Add efficient method for gathering children and parents of multiple terms

This is especially true for children as we only need to walk once
through the statement to gather those via "part of" and "proper part of".

Parents no longer include owl:Thing and children owl:Nothing nor
deprecated terms. There's a new option to retain them.

Return an ExtendedIterator in OntologySearch so that the service can
perform conversion and filtering of obsolete terms itself.

Move Jena-specific implementation details under ubic.basecode.ontology.jena

This package is now considered implementation details and should not be
used externally.

Author: arteymix

src/ubic/basecode/ontology/OntologyUtil.java

@@ -12,10 +12,9 @@
  * an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the
  * specific language governing permissions and limitations under the License.
  */
-package ubic.basecode.ontology.providers;
+package ubic.basecode.ontology.jena;
 
 import com.hp.hpl.jena.ontology.OntModel;
-import ubic.basecode.ontology.OntologyLoader;
 
 /**
  * This class has some stuff that's specific to in-memory ontologies. Unlike database backed ontologies we don't use a
@@ -29,5 +28,4 @@ public abstract class AbstractOntologyMemoryBackedService extends AbstractOntolo
     protected synchronized OntModel loadModel() {
         return OntologyLoader.loadMemoryModel( this.getOntologyUrl(), this.getOntologyName() );
     }
-
 }

…AbstractOntologyMemoryBackedService.java …AbstractOntologyMemoryBackedService.javasrc/ubic/basecode/ontology/providers/AbstractOntologyMemoryBackedService.java renamed to src/ubic/basecode/ontology/jena/AbstractOntologyMemoryBackedService.java src/ubic/basecode/ontology/providers/AbstractOntologyMemoryBackedService.java renamed to src/ubic/basecode/ontology/jena/AbstractOntologyMemoryBackedService.java

@@ -1,8 +1,8 @@
 /*
  * The basecode project
- * 
+ *
  * Copyright (c) 2007-2019 University of British Columbia
- * 
+ *
  * Licensed under the Apache License, Version 2.0 (the "License");
  * you may not use this file except in compliance with the License.
  * You may obtain a copy of the License at
@@ -16,32 +16,68 @@
  * limitations under the License.
  *
  */
-package ubic.basecode.ontology.model;
+package ubic.basecode.ontology.jena;
 
+import com.hp.hpl.jena.ontology.OntResource;
+import com.hp.hpl.jena.rdf.model.Resource;
+import com.hp.hpl.jena.vocabulary.OWL2;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
+import ubic.basecode.ontology.model.OntologyResource;
+
+import java.util.Comparator;
+import java.util.Objects;
 
 /**
  * @author pavlidis
- * 
  */
 public abstract class AbstractOntologyResource implements OntologyResource {
 
     protected static Logger log = LoggerFactory.getLogger( AbstractOntologyResource.class );
 
     private static final long serialVersionUID = 1L;
 
+    private transient final OntResource res;
+
+    protected AbstractOntologyResource( OntResource resource ) {
+        this.res = resource;
+    }
+
+    @Override
+    public String getUri() {
+        return res.getURI();
+    }
+
+    public String getLabel() {
+        String label = res.getLabel( "EN" );
+        if ( label == null ) {
+            label = res.getLabel( null );
+        }
+        if ( label == null ) {
+            label = res.getLocalName();
+        }
+        if ( label == null ) {
+            label = res.getURI();
+        }
+        return label;
+    }
+
+    @Override
+    public boolean isObsolete() {
+        return res.hasLiteral( OWL2.deprecated, true );
+    }
+
     @Override
     public int compareTo( OntologyResource other ) {
-        return this.getUri().compareTo( other.getUri() );
+        return Objects.compare( getUri(), other.getUri(), Comparator.nullsLast( Comparator.naturalOrder() ) );
     }
 
     @Override
     public boolean equals( Object obj ) {
         if ( this == obj ) return true;
         if ( obj == null ) return false;
         if ( getClass() != obj.getClass() ) return false;
-        final AbstractOntologyResource other = ( AbstractOntologyResource ) obj;
+        final OntologyResource other = ( OntologyResource ) obj;
         if ( getLabel() == null ) {
             if ( other.getLabel() != null ) return false;
         } else if ( !getLabel().equals( other.getLabel() ) ) return false;
@@ -51,16 +87,17 @@ public boolean equals( Object obj ) {
         return true;
     }
 
-    @Override
-    public abstract String getUri();
-
     @Override
     public int hashCode() {
-        final int PRIME = 31;
-        int result = 1;
-        result = PRIME * result + ( ( getLabel() == null ) ? 0 : getLabel().hashCode() );
-        result = PRIME * result + ( ( getUri() == null ) ? 0 : getUri().hashCode() );
-        return result;
+        return Objects.hash( getLabel(), getUri() );
     }
 
-}
+    @Override
+    public String toString() {
+        String s = getLabel();
+        if ( s == null ) {
+            s = res.toString();
+        }
+        return s;
+    }
+}