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Posted to commits@ctakes.apache.org by se...@apache.org on 2017/03/28 15:15:04 UTC
svn commit: r1789161 - in
/ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary:
DictionaryBuilder.java umls/ConceptMapFactory.java umls/MrconsoParser.java
umls/SourceTableModel.java
Author: seanfinan
Date: Tue Mar 28 15:15:03 2017
New Revision: 1789161
URL: http://svn.apache.org/viewvc?rev=1789161&view=rev
Log:
ctakes-424 : improved source vocabulary use
Modified:
ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/DictionaryBuilder.java
ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/ConceptMapFactory.java
ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/MrconsoParser.java
ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/SourceTableModel.java
Modified: ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/DictionaryBuilder.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/DictionaryBuilder.java?rev=1789161&r1=1789160&r2=1789161&view=diff
==============================================================================
--- ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/DictionaryBuilder.java (original)
+++ ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/DictionaryBuilder.java Tue Mar 28 15:15:03 2017
@@ -62,7 +62,7 @@ final class DictionaryBuilder {
LOGGER.info( "Parsing Concepts" );
// Create a map of Cuis to empty Concepts for all wanted Tuis and source vocabularies
final Map<Long, Concept> conceptMap
- = ConceptMapFactory.createInitialConceptMap( umlsDirPath, wantedTargets, wantedTuis );
+ = ConceptMapFactory.createInitialConceptMap( umlsDirPath, wantedSources, wantedTuis );
// Fill in information for all valid concepts
MrconsoParser.parseAllConcepts( umlsDirPath, conceptMap, wantedSources, wantedTargets, umlsTermUtil,
wantedLanguages, true, MIN_CHAR_LENGTH, MAX_CHAR_LENGTH, MAX_WORD_COUNT, MAX_SYM_COUNT );
Modified: ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/ConceptMapFactory.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/ConceptMapFactory.java?rev=1789161&r1=1789160&r2=1789161&view=diff
==============================================================================
--- ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/ConceptMapFactory.java (original)
+++ ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/ConceptMapFactory.java Tue Mar 28 15:15:03 2017
@@ -12,15 +12,18 @@ import java.util.Map;
* @version %I%
* @since 12/11/2015
*/
-public class ConceptMapFactory {
+final public class ConceptMapFactory {
static private final Logger LOGGER = Logger.getLogger( "ConceptMapFactory" );
+ private ConceptMapFactory() {
+ }
+
static public Map<Long, Concept> createInitialConceptMap( final String umlsDirPath,
- final Collection<String> wantedTargets,
+ final Collection<String> wantedSources,
final Collection<Tui> wantedTuis ) {
- if ( wantedTargets.isEmpty() ) {
- LOGGER.warn( "No target vocabularies specified" );
+ if ( wantedSources.isEmpty() ) {
+ LOGGER.warn( "No source vocabularies specified" );
return Collections.emptyMap();
}
if ( wantedTuis.isEmpty() ) {
@@ -30,7 +33,7 @@ public class ConceptMapFactory {
// get the valid Cuis for all wanted Tuis
final Map<Long, Concept> concepts = MrstyParser.createConceptsForTuis( umlsDirPath, wantedTuis );
// filter out the Cuis that do not belong to the given sources
- final Collection<Long> validVocabularyCuis = MrconsoParser.getValidVocabularyCuis( umlsDirPath, wantedTargets );
+ final Collection<Long> validVocabularyCuis = MrconsoParser.getValidVocabularyCuis( umlsDirPath, wantedSources );
concepts.keySet().retainAll( validVocabularyCuis );
LOGGER.info( "Total Valid Cuis " + concepts.size() + "\t from wanted Tuis and Vocabularies" );
return concepts;
Modified: ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/MrconsoParser.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/MrconsoParser.java?rev=1789161&r1=1789160&r2=1789161&view=diff
==============================================================================
--- ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/MrconsoParser.java (original)
+++ ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/MrconsoParser.java Tue Mar 28 15:15:03 2017
@@ -147,10 +147,10 @@ final public class MrconsoParser {
if ( isPreferredTerm( tokens ) ) {
concept.setPreferredText( text );
}
- if ( !isSourceOk( tokens, wantedSources ) ) {
- tokens = FileUtil.readBsvTokens( reader, mrconsoPath );
- continue;
- }
+// if ( !isSourceOk( tokens, wantedSources ) ) {
+// tokens = FileUtil.readBsvTokens( reader, mrconsoPath );
+// continue;
+// }
// Get tokenized text
final String tokenizedText = TextTokenizer.getTokenizedText( text );
if ( tokenizedText == null || tokenizedText.isEmpty()
Modified: ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/SourceTableModel.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/SourceTableModel.java?rev=1789161&r1=1789160&r2=1789161&view=diff
==============================================================================
--- ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/SourceTableModel.java (original)
+++ ctakes/trunk/ctakes-gui/src/main/java/org/apache/ctakes/gui/dictionary/umls/SourceTableModel.java Tue Mar 28 15:15:03 2017
@@ -35,8 +35,6 @@ final public class SourceTableModel impl
_wantedTargets.clear();
_sources.addAll( sources );
Collections.sort( _sources );
- // by default, use all sources
- _wantedSources.addAll( sources );
_wantedSources.addAll( Arrays.asList( CTAKES_SOURCES ) );
_wantedTargets.addAll( Arrays.asList( CTAKES_SOURCES ) );
fireTableChanged( new TableModelEvent( this ) );