxSize = maxListSize;
}
public NamedEntityLookupConsumerImpl( final UimaContext aCtx, final Properties props ) {
// TODO property validation could be done here
_properties = props;
}
private int countUniqueCodes( final Collection<LookupHit> hitsAtOffset ) {
final String CODE_MF = _properties.getProperty( CODE_MF_PRP_KEY );
final Set<String> codes = new HashSet<>();
for ( LookupHit lookupHit : hitsAtOffset ) {
final MetaDataHit mdh = lookupHit.getDictMetaDataHit();
final String code = mdh.getMetaFieldValue( CODE_MF );
codes.add( code );
}
return codes.size();
}
/**
* {@inheritDoc}
*/
@Override
public void consumeHits( final JCas jcas, final Iterator<LookupHit> lhItr ) throws AnalysisEngineProcessException {
final String TYPE_ID = _properties.getProperty( TYPE_ID_FIELD );
final String CODE_MF = _properties.getProperty( CODE_MF_PRP_KEY );
final String CODING_SCHEME = _properties.getProperty( CODING_SCHEME_PRP_KEY );
int typeId = CONST.NE_TYPE_ID_UNKNOWN;
if ( TYPE_ID != null ) {
try {
typeId = Integer.parseInt( TYPE_ID );
} catch ( NumberFormatException nfe ) {
typeId = CONST.NE_TYPE_ID_UNKNOWN;
}
}
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 );
}
}
IdentifiedAnnotation neAnnot = new IdentifiedAnnotation(jcas);
if ( typeId == CONST.NE_TYPE_ID_DRUG ) {
neAnnot = new MedicationMention( jcas );
} else if ( typeId == CONST.NE_TYPE_ID_ANATOMICAL_SITE ) {
neAnnot = new AnatomicalSiteMention( jcas );
} else if ( typeId == CONST.NE_TYPE_ID_DISORDER ) {
neAnnot = new DiseaseDisorderMention( jcas );
} else if ( typeId == CONST.NE_TYPE_ID_FINDING ) {
neAnnot = new SignSymptomMention( jcas );
} else if ( typeId == CONST.NE_TYPE_ID_LAB ) {
neAnnot = new LabMention( jcas );
} else if ( typeId == CONST.NE_TYPE_ID_PROCEDURE ) {
neAnnot = new ProcedureMention( jcas );
} else {
neAnnot = new EntityMention( jcas );
}
final int neBegin = entry.getKey().__start;
final int neEnd = entry.getKey().__end;
neAnnot.setBegin( neBegin );
neAnnot.setEnd( neEnd );
neAnnot.setDiscoveryTechnique( CONST.NE_DISCOVERY_TECH_DICT_LOOKUP );
neAnnot.setOntologyConceptArr( ocArr );
neAnnot.setTypeID( typeId );
neAnnot.addToIndexes();
}
}
}