/**
* 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.ytex.uima.annotators;
import java.io.IOException;
import java.util.Arrays;
import java.util.HashSet;
import java.util.Iterator;
import java.util.Set;
import org.apache.ctakes.typesystem.type.textsem.EntityMention;
import org.apache.ctakes.typesystem.type.textspan.Segment;
import org.apache.ctakes.ytex.uima.model.NamedEntityRegex;
import org.apache.ctakes.ytex.uima.model.SegmentRegex;
import org.apache.uima.UIMAException;
import org.apache.uima.cas.text.AnnotationIndex;
import org.apache.uima.jcas.JCas;
import org.apache.uima.jcas.tcas.Annotation;
import org.junit.Assert;
import org.junit.Test;
import org.uimafit.factory.JCasFactory;
/**
* TODO get rid of hard-coded path to Types.xml - load from classpath
*
* @author vgarla
*
*/
public class SegmentRegexTest {
/**
* Verify that date parsing with a manually created date works
*
* @throws UIMAException
* @throws Exception
*/
@Test
public void testRegex() throws UIMAException, IOException {
SegmentRegexAnnotator ner = new SegmentRegexAnnotator();
SegmentRegex segTitle = new SegmentRegex();
segTitle.setRegex("(?i)title:\\s*(.*)\\n");
segTitle.setLimitToRegex(true);
segTitle.setSegmentID("TITLE");
segTitle.setSegmentRegexID(1);
SegmentRegex segHistory = new SegmentRegex();
segHistory.setRegex("(?i)history:");
segHistory.setLimitToRegex(false);
segHistory.setSegmentID("HISTORY");
segHistory.setSegmentRegexID(2);
ner.initRegexMap(Arrays.asList(segTitle, segHistory));
JCas jCas = JCasFactory
.createJCasFromPath("src/main/resources/org/apache/ctakes/ytex/types/TypeSystem.xml");
String text = "Title: US Left Upper Quadrant\nDr. Doolitle asked patient\nto take a deep breath\nand exhale slowly. \nHistory: Patient coughed.";
jCas.setDocumentText(text);
ner.process(jCas);
// run the analysis engine
AnnotationIndex<Annotation> mentions = jCas
.getAnnotationIndex(Segment.type);
Iterator<Annotation> iter = mentions.iterator();
Set<String> uniqueSegments = new HashSet<String>();
int emCount = 0;
while (iter.hasNext()) {
Segment em = (Segment) iter.next();
uniqueSegments.add(em.getId());
System.out.println(em.getId() + " [" + em.getCoveredText() + "]");
emCount++;
}
// should be 4 segments - default/title/default/history
Assert.assertTrue(emCount == 4);
// should be 3 unique segments
Assert.assertTrue(uniqueSegments.size() == 3);
}
}