svn commit: r1587978 - /ctakes/trunk/ctakes-core/src/test/java/org/apache/ctakes/core/ae/SentenceDetectorAnnotatorTest.java

[tm...@apache.org]

Author: tmill
Date: Wed Apr 16 16:58:42 2014
New Revision: 1587978

URL: http://svn.apache.org/r1587978
Log:
CTAKES-70: Adds unit test for sentence detector.

Added:
    ctakes/trunk/ctakes-core/src/test/java/org/apache/ctakes/core/ae/SentenceDetectorAnnotatorTest.java

Added: ctakes/trunk/ctakes-core/src/test/java/org/apache/ctakes/core/ae/SentenceDetectorAnnotatorTest.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/test/java/org/apache/ctakes/core/ae/SentenceDetectorAnnotatorTest.java?rev=1587978&view=auto
==============================================================================
--- ctakes/trunk/ctakes-core/src/test/java/org/apache/ctakes/core/ae/SentenceDetectorAnnotatorTest.java (added)
+++ ctakes/trunk/ctakes-core/src/test/java/org/apache/ctakes/core/ae/SentenceDetectorAnnotatorTest.java Wed Apr 16 16:58:42 2014
@@ -0,0 +1,90 @@
+package org.apache.ctakes.core.ae;
+
+import static org.junit.Assert.assertEquals;
+
+import java.io.IOException;
+import java.util.Collection;
+
+import org.apache.ctakes.typesystem.type.textspan.Segment;
+import org.apache.ctakes.typesystem.type.textspan.Sentence;
+import org.apache.uima.UIMAException;
+import org.apache.uima.analysis_engine.AnalysisEngine;
+import org.apache.uima.jcas.JCas;
+import org.apache.uima.resource.ResourceInitializationException;
+import org.junit.Test;
+import org.uimafit.factory.AggregateBuilder;
+import org.uimafit.factory.AnalysisEngineFactory;
+import org.uimafit.factory.JCasFactory;
+import org.uimafit.pipeline.SimplePipeline;
+import org.uimafit.util.JCasUtil;
+
+public class SentenceDetectorAnnotatorTest {
+
+  public static final String note = "" +
+      "Medications:\n" +
+      "Hibernol, jamitol, triopenin, sproingo\n\n" +
+      "Physical exam:\n" +
+      "Patient is doing fine but probably taking too many fictional drugs. Cholesterol is acceptable. Heartrate is elevated. \n" +
+      "Instructions:\n" +
+      "Patient should quit smoking and taunting sharks.";
+
+  @Test
+  public void testSentenceDetectorInitialization() throws UIMAException, IOException{
+    
+    JCas jcas = JCasFactory.createJCas();
+    jcas.setDocumentText(note);
+    SimplePipeline.runPipeline(jcas, getSegmentingPipeline());
+    
+    Collection<Segment> segs = JCasUtil.select(jcas, Segment.class);
+    assertEquals(segs.size(), 3);
+    
+    // test # sentences -- if it skips MEDS and Instructions it should be 3 from the physical exam section only.
+    Collection<Sentence> sents = JCasUtil.select(jcas, Sentence.class);
+    assertEquals(sents.size(), 3);
+    
+    jcas = JCasFactory.createJCas();
+    jcas.setDocumentText(note);
+    SimplePipeline.runPipeline(jcas, getBasicPipeline());
+    segs = JCasUtil.select(jcas, Segment.class);
+    assertEquals(segs.size(), 1);
+    
+    // test # sentences -- if it skips MEDS and Instructions it should be 3 from the physical exam section only.
+    sents = JCasUtil.select(jcas, Sentence.class);
+    assertEquals(sents.size(), 8);
+  }
+  
+  private static AnalysisEngine getSegmentingPipeline() throws ResourceInitializationException{
+    AggregateBuilder aggregateBuilder = new AggregateBuilder();
+
+    // identify segments; use simple segment annotator on non-mayo notes
+    // aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(SegmentsFromBracketedSectionTagsAnnotator.class));
+    aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(CDASegmentAnnotator.class));
+
+    // identify sentences
+    aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(
+        SentenceDetector.class,
+        SentenceDetector.SD_MODEL_FILE_PARAM,
+        "org/apache/ctakes/core/sentdetect/sd-med-model.zip",
+        SentenceDetector.PARAM_SEGMENTS_TO_SKIP,
+        new String[]{"2.16.840.1.113883.10.20.22.2.1.1" /*Medications*/, "2.16.840.1.113883.10.20.22.2.45" /*Instructions*/}));
+
+    return aggregateBuilder.createAggregate();
+  }
+  
+  private static AnalysisEngine getBasicPipeline() throws ResourceInitializationException{
+    AggregateBuilder aggregateBuilder = new AggregateBuilder();
+
+    // identify segments; use simple segment annotator on non-mayo notes
+    // aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(SegmentsFromBracketedSectionTagsAnnotator.class));
+    aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(SimpleSegmentAnnotator.class));
+
+    // identify sentences
+    aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(
+        SentenceDetector.class,
+        SentenceDetector.SD_MODEL_FILE_PARAM,
+        "org/apache/ctakes/core/sentdetect/sd-med-model.zip"
+        ));
+
+    return aggregateBuilder.createAggregate();
+  }
+}