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Posted to commits@ctakes.apache.org by ja...@apache.org on 2013/07/01 19:28:08 UTC
svn commit: r1498581 - in
/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae:
OrangeBookFilterConsumerImpl.java UmlsToSnomedConsumerImpl.java
Author: james-masanz
Date: Mon Jul 1 17:28:07 2013
New Revision: 1498581
URL: http://svn.apache.org/r1498581
Log:
CTAKES-190 - more related to MedicationMention being used instead of MedicationEventMention as of 3.1. (Will make several separate commits because of timeouts occurring while svn is temporarily routed through EU)
Modified:
ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/OrangeBookFilterConsumerImpl.java
ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/UmlsToSnomedConsumerImpl.java
Modified: ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/OrangeBookFilterConsumerImpl.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/OrangeBookFilterConsumerImpl.java?rev=1498581&r1=1498580&r2=1498581&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/OrangeBookFilterConsumerImpl.java (original)
+++ ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/OrangeBookFilterConsumerImpl.java Mon Jul 1 17:28:07 2013
@@ -24,7 +24,7 @@ import org.apache.ctakes.dictionary.look
import org.apache.ctakes.typesystem.type.constants.CONST;
import org.apache.ctakes.typesystem.type.refsem.OntologyConcept;
import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
-import org.apache.ctakes.typesystem.type.textsem.MedicationEventMention;
+import org.apache.ctakes.typesystem.type.textsem.MedicationMention;
import org.apache.log4j.Logger;
import org.apache.lucene.index.Term;
import org.apache.lucene.search.*;
@@ -99,7 +99,7 @@ public class OrangeBookFilterConsumerImp
validCodes.add( code );
}
final FSArray ocArr = createOntologyConceptArr( jcas, validCodes );
- IdentifiedAnnotation neAnnot = new MedicationEventMention( jcas ); // medication NEs are EventMention
+ IdentifiedAnnotation neAnnot = new MedicationMention( jcas ); // medication NEs are EventMention
neAnnot.setTypeID( CONST.NE_TYPE_ID_DRUG );
neAnnot.setBegin( neBegin );
neAnnot.setEnd( neEnd );
Modified: ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/UmlsToSnomedConsumerImpl.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/UmlsToSnomedConsumerImpl.java?rev=1498581&r1=1498580&r2=1498581&view=diff
==============================================================================
--- ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/UmlsToSnomedConsumerImpl.java (original)
+++ ctakes/trunk/ctakes-dictionary-lookup/src/main/java/org/apache/ctakes/dictionary/lookup/ae/UmlsToSnomedConsumerImpl.java Mon Jul 1 17:28:07 2013
@@ -98,100 +98,6 @@ public abstract class UmlsToSnomedConsum
protected abstract Set<String> getSnomedCodes( final String umlsCode ) throws SQLException, DictionaryException;
-// /**
-// * {@inheritDoc}
-// */
-// @Override
-// public void consumeHits( final JCas jcas, final Iterator<LookupHit> lhItr ) throws AnalysisEngineProcessException {
-// try {
-// final String cuiPropKey = props.getProperty( CUI_MF_PRP_KEY );
-// final String tuiPropKey = props.getProperty( TUI_MF_PRP_KEY );
-// final Iterator hitsByOffsetItr = organizeByOffset( lhItr );
-// while ( hitsByOffsetItr.hasNext() ) {
-// final Collection hitsAtOffsetCol = (Collection) hitsByOffsetItr.next();
-//
-// // Iterate over the LookupHit objects and group Snomed codes by NE type
-// // For each NE type for which there is a hit, get all the Snomed codes
-// // that map to the given CUI.
-//
-// // Use key "cui,tui" to avoid duplicates at this offset
-// final Set<String> cuiTuiSet = new HashSet<String>();
-//
-// // key = type of named entity (java.lang.Integer)
-// // val = set of UmlsConcept objects (java.util.Set)
-// final Map<Integer,Set<UmlsConcept>> conceptMap = new HashMap<Integer,Set<UmlsConcept>>();
-//
-// final Iterator lhAtOffsetItr = hitsAtOffsetCol.iterator();
-// int neBegin = -1;
-// int neEnd = -1;
-// while ( lhAtOffsetItr.hasNext() ) {
-// final LookupHit lh = (LookupHit) lhAtOffsetItr.next();
-// neBegin = lh.getStartOffset();
-// neEnd = lh.getEndOffset();
-//
-// final MetaDataHit mdh = lh.getDictMetaDataHit();
-// final String cui = mdh.getMetaFieldValue( cuiPropKey );
-// final String tui = mdh.getMetaFieldValue( tuiPropKey );
-//
-// //String text = lh.getDictMetaDataHit().getMetaFieldValue("text");
-// if ( !_validTuiSet.contains( tui ) ) {
-// continue;
-// }
-// final String cuiTuiKey = getUniqueKey( cui, tui );
-// if ( cuiTuiSet.contains( cuiTuiKey ) ) {
-// continue;
-// }
-// cuiTuiSet.add( cuiTuiKey );
-// final Set<String> snomedCodeSet = getSnomedCodes( cui );
-// if ( !snomedCodeSet.isEmpty() ) {
-// final Integer neType = getNamedEntityType( tui );
-// Set<UmlsConcept> conceptSet;
-// if ( conceptMap.containsKey( neType ) ) {
-// conceptSet = conceptMap.get( neType );
-// } else {
-// conceptSet = new HashSet<UmlsConcept>();
-// }
-// final Collection<UmlsConcept> conceptCol = createConceptCol( jcas, cui, tui, snomedCodeSet );
-// conceptSet.addAll( conceptCol );
-// conceptMap.put( neType, conceptSet );
-// }
-// }
-//
-// final Collection<Integer> conceptKeys = conceptMap.keySet();
-// for ( Integer conceptKey : conceptKeys ) {
-// final Set<UmlsConcept> conceptSet = conceptMap.get( conceptKey );
-//
-// // Skip updating CAS if all Concepts for this type were filtered out
-// // for this span.
-// if ( !conceptSet.isEmpty() ) {
-// FSArray conceptArr = new FSArray( jcas, conceptSet.size() );
-// int arrIdx = 0;
-// for ( UmlsConcept umlsConcept : conceptSet ) {
-// conceptArr.set( arrIdx, umlsConcept );
-// arrIdx++;
-// }
-//
-// IdentifiedAnnotation neAnnot;
-// if ( conceptKey == CONST.NE_TYPE_ID_DRUG ) {
-// neAnnot = new MedicationEventMention( jcas );
-// } else {
-// neAnnot = new EntityMention( jcas );
-// }
-// neAnnot.setTypeID( conceptKey );
-// neAnnot.setBegin( neBegin );
-// neAnnot.setEnd( neEnd );
-// neAnnot.setDiscoveryTechnique( CONST.NE_DISCOVERY_TECH_DICT_LOOKUP );
-// neAnnot.setOntologyConceptArr( conceptArr );
-// neAnnot.addToIndexes();
-// }
-// }
-// }
-// } catch ( Exception e ) {
-// throw new AnalysisEngineProcessException( e );
-// }
-// }
-
-
/**
* {@inheritDoc}
*/