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Posted to commits@ctakes.apache.org by st...@apache.org on 2012/10/23 23:06:21 UTC
svn commit: r1401480 - in /incubator/ctakes/trunk/ctakes-relation-extractor:
models/ src/main/java/org/apache/ctakes/relationextractor/eval/
src/main/java/org/apache/ctakes/relationextractor/pipelines/
Author: stevenbethard
Date: Tue Oct 23 21:06:20 2012
New Revision: 1401480
URL: http://svn.apache.org/viewvc?rev=1401480&view=rev
Log:
Fixes a bunch of paths for models in relation-extractor
Removed:
incubator/ctakes/trunk/ctakes-relation-extractor/models/
Modified:
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/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationAnnotationAnalysis.java
incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationExtractorPipeline.java
incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationExtractorPipelineSingleCas.java
incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationExtractorTrain.java
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=1401480&r1=1401479&r2=1401480&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 Tue Oct 23 21:06:20 2012
@@ -62,7 +62,7 @@ public class ModifierExtractorEvaluation
Options options = new Options();
options.parseOptions(args);
List<File> trainFiles = Arrays.asList(options.trainDirectory.listFiles());
- File modelsDir = new File("models/modifier");
+ File modelsDir = new File("target/models/modifier");
ModifierExtractorEvaluation evaluation = new ModifierExtractorEvaluation(
modelsDir,
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=1401480&r1=1401479&r2=1401480&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 Tue Oct 23 21:06:20 2012
@@ -110,8 +110,8 @@ public class RelationExtractorEvaluation
// define the output directory for models
File modelsDir = options.runDegreeOf
- ? new File("models/degree_of")
- : new File("models/em_pair");
+ ? new File("target/models/degree_of")
+ : new File("target/models/em_pair");
// determine class for the classifier annotator
Class<? extends RelationExtractorAnnotator> annotatorClass = options.runDegreeOf
Modified: incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationAnnotationAnalysis.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationAnnotationAnalysis.java?rev=1401480&r1=1401479&r2=1401480&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationAnnotationAnalysis.java (original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationAnnotationAnalysis.java Tue Oct 23 21:06:20 2012
@@ -25,12 +25,10 @@ import java.util.List;
import org.apache.ctakes.relationextractor.eval.XMIReader;
import org.apache.uima.analysis_engine.AnalysisEngine;
import org.apache.uima.collection.CollectionReader;
-import org.apache.uima.resource.metadata.TypeSystemDescription;
import org.cleartk.util.Options_ImplBase;
import org.kohsuke.args4j.Option;
import org.uimafit.factory.AnalysisEngineFactory;
import org.uimafit.factory.CollectionReaderFactory;
-import org.uimafit.factory.TypeSystemDescriptionFactory;
import org.uimafit.pipeline.SimplePipeline;
/**
@@ -57,11 +55,8 @@ public class RelationAnnotationAnalysis
Options options = new Options();
options.parseOptions(args);
- TypeSystemDescription typeSystemDescription = TypeSystemDescriptionFactory.createTypeSystemDescriptionFromPath(
- "../ctakes-type-system/desc/common_type_system.xml");
-
List<File> trainFiles = Arrays.asList(options.inputDirectory.listFiles());
- CollectionReader collectionReader = getCollectionReader(trainFiles, typeSystemDescription);
+ CollectionReader collectionReader = getCollectionReader(trainFiles);
AnalysisEngine relationExtractorConsumer = AnalysisEngineFactory.createPrimitive(
RelationExtractorConsumer.class);
@@ -69,8 +64,7 @@ public class RelationAnnotationAnalysis
SimplePipeline.runPipeline(collectionReader, relationExtractorConsumer);
}
- private static CollectionReader getCollectionReader(List<File> items,
- TypeSystemDescription typeSystemDescription) throws Exception {
+ private static CollectionReader getCollectionReader(List<File> items) throws Exception {
// convert the List<File> to a String[]
String[] paths = new String[items.size()];
@@ -81,7 +75,6 @@ public class RelationAnnotationAnalysis
// return a reader that will load each of the XMI files
return CollectionReaderFactory.createCollectionReader(
XMIReader.class,
- typeSystemDescription,
XMIReader.PARAM_FILES,
paths);
}
Modified: incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationExtractorPipeline.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationExtractorPipeline.java?rev=1401480&r1=1401479&r2=1401480&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationExtractorPipeline.java (original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationExtractorPipeline.java Tue Oct 23 21:06:20 2012
@@ -24,13 +24,11 @@ import org.apache.ctakes.core.cr.FilesIn
import org.apache.uima.UIMAException;
import org.apache.uima.analysis_engine.AnalysisEngine;
import org.apache.uima.collection.CollectionReader;
-import org.apache.uima.resource.metadata.TypeSystemDescription;
import org.cleartk.util.Options_ImplBase;
import org.kohsuke.args4j.Option;
import org.uimafit.component.xwriter.XWriter;
import org.uimafit.factory.AnalysisEngineFactory;
import org.uimafit.factory.CollectionReaderFactory;
-import org.uimafit.factory.TypeSystemDescriptionFactory;
import org.uimafit.pipeline.SimplePipeline;
/**
@@ -64,9 +62,6 @@ public class RelationExtractorPipeline {
Options options = new Options();
options.parseOptions(args);
- TypeSystemDescription typeSystemDescription = TypeSystemDescriptionFactory.createTypeSystemDescriptionFromPath(
- "../ctakes-type-system/desc/common_type_system.xml");
-
CollectionReader collectionReader = CollectionReaderFactory.createCollectionReaderFromPath(
"../ctakes-core/desc/collection_reader/FilesInDirectoryCollectionReader.xml",
FilesInDirectoryCollectionReader.PARAM_INPUTDIR,
@@ -78,7 +73,6 @@ public class RelationExtractorPipeline {
AnalysisEngine xWriter = AnalysisEngineFactory.createPrimitive(
XWriter.class,
- typeSystemDescription,
XWriter.PARAM_OUTPUT_DIRECTORY_NAME,
options.outputDirectory);
Modified: incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationExtractorPipelineSingleCas.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationExtractorPipelineSingleCas.java?rev=1401480&r1=1401479&r2=1401480&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationExtractorPipelineSingleCas.java (original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationExtractorPipelineSingleCas.java Tue Oct 23 21:06:20 2012
@@ -47,11 +47,8 @@ import java.io.IOException;
import org.apache.uima.UIMAException;
import org.apache.uima.analysis_engine.AnalysisEngine;
import org.apache.uima.jcas.JCas;
-import org.apache.uima.resource.metadata.TypeSystemDescription;
-import org.cleartk.util.Options_ImplBase;
import org.uimafit.factory.AnalysisEngineFactory;
import org.uimafit.factory.JCasFactory;
-import org.uimafit.factory.TypeSystemDescriptionFactory;
import org.uimafit.pipeline.SimplePipeline;
/**
@@ -62,16 +59,11 @@ import org.uimafit.pipeline.SimplePipeli
*/
public class RelationExtractorPipelineSingleCas {
- public static class Options extends Options_ImplBase {
-
public static void main(String[] args) throws UIMAException, IOException {
String sampleSentence = "Abdomen: Soft, nontender without hepatosplenomegaly or masses";
- TypeSystemDescription typeSystemDescription = TypeSystemDescriptionFactory.createTypeSystemDescriptionFromPath(
- "../ctakes-type-system/desc/common_type_system.xml");
-
- JCas jCas = JCasFactory.createJCas(typeSystemDescription);
+ JCas jCas = JCasFactory.createJCas();
jCas.setDocumentText(sampleSentence);
AnalysisEngine relationExtractor = AnalysisEngineFactory.createAnalysisEngineFromPath(
@@ -82,5 +74,4 @@ public class RelationExtractorPipelineSi
SimplePipeline.runPipeline(jCas, relationExtractor, relationConsumer);
}
- }
}
Modified: incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationExtractorTrain.java
URL: http://svn.apache.org/viewvc/incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationExtractorTrain.java?rev=1401480&r1=1401479&r2=1401480&view=diff
==============================================================================
--- incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationExtractorTrain.java (original)
+++ incubator/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/RelationExtractorTrain.java Tue Oct 23 21:06:20 2012
@@ -151,7 +151,7 @@ public class RelationExtractorTrain {
List<File> trainFiles = Arrays.asList(options.trainDirectory.listFiles());
// Initialize model directories
- File modelsDirBase = new File("resources/models");
+ File modelsDirBase = new File("src/main/resources/org/apache/ctakes/relationextractor/models");
File modelsDirModExtractor = new File(modelsDirBase, "modifier_extractor");
File modelsDirDegreeOf = new File(modelsDirBase, "degree_of");
File modelsDirEMPair = new File(modelsDirBase, "em_pair");