Author: seanfinan
Date: Fri Oct 23 15:48:47 2020
New Revision: 1882785
URL: http://svn.apache.org/viewvc?rev=1882785&view=rev
Log:
Add get methods that take multiple cuis, tuis, codes
Add get methods that take SemanticTui, SemanticGroup
Modified:
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/annotation/OntologyConceptUtil.java
Modified:
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/annotation/OntologyConceptUtil.java
URL:
http://svn.apache.org/viewvc/ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/annotation/OntologyConceptUtil.java?rev=1882785&r1=1882784&r2=1882785&view=diff
==============================================================================
---
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/annotation/OntologyConceptUtil.java
(original)
+++
ctakes/trunk/ctakes-core/src/main/java/org/apache/ctakes/core/util/annotation/OntologyConceptUtil.java
Fri Oct 23 15:48:47 2020
@@ -69,10 +69,10 @@ final public class OntologyConceptUtil {
*/
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 );
+ .filter( OntologyConcept.class::isInstance )
+ .map( fs -> (OntologyConcept)fs )
+ .filter( isSchemeOk )
+ .filter( isCodeOk );
}
/**
@@ -89,8 +89,8 @@ final public class OntologyConceptUtil {
*/
static public Stream<UmlsConcept> getUmlsConceptStream( final
IdentifiedAnnotation annotation ) {
return Arrays.stream( getConceptFeatureStructures( annotation ) )
- .filter( UmlsConcept.class::isInstance )
- .map( fs -> (UmlsConcept)fs );
+ .filter( UmlsConcept.class::isInstance )
+ .map( fs -> (UmlsConcept)fs );
}
/**
@@ -118,8 +118,6 @@ final public class OntologyConceptUtil {
}
}
- ;
-
/**
* @param annotation -
@@ -263,6 +261,21 @@ final public class OntologyConceptUtil {
return getCodes( JCasUtil.select( jcas, IdentifiedAnnotation.class ),
schemeName );
}
+ /**
+ * @param jcas -
+ * @return set of all semantic Types in jcas
+ */
+ static public Collection<SemanticTui> getSemanticTuis( final JCas jcas ) {
+ return getSemanticTuis( JCasUtil.select( jcas,
IdentifiedAnnotation.class ) );
+ }
+
+ /**
+ * @param jcas -
+ * @return set of all semantic groups in jcas
+ */
+ static public Collection<SemanticGroup> getSemanticGroups( final JCas jcas
) {
+ return getSemanticGroups( JCasUtil.select( jcas,
IdentifiedAnnotation.class ) );
+ }
//
// Get cuis, tuis, or codes for all IdentifiedAnnotations in a lookup
window
@@ -327,9 +340,9 @@ final public class OntologyConceptUtil {
*/
static public Collection<String> getCuis( final
Collection<IdentifiedAnnotation> annotations ) {
return annotations.stream()
- .map( OntologyConceptUtil::getCuis )
- .flatMap( Collection::stream )
- .collect( Collectors.toSet() );
+ .map( OntologyConceptUtil::getCuis )
+ .flatMap( Collection::stream )
+ .collect( Collectors.toSet() );
}
/**
@@ -338,9 +351,9 @@ final public class OntologyConceptUtil {
*/
static public Map<String, Long> getCuiCounts( final
Collection<IdentifiedAnnotation> annotations ) {
return annotations.stream()
- .map( OntologyConceptUtil::getCuis )
- .flatMap( Collection::stream )
- .collect( Collectors.groupingBy( Function.identity(),
Collectors.counting() ) );
+ .map( OntologyConceptUtil::getCuis )
+ .flatMap( Collection::stream )
+ .collect( Collectors.groupingBy( Function.identity(),
Collectors.counting() ) );
}
/**
@@ -349,9 +362,9 @@ final public class OntologyConceptUtil {
*/
static public Collection<String> getTuis( final
Collection<IdentifiedAnnotation> annotations ) {
return annotations.stream()
- .map( OntologyConceptUtil::getTuis )
- .flatMap( Collection::stream )
- .collect( Collectors.toSet() );
+ .map( OntologyConceptUtil::getTuis )
+ .flatMap( Collection::stream )
+ .collect( Collectors.toSet() );
}
@@ -361,10 +374,10 @@ final public class OntologyConceptUtil {
*/
static public Map<String, Collection<String>> getSchemeCodes( final
Collection<IdentifiedAnnotation> annotations ) {
return annotations.stream()
- .map( OntologyConceptUtil::getSchemeCodes )
- .map( Map::entrySet )
- .flatMap( Collection::stream )
- .collect( Collectors.toMap( Map.Entry::getKey,
Map.Entry::getValue, mergeSets ) );
+ .map( OntologyConceptUtil::getSchemeCodes )
+ .map( Map::entrySet )
+ .flatMap( Collection::stream )
+ .collect( Collectors.toMap( Map.Entry::getKey,
Map.Entry::getValue, mergeSets ) );
}
/**
@@ -373,9 +386,9 @@ final public class OntologyConceptUtil {
*/
static public Collection<String> getCodes( final
Collection<IdentifiedAnnotation> annotations ) {
return annotations.stream()
- .map( OntologyConceptUtil::getCodes )
- .flatMap( Collection::stream )
- .collect( Collectors.toSet() );
+ .map( OntologyConceptUtil::getCodes )
+ .flatMap( Collection::stream )
+ .collect( Collectors.toSet() );
}
/**
@@ -386,12 +399,34 @@ final public class OntologyConceptUtil {
static public Collection<String> getCodes( final
Collection<IdentifiedAnnotation> annotations,
final String schemeName ) {
return annotations.stream()
- .map( annotation -> getCodes( annotation, schemeName ) )
- .flatMap( Collection::stream )
- .collect( Collectors.toSet() );
+ .map( annotation -> getCodes( annotation, schemeName )
)
+ .flatMap( Collection::stream )
+ .collect( Collectors.toSet() );
}
+ /**
+ * @param annotations -
+ * @return set of Semantic Types associated the named scheme
+ */
+ static public Collection<SemanticTui> getSemanticTuis( final
Collection<IdentifiedAnnotation> annotations ) {
+ return annotations.stream()
+ .map( SemanticTui::getTuis )
+ .flatMap( Collection::stream )
+ .collect( Collectors.toSet() );
+ }
+
+ /**
+ * @param annotations -
+ * @return set of ontology codes associated the named scheme
+ */
+ static public Collection<SemanticGroup> getSemanticGroups( final
Collection<IdentifiedAnnotation> annotations ) {
+ return annotations.stream()
+ .map( SemanticGroup::getGroups )
+ .flatMap( Collection::stream )
+ .collect( Collectors.toSet() );
+ }
+
//
// Get all IdentifiedAnnotations in jcas with given cui, tui, or code
//
@@ -426,6 +461,76 @@ final public class OntologyConceptUtil {
return getAnnotationsByCode( JCasUtil.select( jcas,
IdentifiedAnnotation.class ), code );
}
+ /**
+ * @param jcas -
+ * @param tui semantic type of interest
+ * @return all IdentifiedAnnotations that have the given tui
+ */
+ static public Collection<IdentifiedAnnotation> getAnnotationsBySemanticTui(
final JCas jcas,
+
final SemanticTui tui ) {
+ return getAnnotationsBySemanticTui( JCasUtil.select( jcas,
IdentifiedAnnotation.class ), tui );
+ }
+
+ /**
+ * @param jcas -
+ * @param group semantic group of interest
+ * @return all IdentifiedAnnotations that have the given tui
+ */
+ static public Collection<IdentifiedAnnotation>
getAnnotationsBySemanticGroup( final JCas jcas,
+
final SemanticGroup group ) {
+ return getAnnotationsBySemanticGroup( JCasUtil.select( jcas,
IdentifiedAnnotation.class ), group );
+ }
+
+ /**
+ * @param jcas -
+ * @param cuis cuis of interest
+ * @return all IdentifiedAnnotations that have the given tui
+ */
+ static public Collection<IdentifiedAnnotation> getAnnotationsByCuis( final
JCas jcas,
+ final
String... cuis ) {
+ return getAnnotationsByCuis( JCasUtil.select( jcas,
IdentifiedAnnotation.class ), cuis );
+ }
+
+ /**
+ * @param jcas -
+ * @param tuis tuis of interest
+ * @return all IdentifiedAnnotations that have the given tui
+ */
+ static public Collection<IdentifiedAnnotation> getAnnotationsByTuis( final
JCas jcas,
+ final
String... tuis ) {
+ return getAnnotationsByTuis( JCasUtil.select( jcas,
IdentifiedAnnotation.class ), tuis );
+ }
+
+ /**
+ * @param jcas -
+ * @param codes codes of interest
+ * @return all IdentifiedAnnotations that have the given tui
+ */
+ static public Collection<IdentifiedAnnotation> getAnnotationsByCodes( final
JCas jcas,
+ final
String... codes ) {
+ return getAnnotationsByCodes( JCasUtil.select( jcas,
IdentifiedAnnotation.class ), codes );
+ }
+
+ /**
+ * @param jcas -
+ * @param tuis tuis of interest
+ * @return all IdentifiedAnnotations that have the given tui
+ */
+ static public Collection<IdentifiedAnnotation>
getAnnotationsBySemanticTuis( final JCas jcas,
+
final SemanticTui... tuis ) {
+ return getAnnotationsBySemanticTuis( JCasUtil.select( jcas,
IdentifiedAnnotation.class ), tuis );
+ }
+
+ /**
+ * @param jcas -
+ * @param groups tuis of interest
+ * @return all IdentifiedAnnotations that have the given tui
+ */
+ static public Collection<IdentifiedAnnotation>
getAnnotationsBySemanticGroups( final JCas jcas,
+
final SemanticGroup... groups ) {
+ return getAnnotationsBySemanticGroups( JCasUtil.select( jcas,
IdentifiedAnnotation.class ), groups );
+ }
+
//
// Get all IdentifiedAnnotations in lookup window with given cui, tui, or
code
@@ -481,8 +586,8 @@ final public class OntologyConceptUtil {
final Collection<IdentifiedAnnotation> annotations,
final String cui ) {
return annotations.stream()
- .filter( annotation -> getCuis( annotation ).contains( cui ) )
- .collect( Collectors.toSet() );
+ .filter( annotation -> getCuis( annotation ).contains(
cui ) )
+ .collect( Collectors.toSet() );
}
@@ -495,8 +600,8 @@ final public class OntologyConceptUtil {
final Collection<IdentifiedAnnotation> annotations,
final String tui ) {
return annotations.stream()
- .filter( annotation -> getTuis( annotation ).contains( tui ) )
- .collect( Collectors.toSet() );
+ .filter( annotation -> getTuis( annotation ).contains(
tui ) )
+ .collect( Collectors.toSet() );
}
@@ -509,8 +614,114 @@ final public class OntologyConceptUtil {
final Collection<IdentifiedAnnotation> annotations,
final String code ) {
return annotations.stream()
- .filter( annotation -> getCodes( annotation ).contains( code ) )
- .collect( Collectors.toSet() );
+ .filter( annotation -> getCodes( annotation
).contains( code ) )
+ .collect( Collectors.toSet() );
+ }
+
+ /**
+ * @param annotations annotations for which codes should be found
+ * @param tui semantic type of interest
+ * @return all IdentifiedAnnotations that have the given tui
+ */
+ static public Collection<IdentifiedAnnotation> getAnnotationsBySemanticTui(
+ final Collection<IdentifiedAnnotation> annotations,
+ final SemanticTui tui ) {
+ return annotations.stream()
+ .filter( annotation -> SemanticTui.getTuis( annotation
).contains( tui ) )
+ .collect( Collectors.toSet() );
+ }
+
+ /**
+ * @param annotations annotations for which codes should be found
+ * @param group semantic group of interest
+ * @return all IdentifiedAnnotations that have the given tui
+ */
+ static public Collection<IdentifiedAnnotation>
getAnnotationsBySemanticGroup(
+ final Collection<IdentifiedAnnotation> annotations,
+ final SemanticGroup group ) {
+ return annotations.stream()
+ .filter( annotation -> SemanticGroup.getGroups(
annotation ).contains( group ) )
+ .collect( Collectors.toSet() );
+ }
+
+ /**
+ * @param annotations annotations for which codes should be found
+ * @param cuis cuis of interest
+ * @return all IdentifiedAnnotations that have the given cui
+ */
+ static public Collection<IdentifiedAnnotation> getAnnotationsByCuis(
+ final Collection<IdentifiedAnnotation> annotations,
+ final String... cuis ) {
+ final Collection<String> cuiSet = new HashSet<>( Arrays.asList( cuis ) );
+ final Predicate<IdentifiedAnnotation> cuiMatch
+ = a -> getCuis( a ).stream().anyMatch( cuiSet::contains );
+ return annotations.stream()
+ .filter( cuiMatch )
+ .collect( Collectors.toSet() );
+ }
+
+ /**
+ * @param annotations annotations for which codes should be found
+ * @param tuis tuis of interest
+ * @return all IdentifiedAnnotations that have the given tui
+ */
+ static public Collection<IdentifiedAnnotation> getAnnotationsByTuis(
+ final Collection<IdentifiedAnnotation> annotations,
+ final String... tuis ) {
+ final Collection<String> tuiSet = new HashSet<>( Arrays.asList( tuis ) );
+ final Predicate<IdentifiedAnnotation> tuiMatch
+ = a -> getTuis( a ).stream().anyMatch( tuiSet::contains );
+ return annotations.stream()
+ .filter( tuiMatch )
+ .collect( Collectors.toSet() );
+ }
+
+ /**
+ * @param annotations annotations for which codes should be found
+ * @param codes codes of interest
+ * @return all IdentifiedAnnotations that have the given code
+ */
+ static public Collection<IdentifiedAnnotation> getAnnotationsByCodes(
+ final Collection<IdentifiedAnnotation> annotations,
+ final String... codes ) {
+ final Collection<String> codeSet = new HashSet<>( Arrays.asList( codes )
);
+ final Predicate<IdentifiedAnnotation> codeMatch
+ = a -> getCodes( a ).stream().anyMatch( codeSet::contains );
+ return annotations.stream()
+ .filter( codeMatch )
+ .collect( Collectors.toSet() );
+ }
+
+ /**
+ * @param annotations annotations for which codes should be found
+ * @param tuis semantic types of interest
+ * @return all IdentifiedAnnotations that have the given code
+ */
+ static public Collection<IdentifiedAnnotation> getAnnotationsBySemanticTuis(
+ final Collection<IdentifiedAnnotation> annotations,
+ final SemanticTui... tuis ) {
+ final Collection<SemanticTui> tuiSet = new HashSet<>( Arrays.asList(
tuis ) );
+ final Predicate<IdentifiedAnnotation> tuiMatch
+ = a -> SemanticTui.getTuis( a ).stream().anyMatch(
tuiSet::contains );
+ return annotations.stream()
+ .filter( tuiMatch )
+ .collect( Collectors.toSet() );
+ }
+
+ /**
+ * @param annotations annotations for which codes should be found
+ * @param groups semantic groups of interest
+ * @return all IdentifiedAnnotations that have the given code
+ */
+ static public Collection<IdentifiedAnnotation>
getAnnotationsBySemanticGroups(
+ final Collection<IdentifiedAnnotation> annotations,
+ final SemanticGroup... groups ) {
+ final Collection<SemanticGroup> groupSet = new HashSet<>( Arrays.asList(
groups ) );
+ final Predicate<IdentifiedAnnotation> groupMatch
+ = a -> SemanticGroup.getGroups( a ).stream().anyMatch(
groupSet::contains );
+ return annotations.stream()
+ .filter( groupMatch )
+ .collect( Collectors.toSet() );
}
}
