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From seanfi...@apache.org
Subject svn commit: r1742321 - in /ctakes/trunk/ctakes-core/src: main/java/org/apache/ctakes/core/cc/ main/java/org/apache/ctakes/core/cc/pretty/plaintext/ main/java/org/apache/ctakes/core/cc/property/plaintext/ main/java/org/apache/ctakes/core/util/ test/java...
Date Wed, 04 May 2016 19:19:02 GMT
Author: seanfinan
Date: Wed May  4 19:19:02 2016
New Revision: 1742321

URL: http://svn.apache.org/viewvc?rev=1742321&view=rev
Log:
minor refactoring in OntologyConceptUtil

Modified:
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/JdbcWriterTemplate.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/plaintext/PrettyTextWriter.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/property/plaintext/PropertyTextWriter.java
    ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/OntologyConceptUtil.java
    ctakes/trunk/ctakes-core/src/test/java/org/apache/ctakes/core/util/OntologyConceptUtilTester.java

Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/JdbcWriterTemplate.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/JdbcWriterTemplate.java?rev=1742321&r1=1742320&r2=1742321&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/JdbcWriterTemplate.java
(original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/JdbcWriterTemplate.java
Wed May  4 19:19:02 2016
@@ -148,7 +148,7 @@ public class JdbcWriterTemplate extends
       for ( Annotation annotation : identifiedsIndex ) {
          if ( annotation instanceof IdentifiedAnnotation ) {
             final Collection<UmlsConcept> umlsConcepts
-                  = OntologyConceptUtil.getConcepts( (IdentifiedAnnotation)annotation );
+                  = OntologyConceptUtil.getUmlsConcepts( (IdentifiedAnnotation)annotation
);
             final Collection<I2b2Concept> i2b2Concepts = createI2b2Concepts( umlsConcepts
);
             for ( I2b2Concept i2b2Concept : i2b2Concepts ) {
                Collection<IdentifiedAnnotation> annotationList = cuiAnnotationListMap.get(
i2b2Concept );

Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/plaintext/PrettyTextWriter.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/plaintext/PrettyTextWriter.java?rev=1742321&r1=1742320&r2=1742321&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/plaintext/PrettyTextWriter.java
(original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/pretty/plaintext/PrettyTextWriter.java
Wed May  4 19:19:02 2016
@@ -402,7 +402,7 @@ final public class PrettyTextWriter {
     * @return map of semantic type names and cuis within those types as they apply to the
annotation
     */
    static private Map<String, Collection<String>> getSemanticCuis( final IdentifiedAnnotation
identifiedAnnotation ) {
-      final Collection<UmlsConcept> umlsConcepts = OntologyConceptUtil.getConcepts(
identifiedAnnotation );
+      final Collection<UmlsConcept> umlsConcepts = OntologyConceptUtil.getUmlsConcepts(
identifiedAnnotation );
       if ( umlsConcepts == null || umlsConcepts.isEmpty() ) {
          return Collections.emptyMap();
       }

Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/property/plaintext/PropertyTextWriter.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/property/plaintext/PropertyTextWriter.java?rev=1742321&r1=1742320&r2=1742321&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/property/plaintext/PropertyTextWriter.java
(original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/cc/property/plaintext/PropertyTextWriter.java
Wed May  4 19:19:02 2016
@@ -149,7 +149,7 @@ public class PropertyTextWriter {
     */
    static private Map<String, Collection<UmlsConcept>> getSemanticConcepts(
          final IdentifiedAnnotation identifiedAnnotation ) {
-      final Collection<UmlsConcept> umlsConcepts = OntologyConceptUtil.getConcepts(
identifiedAnnotation );
+      final Collection<UmlsConcept> umlsConcepts = OntologyConceptUtil.getUmlsConcepts(
identifiedAnnotation );
       if ( umlsConcepts == null || umlsConcepts.isEmpty() ) {
          return Collections.emptyMap();
       }

Modified: ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/OntologyConceptUtil.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/OntologyConceptUtil.java?rev=1742321&r1=1742320&r2=1742321&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/OntologyConceptUtil.java
(original)
+++ ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/OntologyConceptUtil.java
Wed May  4 19:19:02 2016
@@ -52,7 +52,7 @@ final public class OntologyConceptUtil {
     * @param annotation -
     * @return array of FeatureStructure castable to array of OntologyConcept
     */
-   static private FeatureStructure[] getOntologyConcepts( final IdentifiedAnnotation annotation
) {
+   static public FeatureStructure[] getConceptFeatureStructures( final IdentifiedAnnotation
annotation ) {
       if ( annotation == null ) {
          return EMPTY_FEATURE_ARRAY;
       }
@@ -65,26 +65,40 @@ final public class OntologyConceptUtil {
 
    /**
     * @param annotation -
-    * @return steram of OntologyConcept
+    * @return stream of OntologyConcept
     */
-   static private Stream<OntologyConcept> getOntologyConceptStream( final IdentifiedAnnotation
annotation ) {
-      return Arrays.stream( getOntologyConcepts( annotation ) )
+   static public Stream<OntologyConcept> getOntologyConceptStream( final IdentifiedAnnotation
annotation ) {
+      return Arrays.stream( getConceptFeatureStructures( annotation ) )
             .filter( OntologyConcept.class::isInstance )
             .map( fs -> (OntologyConcept)fs )
             .filter( isSchemeOk )
             .filter( isCodeOk );
    }
 
+   /**
+    * @param annotation -
+    * @return stream of OntologyConcept
+    */
+   static public Collection<OntologyConcept> getOntologyConcepts( final IdentifiedAnnotation
annotation ) {
+      return getOntologyConceptStream( annotation ).collect( Collectors.toSet() );
+   }
 
    /**
     * @param annotation -
-    * @return set of all Umls Concepts associated with the annotation
+    * @return stream of all Umls Concepts associated with the annotation
     */
-   static public Collection<UmlsConcept> getConcepts( final IdentifiedAnnotation annotation
) {
-      return Arrays.stream( getOntologyConcepts( annotation ) )
+   static public Stream<UmlsConcept> getUmlsConceptStream( final IdentifiedAnnotation
annotation ) {
+      return getOntologyConceptStream( annotation )
             .filter( UmlsConcept.class::isInstance )
-            .map( fs -> (UmlsConcept)fs )
-            .collect( Collectors.toSet() );
+            .map( fs -> (UmlsConcept)fs );
+   }
+
+   /**
+    * @param annotation -
+    * @return set of all Umls Concepts associated with the annotation
+    */
+   static public Collection<UmlsConcept> getUmlsConcepts( final IdentifiedAnnotation
annotation ) {
+      return getUmlsConceptStream( annotation ).collect( Collectors.toSet() );
    }
 
 
@@ -97,8 +111,7 @@ final public class OntologyConceptUtil {
     * @return set of all Umls cuis associated with the annotation
     */
    static public Collection<String> getCuis( final IdentifiedAnnotation annotation
) {
-      return getConcepts( annotation )
-            .stream()
+      return getUmlsConceptStream( annotation )
             .map( UmlsConcept::getCui )
             .collect( Collectors.toSet() );
    }
@@ -108,8 +121,7 @@ final public class OntologyConceptUtil {
     * @return set of all Umls tuis associated with the annotation
     */
    static public Collection<String> getTuis( final IdentifiedAnnotation annotation
) {
-      return getConcepts( annotation )
-            .stream()
+      return getUmlsConceptStream( annotation )
             .map( UmlsConcept::getTui )
             .collect( Collectors.toSet() );
    }

Modified: ctakes/trunk/ctakes-core/src/test/java/org/apache/ctakes/core/util/OntologyConceptUtilTester.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/test/java/org/apache/ctakes/core/util/OntologyConceptUtilTester.java?rev=1742321&r1=1742320&r2=1742321&view=diff
==============================================================================
--- ctakes/trunk/ctakes-core/src/test/java/org/apache/ctakes/core/util/OntologyConceptUtilTester.java
(original)
+++ ctakes/trunk/ctakes-core/src/test/java/org/apache/ctakes/core/util/OntologyConceptUtilTester.java
Wed May  4 19:19:02 2016
@@ -156,7 +156,7 @@ public class OntologyConceptUtilTester {
    @Test
    public void testGetConcepts() {
       assertEquals( "Null IdentifiedAnnotation should have no concepts", 0,
-            OntologyConceptUtil.getConcepts( null ).size() );
+            OntologyConceptUtil.getUmlsConcepts( null ).size() );
       assertConceptCount( TUI_1_CUI_1, 1 );
       assertConceptCount( TUI_1_CUI_2_CODE_A1, 1 );
       assertConceptCount( TUI_2_CUI_3_CODE_B3, 1 );
@@ -166,7 +166,7 @@ public class OntologyConceptUtilTester {
 
    static private void assertConceptCount( final IdentifiedAnnotation annotation, final int
wantedCount ) {
       assertEquals( "Incorrect number of UmlsConcepts", wantedCount,
-            OntologyConceptUtil.getConcepts( annotation ).size() );
+            OntologyConceptUtil.getUmlsConcepts( annotation ).size() );
    }
 
    @Test



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