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From r...@apache.org
Subject [05/14] clerezza git commit: CLEREZZA-966: moved rdf.utils into the hierarchy
Date Sun, 22 Mar 2015 22:04:48 GMT
CLEREZZA-966: moved rdf.utils into the hierarchy

Project: http://git-wip-us.apache.org/repos/asf/clerezza/repo
Commit: http://git-wip-us.apache.org/repos/asf/clerezza/commit/74f5fdb3
Tree: http://git-wip-us.apache.org/repos/asf/clerezza/tree/74f5fdb3
Diff: http://git-wip-us.apache.org/repos/asf/clerezza/diff/74f5fdb3

Branch: refs/heads/rdf-commons
Commit: 74f5fdb34ab823b7fe0f6f733499b766e60bf68e
Parents: ed16bac
Author: Reto Gmuer <reto@apache.org>
Authored: Sun Mar 22 17:38:06 2015 +0000
Committer: Reto Gmuer <reto@apache.org>
Committed: Sun Mar 22 17:38:06 2015 +0000

----------------------------------------------------------------------
 rdf.utils/LICENSE                               | 201 ------
 rdf.utils/pom.xml                               |  69 --
 .../apache/clerezza/rdf/utils/GraphNode.java    | 722 -------------------
 .../apache/clerezza/rdf/utils/GraphUtils.java   | 163 -----
 .../org/apache/clerezza/rdf/utils/IriUtil.java  |  63 --
 .../org/apache/clerezza/rdf/utils/RdfList.java  | 358 ---------
 .../clerezza/rdf/utils/SeeAlsoExpander.java     | 113 ---
 .../org/apache/clerezza/rdf/utils/Smusher.java  |  61 --
 .../apache/clerezza/rdf/utils/UnionGraph.java   | 286 --------
 .../clerezza/rdf/utils/UnionWatchableGraph.java |  54 --
 .../clerezza/rdf/utils/UriMutatingGraph.java    | 223 ------
 .../graphnodeprovider/GraphNodeProvider.java    |  51 --
 .../rdf/utils/smushing/BaseSmusher.java         | 135 ----
 .../clerezza/rdf/utils/smushing/IfpSmusher.java | 174 -----
 .../rdf/utils/smushing/SameAsSmusher.java       | 113 ---
 .../clerezza/rdf/utils/GraphUtilsTest.java      | 104 ---
 .../apache/clerezza/rdf/utils/IfpSmushTest.java | 115 ---
 .../apache/clerezza/rdf/utils/RdfListTest.java  | 183 -----
 .../clerezza/rdf/utils/SameAsSmushTest.java     |  78 --
 .../clerezza/rdf/utils/TestGraphNode.java       | 271 -------
 .../clerezza/rdf/utils/UnionGraphTest.java      |  78 --
 .../rdf/utils/smushing/SameAsSmushTest.java     |  92 ---
 rdf/pom.xml                                     |   7 +-
 rdf/utils/LICENSE                               | 201 ++++++
 rdf/utils/pom.xml                               |  69 ++
 .../apache/clerezza/rdf/utils/GraphNode.java    | 722 +++++++++++++++++++
 .../apache/clerezza/rdf/utils/GraphUtils.java   | 163 +++++
 .../org/apache/clerezza/rdf/utils/IriUtil.java  |  63 ++
 .../org/apache/clerezza/rdf/utils/RdfList.java  | 358 +++++++++
 .../clerezza/rdf/utils/SeeAlsoExpander.java     | 113 +++
 .../org/apache/clerezza/rdf/utils/Smusher.java  |  61 ++
 .../apache/clerezza/rdf/utils/UnionGraph.java   | 286 ++++++++
 .../clerezza/rdf/utils/UnionWatchableGraph.java |  54 ++
 .../clerezza/rdf/utils/UriMutatingGraph.java    | 223 ++++++
 .../graphnodeprovider/GraphNodeProvider.java    |  51 ++
 .../rdf/utils/smushing/BaseSmusher.java         | 135 ++++
 .../clerezza/rdf/utils/smushing/IfpSmusher.java | 174 +++++
 .../rdf/utils/smushing/SameAsSmusher.java       | 113 +++
 .../clerezza/rdf/utils/GraphUtilsTest.java      | 104 +++
 .../apache/clerezza/rdf/utils/IfpSmushTest.java | 115 +++
 .../apache/clerezza/rdf/utils/RdfListTest.java  | 183 +++++
 .../clerezza/rdf/utils/SameAsSmushTest.java     |  78 ++
 .../clerezza/rdf/utils/TestGraphNode.java       | 271 +++++++
 .../clerezza/rdf/utils/UnionGraphTest.java      |  78 ++
 .../rdf/utils/smushing/SameAsSmushTest.java     |  92 +++
 45 files changed, 3711 insertions(+), 3710 deletions(-)
----------------------------------------------------------------------


http://git-wip-us.apache.org/repos/asf/clerezza/blob/74f5fdb3/rdf.utils/LICENSE
----------------------------------------------------------------------
diff --git a/rdf.utils/LICENSE b/rdf.utils/LICENSE
deleted file mode 100644
index 261eeb9..0000000
--- a/rdf.utils/LICENSE
+++ /dev/null
@@ -1,201 +0,0 @@
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http://git-wip-us.apache.org/repos/asf/clerezza/blob/74f5fdb3/rdf.utils/pom.xml
----------------------------------------------------------------------
diff --git a/rdf.utils/pom.xml b/rdf.utils/pom.xml
deleted file mode 100644
index 0f6b648..0000000
--- a/rdf.utils/pom.xml
+++ /dev/null
@@ -1,69 +0,0 @@
-<?xml version="1.0" encoding="UTF-8" standalone="no"?><project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
-<!--
-
- 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.
-
--->
-
-    <modelVersion>4.0.0</modelVersion>
-    <parent>
-        <artifactId>clerezza</artifactId>
-        <groupId>org.apache.clerezza</groupId>
-        <version>7-SNAPSHOT</version>
-        <relativePath>../parent</relativePath>
-    </parent>
-    <groupId>org.apache.clerezza</groupId>
-    <artifactId>rdf.utils</artifactId>
-    <packaging>bundle</packaging>
-    <version>1.0.0-SNAPSHOT</version>
-    <name>Clerezza - RDF - Utilities</name>
-    <description>Utility classed to deal with Clerezza Models</description>
-    <dependencies>
-        <dependency>
-            <groupId>junit</groupId>
-            <artifactId>junit</artifactId>
-            <scope>test</scope>
-        </dependency>
-        <dependency>
-            <groupId>org.apache.clerezza</groupId>
-            <artifactId>rdf.core</artifactId>
-            <version>1.0.0-SNAPSHOT</version>
-        </dependency>
-        <dependency>
-            <groupId>org.apache.clerezza.commons-rdf</groupId>
-            <artifactId>commons-rdf-api</artifactId>
-            <version>0.1-SNAPSHOT</version>
-        </dependency>
-        <dependency>
-            <groupId>org.apache.clerezza.commons-rdf</groupId>
-            <artifactId>commons-rdf-impl-utils</artifactId>
-            <version>0.1-SNAPSHOT</version>
-        </dependency>
-        <dependency>
-            <groupId>org.apache.clerezza</groupId>
-            <artifactId>rdf.ontologies</artifactId>
-            <version>1.0.0-SNAPSHOT</version>
-        </dependency>
-        <dependency>
-            <groupId>org.apache.clerezza</groupId>
-            <artifactId>rdf.core.test</artifactId>
-            <version>1.0.0-SNAPSHOT</version>
-            <scope>test</scope>
-        </dependency>
-    </dependencies>
-</project>
\ No newline at end of file

http://git-wip-us.apache.org/repos/asf/clerezza/blob/74f5fdb3/rdf.utils/src/main/java/org/apache/clerezza/rdf/utils/GraphNode.java
----------------------------------------------------------------------
diff --git a/rdf.utils/src/main/java/org/apache/clerezza/rdf/utils/GraphNode.java b/rdf.utils/src/main/java/org/apache/clerezza/rdf/utils/GraphNode.java
deleted file mode 100644
index 8a1365f..0000000
--- a/rdf.utils/src/main/java/org/apache/clerezza/rdf/utils/GraphNode.java
+++ /dev/null
@@ -1,722 +0,0 @@
-/*
- * 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.clerezza.rdf.utils;
-
-import org.apache.commons.rdf.impl.*;
-import org.apache.commons.rdf.impl.utils.*;
-import org.apache.commons.rdf.impl.utils.simple.SimpleGraph;
-import org.apache.commons.rdf.impl.utils.TripleImpl;
-
-import java.util.*;
-import java.util.concurrent.locks.Lock;
-import org.apache.clerezza.rdf.core.LiteralFactory;
-import org.apache.commons.rdf.*;
-
-/**
- * This class represents a node in the context of a graph. It provides
- * utility methods to explore and modify its neighbourhood. The method
- * modifying the graph will throw an {@link UnsupportedOperationException}
- * it the underlying Graph in immutable (i.e. is a {@link ImmutableGraph}.
- *
- * @since 0.2
- * @author reto, mir
- */
-public class GraphNode {
-
-    private final RdfTerm resource;
-    private final Graph graph;
-
-    /**
-     * Create a GraphNode representing resource within graph.
-     *
-     * @param resource the resource this GraphNode represents
-     * @param graph the Graph that describes the resource
-     */
-    public GraphNode(RdfTerm resource, Graph graph) {
-        if (resource == null) {
-            throw new IllegalArgumentException("resource may not be null");
-        }
-        if (graph == null) {
-            throw new IllegalArgumentException("graph may not be null");
-        }
-        this.resource = resource;
-        this.graph = graph;
-    }
-
-    /**
-     * Gets the graph the node represented by this instance is in
-     *
-     * @return the graph of this GraphNode
-     */
-    public Graph getGraph() {
-        return graph;
-    }
-
-    /**
-     * Gets the unwrapped node
-     *
-     * @return the node represented by this GraphNode
-     */
-    public RdfTerm getNode() {
-        return resource;
-    }
-
-    /**
-     * Deletes the context of a node
-     * @see getNodeContext()
-     */
-    public void deleteNodeContext() {
-        for (Triple triple : getNodeContext()) {
-            graph.remove(triple);
-        }
-    }
-
-    /**
-     * The context of a node are the triples containing a node
-     * as subject or object and recursively the context of the b-nodes in any
-     * of these statements.
-     *
-     * The triples in the ImmutableGraph returned by this method contain the same bnode
-     * instances as in the original graph.
-     *
-     * @return the context of the node represented by the instance
-     */
-    public ImmutableGraph getNodeContext() {
-        Lock l = readLock();
-        l.lock();
-        try {
-            final HashSet<RdfTerm> dontExpand = new HashSet<RdfTerm>();
-            dontExpand.add(resource);
-            if (resource instanceof Iri) {
-                return getContextOf((Iri) resource, dontExpand).getImmutableGraph();
-            }
-            return getContextOf(resource, dontExpand).getImmutableGraph();
-        } finally {
-            l.unlock();
-        }
-
-    }
-
-    private Graph getContextOf(Iri node, final Set<RdfTerm> dontExpand) {
-        final String uriPrefix = node.getUnicodeString()+'#';
-        return getContextOf(node, dontExpand, new Acceptor() {
-
-            @Override
-            public boolean expand(RdfTerm resource) {
-                if (resource instanceof BlankNode) {
-                    return true;
-                }
-                if (resource instanceof Iri) {
-                    return ((Iri)resource).getUnicodeString().startsWith(uriPrefix);
-                }
-                return false;
-            }
-        });
-    }
-
-    /**
-     * Returns the context of a <code>BlankNodeOrIri</code>
-     *
-     * @param node
-     * @param dontExpand a list of bnodes at which to stop expansion, if node
-     * is a BlankNode it should be contained (potentially faster)
-     * @return the context of a node
-     */
-    private Graph getContextOf(RdfTerm node, final Set<RdfTerm> dontExpand) {
-        return getContextOf(node, dontExpand, new Acceptor() {
-
-            @Override
-            public boolean expand(RdfTerm resource) {
-                if (resource instanceof BlankNode) {
-                    return true;
-                }
-                return false;
-            }
-        });
-    }
-
-    private interface Acceptor {
-        boolean expand(RdfTerm resource);
-    }
-    private Graph getContextOf(RdfTerm node, final Set<RdfTerm> dontExpand, Acceptor acceptor) {
-        Graph result = new SimpleGraph();
-        if (node instanceof BlankNodeOrIri) {
-            Iterator<Triple> forwardProperties = graph.filter((BlankNodeOrIri) node, null, null);
-            while (forwardProperties.hasNext()) {
-                Triple triple = forwardProperties.next();
-                result.add(triple);
-                RdfTerm object = triple.getObject();
-                if (acceptor.expand(object) && !dontExpand.contains(object)) {
-                    dontExpand.add(object);
-                    result.addAll(getContextOf(object, dontExpand, acceptor));
-                }
-            }
-        }
-        Iterator<Triple> backwardProperties = graph.filter(null, null, node);
-        while (backwardProperties.hasNext()) {
-            Triple triple = backwardProperties.next();
-            result.add(triple);
-            BlankNodeOrIri subject = triple.getSubject();
-            if (acceptor.expand(subject) && !dontExpand.contains(subject)) {
-                dontExpand.add(subject);
-                result.addAll(getContextOf(subject, dontExpand, acceptor));
-            }
-        }
-        return result;
-    }
-
-    private <T> Iterator<T> getTypeSelectedObjects(Iri property, final Class<T> type) {
-        final Iterator<RdfTerm> objects = getObjects(property);
-        return new Iterator<T>() {
-
-            T next = prepareNext();
-
-            @Override
-            public boolean hasNext() {
-                return next != null;
-            }
-
-            @Override
-            public T next() {
-                T result = next;
-                next = prepareNext();
-                return result;
-            }
-
-            @Override
-            public void remove() {
-                throw new UnsupportedOperationException("Not supported yet.");
-            }
-
-            private T prepareNext() {
-                while (objects.hasNext()) {
-                    RdfTerm nextObject = objects.next();
-                    if (type.isAssignableFrom(nextObject.getClass())) {
-                        return (T) nextObject;
-                    }
-                }
-                return null;
-            }
-        };
-    }
-
-    public Iterator<Literal> getLiterals(Iri property) {
-        final Iterator<RdfTerm> objects = getObjects(property);
-        return new Iterator<Literal>() {
-
-            Literal next = prepareNext();
-
-            @Override
-            public boolean hasNext() {
-                return next != null;
-            }
-
-            @Override
-            public Literal next() {
-                Literal result = next;
-                next = prepareNext();
-                return result;
-            }
-
-            @Override
-            public void remove() {
-                throw new UnsupportedOperationException("Not supported yet.");
-            }
-
-            private Literal prepareNext() {
-                while (objects.hasNext()) {
-                    RdfTerm nextObject = objects.next();
-                    if (nextObject instanceof Literal) {
-                        return (Literal) nextObject;
-                    }
-                }
-                return null;
-            }
-        };
-    }
-
-    /**
-     * Count the number of triples in the underlying triple-collection
-     * with this node as subject and a specified property as predicate.
-     *
-     * @param property the property to be examined
-     * @return the number of triples in the underlying triple-collection
-     *        which meet the specified condition
-     */
-    public int countObjects(Iri property) {
-        return countTriples(graph.filter((BlankNodeOrIri) resource, property, null));
-    }
-
-    private int countTriples(final Iterator<Triple> triples) {
-        int count = 0;
-        while (triples.hasNext()) {
-            triples.next();
-            count++;
-        }
-        return count;
-    }
-
-    /**
-     * Get the objects of statements with this node as subject and a specified
-     * property as predicate.
-     *
-     * @param property the property
-     * @return
-     */
-    public Iterator<RdfTerm> getObjects(Iri property) {
-        if (resource instanceof BlankNodeOrIri) {
-            final Iterator<Triple> triples = graph.filter((BlankNodeOrIri) resource, property, null);
-            return new Iterator<RdfTerm>() {
-
-                @Override
-                public boolean hasNext() {
-                    return triples.hasNext();
-                }
-
-                @Override
-                public RdfTerm next() {
-                    final Triple triple = triples.next();
-                    if (triple != null) {
-                        return triple.getObject();
-                    } else {
-                        return null;
-                    }
-                }
-
-                @Override
-                public void remove() {
-                    throw new UnsupportedOperationException("Not supported yet.");
-                }
-            };
-        } else {
-            return new Iterator<RdfTerm>() {
-
-                @Override
-                public boolean hasNext() {
-                    return false;
-                }
-
-                @Override
-                public RdfTerm next() {
-                    return null;
-                }
-
-                @Override
-                public void remove() {
-                    throw new UnsupportedOperationException("Not supported yet.");
-                }
-            };
-        }
-    }
-
-    /**
-     * Checks wether this node has the given property with the given value.
-     * If the given value is null, then it is checked if this node has the
-     * specified property regardless of its value.
-     *
-     * @param property
-     * @param object
-     * @return true if the node represented by this object is the subject of a
-     *         statement with the given prediate and object, false otherwise
-     */
-    public boolean hasProperty(Iri property, RdfTerm object) {
-        Lock l = readLock();
-        l.lock();
-        try {
-            Iterator<RdfTerm> objects = getObjects(property);
-            if (object == null) {
-                return objects.hasNext();
-            }
-            while (objects.hasNext()) {
-                if (objects.next().equals(object)) {
-                    return true;
-                }
-            }
-            return false;
-        } finally {
-            l.unlock();
-        }
-    }
-
-    /**
-     * Count the number of triples in the underlying triple-collection
-     * with this node as object and a specified property as predicate.
-     *
-     * @param property the property to be examined
-     * @return the number of triples in the underlying triple-collection
-     *        which meet the specified condition
-     */
-    public int countSubjects(Iri property) {
-        Lock l = readLock();
-        l.lock();
-        try {
-            return countTriples(graph.filter(null, property, resource));
-        } finally {
-            l.unlock();
-        }
-    }
-
-    /**
-     * Get the subjects of statements with this node as object and a specified
-     * property as predicate.
-     *
-     * @param property the property
-     * @return
-     */
-    public Iterator<BlankNodeOrIri> getSubjects(Iri property) {
-        final Iterator<Triple> triples = graph.filter(null, property, resource);
-        return new Iterator<BlankNodeOrIri>() {
-
-            @Override
-            public boolean hasNext() {
-                return triples.hasNext();
-            }
-
-            @Override
-            public BlankNodeOrIri next() {
-                return triples.next().getSubject();
-            }
-
-            @Override
-            public void remove() {
-                throw new UnsupportedOperationException("Not supported yet.");
-            }
-        };
-    }
-
-    public Iterator<Iri> getIriObjects(Iri property) {
-        return getTypeSelectedObjects(property, Iri.class);
-
-    }
-
-    /**
-     * Get all available properties as an {@link Iterator}<{@link Iri}>.
-     * You can use <code>getObjects(Iri property)</code> to get the values of
-     * each property
-     *
-     * @return an iterator over properties of this node
-     */
-    public Iterator<Iri> getProperties() {
-        if (resource instanceof BlankNodeOrIri) {
-            final Iterator<Triple> triples = graph.filter((BlankNodeOrIri) resource, null, null);
-            return getUniquePredicates(triples);
-        } else {
-            return new Iterator<Iri>() {
-
-                @Override
-                public boolean hasNext() {
-                    return false;
-                }
-
-                @Override
-                public Iri next() {
-                    return null;
-                }
-
-                @Override
-                public void remove() {
-                    throw new UnsupportedOperationException("Not supported yet.");
-                }
-            };
-        }
-    }
-
-    /**
-     * Get all inverse properties as an {@link Iterator}<{@link Iri}>.
-     * You can use <code>getSubject(Iri property)</code> to get the values of
-     * each inverse property
-     *
-     * @return an iterator over properties pointing to this node
-     */
-    public Iterator<Iri> getInverseProperties() {
-        final Iterator<Triple> triples = graph.filter(null, null, resource);
-        return getUniquePredicates(triples);
-    }
-
-    /**
-     *
-     * @param triples
-     * @returnan {@link Iterator}<{@link Iri}> containing the predicates from
-     * an {@link Iterator}<{@link Triple}>
-     */
-    private Iterator<Iri> getUniquePredicates(final Iterator<Triple> triples) {
-        final Set<Iri> resultSet = new HashSet<Iri>();
-        while (triples.hasNext()) {
-            resultSet.add(triples.next().getPredicate());
-        }
-        return resultSet.iterator();
-    }
-
-    /**
-     * Adds a property to the node with the specified predicate and object
-     *
-     * @param predicate
-     * @param object
-     */
-    public void addProperty(Iri predicate, RdfTerm object) {
-        if (resource instanceof BlankNodeOrIri) {
-            graph.add(new TripleImpl((BlankNodeOrIri) resource, predicate, object));
-        } else {
-            throw new RuntimeException("Literals cannot be the subject of a statement");
-        }
-    }
-
-
-    /**
-     * Coverts the value into a typed literals and sets it as object of the
-     * specified property
-     *
-     * @param property the predicate of the triple to be created
-     * @param value the value of the typed literal object
-     */
-    public void addPropertyValue(Iri property, Object value) {
-        addProperty(property,
-                LiteralFactory.getInstance().createTypedLiteral(value));
-    }
-
-    /**
-     * Adds a property to the node with the inverse of the specified predicate and object
-     * In other words <code>subject</code> will be related via the property <code>relation</code> to this node.
-     *
-     * @param predicate
-     * @param subject
-     */
-    public void addInverseProperty(Iri predicate, RdfTerm subject) {
-        if (subject instanceof BlankNodeOrIri) {
-            graph.add(new TripleImpl((BlankNodeOrIri) subject, predicate, resource));
-        } else {
-            throw new RuntimeException("Literals cannot be the subject of a statement");
-        }
-    }
-
-
-    /**
-     * creates and returns an <code>RdfList</code> for the node and
-     * Graph represented by this object.
-     *
-     * @return a List to easy access the rdf:List represented by this node
-     */
-    public List<RdfTerm> asList() {
-        if (resource instanceof BlankNodeOrIri) {
-            return new RdfList((BlankNodeOrIri) resource, graph);
-        } else {
-            throw new RuntimeException("Literals cannot be the subject of a List");
-        }
-    }
-
-    /**
-     * Deletes all statement with the current node as subject and the specified
-     * predicate
-     *
-     * @param predicate
-     */
-    public void deleteProperties(Iri predicate) {
-        if (resource instanceof BlankNodeOrIri) {
-            Iterator<Triple> tripleIter = graph.filter((BlankNodeOrIri) resource, predicate, null);
-            Collection<Triple> toDelete = new ArrayList<Triple>();
-            while (tripleIter.hasNext()) {
-                Triple triple = tripleIter.next();
-                toDelete.add(triple);
-            }
-            for (Triple triple : toDelete) {
-                graph.remove(triple);
-            }
-        }
-    }
-
-    /**
-     * Delete property to the node with the specified predicate and object
-     *
-     * @param predicate
-     * @param object
-     */
-    public void deleteProperty(Iri predicate, RdfTerm object) {
-        if (resource instanceof BlankNodeOrIri) {
-            graph.remove(new TripleImpl((BlankNodeOrIri) resource, predicate, object));
-        }
-    }
-
-    @Override
-    public String toString() {
-        return resource.toString();
-    }
-
-    /**
-     * Replaces the graph node resouce with the specified <code>BlankNodeOrIri</code>.
-     * The resource is only replaced where it is either subject or object.
-     * @param replacement
-     * @return a GraphNode representing the replecement node
-     */
-    public GraphNode replaceWith(BlankNodeOrIri replacement) {
-        return replaceWith(replacement, false);
-    }
-
-    /**
-     * Replaces the graph node resouce with the specified <code>BlankNodeOrIri</code>.
-     * Over the boolean <code>checkPredicate</code> it can be specified if the
-     * resource should also be replaced where it is used as predicate.
-     * @param replacement
-     * @param checkPredicates
-     * @return a GraphNode representing the replecement node
-     */
-    public GraphNode replaceWith(BlankNodeOrIri replacement, boolean checkPredicates) {
-        Graph newTriples = new SimpleGraph();
-        if (!(resource instanceof Literal)) {
-            Iterator<Triple> subjectTriples = graph.filter((BlankNodeOrIri) resource, null,
-                    null);
-            while (subjectTriples.hasNext()) {
-                Triple triple = subjectTriples.next();
-                Triple newTriple = new TripleImpl(replacement, triple.getPredicate(),
-                        triple.getObject());
-                subjectTriples.remove();
-                newTriples.add(newTriple);
-            }
-            graph.addAll(newTriples);
-            newTriples.clear();
-        }
-
-        Iterator<Triple> objectTriples = graph.filter(null, null, resource);
-        while (objectTriples.hasNext()) {
-            Triple triple = objectTriples.next();
-            Triple newTriple = new TripleImpl(triple.getSubject(),
-                    triple.getPredicate(), replacement);
-            objectTriples.remove();
-            newTriples.add(newTriple);
-        }
-        graph.addAll(newTriples);
-        newTriples.clear();
-
-        if (checkPredicates && replacement instanceof Iri
-                && resource instanceof Iri) {
-            Iterator<Triple> predicateTriples = graph.filter(null,
-                    (Iri) resource, null);
-            while (predicateTriples.hasNext()) {
-                Triple triple = predicateTriples.next();
-                Triple newTriple = new TripleImpl(triple.getSubject(),
-                        (Iri) replacement, triple.getObject());
-                predicateTriples.remove();
-                newTriples.add(newTriple);
-            }
-            graph.addAll(newTriples);
-        }
-        return new GraphNode(replacement, graph);
-    }
-
-    /**
-     * Returns a iterator containing all objects of the triples where this
-     * graph node is the subject and has the specified property. The objects
-     * are returned as <code>GraphNode</code>s.
-     *
-     * @param property
-     * @return
-     */
-    public Iterator<GraphNode> getObjectNodes(Iri property) {
-        final Iterator<RdfTerm> objects = this.getObjects(property);
-        return new Iterator<GraphNode>() {
-
-            @Override
-            public boolean hasNext() {
-                return objects.hasNext();
-            }
-
-            @Override
-            public GraphNode next() {
-                RdfTerm object = objects.next();
-                return new GraphNode(object, graph);
-
-            }
-
-            @Override
-            public void remove() {
-                objects.remove();
-            }
-        };
-    }
-
-    /**
-     * Returns a iterator containing all subjects of the triples where this
-     * graph node is the object and has the specified property. The subjects
-     * are returned as <code>GraphNode</code>s.
-     *
-     * @param property
-     * @return
-     */
-    public Iterator<GraphNode> getSubjectNodes(Iri property) {
-        final Iterator<BlankNodeOrIri> subjects = this.getSubjects(property);
-        return new Iterator<GraphNode>() {
-
-            @Override
-            public boolean hasNext() {
-                return subjects.hasNext();
-            }
-
-            @Override
-            public GraphNode next() {
-                RdfTerm object = subjects.next();
-                return new GraphNode(object, graph);
-
-            }
-
-            @Override
-            public void remove() {
-                subjects.remove();
-            }
-        };
-    }
-
-    /**
-     *
-     * @param obj
-     * @return true if obj is an instance of the same class represening the same
-     * node in the same graph, subclasses may have different identity criteria.
-     */
-    @Override
-    public boolean equals(Object obj) {
-        if (obj == null || !(obj.getClass().equals(getClass()))) {
-            return false;
-        }
-        GraphNode other = (GraphNode) obj;
-        return getNode().equals(other.getNode())
-                && getGraph().equals(other.getGraph());
-    }
-
-    @Override
-    public int hashCode() {
-        return 13 * getNode().hashCode() + getGraph().hashCode();
-    }
-
-    /**
-     * @return a ReadLock if the underlying ImmutableGraph is a LockableGraph it returns its lock, otherwise null
-     */
-    public Lock readLock() {
-
-            return getGraph().getLock().readLock();
-
-    }
-
-    /**
-     *
-     * @return
-     */
-    public Lock writeLock() {
-
-            return (getGraph()).getLock().writeLock();
-
-    }
-}

http://git-wip-us.apache.org/repos/asf/clerezza/blob/74f5fdb3/rdf.utils/src/main/java/org/apache/clerezza/rdf/utils/GraphUtils.java
----------------------------------------------------------------------
diff --git a/rdf.utils/src/main/java/org/apache/clerezza/rdf/utils/GraphUtils.java b/rdf.utils/src/main/java/org/apache/clerezza/rdf/utils/GraphUtils.java
deleted file mode 100644
index dc3943b..0000000
--- a/rdf.utils/src/main/java/org/apache/clerezza/rdf/utils/GraphUtils.java
+++ /dev/null
@@ -1,163 +0,0 @@
-/*
- * 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.clerezza.rdf.utils;
-
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.Set;
-import org.apache.commons.rdf.BlankNode;
-import org.apache.commons.rdf.ImmutableGraph;
-import org.apache.commons.rdf.Graph;
-import org.apache.commons.rdf.BlankNodeOrIri;
-import org.apache.commons.rdf.RdfTerm;
-import org.apache.commons.rdf.Triple;
-import org.apache.commons.rdf.impl.utils.simple.SimpleGraph;
-
-/**
- * Utility methods to manipulate <code>Graph</code>s
- *
- * @author reto
- */
-public class GraphUtils {
-
-    /**
-     * Removes a subGraph from an Graph. The subGraph must match a subgraph of
-     * Graph so that for every node in <code>subGraph</code>
-     * each triple it appears in is also present in <code>mGraph</code>. Two
-     * bnodes are considered equals if their contexts (as returned by
-     * <code>GraphNode.getNodeContext</code> are equals.
-     *
-     * @param mGraph
-     * @param subGraph
-     * @throws org.apache.clerezza.rdf.utils.GraphUtils.NoSuchSubGraphException
-     */
-    public static void removeSubGraph(Graph mGraph, Graph subGraph)
-            throws NoSuchSubGraphException {
-        //point to triples of mGraph that are to be removed (if something is removed)
-        final Set<Triple> removingTriples = new HashSet<Triple>();
-        //we first check only the grounded triples and put the non-grounded in here:
-        final Graph unGroundedTriples = new SimpleGraph();
-        for (Triple triple : subGraph) {
-            if (isGrounded(triple)) {
-                if (!mGraph.contains(triple)) {
-                    throw new NoSuchSubGraphException();
-                }
-                removingTriples.add(triple);
-            } else {
-                unGroundedTriples.add(triple);
-            }
-        }
-
-        //we first remove the context of bnodes we find in object position
-        OBJ_BNODE_LOOP: while (true) {
-            final Triple triple = getTripleWithBlankNodeObject(unGroundedTriples);
-            if (triple == null) {
-                break;
-            }
-            final GraphNode objectGN = new GraphNode(triple.getObject(), unGroundedTriples);
-            BlankNodeOrIri subject = triple.getSubject();
-            ImmutableGraph context = objectGN.getNodeContext();
-            Iterator<Triple> potentialIter = mGraph.filter(subject, triple.getPredicate(), null);
-            while (potentialIter.hasNext()) {
-                try {
-                    final Triple potentialTriple = potentialIter.next();
-                    BlankNode potentialMatch = (BlankNode)potentialTriple.getObject();
-                    final ImmutableGraph potentialContext = new GraphNode(potentialMatch, mGraph).getNodeContext();
-                    if (potentialContext.equals(context)) {
-                        removingTriples.addAll(potentialContext);
-                        unGroundedTriples.removeAll(context);
-                        continue OBJ_BNODE_LOOP;
-                    }
-                } catch (ClassCastException e) {
-                    continue;
-                }
-            }
-            throw new NoSuchSubGraphException();
-        }
-        SUBJ_BNODE_LOOP: while (true) {
-            final Triple triple = getTripleWithBlankNodeSubject(unGroundedTriples);
-            if (triple == null) {
-                break;
-            }
-            final GraphNode subjectGN = new GraphNode(triple.getSubject(), unGroundedTriples);
-            RdfTerm object = triple.getObject();
-            if (object instanceof BlankNode) {
-                object = null;
-            }
-            ImmutableGraph context = subjectGN.getNodeContext();
-            Iterator<Triple> potentialIter = mGraph.filter(null, triple.getPredicate(), object);
-            while (potentialIter.hasNext()) {
-                try {
-                    final Triple potentialTriple = potentialIter.next();
-                    BlankNode potentialMatch = (BlankNode)potentialTriple.getSubject();
-                    final ImmutableGraph potentialContext = new GraphNode(potentialMatch, mGraph).getNodeContext();
-                    if (potentialContext.equals(context)) {
-                        removingTriples.addAll(potentialContext);
-                        unGroundedTriples.removeAll(context);
-                        continue SUBJ_BNODE_LOOP;
-                    }
-                } catch (ClassCastException e) {
-                    continue;
-                }
-            }
-            throw new NoSuchSubGraphException();
-        }
-        mGraph.removeAll(removingTriples);
-    }
-
-    private static boolean isGrounded(Triple triple) {
-        if (triple.getSubject() instanceof BlankNode) {
-            return false;
-        }
-        if (triple.getObject() instanceof BlankNode) {
-            return false;
-        }
-        return true;
-    }
-
-    /** retrun triples with a bnode only at object position
-     *
-     * @param triples
-     * @return
-     */
-    private static Triple getTripleWithBlankNodeObject(Graph triples) {
-        for (Triple triple : triples) {
-            if (triple.getSubject() instanceof BlankNode) {
-                continue;
-            }
-            if (triple.getObject() instanceof BlankNode) {
-                return triple;
-            }
-        }
-        return null;
-    }
-    private static Triple getTripleWithBlankNodeSubject(Graph triples) {
-        for (Triple triple : triples) {
-            if (triple.getSubject() instanceof BlankNode) {
-                return triple;
-            }
-        }
-        return null;
-    }
-
-    public static class NoSuchSubGraphException extends Exception {
-    }
-
-}

http://git-wip-us.apache.org/repos/asf/clerezza/blob/74f5fdb3/rdf.utils/src/main/java/org/apache/clerezza/rdf/utils/IriUtil.java
----------------------------------------------------------------------
diff --git a/rdf.utils/src/main/java/org/apache/clerezza/rdf/utils/IriUtil.java b/rdf.utils/src/main/java/org/apache/clerezza/rdf/utils/IriUtil.java
deleted file mode 100644
index 323c9f2..0000000
--- a/rdf.utils/src/main/java/org/apache/clerezza/rdf/utils/IriUtil.java
+++ /dev/null
@@ -1,63 +0,0 @@
-/*
- * 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.clerezza.rdf.utils;
-
-
-/**
- * A utility class for Iri and String manipulations.
- *
- * @author tio
- */
-public class IriUtil {
-
-    /**
-     * Strips #x00 - #x1F and #x7F-#x9F from a Unicode string
-     * @see <a href="http://www.w3.org/TR/rdf-concepts/#dfn-URI-reference">
-     * http://www.w3.org/TR/rdf-concepts/#dfn-URI-reference</a> and
-     * replaces all US-ASCII space character with a "+".
-     *
-     * @param inputChars
-     * @return the stripped string
-     * 
-     */
-    public static String stripNonIriChars(CharSequence inputChars) {
-
-        if (inputChars == null) {
-            return "";
-        }
-
-        StringBuffer buffer = new StringBuffer();
-
-        for (int i = 0; i < inputChars.length(); i++) {
-            char c = inputChars.charAt(i);
-
-            if (!isIllegal(c)) {
-                buffer.append(c);
-            }
-        }
-        return buffer.toString().replaceAll("\\s+", "+");
-    }
-
-    private static boolean isIllegal(char ch) {
-        if ((ch >= 0x7F) && (ch <= 0x9F)) {
-            return true;
-        }
-        return false;
-    }
-}

http://git-wip-us.apache.org/repos/asf/clerezza/blob/74f5fdb3/rdf.utils/src/main/java/org/apache/clerezza/rdf/utils/RdfList.java
----------------------------------------------------------------------
diff --git a/rdf.utils/src/main/java/org/apache/clerezza/rdf/utils/RdfList.java b/rdf.utils/src/main/java/org/apache/clerezza/rdf/utils/RdfList.java
deleted file mode 100644
index db994e9..0000000
--- a/rdf.utils/src/main/java/org/apache/clerezza/rdf/utils/RdfList.java
+++ /dev/null
@@ -1,358 +0,0 @@
-/*
- * 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.clerezza.rdf.utils;
-
-import java.io.FileOutputStream;
-import java.security.AccessController;
-import java.security.PrivilegedAction;
-import java.util.AbstractList;
-import java.util.ArrayList;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Set;
-import org.apache.commons.rdf.BlankNode;
-import org.apache.commons.rdf.BlankNodeOrIri;
-import org.apache.commons.rdf.RdfTerm;
-import org.apache.commons.rdf.Iri;
-import org.apache.commons.rdf.impl.utils.TripleImpl;
-import org.apache.clerezza.rdf.core.serializedform.Serializer;
-import org.apache.clerezza.rdf.core.serializedform.SupportedFormat;
-import org.apache.clerezza.rdf.ontologies.OWL;
-import org.apache.clerezza.rdf.ontologies.RDF;
-import org.apache.commons.rdf.Graph;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-/**
- * An implementation of an <code>java.util.List</code> backed by an RDF
- * collection (rdf:List). The list allows modification that are reflected
- * to the underlying <code>Graph</code>. It reads the data from the
- * <code>Graph</code> when it is first needed, so changes to the
- * Graph affecting the rdf:List may or may not have an effect on the
- * values returned by instances of this class. For that reason only one
- * instance of this class should be used for accessing an rdf:List of sublists
- * thereof when the lists are being modified, having multiple lists exclusively
- * for read operations (such as for immutable <code>Graph</code>s) is
- * not problematic.
- *
- * @author rbn, mir
- */
-public class RdfList extends AbstractList<RdfTerm> {
-
-    private static final Logger logger = LoggerFactory.getLogger(RdfList.class);
-
-    private final static Iri RDF_NIL =
-            new Iri("http://www.w3.org/1999/02/22-rdf-syntax-ns#nil");
-    /**
-     * a list of the linked rdf:List elements in order
-     */
-    private List<BlankNodeOrIri> listList = new ArrayList<BlankNodeOrIri>();
-    private List<RdfTerm> valueList = new ArrayList<RdfTerm>();
-    private BlankNodeOrIri firstList;
-    private Graph tc;
-    private boolean totallyExpanded = false;
-
-    /**
-     * Get a list for the specified resource.
-     *
-     * If the list is modified using the created instance
-     * <code>listRdfTerm</code> will always be the first list.
-     *
-     * @param listRdfTerm
-     * @param tc
-     */
-    public RdfList(BlankNodeOrIri listRdfTerm, Graph tc) {
-        firstList = listRdfTerm;
-        this.tc = tc;
-
-    }
-
-    /**
-     * Get a list for the specified resource node.
-     *
-     * @param listNode
-     */
-    public RdfList(GraphNode listNode) {
-        this((BlankNodeOrIri)listNode.getNode(), listNode.getGraph());
-    }
-
-    /**
-     * Creates an empty RdfList by writing a triple
-     * "{@code listRdfTerm} owl:sameAs rdf.nil ." to {@code tc}.
-     *
-     * @param listRdfTerm
-     * @param tc
-     * @return    an empty rdf:List.
-     * @throws IllegalArgumentException
-     *        if the provided {@code  listRdfTerm} is a non-empty rdf:List.
-     */
-    public static RdfList createEmptyList(BlankNodeOrIri listRdfTerm, Graph tc)
-            throws IllegalArgumentException {
-
-        if (!tc.filter(listRdfTerm, RDF.first, null).hasNext()) {
-            RdfList list = new RdfList(listRdfTerm, tc);
-            list.tc.add(new TripleImpl(listRdfTerm, OWL.sameAs, RDF_NIL));
-            return list;
-        } else {
-            throw new IllegalArgumentException(listRdfTerm + "is a non-empty rdf:List.");
-        }
-    }
-
-    private void expandTill(int pos) {
-        if (totallyExpanded) {
-            return;
-        }
-        BlankNodeOrIri currentList;
-        if (listList.size() > 0) {
-            currentList = listList.get(listList.size()-1);
-        } else {
-            currentList = firstList;
-            if (!tc.filter(currentList, RDF.first, null).hasNext()) {
-                return;
-            }
-            listList.add(currentList);
-            valueList.add(getFirstEntry(currentList));
-        }
-        if (listList.size() >= pos) {
-            return;
-        }
-        while (true) {                
-            currentList = getRest(currentList);
-            if (currentList.equals(RDF_NIL)) {
-                totallyExpanded = true;
-                break;
-            }
-            if (listList.size() == pos) {
-                break;
-            }
-            valueList.add(getFirstEntry(currentList));
-            listList.add(currentList);
-        }
-    }
-
-
-
-    @Override
-    public RdfTerm get(int index) {
-        expandTill(index + 1);
-        return valueList.get(index);
-    }
-
-    @Override
-    public int size() {
-        expandTill(Integer.MAX_VALUE);        
-        return valueList.size();
-    }
-
-    @Override
-    public void add(int index, RdfTerm element) {
-        expandTill(index);
-        if (index == 0) {
-            //special casing to make sure the first list remains the same resource
-            if (listList.size() == 0) {
-                tc.remove(new TripleImpl(firstList, OWL.sameAs, RDF_NIL));
-                tc.add(new TripleImpl(firstList, RDF.rest, RDF_NIL));
-                tc.add(new TripleImpl(firstList, RDF.first, element));
-                listList.add(firstList);
-            } else {
-                tc.remove(new TripleImpl(listList.get(0), RDF.first, valueList.get(0)));
-                tc.add(new TripleImpl(listList.get(0), RDF.first, element));
-                addInRdfList(1, valueList.get(0));
-            }
-        } else {
-            addInRdfList(index, element);
-        }
-        valueList.add(index, element);
-    }
-    
-    /**
-     *
-     * @param index is > 0
-     * @param element
-     */
-    private void addInRdfList(int index, RdfTerm element) {
-        expandTill(index+1);
-        BlankNodeOrIri newList = new BlankNode() {
-        };
-        tc.add(new TripleImpl(newList, RDF.first, element));
-        if (index < listList.size()) {
-            tc.add(new TripleImpl(newList, RDF.rest, listList.get(index)));
-            tc.remove(new TripleImpl(listList.get(index - 1), RDF.rest, listList.get(index)));
-        } else {
-            tc.remove(new TripleImpl(listList.get(index - 1), RDF.rest, RDF_NIL));
-            tc.add(new TripleImpl(newList, RDF.rest, RDF_NIL));
-
-        }
-        tc.add(new TripleImpl(listList.get(index - 1), RDF.rest, newList));
-        listList.add(index, newList);
-    }
-
-    @Override
-    public RdfTerm remove(int index) {
-        //keeping the first list resource
-        tc.remove(new TripleImpl(listList.get(index), RDF.first, valueList.get(index)));
-        if (index == (listList.size() - 1)) {
-            tc.remove(new TripleImpl(listList.get(index), RDF.rest, RDF_NIL));    
-            if (index > 0) {
-                tc.remove(new TripleImpl(listList.get(index - 1), RDF.rest, listList.get(index)));
-                tc.add(new TripleImpl(listList.get(index - 1), RDF.rest, RDF_NIL));
-            } else {
-                tc.add(new TripleImpl(listList.get(index), OWL.sameAs, RDF_NIL));
-            }
-            listList.remove(index);
-        } else {
-            tc.add(new TripleImpl(listList.get(index), RDF.first, valueList.get(index+1)));
-            tc.remove(new TripleImpl(listList.get(index), RDF.rest, listList.get(index + 1)));
-            tc.remove(new TripleImpl(listList.get(index + 1), RDF.first, valueList.get(index + 1)));
-            if (index == (listList.size() - 2)) {
-                tc.remove(new TripleImpl(listList.get(index + 1), RDF.rest, RDF_NIL));
-                tc.add(new TripleImpl(listList.get(index), RDF.rest, RDF_NIL));
-            } else {
-                tc.remove(new TripleImpl(listList.get(index + 1), RDF.rest, listList.get(index + 2)));
-                tc.add(new TripleImpl(listList.get(index), RDF.rest, listList.get(index + 2)));
-            }
-            listList.remove(index+1);
-        }
-        return valueList.remove(index);
-    }
-
-    private BlankNodeOrIri getRest(BlankNodeOrIri list) {
-        return (BlankNodeOrIri) tc.filter(list, RDF.rest, null).next().getObject();
-    }
-
-    private RdfTerm getFirstEntry(final BlankNodeOrIri listRdfTerm) {
-        try {
-            return tc.filter(listRdfTerm, RDF.first, null).next().getObject();
-        } catch (final NullPointerException e) {
-            RuntimeException runtimeEx = AccessController.doPrivileged(new PrivilegedAction<RuntimeException>() {
-                @Override
-                public RuntimeException run(){
-                    try {
-                        final FileOutputStream fileOutputStream = new FileOutputStream("/tmp/broken-list.nt");
-                        final GraphNode graphNode = new GraphNode(listRdfTerm, tc);
-                        Serializer.getInstance().serialize(fileOutputStream, graphNode.getNodeContext(), SupportedFormat.N_TRIPLE);
-                        fileOutputStream.flush();
-                        logger.warn("GraphNode: " + graphNode);
-                        final Iterator<Iri> properties = graphNode.getProperties();
-                        while (properties.hasNext()) {
-                            logger.warn("available: " + properties.next());
-                        }
-                        return new RuntimeException("broken list " + listRdfTerm, e);
-                    } catch (Exception ex) {
-                        return new RuntimeException(ex);
-                    }
-
-                }
-            });
-            throw runtimeEx;
-        }
-    }
-
-    public BlankNodeOrIri getListRdfTerm() {
-        return firstList;
-    }
-
-    @Override
-    public boolean equals(Object obj) {
-        if (obj == null) {
-            return false;
-        }
-        if (getClass() != obj.getClass()) {
-            return false;
-        }
-        final RdfList other = (RdfList) obj;
-
-        if (!other.firstList.equals(this.firstList)) {
-            return false;
-        }
-
-        if (!other.tc.equals(this.tc)) {
-            return false;
-        }
-
-        return true;
-    }
-
-    @Override
-    public int hashCode() {
-        return 17 * this.firstList.hashCode() + this.tc.hashCode();
-    }
-
-    /**
-     * Returns the rdf lists of which the specified <code>GraphNode</code> is
-     * an element of. Sublists of other lists are not returned.
-     *
-     * @param element
-     * @return
-     */
-    public static Set<RdfList> findContainingLists(GraphNode element) {
-        Set<GraphNode> listNodes = findContainingListNodes(element);
-        if (listNodes.isEmpty()) {
-            return null;
-        }
-
-        Set<RdfList> rdfLists = new HashSet<RdfList>();
-        for (Iterator<GraphNode> it = listNodes.iterator(); it.hasNext();) {
-            GraphNode listNode = it.next();
-            rdfLists.add(new RdfList(listNode));
-        }
-        return rdfLists;
-    }
-
-    /**
-     * Returns a set of <code>GraphNode</code>S which are the first list nodes (meaning
-     * they are not the beginning of a sublist) of the list containing the specified
-     * <code>GraphNode</code> as an element.
-     *
-     * @param element
-     * @return
-     */
-    public static Set<GraphNode> findContainingListNodes(GraphNode element) {
-        Iterator<GraphNode> partOfaListNodesIter = element.getSubjectNodes(RDF.first);
-        if (!partOfaListNodesIter.hasNext()) {
-            return null;
-        }
-        Set<GraphNode> listNodes = new HashSet<GraphNode>();
-
-        while (partOfaListNodesIter.hasNext()) {
-            listNodes.addAll(findAllListNodes(partOfaListNodesIter.next()));
-        }
-        return listNodes;
-    }
-    
-    private static Set<GraphNode> findAllListNodes(GraphNode listPart) {
-        Iterator<GraphNode> invRestNodesIter;
-        Set<GraphNode> listNodes = new HashSet<GraphNode>();
-        do {
-            invRestNodesIter = listPart.getSubjectNodes(RDF.rest);
-            if (invRestNodesIter.hasNext()) {
-                listPart = invRestNodesIter.next();
-                while (invRestNodesIter.hasNext()) {
-                    GraphNode graphNode = invRestNodesIter.next();
-                    listNodes.addAll(findAllListNodes(graphNode));
-                }
-            } else {
-                listNodes.add(listPart);
-                break;
-            }
-        } while (true);
-        return listNodes;
-    }
-}

http://git-wip-us.apache.org/repos/asf/clerezza/blob/74f5fdb3/rdf.utils/src/main/java/org/apache/clerezza/rdf/utils/SeeAlsoExpander.java
----------------------------------------------------------------------
diff --git a/rdf.utils/src/main/java/org/apache/clerezza/rdf/utils/SeeAlsoExpander.java b/rdf.utils/src/main/java/org/apache/clerezza/rdf/utils/SeeAlsoExpander.java
deleted file mode 100644
index fef7e4b..0000000
--- a/rdf.utils/src/main/java/org/apache/clerezza/rdf/utils/SeeAlsoExpander.java
+++ /dev/null
@@ -1,113 +0,0 @@
-/*
- * 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.clerezza.rdf.utils;
-
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.Set;
-import java.util.concurrent.locks.Lock;
-import org.apache.commons.rdf.RdfTerm;
-import org.apache.commons.rdf.Graph;
-import org.apache.commons.rdf.Iri;
-import org.apache.clerezza.rdf.core.access.NoSuchEntityException;
-import org.apache.clerezza.rdf.core.access.TcManager;
-import org.apache.clerezza.rdf.ontologies.RDFS;
-
-/**
- * Expands a GraphNode expanding SeeAlso-References of the node.
- *
- * @author reto
- */
-public class SeeAlsoExpander {
-    /**
-     * using TcManger instead of TcProvider as this ensures LockableGraphs
-     */
-    private final TcManager tcManager;
-    public SeeAlsoExpander(TcManager tcManager) {
-        this.tcManager = tcManager;
-
-    }
-
-    /**
-     * expands a node dereferencing its rdfs:seeAlso references using the
-     * tcManager associated to this instance. If the added TripleCollections
-     * also associate rdfs:seeAlso properties to node this are expanded till
-     * the maximum recursion depth specified.
-     *
-     * @param node the node to be expanded
-     * @param recursion the maximum recursion depth
-     * @return a new GraphNode over the union of the original and all expansion graphs
-     */
-    public GraphNode expand(GraphNode node, int recursion) {
-        Set<Iri> alreadyVisited = new HashSet();
-        Set<Graph> resultTripleCollections = new HashSet<Graph>();
-        resultTripleCollections.add(node.getGraph());
-        for (Iri uriRef : expand(node, alreadyVisited, recursion)) {
-            try {
-                resultTripleCollections.add(tcManager.getGraph(uriRef));
-            } catch (NoSuchEntityException e) {
-                //ignore
-            }
-        }
-        return new GraphNode(node.getNode(),
-                new UnionGraph(resultTripleCollections.toArray(
-                new Graph[resultTripleCollections.size()])));
-
-    }
-
-    private Set<Iri> getSeeAlsoObjectUris(GraphNode node) {
-        Set<Iri> result = new HashSet<Iri>();
-        Lock l = node.readLock();
-        l.lock();
-        try {
-            Iterator<RdfTerm> objects = node.getObjects(RDFS.seeAlso);
-            while (objects.hasNext()) {
-                RdfTerm next = objects.next();
-                if (next instanceof Iri) {
-                    result.add((Iri)next);
-                }
-            }
-        } finally {
-            l.unlock();
-        }
-        return result;
-    }
-
-    private Set<Iri> expand(GraphNode node, Set<Iri> alreadyVisited, int recursion) {
-        Set<Iri> rdfSeeAlsoTargets = getSeeAlsoObjectUris(node);
-        Set<Iri> result = new HashSet<Iri>();
-        result.addAll(rdfSeeAlsoTargets);
-        recursion++;
-        if (recursion > 0) {
-            rdfSeeAlsoTargets.removeAll(alreadyVisited);
-            alreadyVisited.addAll(rdfSeeAlsoTargets);
-            for (Iri target : rdfSeeAlsoTargets) {
-                try {
-                    result.addAll(expand(new GraphNode(node.getNode(),
-                        tcManager.getGraph(target)), alreadyVisited, recursion));
-                } catch (NoSuchEntityException e) {
-                    //ignore
-                }
-            }
-        }
-        return result;
-    }
-
-}

http://git-wip-us.apache.org/repos/asf/clerezza/blob/74f5fdb3/rdf.utils/src/main/java/org/apache/clerezza/rdf/utils/Smusher.java
----------------------------------------------------------------------
diff --git a/rdf.utils/src/main/java/org/apache/clerezza/rdf/utils/Smusher.java b/rdf.utils/src/main/java/org/apache/clerezza/rdf/utils/Smusher.java
deleted file mode 100644
index 8d0ea45..0000000
--- a/rdf.utils/src/main/java/org/apache/clerezza/rdf/utils/Smusher.java
+++ /dev/null
@@ -1,61 +0,0 @@
-/*
- * 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.clerezza.rdf.utils;
-
-import org.apache.commons.rdf.Graph;
-import org.apache.clerezza.rdf.utils.smushing.IfpSmusher;
-import org.apache.clerezza.rdf.utils.smushing.SameAsSmusher;
-import org.slf4j.Logger;
-import org.slf4j.LoggerFactory;
-
-/**
- * A utility to smush equivalent resources. For greater flexibility use the 
- * classes in the smushing package.
- * 
- * @author reto
- */
-public class Smusher {
-
-    static final Logger log = LoggerFactory.getLogger(Smusher.class);
-
-    /**
-     * smush mGaph given the ontological facts. Currently it does only one step
-     * ifp smushin, i.e. only ifps are taken in account and only nodes that have
-     * the same node as ifp object in the orignal graph are equates. (calling
-     * the method a second time might lead to additional smushings.)
-     *
-     * @param mGraph
-     * @param tBox
-     */
-    public static void smush(Graph mGraph, Graph tBox) {
-        new IfpSmusher().smush(mGraph, tBox);
-    }
-
-    /**
-     * Smushes the specified graph adding owl:sameAs statements pointing to the new canonical IRI
-     * 
-     * @param mGraph
-     * @param owlSameStatements 
-     */
-    public static void sameAsSmush(Graph mGraph, Graph owlSameStatements) {
-        new SameAsSmusher().smush(mGraph, owlSameStatements, true);
-    }
-
-
-}

http://git-wip-us.apache.org/repos/asf/clerezza/blob/74f5fdb3/rdf.utils/src/main/java/org/apache/clerezza/rdf/utils/UnionGraph.java
----------------------------------------------------------------------
diff --git a/rdf.utils/src/main/java/org/apache/clerezza/rdf/utils/UnionGraph.java b/rdf.utils/src/main/java/org/apache/clerezza/rdf/utils/UnionGraph.java
deleted file mode 100644
index a928f79..0000000
--- a/rdf.utils/src/main/java/org/apache/clerezza/rdf/utils/UnionGraph.java
+++ /dev/null
@@ -1,286 +0,0 @@
-/*
- * 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.clerezza.rdf.utils;
-
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.HashSet;
-import java.util.Iterator;
-import java.util.Set;
-import java.util.concurrent.TimeUnit;
-import java.util.concurrent.locks.Condition;
-import java.util.concurrent.locks.Lock;
-import java.util.concurrent.locks.ReadWriteLock;
-import org.apache.commons.rdf.BlankNodeOrIri;
-import org.apache.commons.rdf.RdfTerm;
-import org.apache.commons.rdf.Triple;
-import org.apache.commons.rdf.Graph;
-import org.apache.commons.rdf.Iri;
-import org.apache.commons.rdf.impl.utils.AbstractGraph;
-
-/**
- *
- * This class represents the union of multiple triple collections. A UnionGraph
- * appears like a merge of the different graphs (see.
- * http://www.w3.org/TR/rdf-mt/#graphdefs).
- *
- * @author hasan
- */
-public class UnionGraph extends AbstractGraph {
-
-    protected Graph[] baseTripleCollections;
-    private Lock readLock;
-    private Lock writeLock;
-
-    /**
-     * Constructs a UnionGraph over the specified baseTripleCollections. Write
-     * and delete operations are forwarded to the first baseTripleCollections.
-     *
-     * @param baseTripleCollections the baseTripleCollections
-     */
-    public UnionGraph(Graph... baseTripleCollections) {
-        this.baseTripleCollections = baseTripleCollections;
-        readLock = getPartialReadLock(0);
-        writeLock = createWriteLock();
-    }
-
-    @Override
-    public int performSize() {
-        int size = 0;
-        for (Graph graph : baseTripleCollections) {
-            size += graph.size();
-        }
-        return size;
-    }
-
-    @Override
-    public Iterator<Triple> performFilter(final BlankNodeOrIri subject,
-            final Iri predicate, final RdfTerm object) {
-        if (baseTripleCollections.length == 0) {
-            return new HashSet<Triple>(0).iterator();
-        }
-        return new Iterator<Triple>() {
-
-            int currentBaseTC = 0;
-            Iterator<Triple> currentBaseIter = baseTripleCollections[0].filter(
-                    subject, predicate, object);
-            private Triple lastReturned;
-
-            @Override
-            public boolean hasNext() {
-                if (currentBaseIter.hasNext()) {
-                    return true;
-                }
-                if (currentBaseTC == baseTripleCollections.length - 1) {
-                    return false;
-                }
-                currentBaseTC++;
-                currentBaseIter = baseTripleCollections[currentBaseTC].filter(
-                        subject, predicate, object);
-                return hasNext();
-            }
-
-            @Override
-            public Triple next() {
-                lastReturned = hasNext() ? currentBaseIter.next() : null;
-                return lastReturned;
-            }
-
-            @Override
-            public void remove() {
-                if (lastReturned == null) {
-                    throw new IllegalStateException();
-                }
-                if (currentBaseTC == 0) {
-                    currentBaseIter.remove();
-                }
-                lastReturned = null;
-            }
-        };
-    }
-
-    @Override
-    public boolean add(Triple e) {
-        if (baseTripleCollections.length == 0) {
-            throw new RuntimeException("no base graph for adding triples");
-        }
-        return baseTripleCollections[0].add(e);
-    }
-
-    @Override
-    public boolean remove(Object e) {
-        if (baseTripleCollections.length == 0) {
-            throw new RuntimeException("no base graph for removing triples");
-        }
-        return baseTripleCollections[0].remove(e);
-    }
-
-    @Override
-    public boolean equals(Object obj) {
-        if (!(obj.getClass().equals(getClass()))) {
-            return false;
-        }
-        UnionGraph other = (UnionGraph) obj;
-        Set<Graph> otherGraphs
-                = new HashSet(Arrays.asList(other.baseTripleCollections));
-        Set<Graph> thisGraphs
-                = new HashSet(Arrays.asList(baseTripleCollections));
-        return thisGraphs.equals(otherGraphs)
-                && baseTripleCollections[0].equals(other.baseTripleCollections[0]);
-    }
-
-    @Override
-    public int hashCode() {
-        int hash = 0;
-        for (Graph graph : baseTripleCollections) {
-            hash += graph.hashCode();
-        }
-        hash *= baseTripleCollections[0].hashCode();
-        return hash;
-    }
-
-    @Override
-    public ReadWriteLock getLock() {
-        return readWriteLock;
-    }
-    private ReadWriteLock readWriteLock = new ReadWriteLock() {
-
-        @Override
-        public Lock readLock() {
-            return readLock;
-        }
-
-        @Override
-        public Lock writeLock() {
-            return writeLock;
-        }
-    };
-
-    private Lock getPartialReadLock(int startPos) {
-        ArrayList<Lock> resultList = new ArrayList<Lock>();
-        for (int i = startPos; i < baseTripleCollections.length; i++) {
-            Graph graph = baseTripleCollections[i];
-
-            final Lock lock = graph.getLock().readLock();
-            resultList.add(lock);
-        }
-        return new UnionLock(resultList.toArray(new Lock[resultList.size()]));
-    }
-
-    private Lock createWriteLock() {
-        Lock partialReadLock = getPartialReadLock(1);
-
-        Lock baseWriteLock
-                = (baseTripleCollections[0]).getLock().writeLock();
-        return new UnionLock(baseWriteLock, partialReadLock);
-
-    }
-
-    ;
-
-
-    private static class UnionLock implements Lock {
-
-        Lock[] locks;
-
-        public UnionLock(Lock... locks) {
-            this.locks = locks;
-        }
-
-        @Override
-        public void lock() {
-            boolean isLocked = false;
-            while (!isLocked) {
-                try {
-                    isLocked = tryLock(10000, TimeUnit.NANOSECONDS);
-                } catch (InterruptedException ex) {
-
-                }
-            }
-        }
-
-        @Override
-        public void lockInterruptibly() throws InterruptedException {
-            Set<Lock> aquiredLocks = new HashSet<Lock>();
-            try {
-                for (Lock lock : locks) {
-                    lock.lockInterruptibly();
-                    aquiredLocks.add(lock);
-                }
-            } catch (InterruptedException e) {
-                for (Lock lock : aquiredLocks) {
-                    lock.unlock();
-                }
-                throw e;
-            }
-        }
-
-        @Override
-        public boolean tryLock() {
-            Set<Lock> aquiredLocks = new HashSet<Lock>();
-            for (Lock lock : locks) {
-                if (!lock.tryLock()) {
-                    for (Lock aquiredLock : aquiredLocks) {
-                        aquiredLock.unlock();
-                    }
-                    return false;
-                }
-                aquiredLocks.add(lock);
-            }
-            return true;
-        }
-
-        @Override
-        public boolean tryLock(long time, TimeUnit unit) throws InterruptedException {
-            Set<Lock> aquiredLocks = new HashSet<Lock>();
-            long timeInNanos = unit.convert(time, TimeUnit.NANOSECONDS);
-            long startTime = System.nanoTime();
-            try {
-                for (Lock lock : locks) {
-                    if (!lock.tryLock((timeInNanos + startTime) - System.nanoTime(),
-                            TimeUnit.NANOSECONDS)) {
-                        for (Lock aquiredLock : aquiredLocks) {
-                            aquiredLock.unlock();
-                        }
-                        return false;
-                    }
-                    aquiredLocks.add(lock);
-                }
-            } catch (InterruptedException e) {
-                for (Lock lock : aquiredLocks) {
-                    lock.unlock();
-                }
-                throw e;
-            }
-            return true;
-        }
-
-        @Override
-        public void unlock() {
-            for (Lock lock : locks) {
-                lock.unlock();
-            }
-        }
-
-        @Override
-        public Condition newCondition() {
-            throw new UnsupportedOperationException("Conditions not supported.");
-        }
-    }
-}

http://git-wip-us.apache.org/repos/asf/clerezza/blob/74f5fdb3/rdf.utils/src/main/java/org/apache/clerezza/rdf/utils/UnionWatchableGraph.java
----------------------------------------------------------------------
diff --git a/rdf.utils/src/main/java/org/apache/clerezza/rdf/utils/UnionWatchableGraph.java b/rdf.utils/src/main/java/org/apache/clerezza/rdf/utils/UnionWatchableGraph.java
deleted file mode 100644
index 3892811..0000000
--- a/rdf.utils/src/main/java/org/apache/clerezza/rdf/utils/UnionWatchableGraph.java
+++ /dev/null
@@ -1,54 +0,0 @@
-/*
- * Copyright 2015 The Apache Software Foundation.
- *
- * Licensed 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.clerezza.rdf.utils;
-
-import org.apache.commons.rdf.Graph;
-import org.apache.commons.rdf.WatchableGraph;
-import org.apache.commons.rdf.event.FilterTriple;
-import org.apache.commons.rdf.event.GraphListener;
-
-/**
- *
- * @author developer
- */
-public class UnionWatchableGraph extends UnionGraph implements WatchableGraph {
-    
-    public UnionWatchableGraph(WatchableGraph... baseTripleCollections) {
-        super(baseTripleCollections);
-    }
-        @Override
-    public void addGraphListener(GraphListener listener, FilterTriple filter) {
-        for (Graph graph : baseTripleCollections) {
-            ((WatchableGraph)graph).addGraphListener(listener, filter);
-        }
-    }
-
-    @Override
-    public void addGraphListener(GraphListener listener, FilterTriple filter, long delay) {
-        for (Graph graph : baseTripleCollections) {
-            ((WatchableGraph)graph).addGraphListener(listener, filter, delay);
-        }
-    }
-
-    @Override
-    public void removeGraphListener(GraphListener listener) {
-        for (Graph graph : baseTripleCollections) {
-            ((WatchableGraph)graph).removeGraphListener(listener);
-        }
-    }
-
-    
-}


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