ont-api: major renaming com.github.owlcs.ontapi.OntologyModel -> com.github.owlcs.ontapi.Ontology (issue #4)

Author: sszuev

src/main/java/com/github/owlcs/ontapi/OWLAdapter.java

@@ -160,10 +160,10 @@ public OntologyManagerImpl asIMPL(OWLOntologyManager manager) {
      * Performs mapping {@code OWLOntology -> OntologyModel}.
      *
      * @param ont {@link OWLOntology}, not {@code null}
-     * @return {@link OntologyModel}
+     * @return {@link Ontology}
      */
-    public OntologyModel asONT(OWLOntology ont) {
-        return (OntologyModel) ont;
+    public Ontology asONT(OWLOntology ont) {
+        return (Ontology) ont;
     }
 
     /**
@@ -193,10 +193,10 @@ public OntologyFactory asONT(OWLOntologyFactory factory) {
     /**
      * Performs mapping {@code OntologyModel -> InternalModelHolder}.
      *
-     * @param ont {@link OntologyModel}, not {@code null}
+     * @param ont {@link Ontology}, not {@code null}
      * @return {@link BaseModel}
      */
-    public BaseModel asBaseModel(OntologyModel ont) {
+    public BaseModel asBaseModel(Ontology ont) {
         return (BaseModel) ont;
     }
 

src/main/java/com/github/owlcs/ontapi/OWLFactoryWrapper.java

@@ -32,10 +32,11 @@
 
 /**
  * An implementation of {@link OntologyLoader} which is actually {@link OWLOntologyFactory} decorator.
- * Used to load {@link OntologyModel ontology} through pure OWL-API mechanisms (i.e. owl-api parsers).
+ * Used to load {@link Ontology ontology} through pure OWL-API mechanisms (i.e. owl-api parsers).
  * Some formats (such as {@link org.semanticweb.owlapi.formats.ManchesterSyntaxDocumentFormat} or
  * {@link org.semanticweb.owlapi.formats.FunctionalSyntaxDocumentFormat}) are not supported by Jena,
  * so this is the only way to handle them by ONT-API.
+ *
  * @see OntologyLoaderImpl
  * @see com.github.owlcs.ontapi.config.LoadSettings#isUseOWLParsersToLoad()
  */
@@ -108,7 +109,7 @@ public OntLoaderConfiguration optimize(OntLoaderConfiguration config) {
     /**
      * {@inheritDoc}
      *
-     * @param builder {@link OntologyCreator} to construct a fresh {@link OntologyModel} instance
+     * @param builder {@link OntologyCreator} to construct a fresh {@link Ontology} instance
      * @param manager {@link OntologyManager}
      * @param source  {@link OWLOntologyDocumentSource}
      * @param conf    {@link OntLoaderConfiguration}
@@ -119,10 +120,10 @@ public OntLoaderConfiguration optimize(OntLoaderConfiguration config) {
      * @throws OWLOntologyCreationException              if any other problem occurs
      */
     @Override
-    public OntologyModel loadOntology(OntologyCreator builder,
-                                      OntologyManager manager,
-                                      OWLOntologyDocumentSource source,
-                                      OntLoaderConfiguration conf) throws OWLOntologyCreationException {
+    public Ontology loadOntology(OntologyCreator builder,
+                                 OntologyManager manager,
+                                 OWLOntologyDocumentSource source,
+                                 OntLoaderConfiguration conf) throws OWLOntologyCreationException {
         OWLAdapter adapter = getAdapter();
         OWLOntologyFactory factory = new FactoryImpl(builder);
         try {
@@ -131,7 +132,7 @@ public OntologyModel loadOntology(OntologyCreator builder,
                 throw new OntologyFactoryImpl.BadRecursionException("Cycle loading for source " + doc);
             }
             sources.add(doc);
-            OntologyModel res = getAdapter().asONT(factory.loadOWLOntology(manager, source, adapter.asHandler(manager), conf));
+            Ontology res = getAdapter().asONT(factory.loadOWLOntology(manager, source, adapter.asHandler(manager), conf));
             if (LOGGER.isDebugEnabled()) {
                 OntFormat format = OntFormat.get(manager.getOntologyFormat(res));
                 LOGGER.debug("The ontology <{}> is loaded. Format: {}[{}]", res.getOntologyID(), format, source.getClass().getSimpleName());
@@ -230,7 +231,8 @@ public static class FactoryImpl implements OWLOntologyFactory, HasAdapter {
 
         /**
          * Creates an OWL-API compatible factory.
-         * This version cannot be used with ONT-API if the builder does not produce {@link OntologyModel}.
+         * This version cannot be used with ONT-API if the builder does not produce {@link Ontology}.
+         *
          * @param builder {@link OWLOntologyBuilder}, not {@code null}
          */
         public FactoryImpl(OWLOntologyBuilder builder) {

src/main/java/com/github/owlcs/ontapi/OWLOntologyWrapper.java

@@ -33,7 +33,7 @@
 
 /**
  * A decorator for any {@link OWLOntology} instance.
- * Notices that it does not implement {@link OntologyModel} and therefore cannot be used in ONT-API directly.
+ * Notices that it does not implement {@link Ontology} and therefore cannot be used in ONT-API directly.
  * <p>
  * Matthew Horridge Stanford Center for Biomedical Informatics Research 03/04/15
  *

src/main/java/com/github/owlcs/ontapi/OntBaseModelImpl.java

@@ -1104,10 +1104,10 @@ public boolean equals(@Nullable Object obj) {
         if (obj == this) {
             return true;
         }
-        if (!(obj instanceof OntologyModel)) {
+        if (!(obj instanceof Ontology)) {
             return false;
         }
-        OntGraphModel right = ((OntologyModel) obj).asGraphModel();
+        OntGraphModel right = ((Ontology) obj).asGraphModel();
         OntGraphModel left = getBase();
         return left.getID().sameAs(right.getID());
     }

src/main/java/com/github/owlcs/ontapi/OntManagers.java

@@ -14,10 +14,10 @@
 
 package com.github.owlcs.ontapi;
 
+import com.github.owlcs.ontapi.jena.OntModelFactory;
 import com.google.common.collect.LinkedListMultimap;
 import org.semanticweb.owlapi.io.OWLParserFactory;
 import org.semanticweb.owlapi.model.*;
-import com.github.owlcs.ontapi.jena.OntModelFactory;
 
 import java.lang.reflect.Constructor;
 import java.lang.reflect.InvocationTargetException;
@@ -66,7 +66,7 @@ public class OntManagers implements OWLOntologyManagerFactory {
      * <p>
      * Alternative way to assembly ontology is direct working with the {@link org.apache.jena.graph.Graph Graph}
      * through the {@link com.github.owlcs.ontapi.jena.model.OntGraphModel} view of the ontology,
-     * that can be obtained using the method {@link OntologyModel#asGraphModel()}.
+     * that can be obtained using the method {@link Ontology#asGraphModel()}.
      * The first way of ontology editing is native for OWL-API,
      * the second way is native for Apache Jena and provided by ONT-API as a feature,
      * that actually underlies any interaction with ontologies in ONT-API.

src/main/java/com/github/owlcs/ontapi/OntologyModel.java renamed to src/main/java/com/github/owlcs/ontapi/Ontology.java

@@ -14,21 +14,21 @@
 
 package com.github.owlcs.ontapi;
 
-import org.semanticweb.owlapi.model.OWLOntology;
 import com.github.owlcs.ontapi.config.AxiomsSettings;
 import com.github.owlcs.ontapi.jena.model.OntGraphModel;
+import org.semanticweb.owlapi.model.OWLOntology;
 
 /**
- * A Structural Ontological Model, that is an extended {@link OWLOntology OWL-API Ontology}, and
- * represents an <a href="http://www.w3.org/TR/owl2-syntax/#Ontologies">Ontology</a> in the OWL2 specification.
+ * A Structural Ontological Model, that is an extended {@link OWLOntology OWL-API Ontology}.
+ * It represents an <a href="http://www.w3.org/TR/owl2-syntax/#Ontologies">Ontology</a> in the OWL2 specification.
  * This interface provides a wide range of methods inherited from OWL-API
  * for working with structural (OWL Axioms and Annotations) representation of data
  * stored in the form of {@link org.apache.jena.graph.Graph RDF Graph}.
  * In addition to this range, there are also two new methods: {@link #asGraphModel()} and {@link #clearCache()}.
  * <p>
  * Created by szuev on 24.10.2016.
  */
-public interface OntologyModel extends OWLOntology {
+public interface Ontology extends OWLOntology {
 
     /**
      * Returns the jena model shadow,

src/main/java/com/github/owlcs/ontapi/OntologyBuilderImpl.java

@@ -24,7 +24,7 @@
 
 /**
  * An implementation of {@link OntologyFactory.Builder} - a technical factory to create standalone ontology instances.
- * This should be the only way to create {@link OntologyModel} instances.
+ * This should be the only way to create {@link Ontology} instances.
  */
 @SuppressWarnings("WeakerAccess")
 @ParametersAreNonnullByDefault
@@ -36,15 +36,15 @@ public OWLAdapter getAdapter() {
     }
 
     @Override
-    public OntologyModel createOntology(ID id, OntologyManager manager, OntLoaderConfiguration config) {
+    public Ontology createOntology(ID id, OntologyManager manager, OntLoaderConfiguration config) {
         OntologyManagerImpl m = getAdapter().asIMPL(manager);
         OntologyModelImpl res = createOntologyImpl(createGraph(), m, config);
         res.setOntologyID(id);
         return withLock(res, m.getLock());
     }
 
     @Override
-    public OntologyModel createOntology(Graph graph, OntologyManager manager, OntLoaderConfiguration config) {
+    public Ontology createOntology(Graph graph, OntologyManager manager, OntLoaderConfiguration config) {
         OntologyManagerImpl m = getAdapter().asIMPL(manager);
         return withLock(createOntologyImpl(graph, m, config), m.getLock());
     }
@@ -79,11 +79,11 @@ protected ModelConfig createModelConfig(OntologyManagerImpl manager, OntLoaderCo
     /**
      * Wraps the given {@code ont} as a concurrent R/W locked view impl, if it is needed.
      *
-     * @param ont {@link OntologyModelImpl}, not {@code null}
+     * @param ont  {@link OntologyModelImpl}, not {@code null}
      * @param lock {@link ReadWriteLock}, possible {@code null}
-     * @return {@link OntologyModel} instance
+     * @return {@link Ontology} instance
      */
-    protected OntologyModel withLock(OntologyModelImpl ont, ReadWriteLock lock) {
+    protected Ontology withLock(OntologyModelImpl ont, ReadWriteLock lock) {
         if (!NoOpReadWriteLock.isConcurrent(lock)) return ont;
         return new OntologyModelImpl.Concurrent(ont, lock);
     }

src/main/java/com/github/owlcs/ontapi/OntologyCreator.java

@@ -22,8 +22,9 @@
 import java.util.Objects;
 
 /**
- * An interface to create {@link OntologyModel} instances.
+ * An interface to create {@link Ontology} instances.
  * Created by @ssz on 03.06.2019.
+ *
  * @since 1.4.1
  */
 public interface OntologyCreator {
@@ -33,14 +34,14 @@ public interface OntologyCreator {
      * which is associated to the specified manager.
      * Does not change the manager state,
      * although the returned ontology must have a reference to the given manager,
-     * i.e. the method {@link OntologyModel#getOWLOntologyManager()} must return the passed manager instance.
+     * i.e. the method {@link Ontology#getOWLOntologyManager()} must return the passed manager instance.
      *
      * @param id      {@link ID}, not {@code null}
      * @param manager {@link OntologyManager}, not {@code null}
      * @param config  {@link OntLoaderConfiguration} the config, not {@code null}
-     * @return {@link OntologyModel} new instance reflecting manager settings
+     * @return {@link Ontology} new instance reflecting manager settings
      */
-    OntologyModel createOntology(ID id, OntologyManager manager, OntLoaderConfiguration config);
+    Ontology createOntology(ID id, OntologyManager manager, OntLoaderConfiguration config);
 
     /**
      * Creates a new detached ontology model which wraps the specified {@link Graph graph}.
@@ -50,10 +51,10 @@ public interface OntologyCreator {
      * @param graph   {@link Graph} the graph, not {@code null}
      * @param manager {@link OntologyManager} manager, not {@code null}
      * @param config  {@link OntLoaderConfiguration} the config, not {@code null}
-     * @return {@link OntologyModel} new instance reflecting manager settings
+     * @return {@link Ontology} new instance reflecting manager settings
      * @since 1.3.0
      */
-    OntologyModel createOntology(Graph graph, OntologyManager manager, OntLoaderConfiguration config);
+    Ontology createOntology(Graph graph, OntologyManager manager, OntLoaderConfiguration config);
 
     /**
      * Creates a fresh empty {@link Graph RDF Graph} instance.

src/main/java/com/github/owlcs/ontapi/OntologyFactory.java

@@ -52,46 +52,47 @@ public interface OntologyFactory extends OWLOntologyFactory, HasAdapter {
 
     /**
      * Adds the specified ontology into the manager and performs some final tuning actions.
+     *
      * @param manager {@link OntologyManager} the ontology manager, which will hold the {@code model}, not {@code null}
-     * @param model {@link OntologyModel} that has been created by the {@link #getBuilder() Builder}, not {@code null}
+     * @param model   {@link Ontology} that has been created by the {@link #getBuilder() Builder}, not {@code null}
      * @since 1.4.2
      */
-    void includeOntology(OntologyManager manager, OntologyModel model);
+    void includeOntology(OntologyManager manager, Ontology model);
 
     /**
-     * Creates a fresh {@link OntologyModel Ontology Model} inside the manager
+     * Creates a fresh {@link Ontology Ontology Model} inside the manager
      * with the given ID and default configuration.
      *
      * @param manager {@link OntologyManager} the ontology manager to set, not {@code null}
      * @param id      {@link ID} the ID of the ontology to create, not {@code null}
-     * @return {@link OntologyModel}
+     * @return {@link Ontology}
      * @throws OntApiException if something goes wrong
      * @since 1.3.0
      */
-    default OntologyModel createOntology(OntologyManager manager, ID id) throws OntApiException {
-        OntologyModel res = getBuilder().createOntology(id, manager, manager.getOntologyLoaderConfiguration());
+    default Ontology createOntology(OntologyManager manager, ID id) throws OntApiException {
+        Ontology res = getBuilder().createOntology(id, manager, manager.getOntologyLoaderConfiguration());
         includeOntology(manager, res);
         return res;
     }
 
     /**
      * Reads a graph from the given document source and stores
-     * it as a ready to use {@link OntologyModel Ontology Model} in the specified manager.
+     * it as a ready to use {@link Ontology Ontology Model} in the specified manager.
      * {@inheritDoc}
      *
      * @param manager {@link OntologyManager} manager the ontology manager to set, not {@code null}
      * @param source  {@link OWLOntologyDocumentSource} the document source that provides the means
      *                of getting a representation of a document, not {@code null}
      * @param config  {@link OntLoaderConfiguration} settings to manage loading process, not {@code null}
-     * @return {@link OntologyModel}
+     * @return {@link Ontology}
      * @throws OWLOntologyCreationException if the ontology could not be created due to some I/O problem,
      *                                      broken source or incompatible state of manager
      * @throws OntApiException              if something else goes wrong
      * @since 1.3.0
      */
-    default OntologyModel loadOntology(OntologyManager manager,
-                                       OWLOntologyDocumentSource source,
-                                       OntLoaderConfiguration config) throws OWLOntologyCreationException, OntApiException {
+    default Ontology loadOntology(OntologyManager manager,
+                                  OWLOntologyDocumentSource source,
+                                  OntLoaderConfiguration config) throws OWLOntologyCreationException, OntApiException {
         return getLoader().loadOntology(getBuilder(), manager, source, config);
     }
 
@@ -131,14 +132,14 @@ default boolean canAttemptLoading(OWLOntologyDocumentSource source) {
      * @param id          {@link OWLOntologyID} the ID of the ontology to create, not {@code null}
      * @param documentIRI unused parameter
      * @param handler     unused parameter
-     * @return {@link OntologyModel} the newly created ontology
+     * @return {@link Ontology} the newly created ontology
      * @throws OntApiException if something goes wrong
      */
     @Override
-    default OntologyModel createOWLOntology(OWLOntologyManager manager,
-                                            OWLOntologyID id,
-                                            IRI documentIRI,
-                                            OWLOntologyCreationHandler handler) {
+    default Ontology createOWLOntology(OWLOntologyManager manager,
+                                       OWLOntologyID id,
+                                       IRI documentIRI,
+                                       OWLOntologyCreationHandler handler) {
         Adapter adapter = getAdapter();
         return createOntology(adapter.asONT(manager), adapter.asONT(id));
     }
@@ -152,16 +153,16 @@ default OntologyModel createOWLOntology(OWLOntologyManager manager,
      * @param handler unused parameter
      * @param config  {@link OWLOntologyLoaderConfiguration} a configuration object which can be used
      *                to pass various options to th loader, not {@code null}
-     * @return {@link OntologyModel} the newly created and loaded ontology
+     * @return {@link Ontology} the newly created and loaded ontology
      * @throws OWLOntologyCreationException if the ontology could not be created due to some I/O problem,
      *                                      broken source or incompatible state of manager
      * @throws OntApiException              if something else goes wrong
      */
     @Override
-    default OntologyModel loadOWLOntology(OWLOntologyManager manager,
-                                          OWLOntologyDocumentSource source,
-                                          OWLOntologyCreationHandler handler,
-                                          OWLOntologyLoaderConfiguration config) throws OWLOntologyCreationException {
+    default Ontology loadOWLOntology(OWLOntologyManager manager,
+                                     OWLOntologyDocumentSource source,
+                                     OWLOntologyCreationHandler handler,
+                                     OWLOntologyLoaderConfiguration config) throws OWLOntologyCreationException {
         Adapter adapter = getAdapter();
         return loadOntology(adapter.asONT(manager), source, adapter.asONT(config));
     }
@@ -174,7 +175,7 @@ default OntologyModel loadOWLOntology(OWLOntologyManager manager,
     interface Builder extends OntologyCreator, HasAdapter, OWLOntologyBuilder {
 
         @Override
-        default OntologyModel createOWLOntology(OWLOntologyManager manager, OWLOntologyID id) {
+        default Ontology createOWLOntology(OWLOntologyManager manager, OWLOntologyID id) {
             Adapter adapter = getAdapter();
             return createOntology(adapter.asONT(id), adapter.asONT(manager),
                     adapter.asONT(manager.getOntologyLoaderConfiguration()));

src/main/java/com/github/owlcs/ontapi/OntologyFactoryImpl.java

@@ -14,14 +14,14 @@
 
 package com.github.owlcs.ontapi;
 
+import com.github.owlcs.ontapi.jena.utils.Models;
+import com.github.owlcs.ontapi.transforms.TransformException;
 import org.apache.commons.lang3.StringUtils;
 import org.apache.jena.riot.system.ErrorHandlerFactory;
 import org.semanticweb.owlapi.model.IRI;
 import org.semanticweb.owlapi.model.OWLDocumentFormat;
 import org.semanticweb.owlapi.model.OWLOntologyCreationException;
 import org.semanticweb.owlapi.model.OWLOntologyFactory;
-import com.github.owlcs.ontapi.jena.utils.Models;
-import com.github.owlcs.ontapi.transforms.TransformException;
 
 import javax.annotation.ParametersAreNonnullByDefault;
 import java.util.Objects;
@@ -76,7 +76,7 @@ public Loader getLoader() {
      * since it is more readable and more widely used in Jena-world.
      */
     @Override
-    public void includeOntology(OntologyManager manager, OntologyModel model) {
+    public void includeOntology(OntologyManager manager, Ontology model) {
         if (model.getOWLOntologyManager() != manager) {
             throw new OntApiException.IllegalState("The specified ontology is attached to another manager: " + model);
         }