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Sun, 23 Aug 2015 20:33:28 +0000 (UTC) Content-Type: text/plain; charset="utf-8" MIME-Version: 1.0 Content-Transfer-Encoding: 7bit Subject: 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 Date: Sun, 23 Aug 2015 20:33:28 -0000 To: commits@ctakes.apache.org From: seanfinan@apache.org X-Mailer: svnmailer-1.0.9 Message-Id: <20150823203328.7BF78AC0250@hades.apache.org> 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" );