/**
* 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.clinicalpipeline.runtime;
import java.io.IOException;
import java.util.HashSet;
import org.apache.ctakes.typesystem.type.constants.CONST;
import org.apache.ctakes.typesystem.type.refsem.UmlsConcept;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
import org.apache.uima.UIMAException;
import org.apache.uima.jcas.cas.FSArray;
public class BagOfCUIsGenerator extends BagOfAnnotationsGenerator<IdentifiedAnnotation, String> {
public BagOfCUIsGenerator(String inputDir, String outputDir)
throws UIMAException, IOException {
super(inputDir, outputDir);
}
@Override
protected String extractInformation(IdentifiedAnnotation t) {
StringBuilder buff = new StringBuilder();
FSArray mentions = t.getOntologyConceptArr();
HashSet<String> uniqueCuis = new HashSet<String>();
if(mentions == null) return null;
for(int i = 0; i < mentions.size(); i++){
if(mentions.get(i) instanceof UmlsConcept){
UmlsConcept concept = (UmlsConcept) mentions.get(i);
uniqueCuis.add(concept.getCui());
}
}
for(String cui : uniqueCuis){
if(t.getPolarity() == CONST.NE_POLARITY_NEGATION_PRESENT) buff.append("-");
buff.append(cui);
buff.append("\n");
}
if(buff.length() == 0) return null;
return buff.substring(0,buff.length()-1);
}
/**
* @param args
* @throws IOException
* @throws UIMAException
*/
public static void main(String[] args) throws UIMAException, IOException {
(new BagOfCUIsGenerator(args[0], args[1])).process();
}
}