start reasoner in virtuoso

load Model from virtuoso

        VirtGraph set = new VirtGraph(GraphIri, "jdbc:virtuoso://" + uriServer + ":"
                + portJDBC + "", db_user, db_pass);
        System.out.println("Start inference!");
        Reasoner reasoner = PelletReasonerFactory.theInstance().create();
        reasoner = reasoner.bindSchema(set);
        InfModel infModel = ModelFactory.createInfModel(reasoner, modelVirtuoso);
        System.out.println("Stop inference!");

        Model m2 = vd.getNamedModel(GraphIri);


save inference in virtuoso

       
         System.out.print("instancias "+m2.size());
         if(m2.containsAll(infModel)){ System.out.print("no hay inferencia ");
         }else{ System.out.print("hay inferencia "); }
         if(m2.containsAny(infModel)){ System.out.print("es correcto ");
         }else{ System.out.print("es incorrecto "); }
        
        Model inferido = infModel.difference(m2);
        m2.add(inferido);

install virtuoso in windows

Download database virtuoso in http://sourceforge.net/projects/virtuoso/files/latest/download
unzip in virtuoso-opensource and add in variable path virtuoso-opensource\lib

copy  database/virtuoso.ini  as  demo.ini  in virtuoso-opensource
remove in file demo.ini  all character ../

open cmd admin mode
http://networkadminkb.com/KB/a47/how-to-allow-users-to-enumerate-service-remotely.aspx
unable to open sthe service control manager

execute in virtuoso-opensource   ./bin/virtuoso-t.exe -c demo -I Demo -S create
the service has been register

start service openlink virtuoso server [Demo]

open http://localhost:8890/

load OWL file model in virtuoso

If you try save a model from OWL file in Virtuoso with class

VirtuosoUpdateFactory  or VirtuosoQueryExecutionFactory this fail.

http://answers.semanticweb.com/questions/10520/virtrdfinsert-examples
http://answers.semanticweb.com/questions/12513/graph-in-virtuoso

To load in virtuoso used VirtDataSource

    VirtDataSource vd = new VirtDataSource("jdbc:virtuoso://localhost:1111", "dba", "dba");

        ModelMaker maker = ModelFactory.createMemModelMaker();   
        Model m = maker.createModel(BASE, false);
               
        //load owl file in model M
        FileInputStream  fis = new FileInputStream (getClass().getClassLoader().getResource("file.owl").getFile());
        m.read(fis ,null);
        fis.close();

       
        //TODO: if exist BASE in virtuoso FAIL
        //to erase datas conductor SQL> RDF_GLOBAL_RESET ();
        Model m2 =vd.getNamedModel(BASE);
        if(m2 == null)
            vd.addNamedModel(BASE, m);

Neo4j + Sesame + OwlApi + Pellet

 To create inference in pellet and export this inferece to Neo4j with sail connector

function OpenSail 

        Map<String, String> config = new HashMap<String, String>();

        config.put("allow_store_upgrade", "true");

         graph = new MyNeo4jGraph("data/graph.db", 100000, config);

        graph.setCheckElementsInTransaction(true);

        sail = new GraphSail<Neo4jGraph>(graph);



        // sail.

        sail.initialize();



        SailRepository repository = new SailRepository(sail);

        connection = repository.getConnection();

        connection.setAutoCommit(true);

function import ontology
  
     connection.add(getClass().getClassLoader().getResource("Prueba.owl"),
                "etiqueta", RDFFormat.RDFXML);       
        System.out.println("Import stopped ...");
        connection.commit();

function Sparql

TupleQuery durationquery = connection
                .prepareTupleQuery(
                        QueryLanguage.SPARQL,
                        "PREFIX : <http://www.semanticweb.org/ontologies/2012/8/Prueba.owl#> "
                                + "PREFIX Prueba: <http://www.semanticweb.org/ontologies/2012/8/Prueba.owl#> "
                                + "PREFIX owl: <http://www.w3.org/2002/07/owl#>  "
                                + "PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#> "
                                + "PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>  "
                                + "PREFIX xsd: <http://www.w3.org/2001/XMLSchema#>  "
                                + "SELECT ?person " + "WHERE { " +
                                 " Prueba:Jean  Prueba:hasSibling ?person  . "+

                                "}");
        TupleQueryResult result = durationquery.evaluate();
        while (result.hasNext()) {
            BindingSet binding = result.next();
            System.out.println(binding.getBinding("person").getValue());
            Assert.assertEquals("Assert ", binding.getBinding("person").getValue().toString(),
            "http://www.semanticweb.org/ontologies/2012/8/Prueba.owl#Gemma");
        }



reasoner

         //prepare ontology and reasoner 

        OWLOntologyManager manager = OWLManager.createOWLOntologyManager(); 

        //OWLOntology ontology = manager.loadOntologyFromOntologyDocument(IRI.create(BASE_URL)); 

        OWLOntology ontology = manager.loadOntologyFromOntologyDocument(

                IRI.create(getClass().getClassLoader().getResource("Prueba.owl")));

        System.out.println(" Load ontology" );



        OWLReasonerFactory reasonerFactory = PelletReasonerFactory.getInstance(); 

        System.out.println(" Load reasoner" );

        OWLReasoner reasoner = reasonerFactory.createReasoner(ontology, new SimpleConfiguration()); 



        OWLDataFactory factory = manager.getOWLDataFactory(); 

        PrefixOWLOntologyFormat pm = manager.getOntologyFormat(ontology).asPrefixOWLOntologyFormat(); 



        pm.setDefaultPrefix(BASE_URL + "#"); 

        //get class and its individuals 

        OWLClass personClass = factory.getOWLClass(":Person", pm);

        pm.setDefaultPrefix("http://www.semanticweb.org/ontologies/2012/8/Prueba.owl#"); 

        

        OWLObjectProperty hasSibling = factory.getOWLObjectProperty(":hasSibling", pm); 



//export pellet inference to sesame sail neo4j







 for (OWLNamedIndividual person : reasoner.getInstances(personClass, false).getFlattened()) { 

            System.out.println("person : " + renderer.render(person)); 

            

            for (Node<OWLNamedIndividual> siblings : reasoner.getObjectPropertyValues(person, hasSibling)) { 

                for (OWLNamedIndividual sibling : siblings.getEntities()) {

                    System.out.println("Person has sibling: " + sibling.getIRI());

                    

                    Map<OWLObjectPropertyExpression, Set<OWLIndividual>> assertedValues =  person.getObjectPropertyValues(ontology); 

                    for (OWLObjectProperty objProp : ontology.getObjectPropertiesInSignature(true)) { 

                        for (OWLNamedIndividual ind : reasoner.getObjectPropertyValues(person, objProp).getFlattened()) {

                            if (assertedValues.get(objProp)==null ) {//inference

                                System.out.println("inferred object property for :"

                                        + renderer.render(objProp) + " -> " + renderer.render(ind));



                            

                                ValueFactory mValueFactory = connection.getValueFactory();

                                org.openrdf.model.URI predicate = mValueFactory.createURI(hasSibling.getIRI().toURI().toString());

                                Resource subject =  mValueFactory.createURI(person.getIRI().toURI().toString()); // mValueFactory.createURI(subj.getIRI().toURI().toString());

                                Resource resource =  mValueFactory.createBNode();

                                Value object = null;

                                

                                object =  mValueFactory.createURI(ind.getIRI().toURI().toString());

                                

                                try {

                                    System.out.println("Triplet --"+subject+"--"+predicate+"--"+object+"--"+resource+"--");

                                    connection.add(subject, predicate, object,resource);

                                } catch (RepositoryException e) {

                                    System.out.println(e);

                                }

                                                                

                            }else{//asserted

                                boolean asserted = assertedValues.get(objProp).contains(ind); 

                                System.out.println((asserted ? "asserted" : "inferred") + " object property for Martin: " 

                                    + renderer.render(objProp) + " -> " + renderer.render(ind));

                            }

                        } 

                    } 

                }

            } 

        } 

        Assert.assertTrue(reasoner.isConsistent());

java.lang.UnsatisfiedLinkError:

I have a next error with maven and eclipse

[ERROR] Failed to execute goal org.apache.maven.plugins:maven-surefire-plugin:2.10:test (default-test) on project database: Execution default-test of goal org.apache.maven.plugins:maven-surefire-plugin:2.10:test failed: An API incompatibility was encountered while executing org.apache.maven.plugins:maven-surefire-plugin:2.10:test: java.lang.UnsatisfiedLinkError: java.io.WinNTFileSystem.createFileExclusively(Ljava/lang/String;Z)Z

Change version SE java to JDK or other version java. This fix the problem.

NoClassDefFoundError: org/apache/lucene/util/Version

I make a project with blueprint-neo4j-graph and pellet , but pellet use lucene-core  2.3.1 and blueprint-neo4j-graph use lucene-core 3.5.0

I have a new error  in neo4j to load lucene version

Caused by: java.lang.NoClassDefFoundError: org/apache/lucene/util/Version
    at org.neo4j.index.impl.lucene.LuceneDataSource.<clinit>(LuceneDataSource.java:110)
    at org.neo4j.index.lucene.LuceneIndexProvider.load(LuceneIndexProvider.java:70)
    at org.neo4j.kernel.InternalAbstractGraphDatabase$DefaultKernelExtensionLoader.loadIndexImplementations(InternalAbstractGraphDatabase.java:1191)
    at org.neo4j.kernel.InternalAbstractGraphDatabase$DefaultKernelExtensionLoader.init(InternalAbstractGraphDatabase.java:1163)
    at org.neo4j.kernel.lifecycle.LifeSupport$LifecycleInstance.init(LifeSupport.java:382)
    ... 39 more
Caused by: java.lang.ClassNotFoundException: org.apache.lucene.util.Version
    at java.net.URLClassLoader$1.run(Unknown Source)
    at java.security.AccessController.doPrivileged(Native Method)
    at java.net.URLClassLoader.findClass(Unknown Source)
    at java.lang.ClassLoader.loadClass(Unknown Source)
    at sun.misc.Launcher$AppClassLoader.loadClass(Unknown Source)
    at java.lang.ClassLoader.loadClass(Unknown Source)
    ... 44 more



I have pellet dependence
    <dependency>
            <groupId>com.owldl</groupId>
            <artifactId>pellet</artifactId>
            <version>2.3.0</version>
        </dependency>
         <dependency>
            <groupId>com.tinkerpop.blueprints</groupId>
            <artifactId>blueprints-neo4j-graph</artifactId>
            <version>2.1.0</version>
        </dependency>

With plugin m2e resolve depencence add this code in pom.xml project 


    <dependencyManagement>
        <dependencies>
            <dependency>
                <groupId>org.apache.lucene</groupId>
                <artifactId>lucene-core</artifactId>
                <version>3.5.0</version>
            </dependency>
        </dependencies>
    </dependencyManagement>

Install cassandra database

To install cassandra database distribution http://www.datastax.com/download/community

Dont work in 32 bit architecture. java Heap space  error
To see web service
http://<publicIP>:8888/opscenter/

Ubuntu 12, 64 bit

Before
**** remove version of java openjdk and install java oracle
sudo apt-ger purge openjdk*
java 7
sudo add-apt-repository ppa:webupd8team/java
sudo apt-get install oracle-java7-installer

****openssl python
sudo apt-get install libssl0.9.8
sudo apt-get install sysstat
sudo apt-get install python-cql

****Install cassandra, DataStax Community distribution of Cassandra. Read more in http://www.datastax.com/docs/1.1/install/install_deb
sudo apt-get install dsc1.1

****install web service. Read more in http://www.datastax.com/docs/opscenter/install/install_deb
sudo apt-get install opscenter-free

***web service configure
sudo vi /etc/opscenter/opscenterd.conf
***add in file
[cassandra]
seed_hosts=publicIP
[logging]
level=INFO
[jmx]
port =7199


***configure cassadra
sudo vi /etc/cassandra/cassandra.yaml
***change IP and localhost for publiIP

***start cassandra
sudo service cassandra start

***node cassandra
nodetool ring -h publicIP

**start web
sudo service opscenterd start

*** check web service
wget http://publicIP:8888/

***to see log
/var/log/opscenter/opscenterd.log


*** to start client cassandra
cassandra-cli -h publicIP -p 9160

***to see  log of  cassandra
/var/log/cassandra/output.log
/var/log/cassandra/system.log


***  delete database cassandra if you want , stop service before
sudo bash -c '/var/lib/cassandra/data/system/*'