/**
* 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.JdbcConnectionResource;
import org.apache.uima.UimaContext;
import java.sql.Connection;
import java.sql.PreparedStatement;
import java.sql.ResultSet;
import java.sql.SQLException;
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 database
* for SNOMED codes that map to the identified CUI.
*
* @author Mayo Clinic
*/
public class UmlsToSnomedDbConsumerImpl extends UmlsToSnomedConsumerImpl implements LookupConsumer {
static private final String DB_CONN_RESRC_KEY_PRP_KEY = "dbConnExtResrcKey";
static private final String MAP_PREP_STMT_PRP_KEY = "mapPrepStmt";
//ohnlp-Bugs-3296301 fix limited search results to fixed 100 records.
// Added 'MaxListSize'
private static int _maxListSize;
final private PreparedStatement _preparedStatement;
public UmlsToSnomedDbConsumerImpl( final UimaContext uimaContext, final Properties properties, final int maxListSize )
throws Exception {
super( uimaContext, properties );
_maxListSize = maxListSize;
final String resourceName = props.getProperty( DB_CONN_RESRC_KEY_PRP_KEY );
final JdbcConnectionResource resrc = (JdbcConnectionResource) uimaContext.getResourceObject( resourceName );
final String sqlStatement = props.getProperty( MAP_PREP_STMT_PRP_KEY );
final Connection connection = resrc.getConnection();
_preparedStatement = connection.prepareStatement( sqlStatement );
}
public UmlsToSnomedDbConsumerImpl( final UimaContext uimaContext, final Properties properties )
throws Exception {
this( uimaContext, properties, Integer.MAX_VALUE );
}
public void close() {
try {
if ( _preparedStatement != null && !_preparedStatement.isClosed() ) {
_preparedStatement.close();
}
} catch ( SQLException sqlE ) {
// Nothing necessary
}
}
/**
* Queries the given UMLS CUI against the DB. Re`turns a set of SNOMED codes.
*
* @param umlsCode -
* @return -
* @throws SQLException
*/
@Override
protected Set<String> getSnomedCodes( final String umlsCode ) throws SQLException {
final Set<String> codeSet = new HashSet<String>();
_preparedStatement.setString( 1, umlsCode );
final ResultSet rs = _preparedStatement.executeQuery();
while ( rs.next() ) {
final String snomedCode = rs.getString( 1 ).trim();
codeSet.add( snomedCode );
}
rs.close();
return codeSet;
}
}