ont-api: refactoring transformers subsystem (issue #4) - moving/renam…

…ing/removing classes, changing docs

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

@@ -15,6 +15,7 @@
 package com.github.owlcs.ontapi;
 
 import com.github.owlcs.ontapi.jena.utils.Graphs;
+import com.github.owlcs.ontapi.transforms.TransformationModel;
 import org.apache.jena.atlas.web.ContentType;
 import org.apache.jena.graph.Graph;
 import org.apache.jena.riot.Lang;
@@ -67,7 +68,7 @@ public abstract class OntGraphDocumentSource implements OWLOntologyDocumentSourc
      * Answers if the graph must be put in order by the transformations mechanism.
      *
      * @return {@code true} if graph transformations is allowed
-     * @see com.github.owlcs.ontapi.transforms.Transform
+     * @see TransformationModel
      * @since 1.3.2
      */
     public boolean withTransforms() {

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

@@ -19,7 +19,7 @@
 import com.github.owlcs.ontapi.jena.model.OntModel;
 import com.github.owlcs.ontapi.jena.utils.Graphs;
 import com.github.owlcs.ontapi.jena.utils.Models;
-import com.github.owlcs.ontapi.transforms.GraphTransformers;
+import com.github.owlcs.ontapi.transforms.GraphStats;
 import org.apache.commons.io.input.ReaderInputStream;
 import org.apache.jena.graph.*;
 import org.apache.jena.rdf.model.impl.ModelCom;
@@ -225,11 +225,11 @@ public static RDFLiteral literal(Node node) throws IllegalArgumentException {
      * Auxiliary method to produce {@link OWLOntologyLoaderMetaData} object.
      *
      * @param graph {@link Graph}
-     * @param stats {@link GraphTransformers.Stats} transformation outcome, can be null for fake meta-data
+     * @param stats {@link GraphStats} transformation outcome, can be null for fake meta-data
      * @return {@link OWLOntologyLoaderMetaData} object
      * @throws IllegalArgumentException in case {@code graph} and {@code stats} are incompatible
      */
-    protected static OWLOntologyLoaderMetaData makeParserMetaData(Graph graph, GraphTransformers.Stats stats) {
+    protected static OWLOntologyLoaderMetaData makeParserMetaData(Graph graph, GraphStats stats) {
         if (stats == null)
             return OntologyMetaData.createParserMetaData(graph);
         if (Graphs.getBase(graph) != stats.getGraph())

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

@@ -20,7 +20,7 @@
 import com.github.owlcs.ontapi.jena.utils.Graphs;
 import com.github.owlcs.ontapi.jena.utils.OntModels;
 import com.github.owlcs.ontapi.jena.vocabulary.OWL;
-import com.github.owlcs.ontapi.transforms.GraphTransformers;
+import com.github.owlcs.ontapi.transforms.GraphStats;
 import com.github.owlcs.ontapi.transforms.TransformException;
 import org.apache.jena.graph.Graph;
 import org.apache.jena.graph.GraphUtil;
@@ -224,7 +224,7 @@ protected UnionGraph makeUnionGraph(GraphInfo info,
             return graph;
         }
         // process transformations
-        GraphTransformers.Stats stats;
+        GraphStats stats;
         Set<Graph> transformed = graphs.values().stream()
                 .filter(g -> !g.isFresh() || g.noTransforms())
                 .map(GraphInfo::getGraph)
@@ -237,8 +237,8 @@ protected UnionGraph makeUnionGraph(GraphInfo info,
             throw new OntologyFactoryImpl.OWLTransformException(t);
         }
         info.setStats(stats);
-        stats.listStats(true)
-                .filter(GraphTransformers.Stats::isNotEmpty)
+        stats.stats(true)
+                .filter(GraphStats::isNotEmpty)
                 .forEach(s -> {
                     String uri = Graphs.getURI(s.getGraph());
                     if (uri == null) {
@@ -697,7 +697,7 @@ public static class GraphInfo {
         private boolean fresh, transforms;
         private Node ontology;
         private Set<String> imports;
-        private GraphTransformers.Stats stats;
+        private GraphStats stats;
 
         protected GraphInfo(Graph graph, OntFormat format, IRI source, boolean withTransforms) {
             this.graph = graph;
@@ -755,11 +755,11 @@ protected IRI getSource() {
             return source;
         }
 
-        public GraphTransformers.Stats getStats() {
+        public GraphStats getStats() {
             return stats;
         }
 
-        protected void setStats(GraphTransformers.Stats stats) {
+        protected void setStats(GraphStats stats) {
             this.stats = Objects.requireNonNull(stats, "Null transform stats");
         }
     }

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

@@ -17,7 +17,7 @@
 import com.github.owlcs.ontapi.jena.utils.Graphs;
 import com.github.owlcs.ontapi.jena.vocabulary.OWL;
 import com.github.owlcs.ontapi.jena.vocabulary.RDF;
-import com.github.owlcs.ontapi.transforms.GraphTransformers;
+import com.github.owlcs.ontapi.transforms.GraphStats;
 import com.github.owlcs.ontapi.transforms.OWLIDTransform;
 import com.google.common.collect.ArrayListMultimap;
 import com.google.common.collect.Multimap;
@@ -43,12 +43,12 @@
 
 /**
  * Implementation of {@link OWLOntologyLoaderMetaData}.
- * A wrapper for {@link GraphTransformers.Stats Transformation Stats} to satisfy OWL-API.
+ * A wrapper for {@link GraphStats Transformation Stats} to satisfy OWL-API.
  * Constructed while loading to provide some additional information about runtime changes in the source.
  * <p>
  * Created by @szuev on 28.06.2018.
  *
- * @see GraphTransformers.Stats
+ * @see GraphStats
  */
 @SuppressWarnings("WeakerAccess")
 public class OntologyMetaData implements OWLOntologyLoaderMetaData {
@@ -94,26 +94,26 @@ public static OntologyMetaData createParserMetaData(Graph graph) {
 
     /**
      * A factory method.
-     * Creates {@link OWLOntologyLoaderMetaData} from the given {@link GraphTransformers.Stats Transformation Stats}.
+     * Creates {@link OWLOntologyLoaderMetaData} from the given {@link GraphStats Transformation Stats}.
      *
      * @param stats not null
      * @return {@link OntologyMetaData} instance, not null
      */
-    public static OntologyMetaData createParserMetaData(GraphTransformers.Stats stats) {
+    public static OntologyMetaData createParserMetaData(GraphStats stats) {
         Graph graph = Graphs.getBase(Objects.requireNonNull(stats, "Null graph").getGraph());
         RDFOntologyHeaderStatus header = RDFOntologyHeaderStatus.PARSED_ONE_HEADER;
         String idKey = OWLIDTransform.class.getSimpleName();
-        if (stats.hasTriples(GraphTransformers.Stats.Type.ADDED, idKey)) {
+        if (stats.hasTriples(GraphStats.Type.ADDED, idKey)) {
             header = RDFOntologyHeaderStatus.PARSED_ZERO_HEADERS;
         }
-        if (stats.hasTriples(GraphTransformers.Stats.Type.DELETED, idKey)) {
+        if (stats.hasTriples(GraphStats.Type.DELETED, idKey)) {
             header = RDFOntologyHeaderStatus.PARSED_MULTIPLE_HEADERS;
         }
-        Set<RDFTriple> unparsed = stats.triples(GraphTransformers.Stats.Type.UNPARSED)
+        Set<RDFTriple> unparsed = stats.triples(GraphStats.Type.UNPARSED)
                 .map(OntGraphUtils::triple)
                 .collect(Collectors.toSet());
         ArrayListMultimap<IRI, Class<? extends OWLObject>> guessedDeclarations = ArrayListMultimap.create();
-        stats.triples(GraphTransformers.Stats.Type.ADDED)
+        stats.triples(GraphStats.Type.ADDED)
                 .collect(Collectors.toSet())
                 .forEach(t -> {
                     // note: anonymous subject also wrapped as iri

src/main/java/com/github/owlcs/ontapi/config/LoadControl.java

@@ -43,12 +43,12 @@ interface LoadControl<R> extends LoadSettings {
     /**
      * Sets {@code GraphTransformers.Store} collection.
      *
-     * @param t {@link GraphTransformers.Store}, not {@code null}
+     * @param t {@link GraphTransformers}, not {@code null}
      * @return {@link R} (this or copied instance)
      * @see LoadSettings#getGraphTransformers()
      * @see LoadSettings#isPerformTransformation()
      */
-    R setGraphTransformers(GraphTransformers.Store t);
+    R setGraphTransformers(GraphTransformers t);
 
     /**
      * Disables or enables the Graph Transformation mechanism depending on the given flag.

src/main/java/com/github/owlcs/ontapi/config/LoadSettings.java

@@ -17,6 +17,7 @@
 import com.github.owlcs.ontapi.*;
 import com.github.owlcs.ontapi.jena.impl.conf.OntPersonality;
 import com.github.owlcs.ontapi.jena.model.OntModel;
+import com.github.owlcs.ontapi.transforms.GraphFilter;
 import com.github.owlcs.ontapi.transforms.GraphTransformers;
 import org.apache.jena.graph.Graph;
 import org.semanticweb.owlapi.model.IRI;
@@ -51,7 +52,7 @@ public interface LoadSettings {
     OntPersonality getPersonality();
 
     /**
-     * Gets {@link GraphTransformers.Store Transformers Store}.
+     * Gets {@link GraphTransformers Transformers Store}.
      * <p>
      * Transformers Store is a collection of actions that are performed on {@code Graph} before
      * it enters into the main system.
@@ -61,22 +62,22 @@ public interface LoadSettings {
      * or {@link Ontology Axiomatic Model}, but without a proper transformation
      * you might not found valid {@link org.semanticweb.owlapi.model.OWLAxiom Axiom}s inside that data.
      * Transformations can be simply disabled through
-     * the method {@link LoadControl#setGraphTransformers(GraphTransformers.Store)}.
+     * the method {@link LoadControl#setGraphTransformers(GraphTransformers)}.
      * It is recommended to do this in case there is confidence that the data is OWL2,
      * since transformations may take significant processor time.
-     * With the method {@link GraphTransformers.Store#setFilter(GraphTransformers.Filter)}
+     * With the method {@link GraphTransformers#setFilter(GraphFilter)}
      * a whole graph family may be skipped from transformation process.
      * And there is one more facility to selectively turn off transformations:
      * the method {@link OntGraphDocumentSource#withTransforms()},
      * which is used while passing externally loaded graph into the manager
      * (see {@link OntologyManager#addOntology(Graph)}.
      *
-     * @return {@link GraphTransformers.Store}
-     * @see LoadControl#setGraphTransformers(GraphTransformers.Store)
+     * @return {@link GraphTransformers}
+     * @see LoadControl#setGraphTransformers(GraphTransformers)
      * @see LoadControl#setPerformTransformation(boolean)
      * @see OntSettings#ONT_API_LOAD_CONF_TRANSFORMERS
      */
-    GraphTransformers.Store getGraphTransformers();
+    GraphTransformers getGraphTransformers();
 
     /**
      * Answers {@code true} if the mechanism of graph transformers is enabled, which is {@code true} by default.

src/main/java/com/github/owlcs/ontapi/config/OntConfig.java

@@ -14,13 +14,13 @@
 
 package com.github.owlcs.ontapi.config;
 
-import org.semanticweb.owlapi.model.*;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
 import com.github.owlcs.ontapi.NoOpReadWriteLock;
 import com.github.owlcs.ontapi.OntApiException;
 import com.github.owlcs.ontapi.jena.impl.conf.OntPersonality;
 import com.github.owlcs.ontapi.transforms.GraphTransformers;
+import org.semanticweb.owlapi.model.*;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import javax.annotation.Nonnull;
 import java.io.IOException;
@@ -44,7 +44,7 @@
  * <li>{@link #setModelCacheLevel(int, boolean)} (<b>since 1.4.2</b>), {@link #setModelCacheLevel(int)} (<b>since 1.4.0</b>)</li>
  * <li>{@link #useContentCache()}, {@link #useComponentCache()}, {@link #useIteratorCache()} (<b>since 1.4.2</b>)</li>
  * <li>{@link #getPersonality()} and {@link #setPersonality(OntPersonality)}</li>
- * <li>{@link #getGraphTransformers()} amd {@link #setGraphTransformers(GraphTransformers.Store)}</li>
+ * <li>{@link #getGraphTransformers()} amd {@link #setGraphTransformers(GraphTransformers)}</li>
  * <li>{@link #isPerformTransformation()} and {@link #setPerformTransformation(boolean)}</li>
  * <li>{@link #isProcessImports()} and {@link #setProcessImports(boolean)} (<b>since 1.4.1</b>)</li>
  * <li>{@link #getSupportedSchemes()} and {@link #setSupportedSchemes(List)}</li>
@@ -253,20 +253,20 @@ public OntConfig setPersonality(OntPersonality p) {
      * {@inheritDoc}
      */
     @Override
-    public GraphTransformers.Store getGraphTransformers() {
+    public GraphTransformers getGraphTransformers() {
         return get(OntSettings.ONT_API_LOAD_CONF_TRANSFORMERS);
     }
 
     /**
      * An ONT-API manager's load config setter.
      * {@inheritDoc}
      *
-     * @param t {@link com.github.owlcs.ontapi.transforms.GraphTransformers.Store}
+     * @param t {@link GraphTransformers}
      * @return this instance
-     * @see OntLoaderConfiguration#setGraphTransformers(GraphTransformers.Store)
+     * @see OntLoaderConfiguration#setGraphTransformers(GraphTransformers)
      */
     @Override
-    public OntConfig setGraphTransformers(GraphTransformers.Store t) {
+    public OntConfig setGraphTransformers(GraphTransformers t) {
         return put(OntSettings.ONT_API_LOAD_CONF_TRANSFORMERS, t);
     }
 

src/main/java/com/github/owlcs/ontapi/config/OntLoaderConfiguration.java

@@ -14,12 +14,12 @@
 
 package com.github.owlcs.ontapi.config;
 
-import org.semanticweb.owlapi.model.*;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
 import com.github.owlcs.ontapi.OntApiException;
 import com.github.owlcs.ontapi.jena.impl.conf.OntPersonality;
 import com.github.owlcs.ontapi.transforms.GraphTransformers;
+import org.semanticweb.owlapi.model.*;
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
 
 import javax.annotation.Nonnull;
 import java.io.IOException;
@@ -145,19 +145,19 @@ public OntLoaderConfiguration setPerformTransformation(boolean b) {
      * {@inheritDoc}
      */
     @Override
-    public GraphTransformers.Store getGraphTransformers() {
+    public GraphTransformers getGraphTransformers() {
         return get(OntSettings.ONT_API_LOAD_CONF_TRANSFORMERS);
     }
 
     /**
      * An ONT-API config setter.
      * {@inheritDoc}
      *
-     * @param t {@link GraphTransformers.Store} new graph transformers store
+     * @param t {@link GraphTransformers} new graph transformers store
      * @return {@link OntLoaderConfiguration}, a copied (new) or this instance in case no changes is made
      */
     @Override
-    public OntLoaderConfiguration setGraphTransformers(GraphTransformers.Store t) {
+    public OntLoaderConfiguration setGraphTransformers(GraphTransformers t) {
         return set(OntSettings.ONT_API_LOAD_CONF_TRANSFORMERS, t);
     }
 

src/main/java/com/github/owlcs/ontapi/config/OntSettings.java

@@ -14,15 +14,15 @@
 
 package com.github.owlcs.ontapi.config;
 
+import com.github.owlcs.ontapi.OntApiException;
+import com.github.owlcs.ontapi.jena.impl.conf.OntModelConfig;
+import com.github.owlcs.ontapi.jena.vocabulary.*;
+import com.github.owlcs.ontapi.transforms.*;
 import org.apache.jena.vocabulary.RDFS;
 import org.semanticweb.owlapi.model.MissingImportHandlingStrategy;
 import org.semanticweb.owlapi.model.MissingOntologyHeaderStrategy;
 import org.semanticweb.owlapi.model.PriorityCollectionSorting;
 import org.semanticweb.owlapi.model.parameters.ConfigurationOptions;
-import com.github.owlcs.ontapi.OntApiException;
-import com.github.owlcs.ontapi.jena.impl.conf.OntModelConfig;
-import com.github.owlcs.ontapi.jena.vocabulary.*;
-import com.github.owlcs.ontapi.transforms.*;
 
 import java.io.IOException;
 import java.io.InputStream;
@@ -133,20 +133,20 @@ OntModelConfig.StdMode getPersonalityMode() {
             , SWRLTransform.class) {
         @Override
         public Object getDefaultValue() {
-            GraphTransformers.Store res = new GraphTransformers.Store();
-            for (Class<? extends Transform> c : getTransformTypes()) {
-                res = res.add(new GraphTransformers.DefaultMaker(c));
+            GraphTransformers res = new GraphTransformers();
+            for (Class<? extends TransformationModel> c : getTransformTypes()) {
+                res = res.addLast(Transform.Factory.create(c));
             }
             return res;
         }
 
         @SuppressWarnings("unchecked")
-        List<Class<? extends Transform>> getTransformTypes() {
+        List<Class<? extends TransformationModel>> getTransformTypes() {
             List<?> res = PROPERTIES.getListProperty(key);
             if (res == null) {
                 res = (List<?>) secondary;
             }
-            return (List<Class<? extends Transform>>) res;
+            return (List<Class<? extends TransformationModel>>) res;
         }
     };
 

src/main/java/com/github/owlcs/ontapi/jena/OntVocabulary.java

@@ -16,6 +16,7 @@
 
 import com.github.owlcs.ontapi.jena.utils.Iter;
 import com.github.owlcs.ontapi.jena.vocabulary.*;
+import com.github.owlcs.ontapi.transforms.GraphTransformers;
 import org.apache.jena.datatypes.BaseDatatype;
 import org.apache.jena.datatypes.RDFDatatype;
 import org.apache.jena.datatypes.TypeMapper;
@@ -194,7 +195,7 @@ default Set<Resource> getBuiltinOWLEntities() {
      * from the packages {@link com.github.owlcs.ontapi.jena.vocabulary} and {@link org.apache.jena.vocabulary}
      * (such as {@link OWL}).
      * In ONT-API, a {@link OntVocabulary} is used to build {@link com.github.owlcs.ontapi.jena.impl.conf.OntPersonality}
-     * and in {@link com.github.owlcs.ontapi.transforms.GraphTransformers} subsystem.
+     * and in {@link GraphTransformers} subsystem.
      * <p>
      * Created by @szuev on 21.12.2016.
      */
@@ -355,6 +356,7 @@ private static <X> Set<X> toUnmodifiableSet(Collection<X> input) {
          */
         @SuppressWarnings("WeakerAccess")
         protected static class OWLImpl extends Impl {
+            private static final Class<?>[] VOCABULARIES = new Class<?>[]{XSD.class, RDF.class, RDFS.class, OWL.class};
             /**
              * The list of datatypes from owl-2 specification (35 types)
              * (see <a href='https://www.w3.org/TR/owl2-quick-reference/'>Quick References, 3.1 Built-in Datatypes</a>).
@@ -383,7 +385,6 @@ protected static class OWLImpl extends Impl {
                     Stream.of(OWL.topDataProperty, OWL.bottomDataProperty).collect(Iter.toUnmodifiableSet());
             public static final Set<Property> OBJECT_PROPERTIES =
                     Stream.of(OWL.topObjectProperty, OWL.bottomObjectProperty).collect(Iter.toUnmodifiableSet());
-            private static final Class<?>[] VOCABULARIES = new Class<?>[]{XSD.class, RDF.class, RDFS.class, OWL.class};
             public static final Set<Property> PROPERTIES = getConstants(Property.class, VOCABULARIES);
             public static final Set<Resource> RESOURCES = getConstants(Resource.class, VOCABULARIES);
 
@@ -453,8 +454,8 @@ protected SKOSImpl() {
          * @see SWRLB
          */
         protected static class SWRLImpl extends Impl {
-            public static final Set<Resource> BUILTINS = getConstants(Property.class, SWRLB.class);
             private static final Class<?>[] VOCABULARIES = new Class<?>[]{SWRL.class, SWRLB.class};
+            public static final Set<Resource> BUILTINS = getConstants(Property.class, SWRLB.class);
             public static final Set<Property> PROPERTIES = getConstants(Property.class, VOCABULARIES);
             public static final Set<Resource> RESOURCES = getConstants(Resource.class, VOCABULARIES);
 

src/main/java/com/github/owlcs/ontapi/transforms/BaseDeclarator.java

@@ -31,7 +31,7 @@
  * The collection of base methods for {@link ManifestDeclarator} and {@link ReasonerDeclarator}
  */
 @SuppressWarnings({"WeakerAccess", "UnusedReturnValue"})
-public abstract class BaseDeclarator extends Transform {
+public abstract class BaseDeclarator extends TransformationModel {
     private static final List<Property> RESTRICTION_PROPERTY_MARKERS = Stream.of(OWL.onProperty, OWL.allValuesFrom,
             OWL.someValuesFrom, OWL.hasValue, OWL.onClass,
             OWL.onDataRange, OWL.cardinality, OWL.qualifiedCardinality,