Convert OWL/XML in RDF/XML with a simple command line in shell

Question

I'm asking your help to create a converter to transform OWL/XML into RDF/XML. My purpose is to use OWLapi 2 through a simple shell command with bash. My files are in OWL/XML but I have to transform them into RDF/XML to send them in my fuseki database. I could transform each file thanks to Protégé or a converter available online, but I've more than one thousand files to convert.

See my current java file (but I don't know how to use it) :

package owl2rdf;

import java.io.File;
import org.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.io.RDFXMLOntologyFormat;
import org.semanticweb.owlapi.model.IRI;
import org.semanticweb.owlapi.model.OWLOntology;
import org.semanticweb.owlapi.model.OWLOntologyManager;

@SuppressWarnings("deprecation")
public class owl2rdf {

public static void main(String[] args) throws Exception {

    // Get hold of an ontology manager
    OWLOntologyManager manager = OWLManager.createOWLOntologyManager();

    // Load the ontology from a local files
    File file = new File(args[0]);
    System.out.println("Loaded ontology: " + file);
    OWLOntology ontology = manager.loadOntologyFromOntologyDocument(file);

    // Get the ontology format ; in our case it's normally OWL/XML
    OWLOntologyFormat format = manager.OWLOntologyFormat(file);
    System.out.println("    format: " + format);

    // save the file into RDF/XML format
    RDFXMLOntologyFormat rdfxmlFormat = new RDFXMLOntologyFormat();
    manager.saveOntology(ontology, rdfxmlFormat, IRI.create(file));
    }
}

When I execute this code, I've many errors relative to exceptions I don't understand at all, but I saw it's a common error:

Exception in thread "main" java.lang.reflect.InvocationTargetException
Caused by: java.lang.NoClassDefFoundError: com/google/inject/Provider
Caused by: java.lang.ClassNotFoundException: com.google.inject.Provider

Answer 1

To change a entire repository of an OWL/XML file into RDF/XML file:

1- create your package owl2rdf.java

package owl2rdf;

//import all necessary classes
import java.io.File;
import org.semanticweb.owlapi.apibinding.OWLManager;
import org.semanticweb.owlapi.io.RDFXMLOntologyFormat;
import org.semanticweb.owlapi.model.IRI;
import org.semanticweb.owlapi.model.OWLOntology;
import org.semanticweb.owlapi.model.OWLOntologyManager;

@SuppressWarnings("deprecation")
public class owl2rdf {

#create a main() function to take an argument; here in the example one argument only
    public static void main(String[] args) throws Exception {

        // Get hold of an ontology manager
        OWLOntologyManager manager = OWLManager.createOWLOntologyManager();

        // Load the ontology from a local files
        File file = new File(args[0]);
        System.out.println("Loaded ontology: " + file);
        OWLOntology ontology = manager.loadOntologyFromOntologyDocument(file);

        // save the file into RDF/XML format
        //in this case, my ontology file and format already manage prefix
        RDFXMLOntologyFormat rdfxmlFormat = new RDFXMLOntologyFormat();
        manager.saveOntology(ontology, rdfxmlFormat, IRI.create(file));
    }
}

2- Thanks to a Java-IDE such as Eclipse or something else, manages all dependencies (repo Maven, downloads jar, classplath, etc.)

3- create your bash scrip my-scrip.sh; here absolutely not optimized

#!/bin/bash
cd your-dir
for i in *
do
#get the absolute path; be careful, realpath comes with the latest coreutils package
    r=$(realpath "$i")
    #to be not disturb by relative path with java -jar, I put the .jar in the parent directory
    cd ..
    java -jar owl2rdf.jar "$r"
    cd your-dir
done
echo "Conversion finished, see below if there are errors."

4- Execute your script $ chmod +x my-script.sh;./my-script

5- haha moment: all your OWL/XML are converted in RDF/XML. You can for example, import them into fuseki or sesame database.