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Tue, 24 Jun 2014 20:06:56 +0000 Received: from eris.apache.org (localhost [127.0.0.1]) by eris.apache.org (Postfix) with ESMTP id 4167E2388860; Tue, 24 Jun 2014 20:06:31 +0000 (UTC) Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Subject: svn commit: r1605170 - in /ctakes/trunk/ctakes-temporal: ./ src/test/ src/test/java/ src/test/java/org/ src/test/java/org/apach/ src/test/java/org/apach/ctakes/ src/test/java/org/apach/ctakes/temporal/ src/test/java/org/apach/ctakes/temporal/ae/ Date: Tue, 24 Jun 2014 20:06:31 -0000 To: commits@ctakes.apache.org From: chenpei@apache.org X-Mailer: svnmailer-1.0.9 Message-Id: <20140624200631.4167E2388860@eris.apache.org> X-Virus-Checked: Checked by ClamAV on apache.org Author: chenpei Date: Tue Jun 24 20:06:30 2014 New Revision: 1605170 URL: http://svn.apache.org/r1605170 Log: CTAKES-82 Adding some junit test cases to the temporal modules- Backwards TimeAnnotator EventAnnotator DocTimeRel ContextualModality Added: ctakes/trunk/ctakes-temporal/src/test/ ctakes/trunk/ctakes-temporal/src/test/java/ ctakes/trunk/ctakes-temporal/src/test/java/org/ ctakes/trunk/ctakes-temporal/src/test/java/org/apach/ ctakes/trunk/ctakes-temporal/src/test/java/org/apach/ctakes/ ctakes/trunk/ctakes-temporal/src/test/java/org/apach/ctakes/temporal/ ctakes/trunk/ctakes-temporal/src/test/java/org/apach/ctakes/temporal/ae/ ctakes/trunk/ctakes-temporal/src/test/java/org/apach/ctakes/temporal/ae/BackwardsTimeAnnotatorTest.java (with props) ctakes/trunk/ctakes-temporal/src/test/java/org/apach/ctakes/temporal/ae/ContextualModalityAnnotatorTest.java (with props) ctakes/trunk/ctakes-temporal/src/test/java/org/apach/ctakes/temporal/ae/DocTimeRelAnnotatorTest.java (with props) ctakes/trunk/ctakes-temporal/src/test/java/org/apach/ctakes/temporal/ae/EventAnnotatorTest.java (with props) Modified: ctakes/trunk/ctakes-temporal/pom.xml Modified: ctakes/trunk/ctakes-temporal/pom.xml URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/pom.xml?rev=1605170&r1=1605169&r2=1605170&view=diff ============================================================================== --- ctakes/trunk/ctakes-temporal/pom.xml (original) +++ ctakes/trunk/ctakes-temporal/pom.xml Tue Jun 24 20:06:30 2014 @@ -83,11 +83,10 @@ org.apache.ctakes ctakes-constituency-parser - - net.sourceforge.ctakesresources - ctakes-resources-umls2011ab - 3.1.1 - + + org.apache.ctakes + ctakes-clinical-pipeline + org.cleartk cleartk-util Added: ctakes/trunk/ctakes-temporal/src/test/java/org/apach/ctakes/temporal/ae/BackwardsTimeAnnotatorTest.java URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/test/java/org/apach/ctakes/temporal/ae/BackwardsTimeAnnotatorTest.java?rev=1605170&view=auto ============================================================================== --- ctakes/trunk/ctakes-temporal/src/test/java/org/apach/ctakes/temporal/ae/BackwardsTimeAnnotatorTest.java (added) +++ ctakes/trunk/ctakes-temporal/src/test/java/org/apach/ctakes/temporal/ae/BackwardsTimeAnnotatorTest.java Tue Jun 24 20:06:30 2014 @@ -0,0 +1,76 @@ +package org.apach.ctakes.temporal.ae; + +import static org.junit.Assert.*; + +import java.io.File; +import java.io.IOException; +import java.util.ArrayList; +import java.util.Collection; + +import org.apache.ctakes.assertion.medfacts.cleartk.PolarityCleartkAnalysisEngine; +import org.apache.ctakes.clinicalpipeline.ClinicalPipelineFactory; +import org.apache.ctakes.clinicalpipeline.ClinicalPipelineFactory.CopyNPChunksToLookupWindowAnnotations; +import org.apache.ctakes.clinicalpipeline.ClinicalPipelineFactory.RemoveEnclosedLookupWindows; +import org.apache.ctakes.dependency.parser.ae.ClearNLPDependencyParserAE; +import org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator; +import org.apache.ctakes.temporal.ae.BackwardsTimeAnnotator; +import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation; +import org.apache.ctakes.typesystem.type.textsem.TimeMention; +import org.apache.log4j.Logger; +import org.apache.uima.UIMAException; +import org.apache.uima.analysis_engine.AnalysisEngineDescription; +import org.apache.uima.jcas.JCas; +import org.apache.uima.resource.ResourceInitializationException; +import org.cleartk.classifier.CleartkAnnotator; +import org.cleartk.classifier.jar.GenericJarClassifierFactory; +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 BackwardsTimeAnnotatorTest { + + // LOG4J logger based on class name + private Logger LOGGER = Logger.getLogger(getClass().getName()); + + @Test + public void testPipeline() throws UIMAException, IOException { + + String note = "The patient is a 55-year-old man referred by Dr. Good for recently diagnosed colorectal cancer. " + + "The patient was well till 6 months ago, when he started having a little blood with stool."; + JCas jcas = JCasFactory.createJCas(); + jcas.setDocumentText(note); + + //Get the default pipeline with umls dictionary lookup + AggregateBuilder builder = new AggregateBuilder(); + builder.add(ClinicalPipelineFactory.getTokenProcessingPipeline()); + builder.add(AnalysisEngineFactory.createPrimitiveDescription(CopyNPChunksToLookupWindowAnnotations.class)); + builder.add(AnalysisEngineFactory.createPrimitiveDescription(RemoveEnclosedLookupWindows.class)); + builder.add(UmlsDictionaryLookupAnnotator.createAnnotatorDescription()); + builder.add(ClearNLPDependencyParserAE.createAnnotatorDescription()); + + //Add BackwardsTimeAnnotator + builder.add(AnalysisEngineFactory.createPrimitiveDescription( + BackwardsTimeAnnotator.class, + CleartkAnnotator.PARAM_IS_TRAINING, + false, + GenericJarClassifierFactory.PARAM_CLASSIFIER_JAR_PATH, + "/org/apache/ctakes/temporal/ae/timeannotator/model.jar")); + + SimplePipeline.runPipeline(jcas, builder.createAggregateDescription()); + + Collection mentions = JCasUtil.select(jcas, TimeMention.class); + + ArrayList temp = new ArrayList<>(); + for(IdentifiedAnnotation entity : mentions){ + LOGGER.info("Entity: " + entity.getCoveredText()); + temp.add(entity.getCoveredText()); + } + assertEquals(2, temp.size()); + assertTrue(temp.contains("recently")); + assertTrue(temp.contains("6 months ago")); + } + +} Propchange: ctakes/trunk/ctakes-temporal/src/test/java/org/apach/ctakes/temporal/ae/BackwardsTimeAnnotatorTest.java ------------------------------------------------------------------------------ svn:eol-style = native Added: ctakes/trunk/ctakes-temporal/src/test/java/org/apach/ctakes/temporal/ae/ContextualModalityAnnotatorTest.java URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/test/java/org/apach/ctakes/temporal/ae/ContextualModalityAnnotatorTest.java?rev=1605170&view=auto ============================================================================== --- ctakes/trunk/ctakes-temporal/src/test/java/org/apach/ctakes/temporal/ae/ContextualModalityAnnotatorTest.java (added) +++ ctakes/trunk/ctakes-temporal/src/test/java/org/apach/ctakes/temporal/ae/ContextualModalityAnnotatorTest.java Tue Jun 24 20:06:30 2014 @@ -0,0 +1,14 @@ +package org.apach.ctakes.temporal.ae; + +import static org.junit.Assert.*; + +import org.junit.Test; + +public class ContextualModalityAnnotatorTest { + + @Test + public void test() { + fail("Not yet implemented"); + } + +} Propchange: ctakes/trunk/ctakes-temporal/src/test/java/org/apach/ctakes/temporal/ae/ContextualModalityAnnotatorTest.java ------------------------------------------------------------------------------ svn:eol-style = native Added: ctakes/trunk/ctakes-temporal/src/test/java/org/apach/ctakes/temporal/ae/DocTimeRelAnnotatorTest.java URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/test/java/org/apach/ctakes/temporal/ae/DocTimeRelAnnotatorTest.java?rev=1605170&view=auto ============================================================================== --- ctakes/trunk/ctakes-temporal/src/test/java/org/apach/ctakes/temporal/ae/DocTimeRelAnnotatorTest.java (added) +++ ctakes/trunk/ctakes-temporal/src/test/java/org/apach/ctakes/temporal/ae/DocTimeRelAnnotatorTest.java Tue Jun 24 20:06:30 2014 @@ -0,0 +1,14 @@ +package org.apach.ctakes.temporal.ae; + +import static org.junit.Assert.*; + +import org.junit.Test; + +public class DocTimeRelAnnotatorTest { + + @Test + public void test() { + fail("Not yet implemented"); + } + +} Propchange: ctakes/trunk/ctakes-temporal/src/test/java/org/apach/ctakes/temporal/ae/DocTimeRelAnnotatorTest.java ------------------------------------------------------------------------------ svn:eol-style = native Added: ctakes/trunk/ctakes-temporal/src/test/java/org/apach/ctakes/temporal/ae/EventAnnotatorTest.java URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/test/java/org/apach/ctakes/temporal/ae/EventAnnotatorTest.java?rev=1605170&view=auto ============================================================================== --- ctakes/trunk/ctakes-temporal/src/test/java/org/apach/ctakes/temporal/ae/EventAnnotatorTest.java (added) +++ ctakes/trunk/ctakes-temporal/src/test/java/org/apach/ctakes/temporal/ae/EventAnnotatorTest.java Tue Jun 24 20:06:30 2014 @@ -0,0 +1,77 @@ +package org.apach.ctakes.temporal.ae; + +import static org.junit.Assert.*; + +import java.io.IOException; +import java.util.ArrayList; +import java.util.Collection; + +import org.apache.ctakes.clinicalpipeline.ClinicalPipelineFactory; +import org.apache.ctakes.clinicalpipeline.ClinicalPipelineFactory.CopyNPChunksToLookupWindowAnnotations; +import org.apache.ctakes.clinicalpipeline.ClinicalPipelineFactory.RemoveEnclosedLookupWindows; +import org.apache.ctakes.dependency.parser.ae.ClearNLPDependencyParserAE; +import org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator; +import org.apache.ctakes.temporal.ae.BackwardsTimeAnnotator; +import org.apache.ctakes.temporal.ae.EventAnnotator; +import org.apache.ctakes.typesystem.type.textsem.EventMention; +import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation; +import org.apache.ctakes.typesystem.type.textsem.TimeMention; +import org.apache.log4j.Logger; +import org.apache.uima.UIMAException; +import org.apache.uima.jcas.JCas; +import org.cleartk.classifier.CleartkAnnotator; +import org.cleartk.classifier.jar.GenericJarClassifierFactory; +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 EventAnnotatorTest { + + // LOG4J logger based on class name + private Logger LOGGER = Logger.getLogger(getClass().getName()); + + @Test + public void testPipeline() throws UIMAException, IOException { + + String note = "The patient is a 55-year-old man referred by Dr. Good for recently diagnosed colorectal cancer. " + + "The patient was well till 6 months ago, when he started having a little blood with stool."; + JCas jcas = JCasFactory.createJCas(); + jcas.setDocumentText(note); + + //Get the default pipeline with umls dictionary lookup + AggregateBuilder builder = new AggregateBuilder(); + builder.add(ClinicalPipelineFactory.getTokenProcessingPipeline()); + builder.add(AnalysisEngineFactory.createPrimitiveDescription(CopyNPChunksToLookupWindowAnnotations.class)); + builder.add(AnalysisEngineFactory.createPrimitiveDescription(RemoveEnclosedLookupWindows.class)); + builder.add(UmlsDictionaryLookupAnnotator.createAnnotatorDescription()); + builder.add(ClearNLPDependencyParserAE.createAnnotatorDescription()); + + //Add EventAnnotator + builder.add(AnalysisEngineFactory.createPrimitiveDescription( + EventAnnotator.class, + CleartkAnnotator.PARAM_IS_TRAINING, + false, + GenericJarClassifierFactory.PARAM_CLASSIFIER_JAR_PATH, + "/org/apache/ctakes/temporal/ae/eventannotator/model.jar")); + + SimplePipeline.runPipeline(jcas, builder.createAggregateDescription()); + + Collection mentions = JCasUtil.select(jcas, EventMention.class); + + ArrayList temp = new ArrayList<>(); + for(IdentifiedAnnotation entity : mentions){ + LOGGER.info("Entity: " + entity.getCoveredText()); + temp.add(entity.getCoveredText()); + } + assertEquals(7, temp.size()); + assertTrue(temp.contains("old")); + assertTrue(temp.contains("referred")); + assertTrue(temp.contains("cancer")); + assertTrue(temp.contains("till")); + assertTrue(temp.contains("blood")); + assertTrue(temp.contains("stool")); + } +} Propchange: ctakes/trunk/ctakes-temporal/src/test/java/org/apach/ctakes/temporal/ae/EventAnnotatorTest.java ------------------------------------------------------------------------------ svn:eol-style = native