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Posted to commits@ctakes.apache.org by se...@apache.org on 2015/08/23 22:33:28 UTC
svn commit: r1697246 [1/2] - in /ctakes/trunk:
ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineFactory.java
ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/Evaluation_ImplBase.java
Author: seanfinan
Date: Sun Aug 23 20:33:28 2015
New Revision: 1697246
URL: http://svn.apache.org/r1697246
Log:
Boy scouting 2 - continued the uima fit ification of dictionary-fast
Modified:
ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineFactory.java
ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/eval/Evaluation_ImplBase.java
Modified: ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineFactory.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineFactory.java?rev=1697246&r1=1697245&r2=1697246&view=diff
==============================================================================
--- ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineFactory.java (original)
+++ ctakes/trunk/ctakes-clinical-pipeline/src/main/java/org/apache/ctakes/clinicalpipeline/ClinicalPipelineFactory.java Sun Aug 23 20:33:28 2015
@@ -26,13 +26,9 @@ import org.apache.ctakes.contexttokenize
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.dependency.parser.ae.ClearNLPDependencyParserAE;
import org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator;
-import org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator;
import org.apache.ctakes.dictionary.lookup2.ae.DefaultJCasTermAnnotator;
-import org.apache.ctakes.dictionary.lookup2.ae.JCasTermAnnotator;
import org.apache.ctakes.lvg.ae.LvgAnnotator;
import org.apache.ctakes.postagger.POSTagger;
import org.apache.ctakes.typesystem.type.constants.CONST;
@@ -47,7 +43,6 @@ import org.apache.uima.cas.FeatureStruct
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.ExternalResourceFactory;
import org.apache.uima.fit.factory.JCasFactory;
import org.apache.uima.fit.pipeline.SimplePipeline;
import org.apache.uima.fit.util.JCasUtil;
@@ -56,7 +51,6 @@ import org.apache.uima.jcas.cas.FSArray;
import org.apache.uima.resource.ResourceInitializationException;
import org.xml.sax.SAXException;
-import java.io.FileNotFoundException;
import java.io.FileWriter;
import java.io.IOException;
import java.util.*;
@@ -86,11 +80,7 @@ final public class ClinicalPipelineFacto
public static AnalysisEngineDescription getFastPipeline() throws ResourceInitializationException {
AggregateBuilder builder = new AggregateBuilder();
builder.add( getTokenProcessingPipeline() );
- builder.add( AnalysisEngineFactory.createEngineDescription( DefaultJCasTermAnnotator.class,
- AbstractJCasTermAnnotator.PARAM_WINDOW_ANNOT_PRP,
- "org.apache.ctakes.typesystem.type.textspan.Sentence",
- JCasTermAnnotator.DICTIONARY_DESCRIPTOR_KEY,"org/apache/ctakes/dictionary/lookup/fast/cTakesHsql.xml" )
- );
+ builder.add( DefaultJCasTermAnnotator.createAnnotatorDescription() );
builder.add( ClearNLPDependencyParserAE.createAnnotatorDescription() );
builder.add( PolarityCleartkAnalysisEngine.createAnnotatorDescription() );
builder.add( UncertaintyCleartkAnalysisEngine.createAnnotatorDescription() );
@@ -160,7 +150,7 @@ final public class ClinicalPipelineFacto
final JCas jcas = JCasFactory.createJCas();
jcas.setDocumentText( note );
final AnalysisEngineDescription aed = getDefaultPipeline();
-// final AnalysisEngineDescription aed = getFastPipeline(); // Outputs from default and fast pipelines are identical
+// final AnalysisEngineDescription aed = getFastPipeline(); // Outputs from default and fast pipeline are identical
SimplePipeline.runPipeline( jcas, aed );
final boolean printCuis = Arrays.asList( args ).contains( "cuis" );