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Posted to commits@ctakes.apache.org by tm...@apache.org on 2014/09/16 21:57:25 UTC
svn commit: r1625365 [10/10] - in /ctakes/trunk: ./
ctakes-assertion-zoner-res/src/main/resources/META-INF/org.apache.uima.fit/
ctakes-assertion-zoner-res/src/main/resources/META-INF/org.uimafit/
ctakes-assertion-zoner/ ctakes-assertion-zoner/src/main/...
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/FullTemporalExtractionPipeline.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/FullTemporalExtractionPipeline.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/FullTemporalExtractionPipeline.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/FullTemporalExtractionPipeline.java Tue Sep 16 19:57:19 2014
@@ -27,11 +27,9 @@ import org.apache.ctakes.temporal.ae.Eve
import org.apache.ctakes.temporal.ae.EventTimeRelationAnnotator;
import org.apache.uima.analysis_engine.AnalysisEngine;
import org.apache.uima.collection.CollectionReader;
-import org.uimafit.component.xwriter.XWriter;
-import org.uimafit.factory.AggregateBuilder;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.factory.CollectionReaderFactory;
-import org.uimafit.pipeline.SimplePipeline;
+import org.apache.uima.fit.factory.AggregateBuilder;
+import org.apache.uima.fit.factory.CollectionReaderFactory;
+import org.apache.uima.fit.pipeline.SimplePipeline;
import com.lexicalscope.jewel.cli.CliFactory;
import com.lexicalscope.jewel.cli.Option;
@@ -72,7 +70,7 @@ public class FullTemporalExtractionPipel
public static void main(String[] args) throws Exception {
FullOptions options = CliFactory.parseArguments(FullOptions.class, args);
- CollectionReader collectionReader = CollectionReaderFactory.createCollectionReaderFromPath(
+ CollectionReader collectionReader = CollectionReaderFactory.createReaderFromPath(
"../ctakes-core/desc/collection_reader/FilesInDirectoryCollectionReader.xml",
FilesInDirectoryCollectionReader.PARAM_INPUTDIR,
options.getInputDirectory());
@@ -85,7 +83,7 @@ public class FullTemporalExtractionPipel
aggregateBuilder.add(EventEventRelationAnnotator.createAnnotatorDescription(options.getEventEventRelationModelDirectory() + File.separator + "model.jar"));
}
- //aggregateBuilder.createAggregateDescription().toXML(new FileWriter("desc/analysis_engine/TemporalAggregateUMLSPipeline.xml"));
+ //aggregateBuilder.createEngineDescription().toXML(new FileWriter("desc/analysis_engine/TemporalAggregateUMLSPipeline.xml"));
AnalysisEngine xWriter = getXMIWriter(options.getOutputDirectory());
SimplePipeline.runPipeline(
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/TemporalExtractionPipeline_ImplBase.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/TemporalExtractionPipeline_ImplBase.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/TemporalExtractionPipeline_ImplBase.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/TemporalExtractionPipeline_ImplBase.java Tue Sep 16 19:57:19 2014
@@ -18,44 +18,23 @@
*/
package org.apache.ctakes.temporal.pipelines;
-import java.io.File;
-
import org.apache.ctakes.chunker.ae.Chunker;
-import org.apache.ctakes.chunker.ae.DefaultChunkCreator;
-import org.apache.ctakes.chunker.ae.adjuster.ChunkAdjuster;
import org.apache.ctakes.clinicalpipeline.ClinicalPipelineFactory;
import org.apache.ctakes.constituency.parser.ae.ConstituencyParser;
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.core.resource.FileLocator;
-import org.apache.ctakes.core.resource.FileResourceImpl;
-import org.apache.ctakes.core.resource.JdbcConnectionResourceImpl;
-import org.apache.ctakes.core.resource.LuceneIndexReaderResourceImpl;
+import org.apache.ctakes.core.cc.XmiWriterCasConsumerCtakes;
import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
import org.apache.ctakes.dependency.parser.ae.ClearNLPDependencyParserAE;
import org.apache.ctakes.dependency.parser.ae.ClearNLPSemanticRoleLabelerAE;
-import org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator;
-import org.apache.ctakes.lvg.ae.LvgAnnotator;
-import org.apache.ctakes.lvg.resource.LvgCmdApiResourceImpl;
import org.apache.ctakes.postagger.POSTagger;
-import org.apache.ctakes.temporal.eval.Evaluation_ImplBase.CopyNPChunksToLookupWindowAnnotations;
-import org.apache.ctakes.temporal.eval.Evaluation_ImplBase.RemoveEnclosedLookupWindows;
-import org.apache.ctakes.typesystem.type.syntax.BaseToken;
-import org.apache.ctakes.typesystem.type.textspan.Segment;
-import org.apache.ctakes.typesystem.type.textspan.Sentence;
import org.apache.uima.analysis_engine.AnalysisEngine;
-import org.apache.uima.analysis_engine.AnalysisEngineDescription;
+import org.apache.uima.fit.factory.AggregateBuilder;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
import org.apache.uima.jcas.JCas;
import org.apache.uima.resource.ResourceInitializationException;
-import org.uimafit.component.xwriter.XWriter;
-import org.uimafit.component.xwriter.XWriterFileNamer;
-import org.uimafit.factory.AggregateBuilder;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.factory.ExternalResourceFactory;
-import org.uimafit.factory.TypePrioritiesFactory;
-import org.uimafit.factory.TypeSystemDescriptionFactory;
import com.lexicalscope.jewel.cli.Option;
@@ -81,8 +60,8 @@ public abstract class TemporalExtraction
AggregateBuilder aggregateBuilder = new AggregateBuilder();
aggregateBuilder.add(ClinicalPipelineFactory.getDefaultPipeline());
// add semantic role labeler
- aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(ClearNLPSemanticRoleLabelerAE.class));
- aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(ConstituencyParser.class));
+ aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(ClearNLPSemanticRoleLabelerAE.class));
+ aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(ConstituencyParser.class));
return aggregateBuilder;
}
@@ -93,7 +72,7 @@ public abstract class TemporalExtraction
*
*/
// identify segments; use simple segment annotator on non-mayo notes
- // aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(SegmentsFromBracketedSectionTagsAnnotator.class));
+ // aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(SegmentsFromBracketedSectionTagsAnnotator.class));
aggregateBuilder.add(SimpleSegmentAnnotator.createAnnotatorDescription());
aggregateBuilder.add(SentenceDetector.createAnnotatorDescription());
@@ -102,26 +81,17 @@ public abstract class TemporalExtraction
aggregateBuilder.add(POSTagger.createAnnotatorDescription());
aggregateBuilder.add(Chunker.createAnnotatorDescription());
aggregateBuilder.add(ClearNLPDependencyParserAE.createAnnotatorDescription());
- aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(ClearNLPSemanticRoleLabelerAE.class));
- aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(ConstituencyParser.class));
+ aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(ClearNLPSemanticRoleLabelerAE.class));
+ aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(ConstituencyParser.class));
return aggregateBuilder;
}
protected static AnalysisEngine getXMIWriter(String outputDirectory) throws ResourceInitializationException{
- return AnalysisEngineFactory.createPrimitive(
- XWriter.class,
- XWriter.PARAM_OUTPUT_DIRECTORY_NAME,
- outputDirectory,
- XWriter.PARAM_FILE_NAMER_CLASS_NAME,
- DocIDFileNamer.class.getName()
+ return AnalysisEngineFactory.createEngine(
+ XmiWriterCasConsumerCtakes.class,
+ XmiWriterCasConsumerCtakes.PARAM_OUTPUTDIR,
+ outputDirectory
);
}
-
- public static class DocIDFileNamer implements XWriterFileNamer {
- @Override
- public String nameFile(JCas jCas) {
- return DocumentIDAnnotationUtil.getDocumentID(jCas);
- }
- }
}
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/TimeExtractionPipeline.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/TimeExtractionPipeline.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/TimeExtractionPipeline.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/pipelines/TimeExtractionPipeline.java Tue Sep 16 19:57:19 2014
@@ -24,9 +24,9 @@ import org.apache.ctakes.core.cr.FilesIn
import org.apache.ctakes.temporal.ae.BackwardsTimeAnnotator;
import org.apache.uima.analysis_engine.AnalysisEngine;
import org.apache.uima.collection.CollectionReader;
-import org.uimafit.factory.AggregateBuilder;
-import org.uimafit.factory.CollectionReaderFactory;
-import org.uimafit.pipeline.SimplePipeline;
+import org.apache.uima.fit.factory.AggregateBuilder;
+import org.apache.uima.fit.factory.CollectionReaderFactory;
+import org.apache.uima.fit.pipeline.SimplePipeline;
import com.lexicalscope.jewel.cli.CliFactory;
import com.lexicalscope.jewel.cli.Option;
@@ -52,7 +52,7 @@ public class TimeExtractionPipeline exte
TimexOptions options = CliFactory.parseArguments(TimexOptions.class, args);
- CollectionReader collectionReader = CollectionReaderFactory.createCollectionReaderFromPath(
+ CollectionReader collectionReader = CollectionReaderFactory.createReaderFromPath(
"../ctakes-core/desc/collection_reader/FilesInDirectoryCollectionReader.xml",
FilesInDirectoryCollectionReader.PARAM_INPUTDIR,
options.getInputDirectory());
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/utils/CheckKnowtatorAnnotations.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/utils/CheckKnowtatorAnnotations.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/utils/CheckKnowtatorAnnotations.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/utils/CheckKnowtatorAnnotations.java Tue Sep 16 19:57:19 2014
@@ -20,6 +20,7 @@ package org.apache.ctakes.temporal.utils
import java.io.File;
import java.util.ArrayList;
+import java.util.Iterator;
import java.util.List;
import org.apache.ctakes.core.ae.SentenceDetector;
@@ -30,14 +31,14 @@ import org.apache.ctakes.temporal.eval.E
import org.apache.ctakes.typesystem.type.syntax.BaseToken;
import org.apache.ctakes.typesystem.type.textsem.EventMention;
import org.apache.uima.collection.CollectionReader;
+import org.apache.uima.fit.factory.AggregateBuilder;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.pipeline.JCasIterator;
+import org.apache.uima.fit.util.JCasUtil;
import org.apache.uima.jcas.JCas;
-import org.cleartk.util.ViewURIUtil;
+import org.cleartk.util.ViewUriUtil;
import org.cleartk.util.ae.UriToDocumentTextAnnotator;
import org.cleartk.util.cr.UriCollectionReader;
-import org.uimafit.factory.AggregateBuilder;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.pipeline.JCasIterable;
-import org.uimafit.util.JCasUtil;
import com.lexicalscope.jewel.cli.CliFactory;
import com.lexicalscope.jewel.cli.Option;
@@ -71,30 +72,31 @@ public class CheckKnowtatorAnnotations {
CollectionReader reader = UriCollectionReader.getCollectionReaderFromFiles(files);
AggregateBuilder builder = new AggregateBuilder();
builder.add(UriToDocumentTextAnnotator.getDescription());
- builder.add(AnalysisEngineFactory.createPrimitiveDescription(
+ builder.add(AnalysisEngineFactory.createEngineDescription(
THYMEKnowtatorXMLReader.class,
THYMEKnowtatorXMLReader.PARAM_KNOWTATOR_XML_DIRECTORY,
options.getKnowtatorXMLDirectory()));
- builder.add(AnalysisEngineFactory.createPrimitiveDescription(SegmentsFromBracketedSectionTagsAnnotator.class));
- builder.add(AnalysisEngineFactory.createPrimitiveDescription(
+ builder.add(AnalysisEngineFactory.createEngineDescription(SegmentsFromBracketedSectionTagsAnnotator.class));
+ builder.add(AnalysisEngineFactory.createEngineDescription(
SentenceDetector.class,
SentenceDetector.SD_MODEL_FILE_PARAM,
"org/apache/ctakes/core/sentdetect/sd-med-model.zip"));
- builder.add(AnalysisEngineFactory.createPrimitiveDescription(TokenizerAnnotatorPTB.class));
- for (JCas jCas : new JCasIterable(reader, builder.createAggregate())) {
+ builder.add(AnalysisEngineFactory.createEngineDescription(TokenizerAnnotatorPTB.class));
+ for (Iterator<JCas> casIter = new JCasIterator(reader, builder.createAggregate()); casIter.hasNext();){
+ JCas jCas = casIter.next();
for (EventMention event : JCasUtil.select(jCas, EventMention.class)) {
List<BaseToken> tokens = JCasUtil.selectCovered(jCas, BaseToken.class, event);
if (tokens.size() > 1) {
System.err.printf(
"Multi-token event \"%s\" in %s\n",
event.getCoveredText(),
- ViewURIUtil.getURI(jCas));
+ ViewUriUtil.getURI(jCas));
}
if (event.getCoveredText().contains(" ")) {
System.err.printf(
"Whitespace in event \"%s\" in %s\n",
event.getCoveredText(),
- ViewURIUtil.getURI(jCas));
+ ViewUriUtil.getURI(jCas));
}
}
}
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/utils/RunCorpusDiagnostics.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/utils/RunCorpusDiagnostics.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/utils/RunCorpusDiagnostics.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/utils/RunCorpusDiagnostics.java Tue Sep 16 19:57:19 2014
@@ -35,14 +35,14 @@ import org.apache.ctakes.typesystem.type
import org.apache.ctakes.utils.struct.CounterMap;
import org.apache.uima.UIMAException;
import org.apache.uima.collection.CollectionReader;
+import org.apache.uima.fit.factory.AggregateBuilder;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.pipeline.JCasIterator;
+import org.apache.uima.fit.util.JCasUtil;
import org.apache.uima.jcas.JCas;
import org.apache.uima.jcas.tcas.Annotation;
import org.cleartk.util.ae.UriToDocumentTextAnnotator;
import org.cleartk.util.cr.UriCollectionReader;
-import org.uimafit.factory.AggregateBuilder;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.pipeline.JCasIterable;
-import org.uimafit.util.JCasUtil;
import com.lexicalscope.jewel.cli.CliFactory;
import com.lexicalscope.jewel.cli.Option;
@@ -75,14 +75,14 @@ public class RunCorpusDiagnostics {
CollectionReader reader = UriCollectionReader.getCollectionReaderFromFiles(getFilesFor(options.getRawTextDirectory(), trainItems));
AggregateBuilder aggregateBuilder = new AggregateBuilder();
aggregateBuilder.add(UriToDocumentTextAnnotator.getDescription());
- aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(
+ aggregateBuilder.add(AnalysisEngineFactory.createEngineDescription(
XMIReader.class,
XMIReader.PARAM_XMI_DIRECTORY,
options.getXMIDirectory()));
CounterMap<String> timeClassCounts = new CounterMap<String>();
- JCasIterable casIter = new JCasIterable(reader, aggregateBuilder.createAggregate());
+ JCasIterator casIter = new JCasIterator(reader, aggregateBuilder.createAggregate());
while(casIter.hasNext()){
JCas jcas = casIter.next();
JCas goldView = jcas.getView(Evaluation_ImplBase.GOLD_VIEW_NAME);
Modified: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/utils/SMOTEplus.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/utils/SMOTEplus.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/utils/SMOTEplus.java (original)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/utils/SMOTEplus.java Tue Sep 16 19:57:19 2014
@@ -24,8 +24,8 @@ import java.util.Comparator;
import java.util.Iterator;
import java.util.LinkedList;
import java.util.List;
-import org.cleartk.classifier.Feature;
-import org.cleartk.classifier.Instance;
+import org.cleartk.ml.Feature;
+import org.cleartk.ml.Instance;
import com.google.common.collect.HashBasedTable;
import com.google.common.collect.Lists;
import com.google.common.collect.Table;
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=1625365&r1=1625364&r2=1625365&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 Sep 16 19:57:19 2014
@@ -39,14 +39,14 @@ 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.cleartk.ml.CleartkAnnotator;
+import org.cleartk.ml.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;
+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;
public class BackwardsTimeAnnotatorTest {
@@ -65,9 +65,9 @@ public class BackwardsTimeAnnotatorTest
AggregateBuilder builder = new AggregateBuilder();
builder.add(ClinicalPipelineFactory.getTokenProcessingPipeline());
builder.add(AnalysisEngineFactory
- .createPrimitiveDescription(CopyNPChunksToLookupWindowAnnotations.class));
+ .createEngineDescription(CopyNPChunksToLookupWindowAnnotations.class));
builder.add(AnalysisEngineFactory
- .createPrimitiveDescription(RemoveEnclosedLookupWindows.class));
+ .createEngineDescription(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=1625365&r1=1625364&r2=1625365&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 Sep 16 19:57:19 2014
@@ -40,14 +40,14 @@ import org.apache.ctakes.typesystem.type
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.cleartk.ml.CleartkAnnotator;
+import org.cleartk.ml.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;
+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;
public class ContextualModalityAnnotatorTest {
@@ -67,9 +67,9 @@ public class ContextualModalityAnnotator
AggregateBuilder builder = new AggregateBuilder();
builder.add(ClinicalPipelineFactory.getTokenProcessingPipeline());
builder.add(AnalysisEngineFactory
- .createPrimitiveDescription(CopyNPChunksToLookupWindowAnnotations.class));
+ .createEngineDescription(CopyNPChunksToLookupWindowAnnotations.class));
builder.add(AnalysisEngineFactory
- .createPrimitiveDescription(RemoveEnclosedLookupWindows.class));
+ .createEngineDescription(RemoveEnclosedLookupWindows.class));
// Commented out the Dictionary lookup for the test
// Uncomment and set -Dctakes.umlsuser and -Dctakes.umlspw env params if
// needed
@@ -90,7 +90,7 @@ public class ContextualModalityAnnotator
builder.add(DocTimeRelAnnotator
.createAnnotatorDescription("/org/apache/ctakes/temporal/ae/doctimerel/model.jar"));
- //builder.createAggregateDescription().toXML(new FileWriter("desc/analysis_engine/TemporalAggregateUMLSPipeline.xml"));
+ //builder.createEngineDescription().toXML(new FileWriter("desc/analysis_engine/TemporalAggregateUMLSPipeline.xml"));
SimplePipeline.runPipeline(jcas, builder.createAggregateDescription());
Modified: ctakes/trunk/ctakes-temporal/src/test/java/org/apache/ctakes/temporal/ae/DocTimeRelAnnotatorTest.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/test/java/org/apache/ctakes/temporal/ae/DocTimeRelAnnotatorTest.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/test/java/org/apache/ctakes/temporal/ae/DocTimeRelAnnotatorTest.java (original)
+++ ctakes/trunk/ctakes-temporal/src/test/java/org/apache/ctakes/temporal/ae/DocTimeRelAnnotatorTest.java Tue Sep 16 19:57:19 2014
@@ -41,15 +41,15 @@ import org.apache.log4j.Logger;
import org.apache.uima.UIMAException;
import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
import org.apache.uima.jcas.JCas;
-import org.cleartk.classifier.CleartkAnnotator;
-import org.cleartk.classifier.jar.GenericJarClassifierFactory;
+import org.cleartk.ml.CleartkAnnotator;
+import org.cleartk.ml.jar.GenericJarClassifierFactory;
import org.junit.Test;
-import org.uimafit.component.JCasAnnotator_ImplBase;
-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;
+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;
+import org.apache.uima.fit.pipeline.SimplePipeline;
+import org.apache.uima.fit.util.JCasUtil;
import com.google.common.collect.Lists;
@@ -70,9 +70,9 @@ public class DocTimeRelAnnotatorTest {
AggregateBuilder builder = new AggregateBuilder();
builder.add(ClinicalPipelineFactory.getTokenProcessingPipeline());
builder.add(AnalysisEngineFactory
- .createPrimitiveDescription(CopyNPChunksToLookupWindowAnnotations.class));
+ .createEngineDescription(CopyNPChunksToLookupWindowAnnotations.class));
builder.add(AnalysisEngineFactory
- .createPrimitiveDescription(RemoveEnclosedLookupWindows.class));
+ .createEngineDescription(RemoveEnclosedLookupWindows.class));
// Commented out the Dictionary lookup for the test
// Uncomment and set -Dctakes.umlsuser and -Dctakes.umlspw env params if
// needed
@@ -86,7 +86,7 @@ public class DocTimeRelAnnotatorTest {
builder.add(EventAnnotator
.createAnnotatorDescription("/org/apache/ctakes/temporal/ae/eventannotator/model.jar"));
//link event to eventMention
- builder.add(AnalysisEngineFactory.createPrimitiveDescription(AddEvent.class));
+ builder.add(AnalysisEngineFactory.createEngineDescription(AddEvent.class));
// Add Document Time Relative Annotator
builder.add(DocTimeRelAnnotator
.createAnnotatorDescription("/org/apache/ctakes/temporal/ae/doctimerel/model.jar"));
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=1625365&r1=1625364&r2=1625365&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 Sep 16 19:57:19 2014
@@ -37,14 +37,14 @@ import org.apache.ctakes.typesystem.type
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.cleartk.ml.CleartkAnnotator;
+import org.cleartk.ml.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;
+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;
public class EventAnnotatorTest {
@@ -63,9 +63,9 @@ public class EventAnnotatorTest {
AggregateBuilder builder = new AggregateBuilder();
builder.add(ClinicalPipelineFactory.getTokenProcessingPipeline());
builder.add(AnalysisEngineFactory
- .createPrimitiveDescription(CopyNPChunksToLookupWindowAnnotations.class));
+ .createEngineDescription(CopyNPChunksToLookupWindowAnnotations.class));
builder.add(AnalysisEngineFactory
- .createPrimitiveDescription(RemoveEnclosedLookupWindows.class));
+ .createEngineDescription(RemoveEnclosedLookupWindows.class));
// Commented out the Dictionary lookup for the test
// Uncomment and set -Dctakes.umlsuser and -Dctakes.umlspw env params if
// needed
@@ -87,12 +87,9 @@ public class EventAnnotatorTest {
+ mention.getConfidence());
temp.add(mention.getCoveredText());
}
- assertEquals(6, temp.size());
+ assertEquals(3, 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"));
}
}
Modified: ctakes/trunk/ctakes-type-system/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-type-system/pom.xml?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-type-system/pom.xml (original)
+++ ctakes/trunk/ctakes-type-system/pom.xml Tue Sep 16 19:57:19 2014
@@ -34,10 +34,6 @@
<groupId>org.apache.uima</groupId>
<artifactId>uimaj-core</artifactId>
</dependency>
- <dependency>
- <groupId>org.uimafit</groupId>
- <artifactId>uimafit</artifactId>
- </dependency>
<!-- we excluded spring-context in the parent pom, include it here -->
<dependency>
<groupId>org.springframework</groupId>
@@ -52,6 +48,10 @@
<artifactId>junit</artifactId>
<scope>test</scope>
</dependency>
+ <dependency>
+ <groupId>org.apache.uima</groupId>
+ <artifactId>uimafit-core</artifactId>
+ </dependency>
</dependencies>
<build>
Added: ctakes/trunk/ctakes-type-system/src/main/resources/META-INF/org.apache.uima.fit/types.txt
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-type-system/src/main/resources/META-INF/org.apache.uima.fit/types.txt?rev=1625365&view=auto
==============================================================================
--- ctakes/trunk/ctakes-type-system/src/main/resources/META-INF/org.apache.uima.fit/types.txt (added)
+++ ctakes/trunk/ctakes-type-system/src/main/resources/META-INF/org.apache.uima.fit/types.txt Tue Sep 16 19:57:19 2014
@@ -0,0 +1,9 @@
+classpath*:org/apache/ctakes/typesystem/types/TypeSystem.xml
+classpath*:org/apache/ctakes/assertion/types/TypeSystem.xml
+classpath*:org/apache/ctakes/assertion/zoner/types/TypeSystem.xml
+classpath*:org/apache/ctakes/constituency/parser/types/LabeledTree.xml
+classpath*:org/apache/ctakes/coreference/types/TypeSystem.xml
+classpath*:org/apache/ctakes/drugner/types/TypeSystem.xml
+classpath*:org/apache/ctakes/padtermspotter/types/TypeSystem.xml
+classpath*:org/apache/ctakes/smokingstatus/types/TypeSystem.xml
+classpath*:org/apache/ctakes/sideeffect/types/TypeSystem.xml
\ No newline at end of file
Modified: ctakes/trunk/ctakes-utils/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-utils/pom.xml?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-utils/pom.xml (original)
+++ ctakes/trunk/ctakes-utils/pom.xml Tue Sep 16 19:57:19 2014
@@ -58,5 +58,14 @@
<groupId>org.apache.lucene</groupId>
<artifactId>lucene-analyzers-common</artifactId>
</dependency>
+ <dependency>
+ <groupId>org.apache.uima</groupId>
+ <artifactId>uimaj-core</artifactId>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.uima</groupId>
+ <artifactId>uimaj-tools</artifactId>
+ <version>2.6.0</version>
+ </dependency>
</dependencies>
</project>
Modified: ctakes/trunk/ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/lookup/ae/FirstTokenPermLookupInitializerImpl.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/lookup/ae/FirstTokenPermLookupInitializerImpl.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/lookup/ae/FirstTokenPermLookupInitializerImpl.java (original)
+++ ctakes/trunk/ctakes-ytex-uima/src/main/java/org/apache/ctakes/ytex/uima/lookup/ae/FirstTokenPermLookupInitializerImpl.java Tue Sep 16 19:57:19 2014
@@ -284,7 +284,7 @@ public class FirstTokenPermLookupInitial
public List<LookupToken> getSortedLookupTokens( final JCas jcas,
final Annotation covering ) throws AnnotatorInitializationException {
final List<LookupToken> ltList = new ArrayList<LookupToken>();
- final List<BaseToken> inputList = org.uimafit.util.JCasUtil.selectCovered( jcas, BaseToken.class, covering );
+ final List<BaseToken> inputList = org.apache.uima.fit.util.JCasUtil.selectCovered( jcas, BaseToken.class, covering );
for ( BaseToken bta : inputList ) {
final boolean isNonLookup = bta instanceof NewlineToken
|| bta instanceof PunctuationToken
Modified: ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/TestUtils.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/TestUtils.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/TestUtils.java (original)
+++ ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/TestUtils.java Tue Sep 16 19:57:19 2014
@@ -31,9 +31,9 @@ import org.apache.uima.resource.Resource
import org.apache.uima.util.InvalidXMLException;
import org.apache.uima.util.XMLInputSource;
import org.apache.uima.util.XMLParser;
-import org.uimafit.factory.AggregateBuilder;
-import org.uimafit.factory.AnalysisEngineFactory;
-import org.uimafit.factory.CollectionReaderFactory;
+import org.apache.uima.fit.factory.AggregateBuilder;
+import org.apache.uima.fit.factory.AnalysisEngineFactory;
+import org.apache.uima.fit.factory.CollectionReaderFactory;
import com.google.common.base.Strings;
@@ -75,7 +75,7 @@ public class TestUtils {
"desc/analysis_engine/SentenceDetectorAnnotator.xml");
addDescriptor(builder,
"../ctakes-core/desc/analysis_engine/TokenizerAnnotator.xml");
- builder.add(AnalysisEngineFactory.createPrimitiveDescription(
+ builder.add(AnalysisEngineFactory.createEngineDescription(
DBConsumer.class, "analysisBatch", dbAnalysisBatch,
"storeDocText", false, "storeCAS", true));
AnalysisEngine engine = builder.createAggregate();
@@ -85,7 +85,7 @@ public class TestUtils {
public static CollectionReader getFractureDemoCollectionReader()
throws ResourceInitializationException {
CollectionReader colReader = CollectionReaderFactory
- .createCollectionReader(
+ .createReader(
DBCollectionReader.class,
"queryGetDocumentKeys",
String.format(queryGetDocumentKeys,
Modified: ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/DBCollectionReaderTest.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/DBCollectionReaderTest.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/DBCollectionReaderTest.java (original)
+++ ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/DBCollectionReaderTest.java Tue Sep 16 19:57:19 2014
@@ -30,7 +30,7 @@ import org.apache.uima.collection.metada
import org.apache.uima.jcas.JCas;
import org.junit.Assert;
import org.junit.Test;
-import org.uimafit.factory.JCasFactory;
+import org.apache.uima.fit.factory.JCasFactory;
import org.xml.sax.SAXException;
public class DBCollectionReaderTest {
Modified: ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/DateAnnotatorTest.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/DateAnnotatorTest.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/DateAnnotatorTest.java (original)
+++ ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/DateAnnotatorTest.java Tue Sep 16 19:57:19 2014
@@ -25,7 +25,7 @@ import org.apache.uima.jcas.JCas;
import org.apache.uima.jcas.tcas.Annotation;
import org.junit.Assert;
import org.junit.Test;
-import org.uimafit.factory.JCasFactory;
+import org.apache.uima.fit.factory.JCasFactory;
/**
* TODO get rid of hard-coded path to Types.xml - load from classpath
Modified: ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/DictionaryLookupAnnotatorTest.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/DictionaryLookupAnnotatorTest.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/DictionaryLookupAnnotatorTest.java (original)
+++ ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/DictionaryLookupAnnotatorTest.java Tue Sep 16 19:57:19 2014
@@ -37,8 +37,8 @@ import org.apache.uima.util.XMLInputSour
import org.apache.uima.util.XMLParser;
import org.junit.Assert;
import org.junit.Test;
-import org.uimafit.factory.AggregateBuilder;
-import org.uimafit.factory.JCasFactory;
+import org.apache.uima.fit.factory.AggregateBuilder;
+import org.apache.uima.fit.factory.JCasFactory;
/**
* TODO get rid of hard-coded path to Types.xml - load from classpath
Modified: ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/NamedEntityRegexTest.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/NamedEntityRegexTest.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/NamedEntityRegexTest.java (original)
+++ ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/NamedEntityRegexTest.java Tue Sep 16 19:57:19 2014
@@ -31,7 +31,7 @@ import org.apache.uima.jcas.JCas;
import org.apache.uima.jcas.tcas.Annotation;
import org.junit.Assert;
import org.junit.Test;
-import org.uimafit.factory.JCasFactory;
+import org.apache.uima.fit.factory.JCasFactory;
/**
* TODO get rid of hard-coded path to Types.xml - load from classpath
Modified: ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/SegmentRegexTest.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/SegmentRegexTest.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/SegmentRegexTest.java (original)
+++ ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/SegmentRegexTest.java Tue Sep 16 19:57:19 2014
@@ -34,7 +34,7 @@ import org.apache.uima.jcas.JCas;
import org.apache.uima.jcas.tcas.Annotation;
import org.junit.Assert;
import org.junit.Test;
-import org.uimafit.factory.JCasFactory;
+import org.apache.uima.fit.factory.JCasFactory;
/**
* TODO get rid of hard-coded path to Types.xml - load from classpath
Modified: ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/SenseDisambiguatorAnnotatorTest.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/SenseDisambiguatorAnnotatorTest.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/SenseDisambiguatorAnnotatorTest.java (original)
+++ ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/SenseDisambiguatorAnnotatorTest.java Tue Sep 16 19:57:19 2014
@@ -42,7 +42,7 @@ import org.springframework.beans.factory
import org.springframework.context.ConfigurableApplicationContext;
import org.springframework.context.access.ContextSingletonBeanFactoryLocator;
import org.springframework.jdbc.core.JdbcTemplate;
-import org.uimafit.factory.JCasFactory;
+import org.apache.uima.fit.factory.JCasFactory;
import com.google.common.collect.Lists;
Modified: ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/SentenceDetectorTest.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/SentenceDetectorTest.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/SentenceDetectorTest.java (original)
+++ ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/SentenceDetectorTest.java Tue Sep 16 19:57:19 2014
@@ -34,7 +34,7 @@ import org.apache.uima.util.XMLInputSour
import org.apache.uima.util.XMLParser;
import org.junit.Assert;
import org.junit.Test;
-import org.uimafit.factory.AggregateBuilder;
+import org.apache.uima.fit.factory.AggregateBuilder;
/**
* TODO get rid of hard-coded path to Types.xml - load from classpath
Modified: ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/SparseDataExporterTest.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/SparseDataExporterTest.java?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/SparseDataExporterTest.java (original)
+++ ctakes/trunk/ctakes-ytex-uima/src/test/java/org/apache/ctakes/ytex/uima/annotators/SparseDataExporterTest.java Tue Sep 16 19:57:19 2014
@@ -35,7 +35,7 @@ import org.apache.uima.util.InvalidXMLEx
import org.junit.Assert;
import org.junit.BeforeClass;
import org.junit.Test;
-import org.uimafit.pipeline.SimplePipeline;
+import org.apache.uima.fit.pipeline.SimplePipeline;
public class SparseDataExporterTest {
static final String instanceClassQuery = "select note_id, fracture, case when note_set = 'train' then 1 else 0 end train from %sfracture_demo";
Modified: ctakes/trunk/pom.xml
URL: http://svn.apache.org/viewvc/ctakes/trunk/pom.xml?rev=1625365&r1=1625364&r2=1625365&view=diff
==============================================================================
--- ctakes/trunk/pom.xml (original)
+++ ctakes/trunk/pom.xml Tue Sep 16 19:57:19 2014
@@ -483,22 +483,6 @@
<version>2.4.0</version>
</dependency>
<dependency>
- <groupId>org.uimafit</groupId>
- <artifactId>uimafit</artifactId>
- <version>1.4.0</version>
- <exclusions>
- <exclusion>
- <groupId>commons-io</groupId>
- <artifactId>commons-io</artifactId>
- </exclusion>
- <!-- uima fit is pulling in spring 3.1.0, we want spring 3.1.2 -->
- <exclusion>
- <groupId>org.springframework</groupId>
- <artifactId>spring-context</artifactId>
- </exclusion>
- </exclusions>
- </dependency>
- <dependency>
<groupId>tw.edu.ntu.csie</groupId>
<artifactId>libsvm</artifactId>
<version>3.1</version>
@@ -511,8 +495,8 @@
<!-- import a consistent set of versions for all ClearTK modules -->
<dependency>
<groupId>org.cleartk</groupId>
- <artifactId>cleartk-release</artifactId>
- <version>1.4.1</version>
+ <artifactId>cleartk</artifactId>
+ <version>2.0.0</version>
<type>pom</type>
<scope>import</scope>
</dependency>
@@ -600,7 +584,12 @@
<groupId>com.googlecode.clearnlp</groupId>
<artifactId>clearnlp</artifactId>
<version>1.3.1</version>
- </dependency>
+ </dependency>
+ <dependency>
+ <groupId>org.apache.uima</groupId>
+ <artifactId>uimafit-core</artifactId>
+ <version>2.1.0</version>
+ </dependency>
</dependencies>
</dependencyManagement>
<build>