Merge branch 'hotfix-1.1.14'

Author: arteymix

pom.xml

@@ -5,7 +5,7 @@
 	<name>baseCode</name>
 	<groupId>baseCode</groupId>
 	<artifactId>baseCode</artifactId>
-	<version>1.1.13</version>
+	<version>1.1.14</version>
 	<inceptionYear>2003</inceptionYear>
 	<description>
 		<![CDATA[Data structures, math and statistics tools, and utilities that are often needed across projects.]]>

src/ubic/basecode/ontology/jena/JenaUtils.java

@@ -18,17 +18,16 @@ public static Collection<OntClass> getParents( OntModel model, Collection<OntCla
         if ( ontClasses.isEmpty() ) {
             return Collections.emptySet();
         }
-        Collection<OntClass> result = new HashSet<>();
         Iterator<OntClass> it = ontClasses.iterator();
         ExtendedIterator<OntClass> iterator = it.next()
                 .inModel( model )
                 .as( OntClass.class )
-                .listSuperClasses( direct )
-                .filterDrop( new PredicateFilter<>( o -> o.equals( model.getProfile().THING() ) ) );
+                .listSuperClasses( direct );
         while ( it.hasNext() ) {
-            iterator = iterator.andThen( it.next().inModel( model ).as( OntClass.class ).listSuperClasses( true ) );
+            iterator = iterator.andThen( it.next().inModel( model ).as( OntClass.class ).listSuperClasses( direct ) );
         }
 
+        Collection<OntClass> result = new HashSet<>();
         while ( iterator.hasNext() ) {
             OntClass c = iterator.next();
 
@@ -49,6 +48,10 @@ public static Collection<OntClass> getParents( OntModel model, Collection<OntCla
             if ( c.getURI() == null )
                 continue;
 
+            // owl:Thing
+            if ( c.equals( model.getProfile().THING() ) )
+                continue;
+
             result.add( c );
         }
 

src/ubic/basecode/ontology/jena/OntologyTermImpl.java

@@ -194,16 +194,8 @@ public Collection<OntologyRestriction> getRestrictions() {
      */
     @Override
     public String getTerm() {
-        String res;
-        String label = getLabel();
-        String localName = getLocalName();
-        if ( label != null ) {
-            res = label;
-        } else if ( localName != null ) {
-            res = localName;
-        } else if ( this.getUri() != null ) {
-            res = this.getUri();
-        } else {
+        String res = getLabel();
+        if ( res == null ) {
             res = ontResource.toString();
         }
         return res;

src/ubic/basecode/ontology/model/OntologyResource.java

@@ -25,8 +25,14 @@
  */
 public interface OntologyResource extends Serializable, Comparable<OntologyResource> {
 
+    /**
+     * A label, if known, otherwise null.
+     */
     String getLabel();
 
+    /**
+     * A URI if known, otherwise null.
+     */
     String getUri();
 
     /**

src/ubic/basecode/ontology/model/OntologyTerm.java

@@ -80,6 +80,10 @@ default Collection<OntologyTerm> getParents( boolean direct, boolean includeAddi
 
     Collection<OntologyRestriction> getRestrictions();
 
+    /**
+     * @deprecated use {@link #getLabel()} instead.
+     */
+    @Deprecated
     String getTerm();
 
     boolean isRoot();

src/ubic/basecode/ontology/model/OntologyTermSimple.java

@@ -74,12 +74,12 @@ public Collection<OntologyIndividual> getIndividuals( boolean direct ) {
 
     @Override
     public String getLabel() {
-        return this.getTerm();
+        return term;
     }
 
     @Override
     public String getLocalName() {
-        return this.getTerm();
+        return term;
     }
 
     @Override

test/ubic/basecode/ontology/OntologyTermTest.java

@@ -191,7 +191,7 @@ public void testGetParentsFromMultipleTerms() {
         OntologyTerm brain = uberon.getTerm( "http://purl.obolibrary.org/obo/UBERON_0000955" );
         OntologyTerm liver = uberon.getTerm( "http://purl.obolibrary.org/obo/UBERON_0002107" );
         Collection<OntologyTerm> children = uberon.getParents( Arrays.asList( brain, liver ), false, true );
-        assertEquals( 22, children.size() );
+        assertEquals( 30, children.size() );
         assertFalse( children.contains( uberon.getTerm( OWL2.Nothing.getURI() ) ) );
     }