Remove Serializable interface from OntologyResource

It makes no sense to have OntologyResource serializable if the actual
implementation relies on non-serializable states supplied by Jena.

Remove unnecessary transient on Jena fields.

Fix a few fields that should be final.

Author: arteymix

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

@@ -37,13 +37,11 @@ abstract class AbstractOntologyResource implements OntologyResource {
 
     protected static Logger log = LoggerFactory.getLogger( AbstractOntologyResource.class );
 
-    private static final long serialVersionUID = 1L;
-
     private static final Comparator<OntologyResource> comparator = Comparator
             .comparing( OntologyResource::getScore, nullsLast( reverseOrder() ) )
             .thenComparing( OntologyResource::getUri, nullsLast( naturalOrder() ) );
 
-    private transient final OntResource res;
+    private final OntResource res;
     @Nullable
     private final Double score;
 

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

@@ -30,8 +30,6 @@
 import org.apache.commons.lang3.time.StopWatch;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
-import ubic.basecode.ontology.jena.vocabulary.BFO;
-import ubic.basecode.ontology.jena.vocabulary.RO;
 import ubic.basecode.ontology.model.OntologyIndividual;
 import ubic.basecode.ontology.model.OntologyModel;
 import ubic.basecode.ontology.model.OntologyResource;

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

@@ -22,7 +22,6 @@
 import com.hp.hpl.jena.rdf.model.Resource;
 import com.hp.hpl.jena.rdf.model.Statement;
 import com.hp.hpl.jena.vocabulary.RDFS;
-import ubic.basecode.ontology.jena.vocabulary.OBO;
 import ubic.basecode.ontology.model.AnnotationProperty;
 
 import javax.annotation.Nullable;

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

@@ -25,11 +25,6 @@
  */
 class DatatypePropertyImpl extends OntologyPropertyImpl implements DatatypeProperty {
 
-    /**
-     *
-     */
-    private static final long serialVersionUID = 1L;
-
     private final Class<?> type;
 
     public DatatypePropertyImpl( com.hp.hpl.jena.ontology.DatatypeProperty resource ) {

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

@@ -21,7 +21,6 @@
 import com.hp.hpl.jena.rdf.model.*;
 import com.hp.hpl.jena.vocabulary.OWL2;
 import com.hp.hpl.jena.vocabulary.RDFS;
-import ubic.basecode.ontology.jena.vocabulary.OBO;
 
 import java.util.Collection;
 import java.util.HashSet;

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

@@ -34,16 +34,11 @@
  */
 class ObjectPropertyImpl extends OntologyPropertyImpl implements ubic.basecode.ontology.model.ObjectProperty {
 
-    /**
-     *
-     */
-    private static final long serialVersionUID = 1L;
     private final com.hp.hpl.jena.ontology.ObjectProperty resource;
     private final Set<Restriction> additionalRestrictions;
 
     public ObjectPropertyImpl( ObjectProperty resource, Set<Restriction> additionalRestrictions ) {
         super( resource );
-        this.isFunctional = resource.isFunctionalProperty();
         this.resource = resource;
         this.additionalRestrictions = additionalRestrictions;
     }

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

@@ -29,12 +29,8 @@
 class OntologyCardinalityRestrictionImpl extends OntologyRestrictionImpl implements
         OntologyCardinalityRestriction {
 
-    /**
-     *
-     */
-    private static final long serialVersionUID = 1L;
-    int cardinality = 0;
-    CardinalityType cardType;
+    private final int cardinality;
+    private final CardinalityType cardType;
 
     public OntologyCardinalityRestrictionImpl( Restriction resource, Set<Restriction> additionalRestrictions ) {
         super( resource, additionalRestrictions );

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

@@ -34,10 +34,6 @@
  * @author pavlidis
  */
 class OntologyClassRestrictionImpl extends OntologyRestrictionImpl implements OntologyClassRestriction {
-    /**
-     *
-     */
-    private static final long serialVersionUID = 1L;
     private final RDFNode value;
     private final OntologyTerm restrictedTo;
     private final Set<Restriction> additionalRestrictions;

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

@@ -29,10 +29,6 @@
  */
 class OntologyDatatypeRestrictionImpl extends OntologyRestrictionImpl implements OntologyDatatypeRestriction {
 
-    /**
-     *
-     */
-    private static final long serialVersionUID = 1L;
     private final Class<?> type;
 
     public OntologyDatatypeRestrictionImpl( Restriction resource, Set<Restriction> additionalRestrcitions ) {

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

@@ -35,8 +35,6 @@
  */
 class OntologyIndividualImpl extends AbstractOntologyResource implements OntologyIndividual {
 
-    private static final long serialVersionUID = -6164561945940667693L;
-
     private final Individual ind;
     private final Set<Restriction> additionalRestrictions;