[Enhancement #73] Refactor Sesame driver to support the new plural co…

…ntexts supporting axiom descriptors.
kbss-cvut · Sep 24, 2020 · 3753749 · 3753749
1 parent 78975d1
commit 3753749
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Showing 25 changed files with 436 additions and 482 deletions.
diff --git a/ontodriver-sesame/src/main/java/cz/cvut/kbss/ontodriver/sesame/AbstractSesameIterator.java b/ontodriver-sesame/src/main/java/cz/cvut/kbss/ontodriver/sesame/AbstractSesameIterator.java
@@ -25,7 +25,9 @@
 import org.eclipse.rdf4j.model.ValueFactory;
 
 import java.util.Collection;
+import java.util.Collections;
 import java.util.HashSet;
+import java.util.Set;
 
 abstract class AbstractSesameIterator implements SesameIterator {
 
@@ -50,6 +52,10 @@ public AbstractSesameIterator(ListDescriptor listDescriptor, Connector connector
         this.vf = vf;
     }
 
+    protected Set<IRI> contexts() {
+        return context != null ? Collections.singleton(context) : Collections.emptySet();
+    }
+
     protected void checkSuccessorMax(Collection<Statement> stmts, IRI property) {
         // We don't mind the same statement multiple times, it could have been added during transaction
         if (new HashSet<>(stmts).size() > 1) {

diff --git a/ontodriver-sesame/src/main/java/cz/cvut/kbss/ontodriver/sesame/AxiomLoader.java b/ontodriver-sesame/src/main/java/cz/cvut/kbss/ontodriver/sesame/AxiomLoader.java
@@ -1,16 +1,14 @@
 /**
  * Copyright (C) 2020 Czech Technical University in Prague
- *
- * This program is free software: you can redistribute it and/or modify it under
- * the terms of the GNU General Public License as published by the Free Software
- * Foundation, either version 3 of the License, or (at your option) any
- * later version.
- *
- * This program is distributed in the hope that it will be useful, but WITHOUT
- * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
- * FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
- * details. You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ * <p>
+ * This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later
+ * version.
+ * <p>
+ * This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied
+ * warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
+ * details. You should have received a copy of the GNU General Public License along with this program. If not, see
+ * <http://www.gnu.org/licenses/>.
  */
 package cz.cvut.kbss.ontodriver.sesame;
 
@@ -99,12 +97,14 @@ private Assertion processAssertions(AxiomDescriptor descriptor) {
 
     Collection<Axiom<?>> loadAxioms(NamedResource individual, boolean includeInferred, java.net.URI context)
             throws SesameDriverException {
-        final IRI sesameContext = SesameUtils.toSesameIri(context, valueFactory);
+        final Set<IRI> contextIris =
+                context != null ? Collections.singleton(SesameUtils.toSesameIri(context, valueFactory)) :
+                Collections.emptySet();
         final IRI subject = SesameUtils.toSesameIri(individual.getIdentifier(), valueFactory);
         final AxiomBuilder axiomBuilder = new AxiomBuilder(individual, Collections.emptyMap(),
                 Assertion.createUnspecifiedPropertyAssertion(includeInferred));
         final Collection<Statement> statements = connector
-                .findStatements(subject, null, null, includeInferred, sesameContext);
+                .findStatements(subject, null, null, includeInferred, contextIris);
         return statements.stream().map(axiomBuilder::statementToAxiom).collect(Collectors.toSet());
     }
 }
diff --git a/ontodriver-sesame/src/main/java/cz/cvut/kbss/ontodriver/sesame/EpistemicAxiomRemover.java b/ontodriver-sesame/src/main/java/cz/cvut/kbss/ontodriver/sesame/EpistemicAxiomRemover.java
@@ -24,18 +24,16 @@
 import org.eclipse.rdf4j.model.Statement;
 import org.eclipse.rdf4j.model.ValueFactory;
 
-import java.net.URI;
 import java.util.*;
+import java.util.stream.Collectors;
 
 /**
  * This class performs an epistemic remove of axioms described by the axiom descriptor.
  * <p/>
- * Epistemic remove means that only information known to the application is
- * deleted. The assertions in the descriptor represent this information. Thus,
- * only these assertions are removed from the ontology. Note that if the
- * descriptor contains an unspecified property assertion, all property
- * assertions related to the subject individual are removed from the property's
- * context.
+ * Epistemic remove means that only information known to the application is deleted. The assertions in the descriptor
+ * represent this information. Thus, only these assertions are removed from the ontology. Note that if the descriptor
+ * contains an unspecified property assertion, all property assertions related to the subject individual are removed
+ * from the property's context.
  */
 class EpistemicAxiomRemover {
 
@@ -54,11 +52,11 @@ void remove(AbstractAxiomDescriptor axiomDescriptor) throws SesameDriverExceptio
             if (a.isInferred()) {
                 continue;
             }
-            for (URI ctx : axiomDescriptor.getAssertionContexts(a)) {
-                final IRI contextUri = SesameUtils.toSesameIri(ctx, valueFactory);
-                toRemove.addAll(connector.findStatements(individual,
-                        SesameUtils.toSesameIri(a.getIdentifier(), valueFactory), null, a.isInferred(), contextUri));
-            }
+            final Set<IRI> contexts = axiomDescriptor.getAssertionContexts(a).stream()
+                                                     .map(uri -> SesameUtils.toSesameIri(uri, valueFactory))
+                                                     .collect(Collectors.toSet());
+            toRemove.addAll(connector.findStatements(individual,
+                    SesameUtils.toSesameIri(a.getIdentifier(), valueFactory), null, a.isInferred(), contexts));
         }
         connector.removeStatements(toRemove);
     }

diff --git a/ontodriver-sesame/src/main/java/cz/cvut/kbss/ontodriver/sesame/ListHandler.java b/ontodriver-sesame/src/main/java/cz/cvut/kbss/ontodriver/sesame/ListHandler.java
@@ -1,16 +1,14 @@
 /**
  * Copyright (C) 2020 Czech Technical University in Prague
- *
- * This program is free software: you can redistribute it and/or modify it under
- * the terms of the GNU General Public License as published by the Free Software
- * Foundation, either version 3 of the License, or (at your option) any
- * later version.
- *
- * This program is distributed in the hope that it will be useful, but WITHOUT
- * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
- * FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
- * details. You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ * <p>
+ * This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later
+ * version.
+ * <p>
+ * This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied
+ * warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
+ * details. You should have received a copy of the GNU General Public License along with this program. If not, see
+ * <http://www.gnu.org/licenses/>.
  */
 package cz.cvut.kbss.ontodriver.sesame;
 
@@ -23,9 +21,7 @@
 import cz.cvut.kbss.ontodriver.sesame.util.SesameUtils;
 import org.eclipse.rdf4j.model.*;
 
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.List;
+import java.util.*;
 
 /**
  * Base class for list handlers.
@@ -46,8 +42,7 @@ abstract class ListHandler<T extends ListDescriptor, V extends ListValueDescript
     }
 
     /**
-     * Loads axioms representing list described by the specified list
-     * descriptor.
+     * Loads axioms representing list described by the specified list descriptor.
      *
      * @return Collection of axioms representing sequence values
      * @throws SesameDriverException When storage access error occurs
@@ -96,17 +91,17 @@ void updateList(V listValueDescriptor) throws SesameDriverException {
         if (listValueDescriptor.getValues().isEmpty()) {
             clearList(listValueDescriptor);
         } else if (isOldListEmpty(owner(listValueDescriptor), hasList(listValueDescriptor),
-                listValueDescriptor.getListProperty().isInferred(), context(listValueDescriptor))) {
+                listValueDescriptor.getListProperty().isInferred(), contexts(listValueDescriptor))) {
             persistList(listValueDescriptor);
         } else {
             mergeList(listValueDescriptor);
         }
     }
 
     private boolean isOldListEmpty(Resource owner, IRI hasListProperty, boolean includeInferred,
-                                   IRI context) throws SesameDriverException {
+                                   Set<IRI> contexts) throws SesameDriverException {
         final Collection<Statement> stmts = connector.findStatements(owner, hasListProperty, null,
-                includeInferred, context);
+                includeInferred, contexts);
         return stmts.isEmpty();
     }
 
@@ -150,6 +145,11 @@ Resource extractListNode(Collection<Statement> stmts, IRI nodeAssertion) {
         return (Resource) val;
     }
 
+    Set<IRI> contexts(ListDescriptor listDescriptor) {
+        final IRI ctx = sesameIri(listDescriptor.getContext());
+        return ctx != null ? Collections.singleton(ctx) : Collections.emptySet();
+    }
+
     IRI context(ListDescriptor listDescriptor) {
         return sesameIri(listDescriptor.getContext());
     }

diff --git a/ontodriver-sesame/src/main/java/cz/cvut/kbss/ontodriver/sesame/ReferencedListHandler.java b/ontodriver-sesame/src/main/java/cz/cvut/kbss/ontodriver/sesame/ReferencedListHandler.java
@@ -1,33 +1,28 @@
 /**
  * Copyright (C) 2020 Czech Technical University in Prague
- *
- * This program is free software: you can redistribute it and/or modify it under
- * the terms of the GNU General Public License as published by the Free Software
- * Foundation, either version 3 of the License, or (at your option) any
- * later version.
- *
- * This program is distributed in the hope that it will be useful, but WITHOUT
- * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
- * FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
- * details. You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ * <p>
+ * This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later
+ * version.
+ * <p>
+ * This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied
+ * warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
+ * details. You should have received a copy of the GNU General Public License along with this program. If not, see
+ * <http://www.gnu.org/licenses/>.
  */
 package cz.cvut.kbss.ontodriver.sesame;
 
-import cz.cvut.kbss.ontodriver.sesame.connector.Connector;
-import cz.cvut.kbss.ontodriver.sesame.exceptions.SesameDriverException;
 import cz.cvut.kbss.ontodriver.descriptor.ReferencedListDescriptor;
 import cz.cvut.kbss.ontodriver.descriptor.ReferencedListValueDescriptor;
 import cz.cvut.kbss.ontodriver.model.NamedResource;
+import cz.cvut.kbss.ontodriver.sesame.connector.Connector;
+import cz.cvut.kbss.ontodriver.sesame.exceptions.SesameDriverException;
 import org.eclipse.rdf4j.model.IRI;
 import org.eclipse.rdf4j.model.Resource;
 import org.eclipse.rdf4j.model.Statement;
 import org.eclipse.rdf4j.model.ValueFactory;
 
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Iterator;
-import java.util.List;
+import java.util.*;
 
 public class ReferencedListHandler extends
         ListHandler<ReferencedListDescriptor, ReferencedListValueDescriptor> {
@@ -68,7 +63,7 @@ private IRI generateSequenceNode(IRI owner, IRI context) throws SesameDriverExce
         do {
             node = vf.createIRI(uriBase + "-SEQ_" + sequenceCounter++);
             final Collection<Statement> stmts = connector.findStatements(node, null, null, false,
-                    context);
+                    context != null ? Collections.singleton(context) : Collections.emptySet());
             unique = stmts.isEmpty();
         } while (!unique);
         return node;
@@ -107,7 +102,7 @@ void clearList(ReferencedListValueDescriptor listDescriptor) throws SesameDriver
         final IRI hasNext = hasNext(listDescriptor);
         final IRI hasContent = hasContent(listDescriptor);
         final boolean includeInferred = listDescriptor.getListProperty().isInferred();
-        final IRI context = context(listDescriptor);
+        final Set<IRI> context = contexts(listDescriptor);
         Resource previous = owner(listDescriptor);
         IRI currentProperty = hasList(listDescriptor);
         final Collection<Statement> toRemove = new ArrayList<>();

diff --git a/ontodriver-sesame/src/main/java/cz/cvut/kbss/ontodriver/sesame/ReferencedListIterator.java b/ontodriver-sesame/src/main/java/cz/cvut/kbss/ontodriver/sesame/ReferencedListIterator.java
@@ -1,36 +1,33 @@
 /**
  * Copyright (C) 2020 Czech Technical University in Prague
- *
- * This program is free software: you can redistribute it and/or modify it under
- * the terms of the GNU General Public License as published by the Free Software
- * Foundation, either version 3 of the License, or (at your option) any
- * later version.
- *
- * This program is distributed in the hope that it will be useful, but WITHOUT
- * ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
- * FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
- * details. You should have received a copy of the GNU General Public License
- * along with this program. If not, see <http://www.gnu.org/licenses/>.
+ * <p>
+ * This program is free software: you can redistribute it and/or modify it under the terms of the GNU General Public
+ * License as published by the Free Software Foundation, either version 3 of the License, or (at your option) any later
+ * version.
+ * <p>
+ * This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied
+ * warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
+ * details. You should have received a copy of the GNU General Public License along with this program. If not, see
+ * <http://www.gnu.org/licenses/>.
  */
 package cz.cvut.kbss.ontodriver.sesame;
 
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Collections;
-
-import cz.cvut.kbss.ontodriver.sesame.util.SesameUtils;
-
-import cz.cvut.kbss.ontodriver.exception.IntegrityConstraintViolatedException;
-import cz.cvut.kbss.ontodriver.sesame.connector.Connector;
-import cz.cvut.kbss.ontodriver.sesame.exceptions.SesameDriverException;
 import cz.cvut.kbss.ontodriver.descriptor.ReferencedListDescriptor;
+import cz.cvut.kbss.ontodriver.exception.IntegrityConstraintViolatedException;
 import cz.cvut.kbss.ontodriver.model.Axiom;
 import cz.cvut.kbss.ontodriver.model.NamedResource;
+import cz.cvut.kbss.ontodriver.sesame.connector.Connector;
+import cz.cvut.kbss.ontodriver.sesame.exceptions.SesameDriverException;
+import cz.cvut.kbss.ontodriver.sesame.util.SesameUtils;
 import org.eclipse.rdf4j.model.IRI;
 import org.eclipse.rdf4j.model.Resource;
 import org.eclipse.rdf4j.model.Statement;
 import org.eclipse.rdf4j.model.ValueFactory;
 
+import java.util.ArrayList;
+import java.util.Collection;
+import java.util.Collections;
+
 class ReferencedListIterator extends AbstractSesameIterator {
 
     private final ReferencedListDescriptor listDescriptor;
@@ -53,11 +50,11 @@ public ReferencedListIterator(ReferencedListDescriptor listDescriptor, Connector
     }
 
     private void init() throws SesameDriverException {
-        this.next = connector.findStatements(listOwner, hasListProperty, null, includeInferred, context);
+        this.next = connector.findStatements(listOwner, hasListProperty, null, includeInferred, contexts());
     }
 
     @Override
-    public boolean hasNext() throws SesameDriverException {
+    public boolean hasNext() {
         return !next.isEmpty();
     }
 
@@ -77,17 +74,17 @@ private void nextInternal() throws SesameDriverException {
         checkNodeIsResource(currentNode);
         final Resource elem = (Resource) currentNode.getObject();
         this.currentContent = getNodeContent(elem);
-        this.next = connector.findStatements(elem, hasNextProperty, null, includeInferred, context);
+        this.next = connector.findStatements(elem, hasNextProperty, null, includeInferred, contexts());
     }
 
     private Statement getNodeContent(Resource node) throws SesameDriverException {
-        final Collection<Statement> elems = connector.findStatements(node, hasContentProperty,
-                null, includeInferred, context);
-        checkSuccessorMax(elems, hasContentProperty);
-        if (elems.isEmpty()) {
+        final Collection<Statement> elements = connector.findStatements(node, hasContentProperty,
+                null, includeInferred, contexts());
+        checkSuccessorMax(elements, hasContentProperty);
+        if (elements.isEmpty()) {
             throw new IntegrityConstraintViolatedException("Node " + node + " has no content.");
         }
-        final Statement elem = elems.iterator().next();
+        final Statement elem = elements.iterator().next();
         checkNodeIsResource(elem);
         return elem;
     }

diff --git a/ontodriver-sesame/src/main/java/cz/cvut/kbss/ontodriver/sesame/SimpleListHandler.java b/ontodriver-sesame/src/main/java/cz/cvut/kbss/ontodriver/sesame/SimpleListHandler.java
@@ -24,10 +24,7 @@
 import org.eclipse.rdf4j.model.Statement;
 import org.eclipse.rdf4j.model.ValueFactory;
 
-import java.util.ArrayList;
-import java.util.Collection;
-import java.util.Iterator;
-import java.util.List;
+import java.util.*;
 
 class SimpleListHandler extends ListHandler<SimpleListDescriptor, SimpleListValueDescriptor> {
 
@@ -71,15 +68,15 @@ List<Statement> createListRest(IRI head, SimpleListValueDescriptor listValueDesc
      */
     @Override
     void clearList(SimpleListValueDescriptor listValueDescriptor) throws SesameDriverException {
-        final IRI context = context(listValueDescriptor);
+        final Set<IRI> contexts = contexts(listValueDescriptor);
         final Collection<Statement> toRemove = new ArrayList<>();
         IRI currentProperty = hasList(listValueDescriptor);
         final IRI hasNext = hasNext(listValueDescriptor);
         final boolean includeInferred = listValueDescriptor.getNextNode().isInferred();
         Collection<Statement> stmts;
         Resource subject = owner(listValueDescriptor);
         do {
-            stmts = connector.findStatements(subject, currentProperty, null, includeInferred, context);
+            stmts = connector.findStatements(subject, currentProperty, null, includeInferred, contexts);
             if (!stmts.isEmpty()) {
                 subject = extractListNode(stmts, hasNext);
                 toRemove.addAll(stmts);