Added framework to convert the CDK data model into a JEna Model

build.xml

@@ -531,7 +531,7 @@
             list="io,structgen"/>
         <foreach target="compile-module" param="module"
             parallel="${parallel}" maxthreads="${threadCount}"
-            list="pdb,smiles,sdg,inchi,libiocml"/>
+            list="pdb,smiles,sdg,inchi,libiocml,iordf"/>
         <foreach target="compile-module" param="module"
             parallel="${parallel}" maxthreads="${threadCount}"
             list="control,extra,reaction,pdbcml,libiomd"/>
@@ -569,7 +569,7 @@
             parallel="${parallel}" maxthreads="${threadCount}"
             list="test-data,test-qsaratomic,test-qsarbond,
                   test-pdb,test-smiles,test-extra,test-atomtype,
-                  test-structgen"/>
+                  test-structgen,test-iordf"/>
         <foreach target="compile-module" param="module" trim="true"
             parallel="${parallel}" maxthreads="${threadCount}"
             list="test-qsarmolecular,test-builder3d,test-datadebug,

src/META-INF/iordf.cdkdepends

@@ -0,0 +1,7 @@
+cdk-annotation.jar
+cdk-interfaces.jar
+cdk-ioformats.jar
+cdk-core.jar
+cdk-standard.jar
+cdk-atomtype.jar
+cdk-io.jar

src/META-INF/iordf.libdepends

@@ -0,0 +1,16 @@
+vecmath1.2-1.14.jar
+jena/antlr-2.7.5.jar
+jena/arq-extra.jar
+jena/arq.jar
+jena/commons-logging-1.1.1.jar
+jena/concurrent.jar
+jena/icu4j_3_4.jar
+jena/iri.jar
+jena/jena.jar
+jena/json.jar
+jena/log4j-1.2.12.jar
+jena/lucene-core-2.3.1.jar
+jena/slf4j-simple-1.5.0.jar
+jena/stax-api-1.0.jar
+jena/wstx-asl-3.0.0.jar
+jena/xml-apis.jar

src/META-INF/test-iordf.cdkdepends

@@ -0,0 +1,13 @@
+cdk-annotation.jar
+cdk-interfaces.jar
+cdk-ioformats.jar
+cdk-core.jar
+cdk-standard.jar
+cdk-atomtype.jar
+cdk-io.jar
+cdk-iordf.jar
+cdk-diff.jar
+cdk-data.jar
+cdk-nonotify.jar
+cdk-test.jar
+cdk-test-io.jar

src/META-INF/test-iordf.devellibdepends

@@ -0,0 +1,2 @@
+junit-4.5.jar
+

src/META-INF/test-iordf.libdepends

@@ -0,0 +1,16 @@
+vecmath1.2-1.14.jar
+jena/antlr-2.7.5.jar
+jena/arq-extra.jar
+jena/arq.jar
+jena/commons-logging-1.1.1.jar
+jena/concurrent.jar
+jena/icu4j_3_4.jar
+jena/iri.jar
+jena/jena.jar
+jena/json.jar
+jena/log4j-1.2.12.jar
+jena/lucene-core-2.3.1.jar
+jena/slf4j-simple-1.5.0.jar
+jena/stax-api-1.0.jar
+jena/wstx-asl-3.0.0.jar
+jena/xml-apis.jar

src/main/org/openscience/cdk/libio/jena/Convertor.java

@@ -0,0 +1,63 @@
+/* Copyright (C) 2009  Egon Willighagen <egonw@users.sf.net>
+ *
+ * Contact: jchempaint-devel@lists.sourceforge.net
+ *
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ * All we ask is that proper credit is given for our work, which includes
+ * - but is not limited to - adding the above copyright notice to the beginning
+ * of your source code files, and to any copyright notice that you may distribute
+ * with programs based on this work.
+ *
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Lesser General Public License for more details.
+ *
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
+ */
+package org.openscience.cdk.libio.jena;
+
+import org.openscience.cdk.interfaces.IChemObjectBuilder;
+import org.openscience.cdk.interfaces.IMolecule;
+
+import com.hp.hpl.jena.rdf.model.Model;
+import com.hp.hpl.jena.rdf.model.ModelFactory;
+import com.hp.hpl.jena.rdf.model.Resource;
+import com.hp.hpl.jena.vocabulary.RDF;
+
+/**
+ * @cdk.module       iordf
+ * @cdk.githash
+ * @cdk.keyword      Resource Description Framework
+ * @cdk.keyword      Jena
+ * @cdk.keyword      RDF
+ * @cdk.keyword      Web Ontology Language
+ * @cdk.keyword      OWL
+ */
+public class Convertor {
+
+    public static Model molecule2Model(IMolecule molecule) {
+        Model model = ModelFactory.createOntologyModel();
+        model.setNsPrefix("cdk", "http://cdk.sourceforge.net/model.owl#");
+        Resource subject = model.createResource(
+            "http://cdk.sf.net/model/molecule/" + 1
+        );
+        model.add(
+            subject, RDF.type,
+            model.createResource("cdk:Molecule")
+        );
+        return model;
+    }
+
+    public static IMolecule model2Molecule(Model model,
+        IChemObjectBuilder builder) {
+        IMolecule mol = builder.newMolecule();
+        return mol;
+    }
+
+}

src/test/org/openscience/cdk/libio/jena/ConvertorTest.java

@@ -0,0 +1,53 @@
+/* Copyright (C) 2009  Egon Willighagen <egonw@users.sf.net>
+ * 
+ * Contact: cdk-devel@lists.sourceforge.net
+ * 
+ * This program is free software; you can redistribute it and/or
+ * modify it under the terms of the GNU Lesser General Public License
+ * as published by the Free Software Foundation; either version 2.1
+ * of the License, or (at your option) any later version.
+ * All we ask is that proper credit is given for our work, which includes
+ * - but is not limited to - adding the above copyright notice to the beginning
+ * of your source code files, and to any copyright notice that you may distribute
+ * with programs based on this work.
+ * 
+ * This program is distributed in the hope that it will be useful,
+ * but WITHOUT ANY WARRANTY; without even the implied warranty of
+ * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the
+ * GNU Lesser General Public License for more details.
+ * 
+ * You should have received a copy of the GNU Lesser General Public License
+ * along with this program; if not, write to the Free Software
+ * Foundation, Inc., 51 Franklin St, Fifth Floor, Boston, MA 02110-1301 USA.
+ */
+package org.openscience.cdk.libio.jena;
+
+import junit.framework.Assert;
+
+import org.junit.Test;
+import org.openscience.cdk.CDKTestCase;
+import org.openscience.cdk.interfaces.IChemObjectBuilder;
+import org.openscience.cdk.interfaces.IMolecule;
+import org.openscience.cdk.nonotify.NNMolecule;
+import org.openscience.cdk.nonotify.NoNotificationChemObjectBuilder;
+import org.openscience.cdk.tools.diff.AtomContainerDiff;
+
+import com.hp.hpl.jena.rdf.model.Model;
+
+/**
+ * @cdk.module test-iordf
+ */
+public class ConvertorTest extends CDKTestCase {
+
+    private static IChemObjectBuilder builder =
+        NoNotificationChemObjectBuilder.getInstance();
+
+    @Test public void roundtripMolecule() {
+        IMolecule mol = new NNMolecule();
+        Model model = Convertor.molecule2Model(mol);
+        IMolecule rtMol = Convertor.model2Molecule(model, builder);
+        String diff = AtomContainerDiff.diff(mol, rtMol);
+        Assert.assertEquals(0, diff.length());
+    }
+
+}