Few performance optimization based on Gemma profiling

Avoid using getLabel() when hashing or comparing ontology resources
unless both URIs are null.

Lazily cache a label in getLabel().

Ensure that parents or children are collected in a set.

Author: arteymix

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

@@ -45,6 +45,9 @@ abstract class AbstractOntologyResource implements OntologyResource {
     @Nullable
     private final Double score;
 
+    private String _label;
+    private boolean _isLabelNull = false;
+
     protected AbstractOntologyResource( OntResource resource ) {
         this.res = resource;
         this.score = null;
@@ -67,10 +70,15 @@ public String getLocalName() {
 
     @Override
     public String getLabel() {
+        if ( _label != null || _isLabelNull ) {
+            return _label;
+        }
         String label = res.getLabel( "EN" );
         if ( label == null ) {
             label = res.getLabel( null );
         }
+        _label = label;
+        _isLabelNull = label == null;
         return label;
     }
 
@@ -104,19 +112,20 @@ public int compareTo( OntologyResource other ) {
     public boolean equals( Object obj ) {
         if ( this == obj ) return true;
         if ( obj == null ) return false;
-        if ( getClass() != obj.getClass() ) return false;
+        if ( !( obj instanceof OntologyResource ) ) {
+            return false;
+        }
         final OntologyResource other = ( OntologyResource ) obj;
-        if ( getLabel() == null ) {
-            if ( other.getLabel() != null ) return false;
-        } else if ( !getLabel().equals( other.getLabel() ) ) return false;
-        if ( getUri() == null ) {
-            return other.getUri() == null;
-        } else return getUri().equals( other.getUri() );
+        if ( getUri() == null && other.getUri() == null ) {
+            return Objects.equals( getLabel(), other.getLabel() );
+        } else {
+            return Objects.equals( getUri(), other.getUri() );
+        }
     }
 
     @Override
     public int hashCode() {
-        return Objects.hash( getLabel(), getUri() );
+        return Objects.hash( getUri() );
     }
 
     @Override

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

@@ -25,6 +25,7 @@
 import ubic.basecode.ontology.model.AnnotationProperty;
 
 import javax.annotation.Nullable;
+import java.util.Objects;
 
 /**
  * Note that this is a concrete instance of the annotation.
@@ -47,20 +48,6 @@ public AnnotationPropertyImpl( com.hp.hpl.jena.ontology.AnnotationProperty prop,
         this.object = object;
     }
 
-    @Override
-    public boolean equals( @Nullable Object obj ) {
-        if ( this == obj ) return true;
-        if ( obj == null ) return false;
-        if ( getClass() != obj.getClass() ) return false;
-        final AnnotationPropertyImpl other = ( AnnotationPropertyImpl ) obj;
-        if ( object == null ) {
-            if ( other.object != null ) return false;
-        } else if ( !object.equals( other.object ) ) return false;
-        if ( property == null ) {
-            return other.property == null;
-        } else return property.equals( other.property );
-    }
-
     @Override
     public String getProperty() {
         if ( property.getLabel( null ) != null ) {
@@ -95,13 +82,25 @@ public boolean isObsolete() {
         return super.isObsolete() || property.hasSuperProperty( OBO.ObsoleteProperty, false );
     }
 
+    @Override
+    public boolean equals( @Nullable Object obj ) {
+        if ( this == obj ) return true;
+        if ( obj == null ) return false;
+        if ( obj instanceof AnnotationPropertyImpl ) {
+            final AnnotationPropertyImpl other = ( AnnotationPropertyImpl ) obj;
+            return super.equals( other )
+                    && Objects.equals( object, other.object );
+        } else if ( obj instanceof AnnotationProperty ) {
+            final AnnotationProperty other = ( AnnotationProperty ) obj;
+            return super.equals( other )
+                    && Objects.equals( getContents(), other.getContents() );
+        }
+        return false;
+    }
+
     @Override
     public int hashCode() {
-        final int PRIME = 31;
-        int result = 1;
-        result = PRIME * result + ( ( object == null ) ? 0 : object.hashCode() );
-        result = PRIME * result + ( ( property == null ) ? 0 : property.hashCode() );
-        return result;
+        return Objects.hash( super.hashCode(), object );
     }
 
     @Override

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

@@ -46,7 +46,7 @@ private static Collection<OntClass> getParentsInternal( OntModel model, Collecti
                 .map( t -> as( t, OntClass.class ) )
                 .filter( Optional::isPresent )
                 .map( Optional::get )
-                .collect( Collectors.toList() );
+                .collect( Collectors.toSet() );
         if ( ontClasses.isEmpty() ) {
             return Collections.emptySet();
         }
@@ -104,18 +104,18 @@ public static Collection<OntClass> getChildren( OntModel model, Collection<OntCl
     }
 
     public static Collection<OntClass> getChildrenInternal( OntModel model, Collection<OntClass> terms, boolean direct, @Nullable Set<Restriction> additionalRestrictions ) {
-        terms = terms.stream()
+        Set<OntClass> termsSet = terms.stream()
                 .map( t -> t.inModel( model ) )
                 .filter( t -> t.canAs( OntClass.class ) )
                 .map( t -> as( t, OntClass.class ) )
                 .filter( Optional::isPresent )
                 .map( Optional::get )
-                .collect( Collectors.toList() );
-        if ( terms.isEmpty() ) {
+                .collect( Collectors.toSet() );
+        if ( termsSet.isEmpty() ) {
             return Collections.emptySet();
         }
         StopWatch timer = StopWatch.createStarted();
-        Iterator<OntClass> it = terms.iterator();
+        Iterator<OntClass> it = termsSet.iterator();
         ExtendedIterator<OntClass> iterator = it.next().listSubClasses( direct );
         while ( it.hasNext() ) {
             iterator = iterator.andThen( it.next().listSubClasses( direct ) );
@@ -132,7 +132,7 @@ public static Collection<OntClass> getChildrenInternal( OntModel model, Collecti
                 subClassOf = ResourceFactory.createProperty( makeDirect( subClassOf.getURI() ) );
             }
             Set<Restriction> restrictions = UniqueExtendedIterator.create( additionalRestrictions.iterator() )
-                    .filterKeep( new RestrictionWithValuesFromFilter( terms ) )
+                    .filterKeep( new RestrictionWithValuesFromFilter( termsSet ) )
                     .toSet();
             for ( Restriction r : restrictions ) {
                 result.addAll( model.listResourcesWithProperty( subClassOf, r )

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

@@ -4,16 +4,16 @@
 import com.hp.hpl.jena.rdf.model.Resource;
 import com.hp.hpl.jena.util.iterator.Filter;
 
-import java.util.Collection;
+import java.util.Set;
 
 /**
  * Match {@link Restriction} with values from any of the given resources.
  */
 class RestrictionWithValuesFromFilter extends Filter<Restriction> {
 
-    private final Collection<? extends Resource> resource;
+    private final Set<? extends Resource> resource;
 
-    public RestrictionWithValuesFromFilter( Collection<? extends Resource> resource ) {
+    public RestrictionWithValuesFromFilter( Set<? extends Resource> resource ) {
         this.resource = resource;
     }