org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedLuceneConsumerImpl.java Source code

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Here is the source code for org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedLuceneConsumerImpl.java

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/**
 * 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;

    }

}