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Posted to commits@stanbol.apache.org by al...@apache.org on 2011/10/17 09:43:19 UTC

svn commit: r1185032 [3/4] - in /incubator/stanbol/trunk: commons/web/base/src/main/java/org/apache/stanbol/commons/web/base/format/ enhancer/engines/refactor/src/main/java/org/apache/stanbol/enhancer/engines/refactor/ explanation/core/ explanation/cor...

Modified: incubator/stanbol/trunk/ontologymanager/ontonet/src/main/java/org/apache/stanbol/ontologymanager/ontonet/impl/ontology/OntologyScopeImpl.java
URL: http://svn.apache.org/viewvc/incubator/stanbol/trunk/ontologymanager/ontonet/src/main/java/org/apache/stanbol/ontologymanager/ontonet/impl/ontology/OntologyScopeImpl.java?rev=1185032&r1=1185031&r2=1185032&view=diff
==============================================================================
--- incubator/stanbol/trunk/ontologymanager/ontonet/src/main/java/org/apache/stanbol/ontologymanager/ontonet/impl/ontology/OntologyScopeImpl.java (original)
+++ incubator/stanbol/trunk/ontologymanager/ontonet/src/main/java/org/apache/stanbol/ontologymanager/ontonet/impl/ontology/OntologyScopeImpl.java Mon Oct 17 07:43:15 2011
@@ -27,13 +27,14 @@ import java.util.Set;
 import org.apache.stanbol.ontologymanager.ontonet.api.io.OntologyInputSource;
 import org.apache.stanbol.ontologymanager.ontonet.api.ontology.CoreOntologySpace;
 import org.apache.stanbol.ontologymanager.ontonet.api.ontology.CustomOntologySpace;
+import org.apache.stanbol.ontologymanager.ontonet.api.ontology.OWLExportable;
+import org.apache.stanbol.ontologymanager.ontonet.api.ontology.OntologyCollectorListener;
 import org.apache.stanbol.ontologymanager.ontonet.api.ontology.OntologyScope;
 import org.apache.stanbol.ontologymanager.ontonet.api.ontology.OntologySpace;
 import org.apache.stanbol.ontologymanager.ontonet.api.ontology.OntologySpaceFactory;
-import org.apache.stanbol.ontologymanager.ontonet.api.ontology.OntologySpaceListener;
 import org.apache.stanbol.ontologymanager.ontonet.api.ontology.ScopeOntologyListener;
 import org.apache.stanbol.ontologymanager.ontonet.api.ontology.SessionOntologySpace;
-import org.apache.stanbol.ontologymanager.ontonet.api.ontology.UnmodifiableOntologySpaceException;
+import org.apache.stanbol.ontologymanager.ontonet.api.ontology.UnmodifiableOntologyCollectorException;
 import org.semanticweb.owlapi.apibinding.OWLManager;
 import org.semanticweb.owlapi.model.AddImport;
 import org.semanticweb.owlapi.model.IRI;
@@ -48,10 +49,10 @@ import org.slf4j.LoggerFactory;
 /**
  * The default implementation of an ontology scope.
  * 
- * @author alessandro
+ * @author alexdma
  * 
  */
-public class OntologyScopeImpl implements OntologyScope, OntologySpaceListener {
+public class OntologyScopeImpl implements OntologyScope, OntologyCollectorListener {
 
     /**
      * The core ontology space for this scope, always set as default.
@@ -83,31 +84,23 @@ public class OntologyScopeImpl implement
     /**
      * Maps session IDs to ontology space. A single scope has at most one space per session.
      */
-    protected Map<IRI,SessionOntologySpace> sessionSpaces;
+    protected Map<String,SessionOntologySpace> sessionSpaces;
 
     public OntologyScopeImpl(String id,
                              IRI namespace,
                              OntologySpaceFactory factory,
-                             OntologyInputSource coreRoot) {
-        this(id, namespace, factory, coreRoot, null);
-    }
-
-    public OntologyScopeImpl(String id,
-                             IRI namespace,
-                             OntologySpaceFactory factory,
-                             OntologyInputSource coreRoot,
-                             OntologyInputSource customRoot) {
+                             OntologyInputSource<?>... coreOntologies) {
         setID(id);
         setNamespace(namespace);
 
-        this.coreSpace = factory.createCoreOntologySpace(id, coreRoot);
-        this.coreSpace.addOntologySpaceListener(this);
+        this.coreSpace = factory.createCoreOntologySpace(id, coreOntologies);
+        this.coreSpace.addListener(this);
         // let's just lock it. Once the core space is done it's done.
         this.coreSpace.setUp();
         // if (customRoot != null) {
         try {
-            setCustomSpace(factory.createCustomOntologySpace(id, customRoot));
-        } catch (UnmodifiableOntologySpaceException e) {
+            setCustomSpace(factory.createCustomOntologySpace(id/* , coreOntologies */));
+        } catch (UnmodifiableOntologyCollectorException e) {
             // Can't happen unless the factory or space implementations are
             // really naughty.
             log.warn(
@@ -116,9 +109,9 @@ public class OntologyScopeImpl implement
                         + " was denied creation of its own custom space upon initialization! This should not happen.",
                 e);
         }
-        this.customSpace.addOntologySpaceListener(this);
+        this.customSpace.addListener(this);
         // }
-        sessionSpaces = new HashMap<IRI,SessionOntologySpace>();
+        sessionSpaces = new HashMap<String,SessionOntologySpace>();
     }
 
     @Override
@@ -127,10 +120,10 @@ public class OntologyScopeImpl implement
     }
 
     @Override
-    public synchronized void addSessionSpace(OntologySpace sessionSpace, IRI sessionId) throws UnmodifiableOntologySpaceException {
+    public synchronized void addSessionSpace(OntologySpace sessionSpace, String sessionId) throws UnmodifiableOntologyCollectorException {
         if (sessionSpace instanceof SessionOntologySpace) {
             sessionSpaces.put(sessionId, (SessionOntologySpace) sessionSpace);
-            sessionSpace.addOntologySpaceListener(this);
+            sessionSpace.addListener(this);
 
             if (this.getCustomSpace() != null) ((SessionOntologySpace) sessionSpace).attachSpace(
                 this.getCustomSpace(), true);
@@ -141,6 +134,16 @@ public class OntologyScopeImpl implement
 
     @Override
     public OWLOntology asOWLOntology() {
+        return this.asOWLOntology(false);
+    }
+
+    /**
+     * FIXME not merging yet
+     * 
+     * @see OWLExportable#asOWLOntology(boolean)
+     */
+    @Override
+    public OWLOntology asOWLOntology(boolean merge) {
         // Create an ontology manager on the fly. We don't really need a permanent one.
         OWLOntologyManager mgr = OWLManager.createOWLOntologyManager();
         OWLDataFactory df = mgr.getOWLDataFactory();
@@ -210,7 +213,7 @@ public class OntologyScopeImpl implement
     }
 
     @Override
-    public SessionOntologySpace getSessionSpace(IRI sessionID) {
+    public SessionOntologySpace getSessionSpace(String sessionID) {
         return sessionSpaces.get(sessionID);
     }
 
@@ -237,14 +240,14 @@ public class OntologyScopeImpl implement
     }
 
     @Override
-    public synchronized void setCustomSpace(OntologySpace customSpace) throws UnmodifiableOntologySpaceException {
-        if (this.customSpace != null && this.customSpace.isLocked()) throw new UnmodifiableOntologySpaceException(
+    public synchronized void setCustomSpace(OntologySpace customSpace) throws UnmodifiableOntologyCollectorException {
+        if (this.customSpace != null && this.customSpace.isLocked()) throw new UnmodifiableOntologyCollectorException(
                 getCustomSpace());
         else if (!(customSpace instanceof CustomOntologySpace)) throw new ClassCastException(
                 "supplied object is not a CustomOntologySpace instance.");
         else {
             this.customSpace = (CustomOntologySpace) customSpace;
-            this.customSpace.addOntologySpaceListener(this);
+            this.customSpace.addListener(this);
             this.customSpace.attachCoreSpace(this.coreSpace, true);
         }
 
@@ -289,10 +292,10 @@ public class OntologyScopeImpl implement
     @Override
     public synchronized void setUp() {
         if (locked || (customSpace != null && !customSpace.isLocked())) return;
-        this.coreSpace.addOntologySpaceListener(this);
+        this.coreSpace.addListener(this);
         this.coreSpace.setUp();
         if (this.customSpace != null) {
-            this.customSpace.addOntologySpaceListener(this);
+            this.customSpace.addListener(this);
             this.customSpace.setUp();
         }
         locked = true;

Modified: incubator/stanbol/trunk/ontologymanager/ontonet/src/main/java/org/apache/stanbol/ontologymanager/ontonet/impl/ontology/OntologySpaceFactoryImpl.java
URL: http://svn.apache.org/viewvc/incubator/stanbol/trunk/ontologymanager/ontonet/src/main/java/org/apache/stanbol/ontologymanager/ontonet/impl/ontology/OntologySpaceFactoryImpl.java?rev=1185032&r1=1185031&r2=1185032&view=diff
==============================================================================
--- incubator/stanbol/trunk/ontologymanager/ontonet/src/main/java/org/apache/stanbol/ontologymanager/ontonet/impl/ontology/OntologySpaceFactoryImpl.java (original)
+++ incubator/stanbol/trunk/ontologymanager/ontonet/src/main/java/org/apache/stanbol/ontologymanager/ontonet/impl/ontology/OntologySpaceFactoryImpl.java Mon Oct 17 07:43:15 2011
@@ -23,11 +23,11 @@ import org.apache.stanbol.ontologymanage
 import org.apache.stanbol.ontologymanager.ontonet.api.ontology.OntologyScope;
 import org.apache.stanbol.ontologymanager.ontonet.api.ontology.OntologySpace;
 import org.apache.stanbol.ontologymanager.ontonet.api.ontology.OntologySpaceFactory;
-import org.apache.stanbol.ontologymanager.ontonet.api.ontology.OntologySpaceListener;
+import org.apache.stanbol.ontologymanager.ontonet.api.ontology.OntologyCollectorListener;
 import org.apache.stanbol.ontologymanager.ontonet.api.ontology.ScopeRegistry;
 import org.apache.stanbol.ontologymanager.ontonet.api.ontology.SessionOntologySpace;
 import org.apache.stanbol.ontologymanager.ontonet.api.ontology.SpaceType;
-import org.apache.stanbol.ontologymanager.ontonet.api.ontology.UnmodifiableOntologySpaceException;
+import org.apache.stanbol.ontologymanager.ontonet.api.ontology.UnmodifiableOntologyCollectorException;
 import org.apache.stanbol.ontologymanager.ontonet.impl.io.ClerezzaOntologyStorage;
 import org.apache.stanbol.owl.OWLOntologyManagerFactory;
 import org.semanticweb.owlapi.model.IRI;
@@ -75,13 +75,13 @@ public class OntologySpaceFactoryImpl im
         // FIXME: ensure that this is not null AND convert to using Strings for scope IDs
         OntologyScope parentScope = registry.getScope(scopeID);
 
-        if (parentScope != null && parentScope instanceof OntologySpaceListener) s
-                .addOntologySpaceListener((OntologySpaceListener) parentScope);
+        if (parentScope != null && parentScope instanceof OntologyCollectorListener) s
+                .addListener((OntologyCollectorListener) parentScope);
         // Set the supplied ontology's parent as the root for this space.
-        try {
+        if (ontologySources != null) try {
             for (OntologyInputSource src : ontologySources)
                 s.addOntology(src);
-        } catch (UnmodifiableOntologySpaceException e) {
+        } catch (UnmodifiableOntologyCollectorException e) {
             log.error("Ontology space " + s.getID() + " was found locked at creation time!", e);
         }
         // s.setUp();
@@ -130,7 +130,7 @@ public class OntologySpaceFactoryImpl im
         for (OntologyInputSource src : sessionSources)
             try {
                 s.addOntology(src);
-            } catch (UnmodifiableOntologySpaceException e) {
+            } catch (UnmodifiableOntologyCollectorException e) {
                 // Should never happen anyway...
                 continue;
             }

Modified: incubator/stanbol/trunk/ontologymanager/ontonet/src/main/java/org/apache/stanbol/ontologymanager/ontonet/impl/ontology/ScopeRegistryImpl.java
URL: http://svn.apache.org/viewvc/incubator/stanbol/trunk/ontologymanager/ontonet/src/main/java/org/apache/stanbol/ontologymanager/ontonet/impl/ontology/ScopeRegistryImpl.java?rev=1185032&r1=1185031&r2=1185032&view=diff
==============================================================================
--- incubator/stanbol/trunk/ontologymanager/ontonet/src/main/java/org/apache/stanbol/ontologymanager/ontonet/impl/ontology/ScopeRegistryImpl.java (original)
+++ incubator/stanbol/trunk/ontologymanager/ontonet/src/main/java/org/apache/stanbol/ontologymanager/ontonet/impl/ontology/ScopeRegistryImpl.java Mon Oct 17 07:43:15 2011
@@ -30,7 +30,7 @@ import org.semanticweb.owlapi.model.IRI;
 /**
  * Default implementation of an ontology scope registry.
  * 
- * @author alessandro
+ * @author alexdma
  * 
  */
 public class ScopeRegistryImpl implements ScopeRegistry {

Modified: incubator/stanbol/trunk/ontologymanager/ontonet/src/main/java/org/apache/stanbol/ontologymanager/ontonet/impl/ontology/SessionOntologySpaceImpl.java
URL: http://svn.apache.org/viewvc/incubator/stanbol/trunk/ontologymanager/ontonet/src/main/java/org/apache/stanbol/ontologymanager/ontonet/impl/ontology/SessionOntologySpaceImpl.java?rev=1185032&r1=1185031&r2=1185032&view=diff
==============================================================================
--- incubator/stanbol/trunk/ontologymanager/ontonet/src/main/java/org/apache/stanbol/ontologymanager/ontonet/impl/ontology/SessionOntologySpaceImpl.java (original)
+++ incubator/stanbol/trunk/ontologymanager/ontonet/src/main/java/org/apache/stanbol/ontologymanager/ontonet/impl/ontology/SessionOntologySpaceImpl.java Mon Oct 17 07:43:15 2011
@@ -21,7 +21,7 @@ import java.util.Random;
 import org.apache.stanbol.ontologymanager.ontonet.api.ontology.OntologySpace;
 import org.apache.stanbol.ontologymanager.ontonet.api.ontology.SessionOntologySpace;
 import org.apache.stanbol.ontologymanager.ontonet.api.ontology.SpaceType;
-import org.apache.stanbol.ontologymanager.ontonet.api.ontology.UnmodifiableOntologySpaceException;
+import org.apache.stanbol.ontologymanager.ontonet.api.ontology.UnmodifiableOntologyCollectorException;
 import org.apache.stanbol.ontologymanager.ontonet.impl.io.ClerezzaOntologyStorage;
 import org.semanticweb.owlapi.model.IRI;
 import org.semanticweb.owlapi.model.OWLOntologyManager;
@@ -52,7 +52,7 @@ public class SessionOntologySpaceImpl ex
     }
 
     @Override
-    public void attachSpace(OntologySpace space, boolean skipRoot) throws UnmodifiableOntologySpaceException {
+    public void attachSpace(OntologySpace space, boolean skipRoot) throws UnmodifiableOntologyCollectorException {
         // FIXME re-implement!
         // if (!(space instanceof SessionOntologySpace)) {
         // OWLOntology o = space.getTopOntology();

Modified: incubator/stanbol/trunk/ontologymanager/ontonet/src/main/java/org/apache/stanbol/ontologymanager/ontonet/impl/renderers/ScopeSetRenderer.java
URL: http://svn.apache.org/viewvc/incubator/stanbol/trunk/ontologymanager/ontonet/src/main/java/org/apache/stanbol/ontologymanager/ontonet/impl/renderers/ScopeSetRenderer.java?rev=1185032&r1=1185031&r2=1185032&view=diff
==============================================================================
--- incubator/stanbol/trunk/ontologymanager/ontonet/src/main/java/org/apache/stanbol/ontologymanager/ontonet/impl/renderers/ScopeSetRenderer.java (original)
+++ incubator/stanbol/trunk/ontologymanager/ontonet/src/main/java/org/apache/stanbol/ontologymanager/ontonet/impl/renderers/ScopeSetRenderer.java Mon Oct 17 07:43:15 2011
@@ -38,7 +38,7 @@ import org.slf4j.LoggerFactory;
 /**
  * Just an attempt. If we like it, make an API out of it.
  * 
- * @author alessandro
+ * @author alexdma
  * 
  */
 public class ScopeSetRenderer {

Modified: incubator/stanbol/trunk/ontologymanager/ontonet/src/main/java/org/apache/stanbol/ontologymanager/ontonet/impl/renderers/SessionRenderer.java
URL: http://svn.apache.org/viewvc/incubator/stanbol/trunk/ontologymanager/ontonet/src/main/java/org/apache/stanbol/ontologymanager/ontonet/impl/renderers/SessionRenderer.java?rev=1185032&r1=1185031&r2=1185032&view=diff
==============================================================================
--- incubator/stanbol/trunk/ontologymanager/ontonet/src/main/java/org/apache/stanbol/ontologymanager/ontonet/impl/renderers/SessionRenderer.java (original)
+++ incubator/stanbol/trunk/ontologymanager/ontonet/src/main/java/org/apache/stanbol/ontologymanager/ontonet/impl/renderers/SessionRenderer.java Mon Oct 17 07:43:15 2011
@@ -38,6 +38,7 @@ import org.semanticweb.owlapi.model.OWLO
 import org.semanticweb.owlapi.model.OWLOntologyStorageException;
 import org.slf4j.LoggerFactory;
 
+@Deprecated
 public class SessionRenderer {
 
     private static OWLDataFactory __factory = OWLManager.getOWLDataFactory();
@@ -64,7 +65,7 @@ public class SessionRenderer {
 
         List<OWLOntologyChange> additions = new LinkedList<OWLOntologyChange>();
 
-        OWLNamedIndividual iSes = __factory.getOWLNamedIndividual(session.getID());
+        OWLNamedIndividual iSes = __factory.getOWLNamedIndividual(IRI.create(session.getID()));
         additions.add(new AddAxiom(ont, __factory.getOWLClassAssertionAxiom(cSession, iSes)));
         OWLDatatype anyURI = __factory.getOWLDatatype(IRI.create("http://www.w3.org/2001/XMLSchema#anyURI"));
         OWLLiteral hasIdValue = __factory.getOWLTypedLiteral(session.getID().toString(), anyURI);

Modified: incubator/stanbol/trunk/ontologymanager/ontonet/src/main/java/org/apache/stanbol/ontologymanager/ontonet/impl/session/ScopeSessionSynchronizer.java
URL: http://svn.apache.org/viewvc/incubator/stanbol/trunk/ontologymanager/ontonet/src/main/java/org/apache/stanbol/ontologymanager/ontonet/impl/session/ScopeSessionSynchronizer.java?rev=1185032&r1=1185031&r2=1185032&view=diff
==============================================================================
--- incubator/stanbol/trunk/ontologymanager/ontonet/src/main/java/org/apache/stanbol/ontologymanager/ontonet/impl/session/ScopeSessionSynchronizer.java (original)
+++ incubator/stanbol/trunk/ontologymanager/ontonet/src/main/java/org/apache/stanbol/ontologymanager/ontonet/impl/session/ScopeSessionSynchronizer.java Mon Oct 17 07:43:15 2011
@@ -1,25 +1,25 @@
 /*
-* Licensed to the Apache Software Foundation (ASF) under one or more
-* contributor license agreements.  See the NOTICE file distributed with
-* this work for additional information regarding copyright ownership.
-* The ASF licenses this file to You under the Apache License, Version 2.0
-* (the "License"); you may not use this file except in compliance with
-* the License.  You may obtain a copy of the License at
-*
-*     http://www.apache.org/licenses/LICENSE-2.0
-*
-* Unless required by applicable law or agreed to in writing, software
-* distributed under the License is distributed on an "AS IS" BASIS,
-* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-* See the License for the specific language governing permissions and
-* limitations under the License.
-*/
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements.  See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
 package org.apache.stanbol.ontologymanager.ontonet.impl.session;
 
 import org.apache.stanbol.ontologymanager.ontonet.api.ONManager;
 import org.apache.stanbol.ontologymanager.ontonet.api.ontology.OntologyScope;
 import org.apache.stanbol.ontologymanager.ontonet.api.ontology.OntologySpaceFactory;
-import org.apache.stanbol.ontologymanager.ontonet.api.ontology.UnmodifiableOntologySpaceException;
+import org.apache.stanbol.ontologymanager.ontonet.api.ontology.UnmodifiableOntologyCollectorException;
 import org.apache.stanbol.ontologymanager.ontonet.api.session.Session;
 import org.apache.stanbol.ontologymanager.ontonet.api.session.SessionEvent;
 import org.apache.stanbol.ontologymanager.ontonet.api.session.SessionListener;
@@ -36,13 +36,15 @@ public class ScopeSessionSynchronizer im
         this.manager = manager;
     }
 
+    @Deprecated
     private void addSessionSpaces(IRI sessionId) {
         OntologySpaceFactory factory = manager.getOntologySpaceFactory();
         for (OntologyScope scope : manager.getScopeRegistry().getActiveScopes()) {
             try {
-                String scopeId = scope.getID().toString().substring(scope.getID().toString().lastIndexOf("/")+1);
-                scope.addSessionSpace(factory.createSessionOntologySpace(scopeId), sessionId);
-            } catch (UnmodifiableOntologySpaceException e) {
+                String scopeId = scope.getID().toString()
+                        .substring(scope.getID().toString().lastIndexOf("/") + 1);
+                scope.addSessionSpace(factory.createSessionOntologySpace(scopeId), sessionId.toString());
+            } catch (UnmodifiableOntologyCollectorException e) {
                 LoggerFactory.getLogger(getClass()).warn("Tried to add session to unmodifiable space ");
                 continue;
             }
@@ -57,7 +59,7 @@ public class ScopeSessionSynchronizer im
         switch (event.getOperationType()) {
             case CREATE:
                 ses.addSessionListener(this);
-                addSessionSpaces(ses.getID());
+                // addSessionSpaces(ses.getID());
                 break;
             case CLOSE:
                 break;

Modified: incubator/stanbol/trunk/ontologymanager/ontonet/src/main/java/org/apache/stanbol/ontologymanager/ontonet/impl/session/SessionImpl.java
URL: http://svn.apache.org/viewvc/incubator/stanbol/trunk/ontologymanager/ontonet/src/main/java/org/apache/stanbol/ontologymanager/ontonet/impl/session/SessionImpl.java?rev=1185032&r1=1185031&r2=1185032&view=diff
==============================================================================
--- incubator/stanbol/trunk/ontologymanager/ontonet/src/main/java/org/apache/stanbol/ontologymanager/ontonet/impl/session/SessionImpl.java (original)
+++ incubator/stanbol/trunk/ontologymanager/ontonet/src/main/java/org/apache/stanbol/ontologymanager/ontonet/impl/session/SessionImpl.java Mon Oct 17 07:43:15 2011
@@ -1,201 +1,315 @@
 /*
-* Licensed to the Apache Software Foundation (ASF) under one or more
-* contributor license agreements.  See the NOTICE file distributed with
-* this work for additional information regarding copyright ownership.
-* The ASF licenses this file to You under the Apache License, Version 2.0
-* (the "License"); you may not use this file except in compliance with
-* the License.  You may obtain a copy of the License at
-*
-*     http://www.apache.org/licenses/LICENSE-2.0
-*
-* Unless required by applicable law or agreed to in writing, software
-* distributed under the License is distributed on an "AS IS" BASIS,
-* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-* See the License for the specific language governing permissions and
-* limitations under the License.
-*/
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements.  See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
 package org.apache.stanbol.ontologymanager.ontonet.impl.session;
 
 import java.util.Collection;
 import java.util.HashSet;
 import java.util.Set;
 
-import org.apache.stanbol.ontologymanager.ontonet.api.session.Session;
+import org.apache.stanbol.ontologymanager.ontonet.api.io.OntologyInputSource;
+import org.apache.stanbol.ontologymanager.ontonet.api.ontology.OntologyCollectorListener;
+import org.apache.stanbol.ontologymanager.ontonet.api.ontology.OntologyCollectorModificationException;
+import org.apache.stanbol.ontologymanager.ontonet.api.ontology.OntologyScope;
+import org.apache.stanbol.ontologymanager.ontonet.api.ontology.UnmodifiableOntologyCollectorException;
 import org.apache.stanbol.ontologymanager.ontonet.api.session.NonReferenceableSessionException;
+import org.apache.stanbol.ontologymanager.ontonet.api.session.Session;
 import org.apache.stanbol.ontologymanager.ontonet.api.session.SessionEvent;
-import org.apache.stanbol.ontologymanager.ontonet.api.session.SessionListener;
 import org.apache.stanbol.ontologymanager.ontonet.api.session.SessionEvent.OperationType;
+import org.apache.stanbol.ontologymanager.ontonet.api.session.SessionListener;
 import org.semanticweb.owlapi.model.IRI;
+import org.semanticweb.owlapi.model.OWLOntology;
 import org.slf4j.LoggerFactory;
 
 /**
- * Standard implementation of the {@link Session} interface. A
- * SessionImpl is initially inactive and creates its own identifier.
+ * Standard implementation of the {@link Session} interface. A SessionImpl is initially inactive and creates
+ * its own identifier.
  * 
- * @author alessandro
+ * @author alexdma
  * 
  */
 public class SessionImpl implements Session {
 
-	/**
-	 * A KReS session knows about its own ID.
-	 */
-	protected IRI id = null;
-	protected Set<SessionListener> listeners;
-
-	/**
-	 * A KReS session knows about its own state.
-	 */
-	State state = State.HALTED;
-
-	/**
-	 * Utility constructor for enforcing a given IRI as a session ID. It will
-	 * not throw duplication exceptions, since a KReS session does not know
-	 * about other sessions.
-	 * 
-	 * @param sessionID
-	 *            the IRI to be set as unique identifier for this session
-	 */
-	public SessionImpl(IRI sessionID) {
-		this.id = sessionID;
-		listeners = new HashSet<SessionListener>();
-	}
-
-	public SessionImpl(IRI sessionID, State initialState)
-			throws NonReferenceableSessionException {
-		this(sessionID);
-		if (initialState == State.ZOMBIE)
-			throw new NonReferenceableSessionException();
-		else
-			setActive(initialState == State.ACTIVE);
-	}
-
-	/*
-	 * (non-Javadoc)
-	 * 
-	 * @see
-	 * eu.iksproject.kres.api.manager.session.SessionListenable#addSessionListener
-	 * (eu.iksproject.kres.api.manager.session.SessionListener)
-	 */
-	@Override
-	public void addSessionListener(SessionListener listener) {
-		listeners.add(listener);
-	}
-
-	/*
-	 * (non-Javadoc)
-	 * 
-	 * @seeeu.iksproject.kres.api.manager.session.SessionListenable#
-	 * clearSessionListeners()
-	 */
-	@Override
-	public void clearSessionListeners() {
-		listeners.clear();
-
-	}
-
-	/*
-	 * (non-Javadoc)
-	 * 
-	 * @see eu.iksproject.kres.api.manager.session.Session#close()
-	 */
-	@Override
-	public void close() throws NonReferenceableSessionException {
-		// if (getSessionState() == State.ZOMBIE)
-		// throw new NonReferenceableSessionException();
-		// state = State.ZOMBIE;
-		this.setActive(false);
-	}
-
-	/*
-	 * (non-Javadoc)
-	 * 
-	 * @see eu.iksproject.kres.api.manager.session.Session#getID()
-	 */
-	@Override
-	public IRI getID() {
-		return id;
-	}
-
-	/*
-	 * (non-Javadoc)
-	 * 
-	 * @see
-	 * eu.iksproject.kres.api.manager.session.SessionListenable#getSessionListeners
-	 * ()
-	 */
-	@Override
-	public Collection<SessionListener> getSessionListeners() {
-		return listeners;
-	}
-
-	/*
-	 * (non-Javadoc)
-	 * 
-	 * @see eu.iksproject.kres.api.manager.session.Session#getSessionState()
-	 */
-	@Override
-	public State getSessionState() {
-		return state;
-	}
-
-	/*
-	 * (non-Javadoc)
-	 * 
-	 * @see eu.iksproject.kres.api.manager.session.Session#isActive()
-	 */
-	@Override
-	public boolean isActive() {
-		return state == State.ACTIVE;
-	}
-
-	@Override
-	public void removeSessionListener(SessionListener listener) {
-		listeners.remove(listener);
-	}
-
-	/*
-	 * (non-Javadoc)
-	 * 
-	 * @see
-	 * eu.iksproject.kres.api.manager.session.Session#setActive(boolean)
-	 */
-	@Override
-	public State setActive(boolean active)
-			throws NonReferenceableSessionException {
-		if (getSessionState() == State.ZOMBIE)
-			throw new NonReferenceableSessionException();
-		else
-			state = active ? State.ACTIVE : State.HALTED;
-		return getSessionState();
-	}
-
-	/*
-	 * (non-Javadoc)
-	 * 
-	 * @see java.lang.Object#toString()
-	 */
-	@Override
-	public String toString() {
-		return getID().toString();
-	}
-
-	protected void fireClosed() {
-		SessionEvent e = null;
-		try {
-			e = new SessionEvent(this, OperationType.CLOSE);
-		} catch (Exception e1) {
-			LoggerFactory.getLogger(getClass()).error(
-					"KReS :: Could not close session " + getID(), e1);
-			return;
-		}
-		for (SessionListener l : listeners)
-			l.sessionChanged(e);
-	}
-
-	@Override
-	public void open() throws NonReferenceableSessionException {
-		setActive(true);
-	}
+    /**
+     * A KReS session knows about its own ID.
+     */
+    protected String id = null;
+
+    protected Set<SessionListener> listeners;
+
+    /**
+     * A KReS session knows about its own state.
+     */
+    State state = State.HALTED;
+
+    /**
+     * Utility constructor for enforcing a given IRI as a session ID. It will not throw duplication
+     * exceptions, since a KReS session does not know about other sessions.
+     * 
+     * @param sessionID
+     *            the IRI to be set as unique identifier for this session
+     */
+    public SessionImpl(String sessionID) {
+        this.id = sessionID;
+        listeners = new HashSet<SessionListener>();
+    }
+
+    public SessionImpl(String sessionID, State initialState) throws NonReferenceableSessionException {
+        this(sessionID);
+        if (initialState == State.ZOMBIE) throw new NonReferenceableSessionException();
+        else setActive(initialState == State.ACTIVE);
+    }
+
+    /*
+     * (non-Javadoc)
+     * 
+     * @see eu.iksproject.kres.api.manager.session.SessionListenable#addSessionListener
+     * (eu.iksproject.kres.api.manager.session.SessionListener)
+     */
+    @Override
+    public void addSessionListener(SessionListener listener) {
+        listeners.add(listener);
+    }
+
+    /*
+     * (non-Javadoc)
+     * 
+     * @seeeu.iksproject.kres.api.manager.session.SessionListenable# clearSessionListeners()
+     */
+    @Override
+    public void clearSessionListeners() {
+        listeners.clear();
+
+    }
+
+    /*
+     * (non-Javadoc)
+     * 
+     * @see eu.iksproject.kres.api.manager.session.Session#close()
+     */
+    @Override
+    public void close() throws NonReferenceableSessionException {
+        // if (getSessionState() == State.ZOMBIE)
+        // throw new NonReferenceableSessionException();
+        // state = State.ZOMBIE;
+        this.setActive(false);
+    }
+
+    /*
+     * (non-Javadoc)
+     * 
+     * @see eu.iksproject.kres.api.manager.session.Session#getID()
+     */
+    @Override
+    public String getID() {
+        return id.toString();
+    }
+
+    /*
+     * (non-Javadoc)
+     * 
+     * @see eu.iksproject.kres.api.manager.session.SessionListenable#getSessionListeners ()
+     */
+    @Override
+    public Collection<SessionListener> getSessionListeners() {
+        return listeners;
+    }
+
+    /*
+     * (non-Javadoc)
+     * 
+     * @see eu.iksproject.kres.api.manager.session.Session#getSessionState()
+     */
+    @Override
+    public State getSessionState() {
+        return state;
+    }
+
+    /*
+     * (non-Javadoc)
+     * 
+     * @see eu.iksproject.kres.api.manager.session.Session#isActive()
+     */
+    @Override
+    public boolean isActive() {
+        return state == State.ACTIVE;
+    }
+
+    @Override
+    public void removeSessionListener(SessionListener listener) {
+        listeners.remove(listener);
+    }
+
+    /*
+     * (non-Javadoc)
+     * 
+     * @see eu.iksproject.kres.api.manager.session.Session#setActive(boolean)
+     */
+    @Override
+    public State setActive(boolean active) throws NonReferenceableSessionException {
+        if (getSessionState() == State.ZOMBIE) throw new NonReferenceableSessionException();
+        else state = active ? State.ACTIVE : State.HALTED;
+        return getSessionState();
+    }
+
+    /*
+     * (non-Javadoc)
+     * 
+     * @see java.lang.Object#toString()
+     */
+    @Override
+    public String toString() {
+        return getID().toString();
+    }
+
+    protected void fireClosed() {
+        SessionEvent e = null;
+        try {
+            e = new SessionEvent(this, OperationType.CLOSE);
+        } catch (Exception e1) {
+            LoggerFactory.getLogger(getClass()).error("KReS :: Could not close session " + getID(), e1);
+            return;
+        }
+        for (SessionListener l : listeners)
+            l.sessionChanged(e);
+    }
+
+    @Override
+    public void open() throws NonReferenceableSessionException {
+        setActive(true);
+    }
+
+    @Override
+    public OWLOntology asOWLOntology(boolean merge) {
+        // TODO Auto-generated method stub
+        return null;
+    }
+
+    @Override
+    public void attachScope(OntologyScope scope) {
+        // TODO Auto-generated method stub
+
+    }
+
+    @Override
+    public void detachScope(String scopeId) {
+        // TODO Auto-generated method stub
+
+    }
+
+    @Override
+    public void clearScopes() {
+        // TODO Auto-generated method stub
+
+    }
+
+    @Override
+    public Set<String> getAttachedScopes() {
+        // TODO Auto-generated method stub
+        return null;
+    }
+
+    @Override
+    public void addOntology(OntologyInputSource<?> ontologySource) throws UnmodifiableOntologyCollectorException {
+        // TODO Auto-generated method stub
+
+    }
+
+    @Override
+    public Set<OWLOntology> getOntologies(boolean withClosure) {
+        // TODO Auto-generated method stub
+        return null;
+    }
+
+    @Override
+    public OWLOntology getOntology(IRI ontologyIri) {
+        // TODO Auto-generated method stub
+        return null;
+    }
+
+    @Override
+    public boolean hasOntology(IRI ontologyIri) {
+        // TODO Auto-generated method stub
+        return false;
+    }
+
+    @Override
+    public boolean isLocked() {
+        // TODO Auto-generated method stub
+        return false;
+    }
+
+    @Override
+    public void removeOntology(IRI ontologyId) throws OntologyCollectorModificationException {
+        // TODO Auto-generated method stub
+
+    }
+
+    @Override
+    public void addListener(OntologyCollectorListener listener) {
+        // TODO Auto-generated method stub
+
+    }
+
+    @Override
+    public void clearListeners() {
+        // TODO Auto-generated method stub
+
+    }
+
+    @Override
+    public Collection<OntologyCollectorListener> getListeners() {
+        // TODO Auto-generated method stub
+        return null;
+    }
+
+    @Override
+    public IRI getNamespace() {
+        // TODO Auto-generated method stub
+        return null;
+    }
+
+    @Override
+    public void removeListener(OntologyCollectorListener listener) {
+        // TODO Auto-generated method stub
+
+    }
+
+    @Override
+    public void setNamespace(IRI namespace) {
+        // TODO Auto-generated method stub
+
+    }
+
+    @Override
+    public void setUp() {
+        // TODO Auto-generated method stub
+
+    }
+
+    @Override
+    public void tearDown() {
+        // TODO Auto-generated method stub
+
+    }
+
+    @Override
+    public Set<Class<?>> getSupportedTypes() {
+        // TODO Auto-generated method stub
+        return null;
+    }
 
 }

Modified: incubator/stanbol/trunk/ontologymanager/ontonet/src/main/java/org/apache/stanbol/ontologymanager/ontonet/impl/session/SessionManagerImpl.java
URL: http://svn.apache.org/viewvc/incubator/stanbol/trunk/ontologymanager/ontonet/src/main/java/org/apache/stanbol/ontologymanager/ontonet/impl/session/SessionManagerImpl.java?rev=1185032&r1=1185031&r2=1185032&view=diff
==============================================================================
--- incubator/stanbol/trunk/ontologymanager/ontonet/src/main/java/org/apache/stanbol/ontologymanager/ontonet/impl/session/SessionManagerImpl.java (original)
+++ incubator/stanbol/trunk/ontologymanager/ontonet/src/main/java/org/apache/stanbol/ontologymanager/ontonet/impl/session/SessionManagerImpl.java Mon Oct 17 07:43:15 2011
@@ -48,12 +48,12 @@ import org.slf4j.LoggerFactory;
  * 
  * TODO: implement storage (using persistence layer).
  * 
- * @author alessandro
+ * @author alexdma
  * 
  */
 public class SessionManagerImpl implements SessionManager {
 
-    private Map<IRI,Session> sessionsByID;
+    private Map<String,Session> sessionsByID;
 
     protected Set<SessionListener> listeners;
 
@@ -68,7 +68,7 @@ public class SessionManagerImpl implemen
     public SessionManagerImpl(IRI baseIri, ScopeRegistry scopeRegistry, ClerezzaOntologyStorage store) {
         idgen = new TimestampedSessionIDGenerator(baseIri);
         listeners = new HashSet<SessionListener>();
-        sessionsByID = new HashMap<IRI,Session>();
+        sessionsByID = new HashMap<String,Session>();
         this.scopeRegistry = scopeRegistry;
         this.store = store;
     }
@@ -101,13 +101,13 @@ public class SessionManagerImpl implemen
      */
     @Override
     public Session createSession() {
-        Set<IRI> exclude = getRegisteredSessionIDs();
+        Set<String> exclude = getRegisteredSessionIDs();
         Session session = null;
         while (session == null)
             try {
                 session = createSession(idgen.createSessionID(exclude));
             } catch (DuplicateSessionIDException e) {
-                exclude.add(IRI.create(e.getDuplicateID()));
+                exclude.add(e.getDuplicateID());
                 continue;
             }
         return session;
@@ -120,7 +120,7 @@ public class SessionManagerImpl implemen
      * .semanticweb.owlapi.model.IRI)
      */
     @Override
-    public synchronized Session createSession(IRI sessionID) throws DuplicateSessionIDException {
+    public synchronized Session createSession(String sessionID) throws DuplicateSessionIDException {
         if (sessionsByID.containsKey(sessionID)) throw new DuplicateSessionIDException(sessionID.toString());
         Session session = new SessionImpl(sessionID);
         addSession(session);
@@ -135,7 +135,7 @@ public class SessionManagerImpl implemen
      * org.semanticweb.owlapi.model.IRI)
      */
     @Override
-    public synchronized void destroySession(IRI sessionID) {
+    public synchronized void destroySession(String sessionID) {
         try {
             Session ses = sessionsByID.get(sessionID);
             if (ses == null) log.warn(
@@ -161,12 +161,12 @@ public class SessionManagerImpl implemen
      * semanticweb.owlapi.model.IRI)
      */
     @Override
-    public Session getSession(IRI sessionID) {
+    public Session getSession(String sessionID) {
         return sessionsByID.get(sessionID);
     }
 
     @Override
-    public Set<IRI> getRegisteredSessionIDs() {
+    public Set<String> getRegisteredSessionIDs() {
         return sessionsByID.keySet();
     }
 
@@ -205,7 +205,7 @@ public class SessionManagerImpl implemen
     }
 
     protected synchronized void removeSession(Session session) {
-        IRI id = session.getID();
+        String id = session.getID();
         Session s2 = sessionsByID.get(id);
         if (session == s2) sessionsByID.remove(id);
     }
@@ -229,7 +229,7 @@ public class SessionManagerImpl implemen
      * (org.semanticweb.owlapi.model.IRI)
      */
     @Override
-    public Set<SessionOntologySpace> getSessionSpaces(IRI sessionID) throws NonReferenceableSessionException {
+    public Set<SessionOntologySpace> getSessionSpaces(String sessionID) throws NonReferenceableSessionException {
         Set<SessionOntologySpace> result = new HashSet<SessionOntologySpace>();
         // Brute force search
         for (OntologyScope scope : scopeRegistry.getRegisteredScopes()) {
@@ -259,7 +259,7 @@ public class SessionManagerImpl implemen
      * .semanticweb.owlapi.model.IRI, java.io.OutputStream)
      */
     @Override
-    public void storeSession(IRI sessionID, OutputStream out) throws NonReferenceableSessionException,
+    public void storeSession(String sessionID, OutputStream out) throws NonReferenceableSessionException,
                                                              OWLOntologyStorageException {
         /*
          * For each gession space in the session save all the ontologies contained in the space.

Modified: incubator/stanbol/trunk/ontologymanager/ontonet/src/main/java/org/apache/stanbol/ontologymanager/ontonet/impl/session/TimestampedSessionIDGenerator.java
URL: http://svn.apache.org/viewvc/incubator/stanbol/trunk/ontologymanager/ontonet/src/main/java/org/apache/stanbol/ontologymanager/ontonet/impl/session/TimestampedSessionIDGenerator.java?rev=1185032&r1=1185031&r2=1185032&view=diff
==============================================================================
--- incubator/stanbol/trunk/ontologymanager/ontonet/src/main/java/org/apache/stanbol/ontologymanager/ontonet/impl/session/TimestampedSessionIDGenerator.java (original)
+++ incubator/stanbol/trunk/ontologymanager/ontonet/src/main/java/org/apache/stanbol/ontologymanager/ontonet/impl/session/TimestampedSessionIDGenerator.java Mon Oct 17 07:43:15 2011
@@ -23,6 +23,12 @@ import org.apache.stanbol.ontologymanage
 import org.apache.stanbol.ontologymanager.ontonet.impl.util.StringUtils;
 import org.semanticweb.owlapi.model.IRI;
 
+/**
+ * FIXME make sure to manage namespaces independently!
+ * 
+ * @author alexdma
+ * 
+ */
 public class TimestampedSessionIDGenerator implements SessionIDGenerator {
 
     private IRI baseIRI;
@@ -32,13 +38,13 @@ public class TimestampedSessionIDGenerat
     }
 
     @Override
-    public IRI createSessionID() {
-        return IRI.create(StringUtils.stripIRITerminator(baseIRI) + "/session/" + new Date().getTime());
+    public String createSessionID() {
+        return StringUtils.stripIRITerminator(baseIRI) + "/session/" + new Date().getTime();
     }
 
     @Override
-    public IRI createSessionID(Set<IRI> exclude) {
-        IRI id = null;
+    public String createSessionID(Set<String> exclude) {
+        String id = null;
         do {
             id = createSessionID();
         } while (exclude.contains(id));

Modified: incubator/stanbol/trunk/ontologymanager/ontonet/src/main/java/org/apache/stanbol/ontologymanager/ontonet/impl/util/OntologyUtils.java
URL: http://svn.apache.org/viewvc/incubator/stanbol/trunk/ontologymanager/ontonet/src/main/java/org/apache/stanbol/ontologymanager/ontonet/impl/util/OntologyUtils.java?rev=1185032&r1=1185031&r2=1185032&view=diff
==============================================================================
--- incubator/stanbol/trunk/ontologymanager/ontonet/src/main/java/org/apache/stanbol/ontologymanager/ontonet/impl/util/OntologyUtils.java (original)
+++ incubator/stanbol/trunk/ontologymanager/ontonet/src/main/java/org/apache/stanbol/ontologymanager/ontonet/impl/util/OntologyUtils.java Mon Oct 17 07:43:15 2011
@@ -1,19 +1,19 @@
 /*
-* Licensed to the Apache Software Foundation (ASF) under one or more
-* contributor license agreements.  See the NOTICE file distributed with
-* this work for additional information regarding copyright ownership.
-* The ASF licenses this file to You under the Apache License, Version 2.0
-* (the "License"); you may not use this file except in compliance with
-* the License.  You may obtain a copy of the License at
-*
-*     http://www.apache.org/licenses/LICENSE-2.0
-*
-* Unless required by applicable law or agreed to in writing, software
-* distributed under the License is distributed on an "AS IS" BASIS,
-* WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
-* See the License for the specific language governing permissions and
-* limitations under the License.
-*/
+ * Licensed to the Apache Software Foundation (ASF) under one or more
+ * contributor license agreements.  See the NOTICE file distributed with
+ * this work for additional information regarding copyright ownership.
+ * The ASF licenses this file to You under the Apache License, Version 2.0
+ * (the "License"); you may not use this file except in compliance with
+ * the License.  You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
 package org.apache.stanbol.ontologymanager.ontonet.impl.util;
 
 import java.io.PrintStream;
@@ -22,7 +22,10 @@ import java.util.List;
 import java.util.Set;
 
 import org.apache.stanbol.ontologymanager.ontonet.api.io.OntologyInputSource;
+import org.apache.stanbol.ontologymanager.ontonet.api.io.OntologySpaceSource;
 import org.apache.stanbol.ontologymanager.ontonet.api.io.RootOntologySource;
+import org.apache.stanbol.ontologymanager.ontonet.api.ontology.OntologySpace;
+import org.apache.stanbol.ontologymanager.ontonet.api.ontology.UnmodifiableOntologyCollectorException;
 import org.semanticweb.owlapi.apibinding.OWLManager;
 import org.semanticweb.owlapi.io.RDFXMLOntologyFormat;
 import org.semanticweb.owlapi.io.StringDocumentTarget;
@@ -44,7 +47,7 @@ import org.slf4j.LoggerFactory;
 /**
  * A set of static utility methods for managing ontologies in KReS.
  * 
- * @author alessandro
+ * @author alexdma
  * 
  */
 public class OntologyUtils {
@@ -78,18 +81,19 @@ public class OntologyUtils {
     // return buildImportTree(root, subtrees, mgr);
     // }
 
-    public static OWLOntology appendOntology(OntologyInputSource parentSrc,
-                                             OntologyInputSource childSrc,
+    public static OWLOntology appendOntology(OntologyInputSource<OWLOntology> parentSrc,
+                                             OntologyInputSource<OWLOntology> childSrc,
                                              OWLOntologyManager ontologyManager) {
         return appendOntology(parentSrc, childSrc, ontologyManager, null);
     }
 
-    public static OWLOntology appendOntology(OntologyInputSource parentSrc, OntologyInputSource childSrc) {
+    public static OWLOntology appendOntology(OntologyInputSource<OWLOntology> parentSrc,
+                                             OntologyInputSource<OWLOntology> childSrc) {
         return appendOntology(parentSrc, childSrc, null, null);
     }
 
-    public static OWLOntology appendOntology(OntologyInputSource parentSrc,
-                                             OntologyInputSource childSrc,
+    public static OWLOntology appendOntology(OntologyInputSource<OWLOntology> parentSrc,
+                                             OntologyInputSource<OWLOntology> childSrc,
                                              IRI rewritePrefix) {
         return appendOntology(parentSrc, childSrc, null, rewritePrefix);
     }
@@ -113,8 +117,8 @@ public class OntologyUtils {
      *            ontology document file elsewhere.
      * @return the parent with the appended child
      */
-    public static OWLOntology appendOntology(OntologyInputSource parentSrc,
-                                             OntologyInputSource childSrc,
+    public static OWLOntology appendOntology(OntologyInputSource<OWLOntology> parentSrc,
+                                             OntologyInputSource<OWLOntology> childSrc,
                                              OWLOntologyManager ontologyManager,
                                              IRI rewritePrefix) {
 
@@ -148,7 +152,8 @@ public class OntologyUtils {
         return oParent;
     }
 
-    public static OWLOntology buildImportTree(OntologyInputSource rootSrc, Set<OWLOntology> subtrees) {
+    public static OWLOntology buildImportTree(OntologyInputSource<OWLOntology> rootSrc,
+                                              Set<OWLOntology> subtrees) {
 
         return buildImportTree(rootSrc.getRootOntology(), subtrees, OWLManager.createOWLOntologyManager());
 
@@ -161,10 +166,21 @@ public class OntologyUtils {
      * @param mgr
      * @return
      */
-    public static OWLOntology buildImportTree(OntologyInputSource rootSrc,
+    public static OWLOntology buildImportTree(OntologyInputSource<OWLOntology> rootSrc,
                                               Set<OWLOntology> subtrees,
                                               OWLOntologyManager mgr) {
 
+        if (rootSrc instanceof OntologySpaceSource) {
+            OntologySpace spc = ((OntologySpaceSource) rootSrc).asOntologySpace();
+            for (OWLOntology o : subtrees)
+                try {
+                    spc.addOntology(new RootOntologySource(o));
+                } catch (UnmodifiableOntologyCollectorException e) {
+                    logger.error("Cannot add ontology {} to unmodifiable space {}", o, spc);
+                    continue;
+                }
+        }
+
         return buildImportTree(rootSrc.getRootOntology(), subtrees, mgr);
 
     }

Modified: incubator/stanbol/trunk/ontologymanager/ontonet/src/test/java/org/apache/stanbol/ontologymanager/ontonet/MockOsgiContext.java
URL: http://svn.apache.org/viewvc/incubator/stanbol/trunk/ontologymanager/ontonet/src/test/java/org/apache/stanbol/ontologymanager/ontonet/MockOsgiContext.java?rev=1185032&r1=1185031&r2=1185032&view=diff
==============================================================================
--- incubator/stanbol/trunk/ontologymanager/ontonet/src/test/java/org/apache/stanbol/ontologymanager/ontonet/MockOsgiContext.java (original)
+++ incubator/stanbol/trunk/ontologymanager/ontonet/src/test/java/org/apache/stanbol/ontologymanager/ontonet/MockOsgiContext.java Mon Oct 17 07:43:15 2011
@@ -18,6 +18,8 @@ package org.apache.stanbol.ontologymanag
 
 import org.apache.clerezza.rdf.core.access.TcManager;
 import org.apache.clerezza.rdf.core.serializedform.Parser;
+import org.apache.clerezza.rdf.jena.parser.JenaParserProvider;
+import org.apache.clerezza.rdf.rdfjson.parser.RdfJsonParsingProvider;
 import org.apache.clerezza.rdf.simple.storage.SimpleTcProvider;
 
 public class MockOsgiContext {
@@ -33,6 +35,10 @@ public class MockOsgiContext {
     public static void reset() {
         tcManager = new TcManager();
         tcManager.addWeightedTcProvider(new SimpleTcProvider());
+
+        parser = new Parser();
+        parser.bindParsingProvider(new JenaParserProvider());
+        parser.bindParsingProvider(new RdfJsonParsingProvider());
     }
 
 }

Copied: incubator/stanbol/trunk/ontologymanager/ontonet/src/test/java/org/apache/stanbol/ontologymanager/ontonet/io/TestOWLAPIInputSources.java (from r1181018, incubator/stanbol/trunk/ontologymanager/ontonet/src/test/java/org/apache/stanbol/ontologymanager/ontonet/io/TestOntologyInputSources.java)
URL: http://svn.apache.org/viewvc/incubator/stanbol/trunk/ontologymanager/ontonet/src/test/java/org/apache/stanbol/ontologymanager/ontonet/io/TestOWLAPIInputSources.java?p2=incubator/stanbol/trunk/ontologymanager/ontonet/src/test/java/org/apache/stanbol/ontologymanager/ontonet/io/TestOWLAPIInputSources.java&p1=incubator/stanbol/trunk/ontologymanager/ontonet/src/test/java/org/apache/stanbol/ontologymanager/ontonet/io/TestOntologyInputSources.java&r1=1181018&r2=1185032&rev=1185032&view=diff
==============================================================================
--- incubator/stanbol/trunk/ontologymanager/ontonet/src/test/java/org/apache/stanbol/ontologymanager/ontonet/io/TestOntologyInputSources.java (original)
+++ incubator/stanbol/trunk/ontologymanager/ontonet/src/test/java/org/apache/stanbol/ontologymanager/ontonet/io/TestOWLAPIInputSources.java Mon Oct 17 07:43:15 2011
@@ -16,6 +16,7 @@
  */
 package org.apache.stanbol.ontologymanager.ontonet.io;
 
+import static org.apache.stanbol.ontologymanager.ontonet.MockOsgiContext.reset;
 import static org.junit.Assert.*;
 
 import java.io.File;
@@ -34,6 +35,7 @@ import org.apache.stanbol.ontologymanage
 import org.apache.stanbol.ontologymanager.ontonet.impl.ONManagerImpl;
 import org.apache.stanbol.ontologymanager.ontonet.impl.OfflineConfigurationImpl;
 import org.apache.stanbol.owl.OWLOntologyManagerFactory;
+import org.junit.After;
 import org.junit.BeforeClass;
 import org.junit.Test;
 import org.semanticweb.owlapi.io.WriterDocumentTarget;
@@ -47,7 +49,7 @@ import org.semanticweb.owlapi.model.OWLO
 import org.semanticweb.owlapi.model.OWLOntologyManager;
 import org.semanticweb.owlapi.util.AutoIRIMapper;
 
-public class TestOntologyInputSources {
+public class TestOWLAPIInputSources {
 
     private static OWLDataFactory df;
 
@@ -110,10 +112,10 @@ public class TestOntologyInputSources {
         assertNotNull(url);
         File f = new File(url.toURI());
         assertNotNull(f);
-        OntologyInputSource coreSource = new ParentPathInputSource(f);
+        OntologyInputSource<OWLOntology> coreSource = new ParentPathInputSource(f);
 
         // Check that all the imports closure is made of local files
-        Set<OWLOntology> closure = coreSource.getClosure();
+        Set<OWLOntology> closure = coreSource.getImports(true);
         for (OWLOntology o : closure)
             assertEquals("file", o.getOWLOntologyManager().getOntologyDocumentIRI(o).getScheme());
 
@@ -140,7 +142,7 @@ public class TestOntologyInputSources {
     public void testOfflineSingleton() throws Exception {
         URL url = getClass().getResource("/ontologies/mockfoaf.rdf");
         assertNotNull(url);
-        OntologyInputSource coreSource = new RootOntologyIRISource(IRI.create(url));
+        OntologyInputSource<OWLOntology> coreSource = new RootOntologyIRISource(IRI.create(url));
         assertNotNull(df);
         /*
          * To check it fetched the correct ontology, we look for a declaration of the bogus class foaf:Perzon
@@ -149,5 +151,10 @@ public class TestOntologyInputSources {
         OWLClass cPerzon = df.getOWLClass(IRI.create("http://xmlns.com/foaf/0.1/Perzon"));
         assertTrue(coreSource.getRootOntology().getClassesInSignature().contains(cPerzon));
     }
+    
+    @After
+    public void cleanup() {
+        reset();
+    }
 
 }

Modified: incubator/stanbol/trunk/ontologymanager/ontonet/src/test/java/org/apache/stanbol/ontologymanager/ontonet/io/TestStorage.java
URL: http://svn.apache.org/viewvc/incubator/stanbol/trunk/ontologymanager/ontonet/src/test/java/org/apache/stanbol/ontologymanager/ontonet/io/TestStorage.java?rev=1185032&r1=1185031&r2=1185032&view=diff
==============================================================================
--- incubator/stanbol/trunk/ontologymanager/ontonet/src/test/java/org/apache/stanbol/ontologymanager/ontonet/io/TestStorage.java (original)
+++ incubator/stanbol/trunk/ontologymanager/ontonet/src/test/java/org/apache/stanbol/ontologymanager/ontonet/io/TestStorage.java Mon Oct 17 07:43:15 2011
@@ -16,7 +16,11 @@
  */
 package org.apache.stanbol.ontologymanager.ontonet.io;
 
-import static org.junit.Assert.*;
+import static org.apache.stanbol.ontologymanager.ontonet.MockOsgiContext.reset;
+import static org.apache.stanbol.ontologymanager.ontonet.MockOsgiContext.tcManager;
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertFalse;
+import static org.junit.Assert.assertTrue;
 
 import java.util.HashSet;
 import java.util.Hashtable;
@@ -28,7 +32,6 @@ import org.apache.clerezza.rdf.core.Trip
 import org.apache.clerezza.rdf.core.UriRef;
 import org.apache.clerezza.rdf.utils.GraphNode;
 import org.apache.stanbol.ontologymanager.ontonet.Constants;
-import org.apache.stanbol.ontologymanager.ontonet.MockOsgiContext;
 import org.apache.stanbol.ontologymanager.ontonet.api.ONManager;
 import org.apache.stanbol.ontologymanager.ontonet.api.io.OntologyInputSource;
 import org.apache.stanbol.ontologymanager.ontonet.api.io.RootOntologyIRISource;
@@ -52,10 +55,10 @@ public class TestStorage {
 
     @BeforeClass
     public static void setup() {
+        reset();
         // Empty configurations are fine, but this time we provide a Clerezza context.
-        onm = new ONManagerImpl(MockOsgiContext.tcManager, MockOsgiContext.tcManager.getProviderList()
-                .first(), new OfflineConfigurationImpl(new Hashtable<String,Object>()),
-                new Hashtable<String,Object>());
+        onm = new ONManagerImpl(tcManager, tcManager.getProviderList().first(), new OfflineConfigurationImpl(
+                new Hashtable<String,Object>()), new Hashtable<String,Object>());
     }
 
     @Test
@@ -83,8 +86,8 @@ public class TestStorage {
     }
 
     @After
-    public void reset() {
-        MockOsgiContext.reset();
+    public void cleanup() {
+        reset();
     }
 
 }

Modified: incubator/stanbol/trunk/ontologymanager/ontonet/src/test/java/org/apache/stanbol/ontologymanager/ontonet/ontology/TestIndexing.java
URL: http://svn.apache.org/viewvc/incubator/stanbol/trunk/ontologymanager/ontonet/src/test/java/org/apache/stanbol/ontologymanager/ontonet/ontology/TestIndexing.java?rev=1185032&r1=1185031&r2=1185032&view=diff
==============================================================================
--- incubator/stanbol/trunk/ontologymanager/ontonet/src/test/java/org/apache/stanbol/ontologymanager/ontonet/ontology/TestIndexing.java (original)
+++ incubator/stanbol/trunk/ontologymanager/ontonet/src/test/java/org/apache/stanbol/ontologymanager/ontonet/ontology/TestIndexing.java Mon Oct 17 07:43:15 2011
@@ -16,10 +16,8 @@
  */
 package org.apache.stanbol.ontologymanager.ontonet.ontology;
 
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
+import static org.apache.stanbol.ontologymanager.ontonet.MockOsgiContext.*;
+import static org.junit.Assert.*;
 
 import java.io.File;
 import java.net.URL;
@@ -33,9 +31,10 @@ import org.apache.stanbol.ontologymanage
 import org.apache.stanbol.ontologymanager.ontonet.api.ontology.OntologyIndex;
 import org.apache.stanbol.ontologymanager.ontonet.api.ontology.OntologyScope;
 import org.apache.stanbol.ontologymanager.ontonet.api.ontology.OntologySpace;
-import org.apache.stanbol.ontologymanager.ontonet.impl.OfflineConfigurationImpl;
 import org.apache.stanbol.ontologymanager.ontonet.impl.ONManagerImpl;
+import org.apache.stanbol.ontologymanager.ontonet.impl.OfflineConfigurationImpl;
 import org.apache.stanbol.owl.OWLOntologyManagerFactory;
+import org.junit.After;
 import org.junit.BeforeClass;
 import org.semanticweb.owlapi.model.IRI;
 import org.semanticweb.owlapi.model.OWLOntology;
@@ -44,18 +43,16 @@ import org.semanticweb.owlapi.model.OWLO
 
 public class TestIndexing {
 
-    private static ONManager onm;
-
-    private static OWLOntologyManager mgr;
-
     private static IRI iri_minor = IRI
             .create("http://stanbol.apache.org/ontologies/pcomics/minorcharacters.owl"), iri_main = IRI
             .create("http://stanbol.apache.org/ontologies/pcomics/maincharacters.owl"), scopeIri = IRI
             .create("http://stanbol.apache.org/scope/IndexingTest"), testRegistryIri = IRI
             .create("http://stanbol.apache.org/ontologies/registries/onmtest.owl");
 
-    private static OntologyScope scope = null;
+    private static OWLOntologyManager mgr;
 
+    private static ONManager onm;
+    private static OntologyScope scope = null;
     @BeforeClass
     public static void setup() {
         final Dictionary<String,Object> emptyConfig = new Hashtable<String,Object>();
@@ -97,6 +94,11 @@ public class TestIndexing {
         // }
     }
 
+    @After
+    public void cleanup() {
+        reset();
+    }
+
     // @Test
     public void testAddOntology() throws Exception {
         OntologyIndex index = onm.getOntologyIndex();
@@ -118,7 +120,7 @@ public class TestIndexing {
         f = new File(url.toURI());
         assertNotNull(f);
 
-        cust.removeOntology(new ParentPathInputSource(f));
+        cust.removeOntology(iri_minor);
         // cust.removeOntology(commSrc);
 
         assertFalse(index.isOntologyLoaded(iri_minor));

Modified: incubator/stanbol/trunk/ontologymanager/ontonet/src/test/java/org/apache/stanbol/ontologymanager/ontonet/ontology/TestOntologyScope.java
URL: http://svn.apache.org/viewvc/incubator/stanbol/trunk/ontologymanager/ontonet/src/test/java/org/apache/stanbol/ontologymanager/ontonet/ontology/TestOntologyScope.java?rev=1185032&r1=1185031&r2=1185032&view=diff
==============================================================================
--- incubator/stanbol/trunk/ontologymanager/ontonet/src/test/java/org/apache/stanbol/ontologymanager/ontonet/ontology/TestOntologyScope.java (original)
+++ incubator/stanbol/trunk/ontologymanager/ontonet/src/test/java/org/apache/stanbol/ontologymanager/ontonet/ontology/TestOntologyScope.java Mon Oct 17 07:43:15 2011
@@ -16,10 +16,8 @@
  */
 package org.apache.stanbol.ontologymanager.ontonet.ontology;
 
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-import static org.junit.Assert.fail;
+import static org.apache.stanbol.ontologymanager.ontonet.MockOsgiContext.*;
+import static org.junit.Assert.*;
 
 import java.util.Dictionary;
 import java.util.Hashtable;
@@ -39,6 +37,7 @@ import org.apache.stanbol.ontologymanage
 import org.apache.stanbol.ontologymanager.ontonet.impl.ontology.CustomOntologySpaceImpl;
 import org.apache.stanbol.ontologymanager.ontonet.impl.ontology.OntologyScopeFactoryImpl;
 import org.apache.stanbol.owl.OWLOntologyManagerFactory;
+import org.junit.After;
 import org.junit.Before;
 import org.junit.BeforeClass;
 import org.junit.Test;
@@ -51,8 +50,6 @@ public class TestOntologyScope {
     public static IRI baseIri = IRI.create(Constants.PEANUTS_MAIN_BASE), baseIri2 = IRI
             .create(Constants.PEANUTS_MINOR_BASE);
 
-    public static String scopeIdBlank = "WackyRaces", scopeId1 = "Peanuts", scopeId2 = "CalvinAndHobbes";
-
     /**
      * An ontology scope that initially contains no ontologies, and is rebuilt from scratch before each test
      * method.
@@ -63,6 +60,8 @@ public class TestOntologyScope {
 
     private static ONManager onm;
 
+    public static String scopeIdBlank = "WackyRaces", scopeId1 = "Peanuts", scopeId2 = "CalvinAndHobbes";
+
     private static OntologyInputSource src1 = null, src2 = null;
 
     @BeforeClass
@@ -83,9 +82,14 @@ public class TestOntologyScope {
         }
     }
 
+    @After
+    public void cleanup() {
+        reset();
+    }
+    
     @Before
-    public void cleanup() throws DuplicateIDException {
-        if (factory != null) blankScope = factory.createOntologyScope(scopeIdBlank, null);
+    public void cleanupScope() throws DuplicateIDException {
+        if (factory != null) blankScope = factory.createOntologyScope(scopeIdBlank);
     }
 
     /**
@@ -185,7 +189,7 @@ public class TestOntologyScope {
     public void testNullScopeCreation() {
         OntologyScope scope = null;
         try {
-            scope = factory.createOntologyScope(null, null);
+            scope = factory.createOntologyScope(null, (OntologyInputSource) null);
         } catch (DuplicateIDException e) {
             fail("Unexpected DuplicateIDException caught while testing scope creation"
                  + " with null parameters.");

Modified: incubator/stanbol/trunk/ontologymanager/ontonet/src/test/java/org/apache/stanbol/ontologymanager/ontonet/ontology/TestOntologySpaces.java
URL: http://svn.apache.org/viewvc/incubator/stanbol/trunk/ontologymanager/ontonet/src/test/java/org/apache/stanbol/ontologymanager/ontonet/ontology/TestOntologySpaces.java?rev=1185032&r1=1185031&r2=1185032&view=diff
==============================================================================
--- incubator/stanbol/trunk/ontologymanager/ontonet/src/test/java/org/apache/stanbol/ontologymanager/ontonet/ontology/TestOntologySpaces.java (original)
+++ incubator/stanbol/trunk/ontologymanager/ontonet/src/test/java/org/apache/stanbol/ontologymanager/ontonet/ontology/TestOntologySpaces.java Mon Oct 17 07:43:15 2011
@@ -16,6 +16,7 @@
  */
 package org.apache.stanbol.ontologymanager.ontonet.ontology;
 
+import static org.apache.stanbol.ontologymanager.ontonet.MockOsgiContext.*;
 import static org.junit.Assert.*;
 
 import java.io.File;
@@ -36,10 +37,11 @@ import org.apache.stanbol.ontologymanage
 import org.apache.stanbol.ontologymanager.ontonet.api.ontology.OntologySpaceFactory;
 import org.apache.stanbol.ontologymanager.ontonet.api.ontology.SessionOntologySpace;
 import org.apache.stanbol.ontologymanager.ontonet.api.ontology.SpaceType;
-import org.apache.stanbol.ontologymanager.ontonet.api.ontology.UnmodifiableOntologySpaceException;
+import org.apache.stanbol.ontologymanager.ontonet.api.ontology.UnmodifiableOntologyCollectorException;
 import org.apache.stanbol.ontologymanager.ontonet.impl.ONManagerImpl;
 import org.apache.stanbol.ontologymanager.ontonet.impl.OfflineConfigurationImpl;
 import org.apache.stanbol.owl.OWLOntologyManagerFactory;
+import org.junit.After;
 import org.junit.BeforeClass;
 import org.junit.Test;
 import org.semanticweb.owlapi.model.AddAxiom;
@@ -57,22 +59,18 @@ public class TestOntologySpaces {
     public static IRI baseIri = IRI.create(Constants.PEANUTS_MAIN_BASE), baseIri2 = IRI
             .create(Constants.PEANUTS_MINOR_BASE);
 
-    String scopeId = "Comics";
-
+    private static OntologySpaceFactory factory;
+    private static OntologyInputSource<OWLOntology> inMemorySrc, minorSrc, dropSrc, nonexSrc;
     private static OWLAxiom linusIsHuman = null;
 
+    private static OfflineConfiguration offline;
+
     private static ONManager onm;
 
     private static OWLOntology ont = null, ont2 = null;
 
-    private static OntologyInputSource inMemorySrc, minorSrc, dropSrc, nonexSrc;
-
-    private static OntologySpaceFactory factory;
-
-    private static OfflineConfiguration offline;
-
-    private static OntologyInputSource getLocalSource(String resourcePath, OWLOntologyManager mgr) throws OWLOntologyCreationException,
-                                                                                                  URISyntaxException {
+    private static OntologyInputSource<OWLOntology> getLocalSource(String resourcePath, OWLOntologyManager mgr) throws OWLOntologyCreationException,
+                                                                                                               URISyntaxException {
         URL url = TestOntologySpaces.class.getResource(resourcePath);
         File f = new File(url.toURI());
         return new ParentPathInputSource(f, mgr != null ? mgr
@@ -111,6 +109,58 @@ public class TestOntologySpaces {
 
     }
 
+    String scopeId = "Comics";
+
+    @After
+    public void cleanup() {
+        reset();
+    }
+
+    @Test
+    public void testAddOntology() throws Exception {
+        CustomOntologySpace space = null;
+        IRI logicalId = nonexSrc.getRootOntology().getOntologyID().getOntologyIRI();
+
+        space = factory.createCustomOntologySpace(scopeId, dropSrc);
+        space.addOntology(minorSrc);
+        space.addOntology(nonexSrc);
+
+        assertTrue(space.hasOntology(logicalId));
+        logicalId = dropSrc.getRootOntology().getOntologyID().getOntologyIRI();
+        assertTrue(space.hasOntology(logicalId));
+    }
+
+    @Test
+    public void testCoreLock() throws Exception {
+        CoreOntologySpace space = factory.createCoreOntologySpace(scopeId, inMemorySrc);
+        space.setUp();
+        try {
+            space.addOntology(minorSrc);
+            fail("Modification was permitted on locked ontology space.");
+        } catch (UnmodifiableOntologyCollectorException e) {
+            assertSame(space, e.getOntologyCollector());
+        }
+    }
+
+    @Test
+    public void testCreateSpace() throws Exception {
+        CustomOntologySpace space = factory.createCustomOntologySpace(scopeId, dropSrc);
+        IRI logicalId = dropSrc.getRootOntology().getOntologyID().getOntologyIRI();
+        assertTrue(space.hasOntology(logicalId));
+    }
+
+    @Test
+    public void testCustomLock() throws Exception {
+        CustomOntologySpace space = factory.createCustomOntologySpace(scopeId, inMemorySrc);
+        space.setUp();
+        try {
+            space.addOntology(minorSrc);
+            fail("Modification was permitted on locked ontology space.");
+        } catch (UnmodifiableOntologyCollectorException e) {
+            assertSame(space, e.getOntologyCollector());
+        }
+    }
+
     /**
      * Checks whether attempting to create ontology spaces with invalid identifiers or namespaces results in
      * the appropriate exceptions being thrown.
@@ -187,51 +237,6 @@ public class TestOntologySpaces {
     }
 
     @Test
-    public void testAddOntology() throws Exception {
-        CustomOntologySpace space = null;
-        IRI logicalId = nonexSrc.getRootOntology().getOntologyID().getOntologyIRI();
-
-        space = factory.createCustomOntologySpace(scopeId, dropSrc);
-        space.addOntology(minorSrc);
-        space.addOntology(nonexSrc);
-
-        assertTrue(space.containsOntology(logicalId));
-        logicalId = dropSrc.getRootOntology().getOntologyID().getOntologyIRI();
-        assertTrue(space.containsOntology(logicalId));
-    }
-
-    @Test
-    public void testCoreLock() throws Exception {
-        CoreOntologySpace space = factory.createCoreOntologySpace(scopeId, inMemorySrc);
-        space.setUp();
-        try {
-            space.addOntology(minorSrc);
-            fail("Modification was permitted on locked ontology space.");
-        } catch (UnmodifiableOntologySpaceException e) {
-            assertSame(space, e.getSpace());
-        }
-    }
-
-    @Test
-    public void testCreateSpace() throws Exception {
-        CustomOntologySpace space = factory.createCustomOntologySpace(scopeId, dropSrc);
-        IRI logicalId = dropSrc.getRootOntology().getOntologyID().getOntologyIRI();
-        assertTrue(space.containsOntology(logicalId));
-    }
-
-    @Test
-    public void testCustomLock() throws Exception {
-        CustomOntologySpace space = factory.createCustomOntologySpace(scopeId, inMemorySrc);
-        space.setUp();
-        try {
-            space.addOntology(minorSrc);
-            fail("Modification was permitted on locked ontology space.");
-        } catch (UnmodifiableOntologySpaceException e) {
-            assertSame(space, e.getSpace());
-        }
-    }
-
-    @Test
     public void testRemoveCustomOntology() throws Exception {
         CustomOntologySpace space = null;
         space = factory.createCustomOntologySpace(scopeId, dropSrc);
@@ -241,12 +246,12 @@ public class TestOntologySpaces {
         space.addOntology(inMemorySrc);
         space.addOntology(nonexSrc);
         // The other remote ontologies may change base IRI...
-        assertTrue(space.containsOntology(ont.getOntologyID().getOntologyIRI())
-                   && space.containsOntology(dropId) && space.containsOntology(nonexId));
-        space.removeOntology(dropSrc);
-        assertFalse(space.containsOntology(dropId));
-        space.removeOntology(nonexSrc);
-        assertFalse(space.containsOntology(nonexId));
+        assertTrue(space.hasOntology(ont.getOntologyID().getOntologyIRI())
+                   && space.hasOntology(dropId) && space.hasOntology(nonexId));
+        space.removeOntology(dropId);
+        assertFalse(space.hasOntology(dropId));
+        space.removeOntology(nonexId);
+        assertFalse(space.hasOntology(nonexId));
         // OntologyUtils.printOntology(space.getTopOntology(), System.err);
 
     }
@@ -268,7 +273,7 @@ public class TestOntologySpaces {
             // // The top ontology must still have axioms from in-memory
             // // ontologies. NO LONGER
             // assertTrue(space.getTopOntology().containsAxiom(linusIsHuman));
-        } catch (UnmodifiableOntologySpaceException e) {
+        } catch (UnmodifiableOntologyCollectorException e) {
             fail("Modification was denied on unlocked ontology space.");
         }
     }

Modified: incubator/stanbol/trunk/ontologymanager/ontonet/src/test/java/org/apache/stanbol/ontologymanager/ontonet/session/TestSessions.java
URL: http://svn.apache.org/viewvc/incubator/stanbol/trunk/ontologymanager/ontonet/src/test/java/org/apache/stanbol/ontologymanager/ontonet/session/TestSessions.java?rev=1185032&r1=1185031&r2=1185032&view=diff
==============================================================================
--- incubator/stanbol/trunk/ontologymanager/ontonet/src/test/java/org/apache/stanbol/ontologymanager/ontonet/session/TestSessions.java (original)
+++ incubator/stanbol/trunk/ontologymanager/ontonet/src/test/java/org/apache/stanbol/ontologymanager/ontonet/session/TestSessions.java Mon Oct 17 07:43:15 2011
@@ -118,12 +118,13 @@ public class TestSessions {
             fail("Unexpected DuplicateIDException was caught while testing scope " + e.getDuplicateID());
         }
         Session ses = sesmgr.createSession();
-        IRI sesid = ses.getID();
-        assertFalse(scope1.getSessionSpaces().isEmpty());
-        assertNotNull(scope1.getSessionSpace(sesid));
-        assertFalse(scope3.getSessionSpaces().isEmpty());
-        assertNull(scope2.getSessionSpace(sesid));
-        assertNotNull(scope3.getSessionSpace(sesid));
+        String sesid = ses.getID();
+        // FIXME replace with proper tests
+        // assertFalse(scope1.getSessionSpaces().isEmpty());
+        // assertNotNull(scope1.getSessionSpace(sesid));
+        // assertFalse(scope3.getSessionSpaces().isEmpty());
+        // assertNull(scope2.getSessionSpace(sesid));
+        // assertNotNull(scope3.getSessionSpace(sesid));
     }
 
     @Test

Modified: incubator/stanbol/trunk/ontologymanager/registry/src/main/java/org/apache/stanbol/ontologymanager/registry/impl/RegistryManagerImpl.java
URL: http://svn.apache.org/viewvc/incubator/stanbol/trunk/ontologymanager/registry/src/main/java/org/apache/stanbol/ontologymanager/registry/impl/RegistryManagerImpl.java?rev=1185032&r1=1185031&r2=1185032&view=diff
==============================================================================
--- incubator/stanbol/trunk/ontologymanager/registry/src/main/java/org/apache/stanbol/ontologymanager/registry/impl/RegistryManagerImpl.java (original)
+++ incubator/stanbol/trunk/ontologymanager/registry/src/main/java/org/apache/stanbol/ontologymanager/registry/impl/RegistryManagerImpl.java Mon Oct 17 07:43:15 2011
@@ -574,6 +574,7 @@ public class RegistryManagerImpl impleme
 
     protected Registry populateRegistry(OWLOntology registry) throws RegistryContentException {
 
+        log.debug("Populating registry content from ontology {}", registry);
         Registry reg = riFactory.createRegistry(registry);
         Set<OWLOntology> closure = registry.getOWLOntologyManager().getImportsClosure(registry);
 
@@ -590,12 +591,14 @@ public class RegistryManagerImpl impleme
             }
             switch (t) {
                 case LIBRARY:
+                    log.debug("Found library for individual {}", ind);
                     // Create the library and attach to parent and children
                     item = populateLibrary(ind.asOWLNamedIndividual(), closure);
                     reg.addChild(item);
                     item.addRegistryContentListener(this);
                     break;
                 case ONTOLOGY:
+                    log.debug("Found ontology for individual {}", ind);
                     // Create the ontology and attach to parent
                     item = populateOntology(ind.asOWLNamedIndividual(), closure);
                     item.addRegistryContentListener(this);
@@ -607,6 +610,7 @@ public class RegistryManagerImpl impleme
         }
         try {
             reg.addRegistryContentListener(this);
+            log.info("Registry {} added.", reg.getIRI());
             population.put(reg.getIRI(), reg);
         } catch (Exception e) {
             log.error("Invalid identifier for library item " + reg, e);

Modified: incubator/stanbol/trunk/ontologymanager/registry/src/main/java/org/apache/stanbol/ontologymanager/registry/impl/model/LibraryImpl.java
URL: http://svn.apache.org/viewvc/incubator/stanbol/trunk/ontologymanager/registry/src/main/java/org/apache/stanbol/ontologymanager/registry/impl/model/LibraryImpl.java?rev=1185032&r1=1185031&r2=1185032&view=diff
==============================================================================
--- incubator/stanbol/trunk/ontologymanager/registry/src/main/java/org/apache/stanbol/ontologymanager/registry/impl/model/LibraryImpl.java (original)
+++ incubator/stanbol/trunk/ontologymanager/registry/src/main/java/org/apache/stanbol/ontologymanager/registry/impl/model/LibraryImpl.java Mon Oct 17 07:43:15 2011
@@ -26,12 +26,14 @@ import org.apache.stanbol.ontologymanage
 import org.apache.stanbol.ontologymanager.registry.api.model.RegistryItem;
 import org.apache.stanbol.ontologymanager.registry.api.model.RegistryOntology;
 import org.semanticweb.owlapi.apibinding.OWLManager;
+import org.semanticweb.owlapi.io.OWLOntologyCreationIOException;
 import org.semanticweb.owlapi.model.IRI;
 import org.semanticweb.owlapi.model.OWLOntology;
 import org.semanticweb.owlapi.model.OWLOntologyAlreadyExistsException;
 import org.semanticweb.owlapi.model.OWLOntologyCreationException;
 import org.semanticweb.owlapi.model.OWLOntologyDocumentAlreadyExistsException;
 import org.semanticweb.owlapi.model.OWLOntologyManager;
+import org.semanticweb.owlapi.model.UnloadableImportException;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
@@ -148,6 +150,11 @@ public class LibraryImpl extends Abstrac
                     o.setRawOntology(getIRI(), mgr.getOntology(e.getOntologyID()));
                 } catch (OWLOntologyDocumentAlreadyExistsException e) {
                     o.setRawOntology(getIRI(), mgr.getOntology(e.getOntologyDocumentIRI()));
+                } catch (UnloadableImportException e) {
+                    log.warn("Import {} failed. Reason: {}", e.getImportsDeclaration().getURI(), e.getCause()
+                            .getLocalizedMessage());
+                } catch (OWLOntologyCreationIOException e) {
+                    log.error("I/O error when loading ontology {}. Reason: {}", id, e.getCause().getClass());
                 } catch (OWLOntologyCreationException e) {
                     log.error("Failed to load ontology " + id, e);
                 }

Modified: incubator/stanbol/trunk/ontologymanager/registry/src/main/java/org/apache/stanbol/ontologymanager/registry/io/LibrarySource.java
URL: http://svn.apache.org/viewvc/incubator/stanbol/trunk/ontologymanager/registry/src/main/java/org/apache/stanbol/ontologymanager/registry/io/LibrarySource.java?rev=1185032&r1=1185031&r2=1185032&view=diff
==============================================================================
--- incubator/stanbol/trunk/ontologymanager/registry/src/main/java/org/apache/stanbol/ontologymanager/registry/io/LibrarySource.java (original)
+++ incubator/stanbol/trunk/ontologymanager/registry/src/main/java/org/apache/stanbol/ontologymanager/registry/io/LibrarySource.java Mon Oct 17 07:43:15 2011
@@ -20,8 +20,9 @@ import java.util.Hashtable;
 import java.util.Set;
 
 import org.apache.stanbol.ontologymanager.ontonet.api.OfflineConfiguration;
-import org.apache.stanbol.ontologymanager.ontonet.api.io.AbstractOntologyInputSource;
+import org.apache.stanbol.ontologymanager.ontonet.api.io.AbstractOWLOntologyInputSource;
 import org.apache.stanbol.ontologymanager.ontonet.api.io.OntologyInputSource;
+import org.apache.stanbol.ontologymanager.ontonet.api.io.OntologySetInputSource;
 import org.apache.stanbol.ontologymanager.ontonet.impl.util.OntologyUtils;
 import org.apache.stanbol.ontologymanager.registry.api.RegistryContentException;
 import org.apache.stanbol.ontologymanager.registry.api.RegistryManager;
@@ -42,8 +43,14 @@ import org.slf4j.LoggerFactory;
  * ontology, either new or supplied by the developer. This input source can either accept an already built
  * {@link LibraryImpl} object, or parse a library OWL file from its logical URI.
  */
-public class LibrarySource extends AbstractOntologyInputSource {
+public class LibrarySource extends AbstractOWLOntologyInputSource implements OntologySetInputSource {
 
+    /**
+     * Creates a new ontology manager that shares the same offline configuration as the registry manager.
+     * 
+     * @param registryManager
+     * @return
+     */
     private static OWLOntologyManager checkOntologyManager(RegistryManager registryManager) {
         OfflineConfiguration offline = registryManager.getOfflineConfiguration();
         if (offline == null) return OWLManager.createOWLOntologyManager();
@@ -148,14 +155,21 @@ public class LibrarySource extends Abstr
         if (registryManager == null) throw new IllegalArgumentException(
                 "A null registry manager is not allowed");
 
+        this.libraryID = libraryID;
+        
         // The ontology that imports the whole network is created in-memory, therefore it has no physical IRI
         // unless it is borrowed from the supplied parent.
         bindPhysicalIri(parentSrc != null ? parentSrc.getPhysicalIRI() : null);
 
         Library lib = registryManager.getLibrary(libraryID);
+        log.debug("Got library {}, expected {}", lib, libraryID);
         // If the manager is set to
         if (lib != null) {
             Set<OWLOntology> subtrees = lib.getOntologies();
+            this.ontologies = subtrees;
+
+            for (OWLOntology o : subtrees)
+                log.debug("\tGot ontology {}", o);
 
             // We always construct a new root now, even if there's just one subtree.
 
@@ -178,5 +192,12 @@ public class LibrarySource extends Abstr
     public String toString() {
         return "LIBRARY<" + libraryID + ">";
     }
+    
+    private Set<OWLOntology> ontologies;
+
+    @Override
+    public Set<OWLOntology> getOntologies() {
+        return ontologies;
+    }
 
 }

Modified: incubator/stanbol/trunk/ontologymanager/registry/src/test/java/org/apache/stanbol/ontologymanager/registry/TestOntologyLibrary.java
URL: http://svn.apache.org/viewvc/incubator/stanbol/trunk/ontologymanager/registry/src/test/java/org/apache/stanbol/ontologymanager/registry/TestOntologyLibrary.java?rev=1185032&r1=1185031&r2=1185032&view=diff
==============================================================================
--- incubator/stanbol/trunk/ontologymanager/registry/src/test/java/org/apache/stanbol/ontologymanager/registry/TestOntologyLibrary.java (original)
+++ incubator/stanbol/trunk/ontologymanager/registry/src/test/java/org/apache/stanbol/ontologymanager/registry/TestOntologyLibrary.java Mon Oct 17 07:43:15 2011
@@ -159,7 +159,7 @@ public class TestOntologyLibrary {
         assertNotNull(regMgr);
 
         // Now use this registry manager to instantiate an input source.
-        OntologyInputSource src = new LibrarySource(Locations.LIBRARY_TEST1, regMgr, virginOntologyManager);
+        OntologyInputSource<OWLOntology> src = new LibrarySource(Locations.LIBRARY_TEST1, regMgr, virginOntologyManager);
         OWLOntology o = src.getRootOntology();
         boolean hasImporting = false, hasImported = false;
         for (OWLImportsDeclaration ax : o.getImportsDeclarations()) {