Make all Jena-related code package-private

arteymix · arteymix · commit d0ec53509b1a · 2023-06-27T13:33:41.000-07:00
diff --git a/src/ubic/basecode/ontology/jena/AbstractOntologyMemoryBackedService.java b/src/ubic/basecode/ontology/jena/AbstractOntologyMemoryBackedService.java
@@ -14,8 +14,8 @@
  */
 package ubic.basecode.ontology.jena;
 
-import com.hp.hpl.jena.ontology.OntModel;
 import com.hp.hpl.jena.ontology.OntModelSpec;
+import ubic.basecode.ontology.model.OntologyModel;
 import ubic.basecode.util.Configuration;
 
 import java.io.IOException;
@@ -35,13 +35,13 @@ protected String getOntologyUrl() {
     }
 
     @Override
-    protected OntModel loadModel( boolean processImports, InferenceMode inferenceMode ) throws IOException {
-        return OntologyLoader.loadMemoryModel( this.getOntologyUrl(), this.getCacheName(), processImports, this.getSpec( inferenceMode ) );
+    protected OntologyModel loadModel( boolean processImports, InferenceMode inferenceMode ) throws IOException {
+        return new OntologyModelImpl( OntologyLoader.loadMemoryModel( this.getOntologyUrl(), this.getCacheName(), processImports, this.getSpec( inferenceMode ) ) );
     }
 
     @Override
-    protected OntModel loadModelFromStream( InputStream is, boolean processImports, InferenceMode inferenceMode ) {
-        return OntologyLoader.loadMemoryModel( is, this.getOntologyUrl(), processImports, this.getSpec( inferenceMode ) );
+    protected OntologyModel loadModelFromStream( InputStream is, boolean processImports, InferenceMode inferenceMode ) throws IOException {
+        return new OntologyModelImpl( OntologyLoader.loadMemoryModel( is, this.getOntologyUrl(), processImports, this.getSpec( inferenceMode ) ) );
     }
 
     private OntModelSpec getSpec( InferenceMode inferenceMode ) {
diff --git a/src/ubic/basecode/ontology/jena/AbstractOntologyResource.java b/src/ubic/basecode/ontology/jena/AbstractOntologyResource.java
@@ -33,7 +33,7 @@
 /**
  * @author pavlidis
  */
-public abstract class AbstractOntologyResource implements OntologyResource {
+abstract class AbstractOntologyResource implements OntologyResource {
 
     protected static Logger log = LoggerFactory.getLogger( AbstractOntologyResource.class );
 
diff --git a/src/ubic/basecode/ontology/jena/AbstractOntologyService.java b/src/ubic/basecode/ontology/jena/AbstractOntologyService.java
@@ -24,19 +24,16 @@
 import com.hp.hpl.jena.rdf.arp.ParseException;
 import com.hp.hpl.jena.rdf.model.Property;
 import com.hp.hpl.jena.rdf.model.Resource;
-import com.hp.hpl.jena.shared.JenaException;
 import com.hp.hpl.jena.util.iterator.ExtendedIterator;
 import org.apache.commons.lang3.RandomStringUtils;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.commons.lang3.time.StopWatch;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
-import ubic.basecode.ontology.jena.search.OntologyIndexer;
-import ubic.basecode.ontology.jena.search.OntologySearch;
-import ubic.basecode.ontology.jena.search.SearchIndex;
 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;
 import ubic.basecode.ontology.model.OntologyTerm;
 import ubic.basecode.ontology.providers.OntologyService;
@@ -201,7 +198,12 @@ private void initialize( @Nullable InputStream stream, boolean forceLoad, boolea
             return;
 
         try {
-            model = stream != null ? loadModelFromStream( stream, processImports, inferenceMode ) : loadModel( processImports, inferenceMode ); // can take a while.
+            OntologyModel m = stream != null ? loadModelFromStream( stream, processImports, inferenceMode ) : loadModel( processImports, inferenceMode ); // can take a while.
+            if ( m instanceof OntologyModelImpl ) {
+                model = ( ( OntologyModelImpl ) m ).getOntModel();
+            } else {
+                throw new RuntimeException( "Only Jena-based ontology models are supported." );
+            }
         } catch ( Exception e ) {
             if ( isCausedByInterrupt( e ) ) {
                 return;
@@ -491,7 +493,7 @@ public Collection<OntologyIndividual> getTermIndividuals( String uri ) {
 
     @Override
     public Set<OntologyTerm> getParents( Collection<OntologyTerm> terms, boolean direct,
-                                         boolean includeAdditionalProperties, boolean keepObsoletes ) {
+            boolean includeAdditionalProperties, boolean keepObsoletes ) {
         Lock lock = rwLock.readLock();
         try {
             lock.lock();
@@ -510,7 +512,7 @@ public Set<OntologyTerm> getParents( Collection<OntologyTerm> terms, boolean dir
 
     @Override
     public Set<OntologyTerm> getChildren( Collection<OntologyTerm> terms, boolean direct,
-                                          boolean includeAdditionalProperties, boolean keepObsoletes ) {
+            boolean includeAdditionalProperties, boolean keepObsoletes ) {
         Lock lock = rwLock.readLock();
         try {
             lock.lock();
@@ -615,13 +617,13 @@ public void waitForInitializationThread() throws InterruptedException {
      * Delegates the call as to load the model into memory or leave it on disk. Simply delegates to either
      * OntologyLoader.loadMemoryModel( url ); OR OntologyLoader.loadPersistentModel( url, spec );
      */
-    protected abstract OntModel loadModel( boolean processImports, InferenceMode inferenceMode ) throws JenaException, IOException;
+    protected abstract OntologyModel loadModel( boolean processImports, InferenceMode inferenceMode ) throws IOException;
 
 
     /**
      * Load a model from a given input stream.
      */
-    protected abstract OntModel loadModelFromStream( InputStream stream, boolean processImports, InferenceMode inferenceMode ) throws JenaException, IOException;
+    protected abstract OntologyModel loadModelFromStream( InputStream stream, boolean processImports, InferenceMode inferenceMode ) throws IOException;
 
     /**
      * A name for caching this ontology, or null to disable caching.
@@ -633,6 +635,17 @@ protected String getCacheName() {
         return getOntologyName();
     }
 
+    private OntModelSpec getSpec( InferenceMode inferenceMode ) {
+        switch ( inferenceMode ) {
+            case TRANSITIVE:
+                return OntModelSpec.OWL_MEM_TRANS_INF;
+            case NONE:
+                return OntModelSpec.OWL_MEM;
+            default:
+                throw new UnsupportedOperationException( String.format( "Unsupported inference level %s.", inferenceMode ) );
+        }
+    }
+
     @Override
     public void index( boolean force ) {
         String cacheName = getCacheName();
diff --git a/src/ubic/basecode/ontology/jena/AnnotationPropertyImpl.java b/src/ubic/basecode/ontology/jena/AnnotationPropertyImpl.java
@@ -32,7 +32,7 @@
  *
  * @author pavlidis
  */
-public class AnnotationPropertyImpl extends AbstractOntologyResource implements AnnotationProperty {
+class AnnotationPropertyImpl extends AbstractOntologyResource implements AnnotationProperty {
 
     private final String contents;
 
diff --git a/src/ubic/basecode/ontology/jena/BFO.java b/src/ubic/basecode/ontology/jena/BFO.java
@@ -1,8 +1,8 @@
-package ubic.basecode.ontology.jena.vocabulary;
+package ubic.basecode.ontology.jena;
 
 import com.hp.hpl.jena.rdf.model.Property;
 import com.hp.hpl.jena.rdf.model.ResourceFactory;
 
-public class BFO {
+class BFO {
     public static final Property partOf = ResourceFactory.createProperty( "http://purl.obolibrary.org/obo/BFO_0000050" );
 }
diff --git a/src/ubic/basecode/ontology/jena/BnodeFilter.java b/src/ubic/basecode/ontology/jena/BnodeFilter.java
@@ -8,7 +8,7 @@
  *
  * @param <T>
  */
-public class BnodeFilter<T extends Resource> extends Filter<T> {
+class BnodeFilter<T extends Resource> extends Filter<T> {
 
     @Override
     public boolean accept( T o ) {
diff --git a/src/ubic/basecode/ontology/jena/IndexerSelector.java b/src/ubic/basecode/ontology/jena/IndexerSelector.java
@@ -16,7 +16,7 @@
  * limitations under the License.
  *
  */
-package ubic.basecode.ontology.jena.search;
+package ubic.basecode.ontology.jena;
 
 import com.hp.hpl.jena.rdf.model.*;
 import com.hp.hpl.jena.vocabulary.OWL2;
@@ -32,7 +32,7 @@
  *
  * @author paul
  */
-public class IndexerSelector implements Selector {
+class IndexerSelector implements Selector {
 
     private static final Collection<Property> wantedForIndexing;
 
diff --git a/src/ubic/basecode/ontology/jena/JenaUtils.java b/src/ubic/basecode/ontology/jena/JenaUtils.java
@@ -16,7 +16,7 @@
 
 import static com.hp.hpl.jena.reasoner.ReasonerRegistry.makeDirect;
 
-public class JenaUtils {
+class JenaUtils {
 
     public static Collection<OntClass> getParents( OntModel model, Collection<OntClass> ontClasses, boolean direct, @Nullable Set<Restriction> additionalRestrictions ) {
         ontClasses = ontClasses.stream()
diff --git a/src/ubic/basecode/ontology/jena/OBO.java b/src/ubic/basecode/ontology/jena/OBO.java
@@ -1,10 +1,10 @@
-package ubic.basecode.ontology.jena.vocabulary;
+package ubic.basecode.ontology.jena;
 
 import com.hp.hpl.jena.rdf.model.Property;
 import com.hp.hpl.jena.rdf.model.Resource;
 import com.hp.hpl.jena.rdf.model.ResourceFactory;
 
-public class OBO {
+class OBO {
 
     private static final String NS = "http://www.geneontology.org/formats/oboInOwl" + "#";
 
diff --git a/src/ubic/basecode/ontology/jena/ObjectPropertyImpl.java b/src/ubic/basecode/ontology/jena/ObjectPropertyImpl.java
@@ -32,7 +32,7 @@
 /**
  * @author pavlidis
  */
-public class ObjectPropertyImpl extends OntologyPropertyImpl implements ubic.basecode.ontology.model.ObjectProperty {
+class ObjectPropertyImpl extends OntologyPropertyImpl implements ubic.basecode.ontology.model.ObjectProperty {
 
     /**
      *
diff --git a/src/ubic/basecode/ontology/jena/OntologyCardinalityRestrictionImpl.java b/src/ubic/basecode/ontology/jena/OntologyCardinalityRestrictionImpl.java
@@ -26,7 +26,7 @@
 /**
  * @author pavlidis
  */
-public class OntologyCardinalityRestrictionImpl extends OntologyRestrictionImpl implements
+class OntologyCardinalityRestrictionImpl extends OntologyRestrictionImpl implements
         OntologyCardinalityRestriction {
 
     /**
diff --git a/src/ubic/basecode/ontology/jena/OntologyClassRestrictionImpl.java b/src/ubic/basecode/ontology/jena/OntologyClassRestrictionImpl.java
@@ -33,7 +33,7 @@
 /**
  * @author pavlidis
  */
-public class OntologyClassRestrictionImpl extends OntologyRestrictionImpl implements OntologyClassRestriction {
+class OntologyClassRestrictionImpl extends OntologyRestrictionImpl implements OntologyClassRestriction {
     /**
      *
      */
diff --git a/src/ubic/basecode/ontology/jena/OntologyDatatypeRestrictionImpl.java b/src/ubic/basecode/ontology/jena/OntologyDatatypeRestrictionImpl.java
@@ -27,7 +27,7 @@
 /**
  * @author pavlidis
  */
-public class OntologyDatatypeRestrictionImpl extends OntologyRestrictionImpl implements OntologyDatatypeRestriction {
+class OntologyDatatypeRestrictionImpl extends OntologyRestrictionImpl implements OntologyDatatypeRestriction {
 
     /**
      *
diff --git a/src/ubic/basecode/ontology/jena/OntologyIndexer.java b/src/ubic/basecode/ontology/jena/OntologyIndexer.java
@@ -16,7 +16,7 @@
  * limitations under the License.
  *
  */
-package ubic.basecode.ontology.jena.search;
+package ubic.basecode.ontology.jena;
 
 import com.hp.hpl.jena.ontology.OntModel;
 import com.hp.hpl.jena.rdf.model.StmtIterator;
@@ -45,7 +45,7 @@
 /**
  * @author pavlidis
  */
-public class OntologyIndexer {
+class OntologyIndexer {
 
     private static final Logger log = LoggerFactory.getLogger( OntologyIndexer.class );
 
diff --git a/src/ubic/basecode/ontology/jena/OntologyIndividualImpl.java b/src/ubic/basecode/ontology/jena/OntologyIndividualImpl.java
@@ -33,7 +33,7 @@
 /**
  * @author pavlidis
  */
-public class OntologyIndividualImpl extends AbstractOntologyResource implements OntologyIndividual {
+class OntologyIndividualImpl extends AbstractOntologyResource implements OntologyIndividual {
 
     private static final long serialVersionUID = -6164561945940667693L;
 
@@ -56,7 +56,7 @@ public OntologyIndividualImpl( Individual ind, Set<Restriction> additionalRestri
     public OntologyTerm getInstanceOf() {
         Resource type = ind.getRDFType();
 
-        OntClass cl = null;
+        OntClass cl;
         EnhGraph g = new EnhGraph( type.getModel().getGraph(), new GraphPersonality() );
         if ( OntClassImpl.factory.canWrap( type.asNode(), g ) ) {
             cl = new OntClassImpl( type.asNode(), g );
diff --git a/src/ubic/basecode/ontology/jena/OntologyLoader.java b/src/ubic/basecode/ontology/jena/OntologyLoader.java
@@ -46,7 +46,7 @@
  *
  * @author paul
  */
-public class OntologyLoader {
+class OntologyLoader {
 
     private static final Logger log = LoggerFactory.getLogger( OntologyLoader.class );
     private static final String OLD_CACHE_SUFFIX = ".old";
diff --git a/src/ubic/basecode/ontology/jena/OntologyModelImpl.java b/src/ubic/basecode/ontology/jena/OntologyModelImpl.java
@@ -0,0 +1,17 @@
+package ubic.basecode.ontology.jena;
+
+import com.hp.hpl.jena.ontology.OntModel;
+import ubic.basecode.ontology.model.OntologyModel;
+
+class OntologyModelImpl implements OntologyModel {
+
+    private final OntModel ontModel;
+
+    public OntologyModelImpl( OntModel ontModel ) {
+        this.ontModel = ontModel;
+    }
+
+    public OntModel getOntModel() {
+        return ontModel;
+    }
+}
diff --git a/src/ubic/basecode/ontology/jena/OntologyPropertyImpl.java b/src/ubic/basecode/ontology/jena/OntologyPropertyImpl.java
@@ -24,7 +24,7 @@
 /**
  * @author pavlidis
  */
-public abstract class OntologyPropertyImpl extends AbstractOntologyResource implements OntologyProperty {
+abstract class OntologyPropertyImpl extends AbstractOntologyResource implements OntologyProperty {
 
     /**
      *
diff --git a/src/ubic/basecode/ontology/jena/OntologyRestrictionImpl.java b/src/ubic/basecode/ontology/jena/OntologyRestrictionImpl.java
@@ -30,7 +30,7 @@
  *
  * @author Paul
  */
-public abstract class OntologyRestrictionImpl extends OntologyTermImpl implements OntologyRestriction {
+abstract class OntologyRestrictionImpl extends OntologyTermImpl implements OntologyRestriction {
 
     /**
      *
diff --git a/src/ubic/basecode/ontology/jena/OntologySearch.java b/src/ubic/basecode/ontology/jena/OntologySearch.java
@@ -16,7 +16,7 @@
  * limitations under the License.
  *
  */
-package ubic.basecode.ontology.jena.search;
+package ubic.basecode.ontology.jena;
 
 import com.hp.hpl.jena.ontology.Individual;
 import com.hp.hpl.jena.ontology.OntClass;
@@ -46,7 +46,7 @@
 /**
  * @author pavlidis
  */
-public class OntologySearch {
+class OntologySearch {
 
     private static final Logger log = LoggerFactory.getLogger( OntologySearch.class );
 
diff --git a/src/ubic/basecode/ontology/jena/OntologySearchJenaException.java b/src/ubic/basecode/ontology/jena/OntologySearchJenaException.java
@@ -1,12 +1,12 @@
-package ubic.basecode.ontology.jena.search;
+package ubic.basecode.ontology.jena;
 
 import com.hp.hpl.jena.shared.JenaException;
 import ubic.basecode.ontology.search.OntologySearchException;
 
 /**
  * Base class for Jena-related ontology search exceptions.
  */
-public class OntologySearchJenaException extends OntologySearchException {
+class OntologySearchJenaException extends OntologySearchException {
 
     private final JenaException cause;
 
diff --git a/src/ubic/basecode/ontology/jena/OntologyTermImpl.java b/src/ubic/basecode/ontology/jena/OntologyTermImpl.java
@@ -39,7 +39,7 @@
  *
  * @author Paul
  */
-public class OntologyTermImpl extends AbstractOntologyResource implements OntologyTerm {
+class OntologyTermImpl extends AbstractOntologyResource implements OntologyTerm {
 
     private static final String HAS_ALTERNATE_ID = "http://www.geneontology.org/formats/oboInOwl#hasAlternativeId";
 
diff --git a/src/ubic/basecode/ontology/jena/PredicateFilter.java b/src/ubic/basecode/ontology/jena/PredicateFilter.java
@@ -9,7 +9,7 @@
  *
  * @param <T>
  */
-public class PredicateFilter<T> extends Filter<T> {
+class PredicateFilter<T> extends Filter<T> {
     private final Predicate<T> predicate;
 
     public PredicateFilter( Predicate<T> predicate ) {
diff --git a/src/ubic/basecode/ontology/jena/PropertyFactory.java b/src/ubic/basecode/ontology/jena/PropertyFactory.java
@@ -30,7 +30,7 @@
  * @author pavlidis
  * 
  */
-public class PropertyFactory {
+class PropertyFactory {
 
     /**
      * Convert a Jena property.
diff --git a/src/ubic/basecode/ontology/jena/RO.java b/src/ubic/basecode/ontology/jena/RO.java
@@ -1,9 +1,9 @@
-package ubic.basecode.ontology.jena.vocabulary;
+package ubic.basecode.ontology.jena;
 
 import com.hp.hpl.jena.rdf.model.Property;
 import com.hp.hpl.jena.rdf.model.ResourceFactory;
 
-public class RO {
+class RO {
 
     public static final Property properPartOf = ResourceFactory.createProperty( "http://www.obofoundry.org/ro/ro.owl#proper_part_of" );
 }
diff --git a/src/ubic/basecode/ontology/jena/RestrictionFactory.java b/src/ubic/basecode/ontology/jena/RestrictionFactory.java
@@ -29,7 +29,7 @@
  * @author pavlidis
  * 
  */
-public class RestrictionFactory {
+class RestrictionFactory {
 
     public static OntologyRestriction asRestriction( Restriction restriction, Set<Restriction> additionalRestrictions ) {
 
diff --git a/src/ubic/basecode/ontology/jena/RestrictionWithOnPropertyFilter.java b/src/ubic/basecode/ontology/jena/RestrictionWithOnPropertyFilter.java
@@ -9,7 +9,7 @@
 /**
  * Filter that retain only the restrictions on any of the given properties.
  */
-public class RestrictionWithOnPropertyFilter extends Filter<Restriction> {
+class RestrictionWithOnPropertyFilter extends Filter<Restriction> {
     private final Set<Property> properties;
 
     public RestrictionWithOnPropertyFilter( Set<Property> properties ) {
diff --git a/src/ubic/basecode/ontology/jena/RestrictionWithValuesFromFilter.java b/src/ubic/basecode/ontology/jena/RestrictionWithValuesFromFilter.java
diff --git a/src/ubic/basecode/ontology/jena/RetryWithoutWildcardFailedException.java b/src/ubic/basecode/ontology/jena/RetryWithoutWildcardFailedException.java
diff --git a/src/ubic/basecode/ontology/jena/SearchIndex.java b/src/ubic/basecode/ontology/jena/SearchIndex.java
diff --git a/src/ubic/basecode/ontology/jena/search/package-info.java b/src/ubic/basecode/ontology/jena/search/package-info.java
diff --git a/src/ubic/basecode/ontology/jena/vocabulary/package-info.java b/src/ubic/basecode/ontology/jena/vocabulary/package-info.java
diff --git a/src/ubic/basecode/ontology/model/OntologyModel.java b/src/ubic/basecode/ontology/model/OntologyModel.java
diff --git a/src/ubic/basecode/ontology/providers/MedicOntologyService.java b/src/ubic/basecode/ontology/providers/MedicOntologyService.java
diff --git a/src/ubic/basecode/ontology/providers/NIFSTDOntologyService.java b/src/ubic/basecode/ontology/providers/NIFSTDOntologyService.java
diff --git a/src/ubic/basecode/ontology/search/OntologySearchException.java b/src/ubic/basecode/ontology/search/OntologySearchException.java
diff --git a/test/ubic/basecode/ontology/jena/OntologyLoaderTest.java b/test/ubic/basecode/ontology/jena/OntologyLoaderTest.java
diff --git a/test/ubic/basecode/ontology/jena/OntologySearchTest.java b/test/ubic/basecode/ontology/jena/OntologySearchTest.java
diff --git a/test/ubic/basecode/ontology/jena/UberonOntologySearchTest.java b/test/ubic/basecode/ontology/jena/UberonOntologySearchTest.java
diff --git a/test/ubic/basecode/ontology/providers/GenericOntologyServiceTest.java b/test/ubic/basecode/ontology/providers/GenericOntologyServiceTest.java

Original file line number	Diff line number	Diff line change
`@@ -32,7 +32,7 @@`
`32`	`32`	`*`
`33`	`33`	`* @author pavlidis`
`34`	`34`	`*/`
`35`		`-public class AnnotationPropertyImpl extends AbstractOntologyResource implements AnnotationProperty {`
	`35`	`+class AnnotationPropertyImpl extends AbstractOntologyResource implements AnnotationProperty {`
`36`	`36`
`37`	`37`	`private final String contents;`
`38`	`38`
Original file line number	Diff line number	Diff line change
`@@ -1,8 +1,8 @@`
`1`		`-package ubic.basecode.ontology.jena.vocabulary;`
	`1`	`+package ubic.basecode.ontology.jena;`
`2`	`2`
`3`	`3`	`import com.hp.hpl.jena.rdf.model.Property;`
`4`	`4`	`import com.hp.hpl.jena.rdf.model.ResourceFactory;`
`5`	`5`
`6`		`-public class BFO {`
	`6`	`+class BFO {`
`7`	`7`	`public static final Property partOf = ResourceFactory.createProperty( "http://purl.obolibrary.org/obo/BFO_0000050" );`
`8`	`8`	`}`
Original file line number	Diff line number	Diff line change
`@@ -8,7 +8,7 @@`
`8`	`8`	`*`
`9`	`9`	`* @param <T>`
`10`	`10`	`*/`
`11`		`-public class BnodeFilter<T extends Resource> extends Filter<T> {`
	`11`	`+class BnodeFilter<T extends Resource> extends Filter<T> {`
`12`	`12`
`13`	`13`	`@Override`
`14`	`14`	`public boolean accept( T o ) {`
Original file line number	Diff line number	Diff line change
`@@ -16,7 +16,7 @@`
`16`	`16`	`* limitations under the License.`
`17`	`17`	`*`
`18`	`18`	`*/`
`19`		`-package ubic.basecode.ontology.jena.search;`
	`19`	`+package ubic.basecode.ontology.jena;`
`20`	`20`
`21`	`21`	`import com.hp.hpl.jena.rdf.model.*;`
`22`	`22`	`import com.hp.hpl.jena.vocabulary.OWL2;`
`@@ -32,7 +32,7 @@`
`32`	`32`	`*`
`33`	`33`	`* @author paul`
`34`	`34`	`*/`
`35`		`-public class IndexerSelector implements Selector {`
	`35`	`+class IndexerSelector implements Selector {`
`36`	`36`
`37`	`37`	`private static final Collection<Property> wantedForIndexing;`
`38`	`38`