ont-api: cosmetic changes (rename vocabulary & change javadocs for se…

…veral classes, etc)
owlcs · Mar 21, 2023 · 33646b6 · 33646b6
1 parent f56b71f
commit 33646b6
Show file tree

Hide file tree

Showing 10 changed files with 22 additions and 37 deletions.
diff --git a/owlapi-impl/src/main/java/com/github/owlcs/ontapi/Ontology.java b/owlapi-impl/src/main/java/com/github/owlcs/ontapi/Ontology.java
@@ -35,8 +35,7 @@
  * Also, please note that although ONT-API supports the ability to change data simultaneously through both interfaces,
  * this is not always correct: an {@link Ontology} impls use caches,
  * and switching back and forth could flush these caches, which may degrade performance.
- * <p>
- * Created by szuev on 24.10.2016.
+ * @see <a href="https://github.com/owlcs/owlapi/blob/version5/api/src/main/java/org/semanticweb/owlapi/model/OWLOntology.java">org.semanticweb.owlapi.model.OWLOntology</a>
  */
 public interface Ontology extends OWLOntology {
 
@@ -55,6 +54,9 @@ public interface Ontology extends OWLOntology {
      * then the method {@link #clearCache()} may help.
      * Also note: any changes in the RDF-view will reset the internal cache,
      * that means next attempt to retrieve data from axiomatic view (i.e. list axioms) will take the same time as the very first one.
+     * <p>
+     * Note that returning {@code OntModel} is not thread-safe even with {@code ReadWriteLock} (see <a href="https://github.com/owlcs/ont-api/issues/46">issue #46</a>).
+     * But {@code asGraphModel().getGraph()} and {@code asGraphModel().getBaseGraph()} are thread-safe.
      *
      * @return {@link OntModel Ontology RDF Graph Model}, not {@code null}
      * @see org.apache.jena.graph.Graph

diff --git a/owlapi-impl/src/main/java/com/github/owlcs/ontapi/OntologyFactoryImpl.java b/owlapi-impl/src/main/java/com/github/owlcs/ontapi/OntologyFactoryImpl.java
@@ -30,7 +30,7 @@
  * The ontology building and loading factory, the 'core' - the main point to create and load ontologies.
  * See also base interface {@link OWLOntologyFactory} and its single implementation
  * <a href="https://github.com/owlcs/owlapi/blob/version5/impl/src/main/java/uk/ac/manchester/cs/owl/owlapi/OWLOntologyFactoryImpl.java">uk.ac.manchester.cs.owl.owlapi.OWLOntologyFactoryImpl</a> in the OWLAPI-impl module.
- * It is also an outer class for any {@link OWLOntologyCreationException}s sub-classes, which may occur during loading.
+ * It is also an outer class for any {@link OWLOntologyCreationException}s subclasses, which may occur during loading.
  * <p>
  * Created by szuev on 24.10.2016.
  *

diff --git a/owlapi-impl/src/main/java/com/github/owlcs/ontapi/OntologyManager.java b/owlapi-impl/src/main/java/com/github/owlcs/ontapi/OntologyManager.java
@@ -65,8 +65,7 @@
  * <li>{@link #getGraphModel(String, String)}</li>
  * <li>{@link #getDocumentSourceMappers()} - since 1.3.0</li>
  * </ul>
- * <p>
- * Created by szuev on 24.10.2016.
+ * @see <a href="https://github.com/owlcs/owlapi/blob/version5/api/src/main/java/org/semanticweb/owlapi/model/OWLOntologyManager.java">org.semanticweb.owlapi.model.OWLOntologyManager</a>
  */
 @ParametersAreNonnullByDefault
 public interface OntologyManager extends OWLOntologyManager {

diff --git a/owlapi-impl/src/main/java/com/github/owlcs/ontapi/ReflectionUtils.java b/owlapi-impl/src/main/java/com/github/owlcs/ontapi/ReflectionUtils.java
@@ -20,7 +20,6 @@
 import java.lang.reflect.Constructor;
 import java.lang.reflect.InvocationHandler;
 import java.lang.reflect.InvocationTargetException;
-import java.lang.reflect.Method;
 import java.lang.reflect.Proxy;
 import java.text.MessageFormat;
 import java.util.Objects;
@@ -33,22 +32,6 @@
  */
 class ReflectionUtils {
 
-    /**
-     * Finds a static method by the class and its name.
-     *
-     * @param clazz {@link Class}
-     * @param name  String name
-     * @return {@link Method}
-     * @throws OntApiException if no method is found
-     */
-    static Method findStaticMethod(Class<?> clazz, String name) throws OntApiException {
-        try {
-            return clazz.getMethod(name);
-        } catch (NoSuchMethodException e) {
-            throw new OntApiException("Can't find method '" + name + "' in " + clazz, e);
-        }
-    }
-
     /**
      * Returns a proxy instance that implements {@code interfaceType} by dispatching method
      * invocations to {@code handler}.
@@ -110,7 +93,8 @@ static <R> R newInstance(Class<? extends R> interfaceType,
     static <R> R newInstance(Class<R> type) throws OntApiException {
         try {
             return type.getDeclaredConstructor().newInstance();
-        } catch (NoSuchMethodException | InvocationTargetException | InstantiationException | IllegalAccessException e) {
+        } catch (NoSuchMethodException | InvocationTargetException | InstantiationException |
+                 IllegalAccessException e) {
             throw new OntApiException("Can't create instance of " + type.getName(), e);
         }
     }

diff --git a/owlapi-impl/src/main/java/com/github/owlcs/ontapi/transforms/BaseDeclarator.java b/owlapi-impl/src/main/java/com/github/owlcs/ontapi/transforms/BaseDeclarator.java
@@ -16,7 +16,7 @@
 
 import com.github.owlcs.ontapi.jena.utils.Iterators;
 import com.github.owlcs.ontapi.jena.vocabulary.OWL;
-import com.github.owlcs.ontapi.transforms.vocabulary.AVC;
+import com.github.owlcs.ontapi.transforms.vocabulary.ONTAPI;
 import org.apache.jena.graph.Graph;
 import org.apache.jena.rdf.model.Literal;
 import org.apache.jena.rdf.model.Property;
@@ -113,7 +113,7 @@ protected boolean isAnnotationProperty(Resource candidate) {
     }
 
     protected boolean isIndividual(Resource candidate) {
-        return hasType(candidate, OWL.NamedIndividual) || hasType(candidate, AVC.AnonymousIndividual);
+        return hasType(candidate, OWL.NamedIndividual) || hasType(candidate, ONTAPI.AnonymousIndividual);
     }
 
     protected BaseDeclarator declareObjectProperty(Resource resource) {
@@ -153,7 +153,7 @@ protected BaseDeclarator declareIndividual(Resource resource) {
             // test data from owl-api-contact contains such things also:
             undeclare(resource, OWL.NamedIndividual);
             // the temporary declaration:
-            declare(resource, AVC.AnonymousIndividual);
+            declare(resource, ONTAPI.AnonymousIndividual);
         } else {
             declare(resource, OWL.NamedIndividual);
         }

diff --git a/owlapi-impl/src/main/java/com/github/owlcs/ontapi/transforms/ManifestDeclarator.java b/owlapi-impl/src/main/java/com/github/owlcs/ontapi/transforms/ManifestDeclarator.java
@@ -19,7 +19,7 @@
 import com.github.owlcs.ontapi.jena.vocabulary.OWL;
 import com.github.owlcs.ontapi.jena.vocabulary.RDF;
 import com.github.owlcs.ontapi.jena.vocabulary.SWRL;
-import com.github.owlcs.ontapi.transforms.vocabulary.AVC;
+import com.github.owlcs.ontapi.transforms.vocabulary.ONTAPI;
 import org.apache.jena.graph.Graph;
 import org.apache.jena.rdf.model.Property;
 import org.apache.jena.rdf.model.RDFList;
@@ -297,7 +297,7 @@ private ExtendedIterator<Resource> disjointIndividuals(Resource s) {
 
     protected Set<Resource> collectForbiddenClassCandidates() {
         Set<Resource> res = new HashSet<>(builtins.getSystemResources());
-        res.add(AVC.AnonymousIndividual);
+        res.add(ONTAPI.AnonymousIndividual);
         res.removeAll(builtins.getBuiltinClasses());
         return res;
     }

diff --git a/owlapi-impl/src/main/java/com/github/owlcs/ontapi/transforms/OWLCommonTransform.java b/owlapi-impl/src/main/java/com/github/owlcs/ontapi/transforms/OWLCommonTransform.java
@@ -19,8 +19,8 @@
 import com.github.owlcs.ontapi.jena.vocabulary.OWL;
 import com.github.owlcs.ontapi.jena.vocabulary.RDF;
 import com.github.owlcs.ontapi.jena.vocabulary.XSD;
-import com.github.owlcs.ontapi.transforms.vocabulary.AVC;
 import com.github.owlcs.ontapi.transforms.vocabulary.DEPRECATED;
+import com.github.owlcs.ontapi.transforms.vocabulary.ONTAPI;
 import org.apache.jena.datatypes.RDFDatatype;
 import org.apache.jena.datatypes.xsd.XSDDatatype;
 import org.apache.jena.graph.Graph;
@@ -234,9 +234,9 @@ protected void fixDatatype(Resource r) {
                 .forEach(s -> {
                     RDFNode o = s.getObject();
                     if (o.isURIResource()) {
-                        m.remove(s).add(s.getSubject(), OWL.onDatatype, s.getObject());
+                        m.remove(s).add(s.getSubject(), OWL.onDatatype, o);
                     } else if (o.isAnon()) {
-                        Resource auto = AVC.randomIRI().inModel(m);
+                        Resource auto = ONTAPI.randomIRI().inModel(m);
                         m.remove(s).add(s.getSubject(), OWL.onDatatype, auto);
                         auto.addProperty(OWL.equivalentClass, o);
                     }

diff --git a/owlapi-impl/src/main/java/com/github/owlcs/ontapi/transforms/OWLDeclarationTransform.java b/owlapi-impl/src/main/java/com/github/owlcs/ontapi/transforms/OWLDeclarationTransform.java
@@ -16,7 +16,7 @@
 
 import com.github.owlcs.ontapi.jena.vocabulary.OWL;
 import com.github.owlcs.ontapi.jena.vocabulary.RDF;
-import com.github.owlcs.ontapi.transforms.vocabulary.AVC;
+import com.github.owlcs.ontapi.transforms.vocabulary.ONTAPI;
 import org.apache.jena.graph.Graph;
 import org.apache.jena.graph.Triple;
 import org.apache.jena.rdf.model.RDFNode;
@@ -89,7 +89,7 @@ public Stream<Triple> uncertainTriples() {
     }
 
     protected void finalActions() {
-        getWorkModel().removeAll(null, RDF.type, AVC.AnonymousIndividual);
+        getWorkModel().removeAll(null, RDF.type, ONTAPI.AnonymousIndividual);
         // at times the ontology could contain some rdfs garbage,
         // even if other transformers (OWLTransformer, RDFSTransformer) have been used.
         listStatements(null, RDF.type, RDF.Property)

diff --git a/owlapi-impl/src/main/java/com/github/owlcs/ontapi/transforms/RecursiveTransform.java b/owlapi-impl/src/main/java/com/github/owlcs/ontapi/transforms/RecursiveTransform.java
@@ -15,7 +15,7 @@
 package com.github.owlcs.ontapi.transforms;
 
 import com.github.owlcs.ontapi.jena.OntVocabulary;
-import com.github.owlcs.ontapi.transforms.vocabulary.AVC;
+import com.github.owlcs.ontapi.transforms.vocabulary.ONTAPI;
 import org.apache.jena.graph.Graph;
 import org.apache.jena.graph.Node;
 import org.apache.jena.graph.Triple;
@@ -44,7 +44,7 @@
  * Created by @szuev on 24.01.2018.
  * <p>
  * Note: this transform is slow - the complexity is ~O(n*log(n))
- * @see AVC#error(String)
+ * @see ONTAPI#error(String)
  */
 @SuppressWarnings("WeakerAccess")
 public class RecursiveTransform extends TransformationModel {
@@ -158,7 +158,7 @@ public void perform() {
     }
 
     public Triple createReplacement(Triple base) {
-        return createReplacement(base, n -> AVC.error(n).asNode());
+        return createReplacement(base, n -> ONTAPI.error(n).asNode());
     }
 
     public Triple createReplacement(Triple base, UnaryOperator<Node> mapper) {

diff --git a/...lcs/ontapi/transforms/vocabulary/AVC.java → .../ontapi/transforms/vocabulary/ONTAPI.java b/...lcs/ontapi/transforms/vocabulary/AVC.java → .../ontapi/transforms/vocabulary/ONTAPI.java
@@ -25,7 +25,7 @@
  * Vocabulary with (possible, temporary) resources used by ONT-API only.
  * Might be moved to {@link com.github.owlcs.ontapi.jena.vocabulary} if necessary.
  */
-public class AVC {
+public class ONTAPI {
     public final static String URI = "https://github.com/owlcs/ont-api";
     public final static String NS = URI + "#";