Merge branch 'hotfix-1.1.13'

pom.xml

@@ -5,7 +5,7 @@
 	<name>baseCode</name>
 	<groupId>baseCode</groupId>
 	<artifactId>baseCode</artifactId>
-	<version>1.1.12</version>
+	<version>1.1.13</version>
 	<inceptionYear>2003</inceptionYear>
 	<description>
 		<![CDATA[Data structures, math and statistics tools, and utilities that are often needed across projects.]]>

src/ubic/basecode/ontology/providers/AbstractOntologyMemoryBackedService.java → src/ubic/basecode/ontology/jena/AbstractOntologyMemoryBackedService.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() );
     }
-
 }

src/ubic/basecode/ontology/model/AbstractOntologyResource.java → src/ubic/basecode/ontology/jena/AbstractOntologyResource.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;
+    }
+}