/**
* 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.core.resource.FileResource;
import org.apache.ctakes.dictionary.lookup.DictionaryException;
import org.apache.ctakes.dictionary.lookup.MetaDataHit;
import org.apache.ctakes.dictionary.lookup.lucene.LuceneDictionaryImpl;
import org.apache.log4j.Logger;
import org.apache.lucene.index.IndexReader;
import org.apache.lucene.search.IndexSearcher;
import org.apache.lucene.store.FSDirectory;
import org.apache.uima.UimaContext;
import org.apache.uima.analysis_engine.annotator.AnnotatorConfigurationException;
import java.io.File;
import java.io.IOException;
import java.util.Collection;
import java.util.HashSet;
import java.util.Properties;
import java.util.Set;
/**
* Implementation that takes UMLS dictionary lookup hits and stores as NamedEntity
* objects only the ones that have a SNOMED synonym, by looking in a lucene index
* for SNOMED codes that map to the identified CUI.
*
* @author Mayo Clinic
*/
public class UmlsToSnomedLuceneConsumerImpl extends UmlsToSnomedConsumerImpl {
// LOG4J logger based on class name
private Logger logger = Logger.getLogger( getClass().getName() );
//ohnlp-Bugs-3296301 limits the search results to fixed 100 records.
// Added 'MaxListSize'
private static int iv_maxListSize;
private final String SNOMED_MAPPING_PRP_KEY = "snomedCodeMappingField";
private final String CUI_MAPPING_PRP_KEY = "cuiMappingField";
private final String SNOMED_CODE_LIST_CONFIG_PARM = "CodesListIndexDirectory";
private LuceneDictionaryImpl snomedLikeCodesIndex;
public UmlsToSnomedLuceneConsumerImpl( UimaContext aCtx, Properties properties )
throws Exception {
this( aCtx, properties, Integer.MAX_VALUE );
}
// ohnlp Bugs tracker ID: 3390078 do not reload lucene index for each document, load in constructor
public UmlsToSnomedLuceneConsumerImpl( UimaContext aCtx, Properties properties, int maxListSize )
throws Exception {
super( aCtx, properties );
iv_maxListSize = maxListSize;
IndexReader indexReader;
String indexDirAbsPath = null;
try {
// ohnlp Bugs tracker ID: 3425014 SNOMED lucene dictionary lookup hardcodes resource path
FileResource fResrc = (FileResource) aCtx.getResourceObject( SNOMED_CODE_LIST_CONFIG_PARM );
if ( fResrc == null ) {
logger.error( "Unable to find config parm " + SNOMED_CODE_LIST_CONFIG_PARM + "." );
}
File indexDir = fResrc.getFile();
indexDirAbsPath = indexDir.getAbsolutePath();
try {
logger.info( "Using lucene index: " + indexDir.getAbsolutePath() );
} catch ( Exception e ) {
throw new AnnotatorConfigurationException( e );
}
// For the sample dictionary, we use the following lucene index.
//indexPath = "lookup/snomed-like_codes_sample";
indexReader = IndexReader.open( FSDirectory.open( indexDir ) );
IndexSearcher indexSearcher = new IndexSearcher( indexReader );
String lookupFieldName = props.getProperty( CUI_MAPPING_PRP_KEY );
// We will lookup entries based on lookupFieldName
snomedLikeCodesIndex = new LuceneDictionaryImpl( indexSearcher, lookupFieldName, iv_maxListSize );
logger.info( "Loaded Lucene index with " + indexReader.numDocs() + " entries." );
} catch ( IOException ioe ) {
logger.info( "Lucene index: " + indexDirAbsPath );
throw new DictionaryException( ioe );
}
}
/**
* Find all Snomed codes that map to the given UMLS code (CUI),
* by looking in a lucene index
*
* @param umlsCode a UMLS CUI
* @return Set of Snomed codes that map to the given UMLS code (CUI).
* @see getSnomedCodes in <code>UmlsToSnomedConsumerImpl</code> for example of using a database
*/
@Override
protected Set<String> getSnomedCodes( final String umlsCode ) throws DictionaryException {
final Set<String> codeSet = new HashSet<>();
final String valueFieldName = props.getProperty( SNOMED_MAPPING_PRP_KEY );
// Get the entries with field lookupFieldName having value umlsCode
final Collection<MetaDataHit> mdhCollection = snomedLikeCodesIndex.getEntries( umlsCode );
for ( MetaDataHit mdh : mdhCollection ) {
codeSet.add( mdh.getMetaFieldValue( valueFieldName ) );
}
return codeSet;
}
}