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Posted to commits@ctakes.apache.org by tm...@apache.org on 2016/12/06 22:39:59 UTC
svn commit: r1772987 - in /ctakes/trunk/ctakes-temporal: ./
src/test/java/org/apache/ctakes/temporal/ae/
Author: tmill
Date: Tue Dec 6 22:39:59 2016
New Revision: 1772987
URL: http://svn.apache.org/viewvc?rev=1772987&view=rev
Log:
Fix pom and tests that prevoiusly relied on clinical-pipeline
Added:
ctakes/trunk/ctakes-temporal/src/test/java/org/apache/ctakes/temporal/ae/TemporalTest_ImplBase.java
Modified:
ctakes/trunk/ctakes-temporal/pom.xml
ctakes/trunk/ctakes-temporal/src/test/java/org/apache/ctakes/temporal/ae/BackwardsTimeAnnotatorTest.java
ctakes/trunk/ctakes-temporal/src/test/java/org/apache/ctakes/temporal/ae/ContextualModalityAnnotatorTest.java
ctakes/trunk/ctakes-temporal/src/test/java/org/apache/ctakes/temporal/ae/EventAnnotatorTest.java
ctakes/trunk/ctakes-temporal/src/test/java/org/apache/ctakes/temporal/ae/EventEventRelationAnnotatorTest.java
ctakes/trunk/ctakes-temporal/src/test/java/org/apache/ctakes/temporal/ae/EventTimeRelationAnnotatorTest.java
Modified: ctakes/trunk/ctakes-temporal/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/pom.xml?rev=1772987&r1=1772986&r2=1772987&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/pom.xml (original)
+++ ctakes/trunk/ctakes-temporal/pom.xml Tue Dec 6 22:39:59 2016
@@ -84,10 +84,6 @@
<artifactId>ctakes-constituency-parser</artifactId>
</dependency>
<dependency>
- <groupId>org.apache.ctakes</groupId>
- <artifactId>ctakes-clinical-pipeline</artifactId>
- </dependency>
- <dependency>
<groupId>org.cleartk</groupId>
<artifactId>cleartk-util</artifactId>
</dependency>
Modified: ctakes/trunk/ctakes-temporal/src/test/java/org/apache/ctakes/temporal/ae/BackwardsTimeAnnotatorTest.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/test/java/org/apache/ctakes/temporal/ae/BackwardsTimeAnnotatorTest.java?rev=1772987&r1=1772986&r2=1772987&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/test/java/org/apache/ctakes/temporal/ae/BackwardsTimeAnnotatorTest.java (original)
+++ ctakes/trunk/ctakes-temporal/src/test/java/org/apache/ctakes/temporal/ae/BackwardsTimeAnnotatorTest.java Tue Dec 6 22:39:59 2016
@@ -18,37 +18,26 @@
*/
package org.apache.ctakes.temporal.ae;
-import static org.junit.Assert.*;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
-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.ml.CleartkAnnotator;
-import org.cleartk.ml.jar.GenericJarClassifierFactory;
-import org.junit.Test;
import org.apache.uima.fit.factory.AggregateBuilder;
import org.apache.uima.fit.factory.AnalysisEngineFactory;
import org.apache.uima.fit.factory.JCasFactory;
import org.apache.uima.fit.pipeline.SimplePipeline;
import org.apache.uima.fit.util.JCasUtil;
+import org.apache.uima.jcas.JCas;
+import org.junit.Test;
-public class BackwardsTimeAnnotatorTest {
+public class BackwardsTimeAnnotatorTest extends TemporalTest_ImplBase {
// LOG4J logger based on class name
private Logger LOGGER = Logger.getLogger(getClass().getName());
@@ -63,11 +52,11 @@ public class BackwardsTimeAnnotatorTest
// Get the default pipeline with umls dictionary lookup
AggregateBuilder builder = new AggregateBuilder();
- builder.add(ClinicalPipelineFactory.getTokenProcessingPipeline());
+ builder.add(getTokenProcessingPipeline());
builder.add(AnalysisEngineFactory
- .createEngineDescription(CopyNPChunksToLookupWindowAnnotations.class));
+ .createEngineDescription(org.apache.ctakes.temporal.eval.Evaluation_ImplBase.CopyNPChunksToLookupWindowAnnotations.class));
builder.add(AnalysisEngineFactory
- .createEngineDescription(RemoveEnclosedLookupWindows.class));
+ .createEngineDescription(org.apache.ctakes.temporal.eval.Evaluation_ImplBase.RemoveEnclosedLookupWindows.class));
// Commented out the Dictionary lookup for the test
// Uncomment and set -Dctakes.umlsuser and -Dctakes.umlspw env params if
// needed
Modified: ctakes/trunk/ctakes-temporal/src/test/java/org/apache/ctakes/temporal/ae/ContextualModalityAnnotatorTest.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/test/java/org/apache/ctakes/temporal/ae/ContextualModalityAnnotatorTest.java?rev=1772987&r1=1772986&r2=1772987&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/test/java/org/apache/ctakes/temporal/ae/ContextualModalityAnnotatorTest.java (original)
+++ ctakes/trunk/ctakes-temporal/src/test/java/org/apache/ctakes/temporal/ae/ContextualModalityAnnotatorTest.java Tue Dec 6 22:39:59 2016
@@ -18,45 +18,31 @@
*/
package org.apache.ctakes.temporal.ae;
-import static org.junit.Assert.*;
-
-import java.io.FileWriter;
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.ContextualModalityAnnotator;
-import org.apache.ctakes.temporal.ae.DocTimeRelAnnotator;
-import org.apache.ctakes.temporal.ae.EventAnnotator;
+import org.apache.ctakes.temporal.eval.Evaluation_ImplBase.CopyNPChunksToLookupWindowAnnotations;
+import org.apache.ctakes.temporal.eval.Evaluation_ImplBase.RemoveEnclosedLookupWindows;
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.ml.CleartkAnnotator;
-import org.cleartk.ml.jar.GenericJarClassifierFactory;
-import org.junit.Test;
import org.apache.uima.fit.factory.AggregateBuilder;
import org.apache.uima.fit.factory.AnalysisEngineFactory;
import org.apache.uima.fit.factory.JCasFactory;
import org.apache.uima.fit.pipeline.SimplePipeline;
import org.apache.uima.fit.util.JCasUtil;
-import org.xml.sax.SAXException;
+import org.apache.uima.jcas.JCas;
+import org.junit.Test;
-public class ContextualModalityAnnotatorTest {
+public class ContextualModalityAnnotatorTest extends TemporalTest_ImplBase {
// LOG4J logger based on class name
private Logger LOGGER = Logger.getLogger(getClass().getName());
@Test
- public void testPipeline() throws UIMAException, IOException, SAXException {
+ 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.";
@@ -65,7 +51,7 @@ public class ContextualModalityAnnotator
// Get the default pipeline with umls dictionary lookup
AggregateBuilder builder = new AggregateBuilder();
- builder.add(ClinicalPipelineFactory.getTokenProcessingPipeline());
+ builder.add(getTokenProcessingPipeline());
builder.add(AnalysisEngineFactory
.createEngineDescription(CopyNPChunksToLookupWindowAnnotations.class));
builder.add(AnalysisEngineFactory
Modified: ctakes/trunk/ctakes-temporal/src/test/java/org/apache/ctakes/temporal/ae/EventAnnotatorTest.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/test/java/org/apache/ctakes/temporal/ae/EventAnnotatorTest.java?rev=1772987&r1=1772986&r2=1772987&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/test/java/org/apache/ctakes/temporal/ae/EventAnnotatorTest.java (original)
+++ ctakes/trunk/ctakes-temporal/src/test/java/org/apache/ctakes/temporal/ae/EventAnnotatorTest.java Tue Dec 6 22:39:59 2016
@@ -18,10 +18,16 @@
*/
package org.apache.ctakes.temporal.ae;
-import org.apache.ctakes.clinicalpipeline.ClinicalPipelineFactory;
-import org.apache.ctakes.clinicalpipeline.ClinicalPipelineFactory.CopyNPChunksToLookupWindowAnnotations;
-import org.apache.ctakes.clinicalpipeline.ClinicalPipelineFactory.RemoveEnclosedLookupWindows;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.Collection;
+
import org.apache.ctakes.dependency.parser.ae.ClearNLPDependencyParserAE;
+import org.apache.ctakes.temporal.eval.Evaluation_ImplBase.CopyNPChunksToLookupWindowAnnotations;
+import org.apache.ctakes.temporal.eval.Evaluation_ImplBase.RemoveEnclosedLookupWindows;
import org.apache.ctakes.typesystem.type.textsem.EventMention;
import org.apache.log4j.Logger;
import org.apache.uima.UIMAException;
@@ -33,14 +39,7 @@ import org.apache.uima.fit.util.JCasUtil
import org.apache.uima.jcas.JCas;
import org.junit.Test;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Collection;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertTrue;
-
-public class EventAnnotatorTest {
+public class EventAnnotatorTest extends TemporalTest_ImplBase {
// LOG4J logger based on class name
private Logger LOGGER = Logger.getLogger(getClass().getName());
@@ -55,7 +54,7 @@ public class EventAnnotatorTest {
// Get the default pipeline
AggregateBuilder builder = new AggregateBuilder();
- builder.add(ClinicalPipelineFactory.getTokenProcessingPipeline());
+ builder.add(getTokenProcessingPipeline());
builder.add(AnalysisEngineFactory
.createEngineDescription(CopyNPChunksToLookupWindowAnnotations.class));
builder.add(AnalysisEngineFactory
Modified: ctakes/trunk/ctakes-temporal/src/test/java/org/apache/ctakes/temporal/ae/EventEventRelationAnnotatorTest.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/test/java/org/apache/ctakes/temporal/ae/EventEventRelationAnnotatorTest.java?rev=1772987&r1=1772986&r2=1772987&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/test/java/org/apache/ctakes/temporal/ae/EventEventRelationAnnotatorTest.java (original)
+++ ctakes/trunk/ctakes-temporal/src/test/java/org/apache/ctakes/temporal/ae/EventEventRelationAnnotatorTest.java Tue Dec 6 22:39:59 2016
@@ -19,14 +19,11 @@
package org.apache.ctakes.temporal.ae;
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.eval.Evaluation_ImplBase.CopyNPChunksToLookupWindowAnnotations;
+import org.apache.ctakes.temporal.eval.Evaluation_ImplBase.RemoveEnclosedLookupWindows;
import org.apache.ctakes.typesystem.type.refsem.Event;
import org.apache.ctakes.typesystem.type.refsem.EventProperties;
import org.apache.ctakes.typesystem.type.relation.TemporalTextRelation;
@@ -34,7 +31,6 @@ import org.apache.ctakes.typesystem.type
import org.apache.log4j.Logger;
import org.apache.uima.UIMAException;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
-import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
import org.apache.uima.fit.factory.AggregateBuilder;
import org.apache.uima.fit.factory.AnalysisEngineFactory;
import org.apache.uima.fit.factory.JCasFactory;
@@ -45,7 +41,7 @@ import org.junit.Test;
import com.google.common.collect.Lists;
-public class EventEventRelationAnnotatorTest {
+public class EventEventRelationAnnotatorTest extends TemporalTest_ImplBase {
// LOG4J logger based on class name
private Logger LOGGER = Logger.getLogger(getClass().getName());
@@ -60,7 +56,7 @@ public class EventEventRelationAnnotator
// Get the default pipeline with umls dictionary lookup
AggregateBuilder builder = new AggregateBuilder();
- builder.add(ClinicalPipelineFactory.getTokenProcessingPipeline());
+ builder.add(getTokenProcessingPipeline());
builder.add(AnalysisEngineFactory
.createEngineDescription(CopyNPChunksToLookupWindowAnnotations.class));
builder.add(AnalysisEngineFactory
Modified: ctakes/trunk/ctakes-temporal/src/test/java/org/apache/ctakes/temporal/ae/EventTimeRelationAnnotatorTest.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/test/java/org/apache/ctakes/temporal/ae/EventTimeRelationAnnotatorTest.java?rev=1772987&r1=1772986&r2=1772987&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/test/java/org/apache/ctakes/temporal/ae/EventTimeRelationAnnotatorTest.java (original)
+++ ctakes/trunk/ctakes-temporal/src/test/java/org/apache/ctakes/temporal/ae/EventTimeRelationAnnotatorTest.java Tue Dec 6 22:39:59 2016
@@ -19,14 +19,11 @@
package org.apache.ctakes.temporal.ae;
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.eval.Evaluation_ImplBase.CopyNPChunksToLookupWindowAnnotations;
+import org.apache.ctakes.temporal.eval.Evaluation_ImplBase.RemoveEnclosedLookupWindows;
import org.apache.ctakes.typesystem.type.refsem.Event;
import org.apache.ctakes.typesystem.type.refsem.EventProperties;
import org.apache.ctakes.typesystem.type.relation.TemporalTextRelation;
@@ -34,7 +31,6 @@ import org.apache.ctakes.typesystem.type
import org.apache.log4j.Logger;
import org.apache.uima.UIMAException;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
-import org.apache.uima.fit.component.JCasAnnotator_ImplBase;
import org.apache.uima.fit.factory.AggregateBuilder;
import org.apache.uima.fit.factory.AnalysisEngineFactory;
import org.apache.uima.fit.factory.JCasFactory;
@@ -45,7 +41,7 @@ import org.junit.Test;
import com.google.common.collect.Lists;
-public class EventTimeRelationAnnotatorTest {
+public class EventTimeRelationAnnotatorTest extends TemporalTest_ImplBase {
// LOG4J logger based on class name
private Logger LOGGER = Logger.getLogger(getClass().getName());
@@ -60,7 +56,7 @@ public class EventTimeRelationAnnotatorT
// Get the default pipeline with umls dictionary lookup
AggregateBuilder builder = new AggregateBuilder();
- builder.add(ClinicalPipelineFactory.getTokenProcessingPipeline());
+ builder.add(getTokenProcessingPipeline());
builder.add(AnalysisEngineFactory
.createEngineDescription(CopyNPChunksToLookupWindowAnnotations.class));
builder.add(AnalysisEngineFactory
Added: ctakes/trunk/ctakes-temporal/src/test/java/org/apache/ctakes/temporal/ae/TemporalTest_ImplBase.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/test/java/org/apache/ctakes/temporal/ae/TemporalTest_ImplBase.java?rev=1772987&view=auto
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/test/java/org/apache/ctakes/temporal/ae/TemporalTest_ImplBase.java (added)
+++ ctakes/trunk/ctakes-temporal/src/test/java/org/apache/ctakes/temporal/ae/TemporalTest_ImplBase.java Tue Dec 6 22:39:59 2016
@@ -0,0 +1,27 @@
+package org.apache.ctakes.temporal.ae;
+
+import java.net.MalformedURLException;
+
+import org.apache.ctakes.contexttokenizer.ae.ContextDependentTokenizerAnnotator;
+import org.apache.ctakes.core.ae.SentenceDetector;
+import org.apache.ctakes.core.ae.SimpleSegmentAnnotator;
+import org.apache.ctakes.core.ae.TokenizerAnnotatorPTB;
+import org.apache.ctakes.lvg.ae.LvgAnnotator;
+import org.apache.ctakes.postagger.POSTagger;
+import org.apache.uima.analysis_engine.AnalysisEngineDescription;
+import org.apache.uima.fit.factory.AggregateBuilder;
+import org.apache.uima.resource.ResourceInitializationException;
+
+public class TemporalTest_ImplBase {
+ public static AnalysisEngineDescription getTokenProcessingPipeline() throws ResourceInitializationException, MalformedURLException {
+ AggregateBuilder builder = new AggregateBuilder();
+ builder.add( SimpleSegmentAnnotator.createAnnotatorDescription() );
+ builder.add( SentenceDetector.createAnnotatorDescription() );
+ builder.add( TokenizerAnnotatorPTB.createAnnotatorDescription() );
+ builder.add( LvgAnnotator.createAnnotatorDescription() );
+ builder.add( ContextDependentTokenizerAnnotator.createAnnotatorDescription() );
+ builder.add( POSTagger.createAnnotatorDescription() );
+ return builder.createAggregateDescription();
+ }
+
+}