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Posted to commits@ctakes.apache.org by st...@apache.org on 2012/09/28 02:40:11 UTC
svn commit: r1391275 - in /incubator/ctakes/trunk: ./ ctakes-assertion/
ctakes-dependency-parser/ ctakes-relation-extractor/
ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/
ctakes-relation-extractor/src/main/java/org/apa...
Author: stevenbethard
Date: Fri Sep 28 00:40:10 2012
New Revision: 1391275
URL: http://svn.apache.org/viewvc?rev=1391275&view=rev
Log:
Updates to ClearTK 1.2.0, and removes copy of ClearTK 1.2.0-SNAPSHOT code which was in ctakes-relation-extractor
Removed:
incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/chboston/
incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/cleartk/
Modified:
incubator/ctakes/trunk/ctakes-assertion/pom.xml
incubator/ctakes/trunk/ctakes-dependency-parser/pom.xml
incubator/ctakes/trunk/ctakes-relation-extractor/pom.xml
incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/ModifierExtractorAnnotator.java
incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/ModifierExtractorEvaluation.java
incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/RelationExtractorEvaluation.java
incubator/ctakes/trunk/pom.xml
Modified: incubator/ctakes/trunk/ctakes-assertion/pom.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-assertion/pom.xml?rev=1391275&r1=1391274&r2=1391275&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-assertion/pom.xml (original)
+++ incubator/ctakes/trunk/ctakes-assertion/pom.xml Fri Sep 28 00:40:10 2012
@@ -34,10 +34,6 @@
</dependency>
<dependency>
<groupId>org.cleartk</groupId>
- <artifactId>cleartk-chunker</artifactId>
- </dependency>
- <dependency>
- <groupId>org.cleartk</groupId>
<artifactId>cleartk-ml</artifactId>
</dependency>
<dependency>
Modified: incubator/ctakes/trunk/ctakes-dependency-parser/pom.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-dependency-parser/pom.xml?rev=1391275&r1=1391274&r2=1391275&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-dependency-parser/pom.xml (original)
+++ incubator/ctakes/trunk/ctakes-dependency-parser/pom.xml Fri Sep 28 00:40:10 2012
@@ -8,6 +8,13 @@
<artifactId>ctakes</artifactId>
<version>3.0.0-SNAPSHOT</version>
</parent>
+ <!-- necessary for ClearParser -->
+ <repositories>
+ <repository>
+ <id>cleartk-googlecode</id>
+ <url>http://cleartk.googlecode.com/svn/repo/</url>
+ </repository>
+ </repositories>
<dependencies>
<dependency>
<groupId>org.apache.ctakes</groupId>
Modified: incubator/ctakes/trunk/ctakes-relation-extractor/pom.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/pom.xml?rev=1391275&r1=1391274&r2=1391275&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/pom.xml (original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/pom.xml Fri Sep 28 00:40:10 2012
@@ -27,7 +27,7 @@
</dependency>
<dependency>
<groupId>org.cleartk</groupId>
- <artifactId>cleartk-chunker</artifactId>
+ <artifactId>cleartk-eval</artifactId>
</dependency>
<dependency>
<groupId>org.cleartk</groupId>
Modified: incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/ModifierExtractorAnnotator.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/ModifierExtractorAnnotator.java?rev=1391275&r1=1391274&r2=1391275&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/ModifierExtractorAnnotator.java (original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/ae/ModifierExtractorAnnotator.java Fri Sep 28 00:40:10 2012
@@ -69,7 +69,7 @@ public class ModifierExtractorAnnotator
List<String> outcomes;
if (this.isTraining()) {
List<Modifier> modifiers = JCasUtil.selectCovered(jCas, Modifier.class, sentence);
- outcomes = this.chunking.toOutcomes(jCas, tokens, modifiers);
+ outcomes = this.chunking.createOutcomes(jCas, tokens, modifiers);
}
// during prediction, the list of outcomes predicted so far
@@ -115,7 +115,7 @@ public class ModifierExtractorAnnotator
// convert classifications to Modifiers
if (!this.isTraining()) {
- this.chunking.toChunks(jCas, tokens, outcomes);
+ this.chunking.createChunks(jCas, tokens, outcomes);
}
}
Modified: incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/ModifierExtractorEvaluation.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/ModifierExtractorEvaluation.java?rev=1391275&r1=1391274&r2=1391275&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/ModifierExtractorEvaluation.java (original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/ModifierExtractorEvaluation.java Fri Sep 28 00:40:10 2012
@@ -47,7 +47,7 @@ import org.uimafit.util.JCasUtil;
import org.apache.ctakes.relationextractor.ae.ModifierExtractorAnnotator;
import org.apache.ctakes.typesystem.type.textsem.Modifier;
-public class ModifierExtractorEvaluation extends Evaluation_ImplBase<File, AnnotationStatistics> {
+public class ModifierExtractorEvaluation extends Evaluation_ImplBase<File, AnnotationStatistics<String>> {
public static class Options extends Options_ImplBase {
@Option(
@@ -70,8 +70,8 @@ public class ModifierExtractorEvaluation
"-c",
"1000");
- List<AnnotationStatistics> foldStats = evaluation.crossValidation(trainFiles, 2);
- AnnotationStatistics overallStats = AnnotationStatistics.addAll(foldStats);
+ List<AnnotationStatistics<String>> foldStats = evaluation.crossValidation(trainFiles, 2);
+ AnnotationStatistics<String> overallStats = AnnotationStatistics.addAll(foldStats);
System.err.println("Overall:");
System.err.println(overallStats);
}
@@ -111,13 +111,13 @@ public class ModifierExtractorEvaluation
}
@Override
- protected AnnotationStatistics test(CollectionReader collectionReader, File directory)
+ protected AnnotationStatistics<String> test(CollectionReader collectionReader, File directory)
throws Exception {
AnalysisEngine classifierAnnotator = AnalysisEngineFactory.createPrimitive(ModifierExtractorAnnotator.getDescription(
GenericJarClassifierFactory.PARAM_CLASSIFIER_JAR_PATH,
new File(directory, "model.jar").getPath()));
- AnnotationStatistics stats = new AnnotationStatistics();
+ AnnotationStatistics<String> stats = new AnnotationStatistics<String>();
for (JCas jCas : new JCasIterable(collectionReader, classifierAnnotator)) {
JCas goldView;
try {
Modified: incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/RelationExtractorEvaluation.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/RelationExtractorEvaluation.java?rev=1391275&r1=1391274&r2=1391275&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/RelationExtractorEvaluation.java (original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/eval/RelationExtractorEvaluation.java Fri Sep 28 00:40:10 2012
@@ -73,7 +73,7 @@ import org.apache.ctakes.typesystem.type
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
import org.apache.ctakes.typesystem.type.textsem.Modifier;
-public class RelationExtractorEvaluation extends Evaluation_ImplBase<File, AnnotationStatistics> {
+public class RelationExtractorEvaluation extends Evaluation_ImplBase<File, AnnotationStatistics<String>> {
public static class Options extends Options_ImplBase {
@@ -159,7 +159,7 @@ public class RelationExtractorEvaluation
if(options.testDirectory == null) {
// run n-fold cross-validation
- List<AnnotationStatistics> foldStats = evaluation.crossValidation(trainFiles, 2);
+ List<AnnotationStatistics<String>> foldStats = evaluation.crossValidation(trainFiles, 2);
params.stats = AnnotationStatistics.addAll(foldStats);
System.err.println("overall:");
@@ -177,7 +177,8 @@ public class RelationExtractorEvaluation
evaluation.train(trainCollectionReader, modelsDir);
CollectionReader testCollectionReader = evaluation.getCollectionReader(testFiles);
- AnnotationStatistics stats = evaluation.test(testCollectionReader, modelsDir);
+ AnnotationStatistics<String> stats = evaluation.test(testCollectionReader, modelsDir);
+ System.err.print(stats);
return;
}
}
@@ -291,7 +292,7 @@ public class RelationExtractorEvaluation
}
@Override
- protected AnnotationStatistics test(CollectionReader collectionReader, File directory)
+ protected AnnotationStatistics<String> test(CollectionReader collectionReader, File directory)
throws Exception {
AggregateBuilder builder = new AggregateBuilder();
// replace cTAKES entity mentions and modifiers in the system view with the gold annotations
@@ -307,7 +308,14 @@ public class RelationExtractorEvaluation
builder.add(classifierAnnotator);
// statistics will be based on the "category" feature of the BinaryTextRelations
- AnnotationStatistics stats = new AnnotationStatistics("category");
+ AnnotationStatistics<String> stats = new AnnotationStatistics<String>();
+ Function<BinaryTextRelation, HashableArguments> getSpan = new Function<BinaryTextRelation, HashableArguments>() {
+ @Override
+ public HashableArguments apply(BinaryTextRelation relation) {
+ return new HashableArguments(relation);
+ }
+ };
+ Function<BinaryTextRelation, String> getOutcome = AnnotationStatistics.annotationToFeatureValue("category");
// calculate statistics, iterating over the results of the classifier
AnalysisEngine engine = builder.createAggregate();
@@ -333,12 +341,8 @@ public class RelationExtractorEvaluation
stats.add(
goldBinaryTextRelations,
systemBinaryTextRelations,
- new Function<BinaryTextRelation, HashableArguments>() {
- @Override
- public HashableArguments apply(BinaryTextRelation relation) {
- return new HashableArguments(relation);
- }
- });
+ getSpan,
+ getOutcome);
}
System.err.println(directory.getName() + ":");
@@ -426,7 +430,7 @@ public class RelationExtractorEvaluation
public double svmGamma;
- public AnnotationStatistics stats;
+ public AnnotationStatistics<String> stats;
private static List<String> SVM_KERNELS = Arrays.asList(
"linear",
Modified: incubator/ctakes/trunk/pom.xml
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/pom.xml?rev=1391275&r1=1391274&r2=1391275&view=diff
==============================================================================
--- incubator/ctakes/trunk/pom.xml (original)
+++ incubator/ctakes/trunk/pom.xml Fri Sep 28 00:40:10 2012
@@ -13,12 +13,6 @@
<developerConnection>scm:svn:https://svn.apache.org/repos/asf/incubator/ctakes/</developerConnection>
<url>https://svn.apache.org/repos/asf/incubator/ctakes/</url>
</scm>
- <repositories>
- <repository>
- <id>cleartk-googlecode</id>
- <url>http://cleartk.googlecode.com/svn/repo/</url>
- </repository>
- </repositories>
<properties>
<ctakes.version>3.0.0-SNAPSHOT</ctakes.version>
<maven.compiler.source>1.6</maven.compiler.source>
@@ -220,40 +214,13 @@
<artifactId>xercesImpl</artifactId>
<version>2.10.0</version>
</dependency>
+ <!-- import a consistent set of versions for all ClearTK modules -->
<dependency>
<groupId>org.cleartk</groupId>
- <artifactId>cleartk-chunker</artifactId>
- <version>1.0.1</version>
- </dependency>
- <dependency>
- <groupId>org.cleartk</groupId>
- <artifactId>cleartk-eval</artifactId>
- <version>0.8.1</version>
- </dependency>
- <dependency>
- <groupId>org.cleartk</groupId>
- <artifactId>cleartk-ml</artifactId>
- <version>1.0.1</version>
- </dependency>
- <dependency>
- <groupId>org.cleartk</groupId>
- <artifactId>cleartk-ml-libsvm</artifactId>
- <version>1.0.1</version>
- </dependency>
- <dependency>
- <groupId>org.cleartk</groupId>
- <artifactId>cleartk-ml-opennlp-maxent</artifactId>
- <version>1.0.2</version>
- </dependency>
- <dependency>
- <groupId>org.cleartk</groupId>
- <artifactId>cleartk-test-util</artifactId>
- <version>1.0.1</version>
- </dependency>
- <dependency>
- <groupId>org.cleartk</groupId>
- <artifactId>cleartk-util</artifactId>
- <version>0.8.1</version>
+ <artifactId>cleartk-release</artifactId>
+ <version>1.2.0</version>
+ <type>pom</type>
+ <scope>import</scope>
</dependency>
<dependency>
<groupId>args4j</groupId>