Parsing ontology file (.owl, serialized in RDF/XML) to JSON-LD

[luispcosta]

Hello.

I'm trying to create a simple program like the one presented here: https://github.com/jsonld-java/jsonld-java-rdf2go/blob/master/src/test/java/com/github/jsonldjava/rdf2go/RDF2GoRDFParserTest.java

If I understood correctly, RDF/XML is also a valid syntax to be transformed to JSON-LD (correct if I'm wrong) and so this is the code I wrote so far:

import java.io.ByteArrayInputStream;
import java.io.IOException;

import org.ontoware.rdf2go.RDF2Go;
import org.ontoware.rdf2go.exception.ModelRuntimeException;
import org.ontoware.rdf2go.model.Model;
import org.ontoware.rdf2go.model.Syntax;

import com.github.jsonldjava.core.JsonLdError;
import com.github.jsonldjava.core.JsonLdProcessor;
import com.github.jsonldjava.rdf2go.RDF2GoRDFParser;
import com.github.jsonldjava.utils.JsonUtils;

public class Populate {

    public static void main(String[] args) throws JsonLdError, ModelRuntimeException, IOException {

            final String rdfxml = 
                    "<?xml version='1.0'?>" +
                    "<rdf:RDF xmlns='http://protege.stanford.edu/plugins/owl/owl-library/koala.owl#'" +
                    "xmlns:rdf='http://www.w3.org/1999/02/22-rdf-syntax-ns#'" +
                    "xmlns:owl='http://www.w3.org/2002/07/owl#'" +
                    "xmlns:rdfs='http://www.w3.org/2000/01/rdf-schema#'>" +
                    " <owl:Ontology rdf:about='http://protege.stanford.edu/plugins/owl/owl-library/koala.owl'/>" + 

                    "<owl:ObjectProperty rdf:about='http://protege.stanford.edu/plugins/owl/owl-library/koala.owl#hasChildren'>" +
                    "<rdfs:range rdf:resource='http://protege.stanford.edu/plugins/owl/owl-library/koala.owl#Animal'/>" +
                    "<rdfs:domain rdf:resource='http://protege.stanford.edu/plugins/owl/owl-library/koala.owl#Animal'/>" +
                    "</owl:ObjectProperty>" +
                    "</rdf:RDF>";

            final RDF2GoRDFParser parser = new RDF2GoRDFParser();
            final Model modelResult = RDF2Go.getModelFactory().createModel().open();
            modelResult.readFrom(new ByteArrayInputStream(rdfxml.getBytes()), Syntax.RdfXml);
            final Object jsonld = JsonLdProcessor.fromRDF(modelResult, parser);
            String finalObj = JsonUtils.toPrettyString(jsonld);
            System.out.println(finalObj);
    }
}

I'm sure that the Ontology encoded by the the string RdfXml is a valid one.
However when I try to run this code, I always get:

Model runtime exception org.ontoware.rdf2go.exception.ModelRuntimeException: org.openrdf.rio.RDFParseException: Element type "rdf:RDF" must be followed by either attribute specifications, ">" or "/>". [line 1, column 101]

So two questions:

1. Is OWL files (encoded in RDF/XML syntax) accepted?
2. If it is, what's wrong with the code?

Thank you!

Edit: If this actually works and I can solve the problem, I'll gladly open a PR with some tests of RDF/XML to JSON-LD transformations!

[ansell]

You may be missing some whitespace between the "xmlns" attributes inside of the rdf:RDF element declaration.

[luispcosta]

You were right! Thank you for the help. One last question: If, instead I wanted to read the RDF/XML from a .owl file instead directly from a string, how could I do it?

This is what I tried:

final RDF2GoRDFParser parser = new RDF2GoRDFParser();
            final Model modelResult = RDF2Go.getModelFactory().createModel().open();
            modelResult.readFrom(new FileInputStream(ontologyFile), Syntax.RdfXml);
            final Object jsonld = JsonLdProcessor.fromRDF(modelResult, parser);

Map con = new HashMap();
            JsonLdOptions opt = new JsonLdOptions();
            Object compact = JsonLdProcessor.compact(jsonld, con, opt);
            String finalObj = JsonUtils.toPrettyString(jsonld);

System.out.println(finalObj);

The ontology file I'm using is this: http://pastebin.com/BhHHx4RM

I'm getting this error:

[WARNING] 
java.lang.reflect.InvocationTargetException
    at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method)
    at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:62)
    at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
    at java.lang.reflect.Method.invoke(Method.java:497)
    at org.codehaus.mojo.exec.ExecJavaMojo$1.run(ExecJavaMojo.java:297)
    at java.lang.Thread.run(Thread.java:745)
Caused by: java.lang.ClassCastException: Cannot cast a BlankNode to a URI
    at org.ontoware.rdf2go.model.node.impl.AbstractBlankNodeImpl.asURI(AbstractBlankNodeImpl.java:49)
    at com.github.jsonldjava.rdf2go.RDF2GoRDFParser.handleStatement(RDF2GoRDFParser.java:70)
    at com.github.jsonldjava.rdf2go.RDF2GoRDFParser.importModel(RDF2GoRDFParser.java:40)
    at com.github.jsonldjava.rdf2go.RDF2GoRDFParser.parse(RDF2GoRDFParser.java:127)
    at com.github.jsonldjava.core.JsonLdProcessor.fromRDF(JsonLdProcessor.java:420)
    at com.github.jsonldjava.core.JsonLdProcessor.fromRDF(JsonLdProcessor.java:456)
    at luispcosta.db.Populate.storeOntology(Populate.java:85)
    at luispcosta.db.Populate.main(Populate.java:61)

I'm not sure if I need a special configuration on json-ld to read this ontology, or if is a specific problem in the ontology. I'm guessing it is a error in the ontology because of: Caused by: java.lang.ClassCastException: Cannot cast a BlankNode to a URI at
but I'm not sure.

[ansell]

That looks like a bug here as not all non-literal cases are URIs, but I am not familiar with the RDF2Go API:

https://github.com/jsonld-java/jsonld-java-rdf2go/blob/master/src/main/java/com/github/jsonldjava/rdf2go/RDF2GoRDFParser.java#L70

@ismriv may be able to help further with a fix for that.

[luispcosta]

Great! I'll be glad to help out fixing the issue (if it is confirmed as one) as well. Will be waiting

[ismriv]

Hi @luispcosta, sorry I've just seen this now, I'm not actively involve in this anymore. Are you still having the same problem? There seems to be a bug in L70, can you try checking if the object is an instance of BlankNode and call toString() in that case?

[duy-tran]

I'm having the same problem while parsing an RDF graph containing cardinality restriction.
From @luispcosta 's file, the error comes from this block:

 <owl:Class rdf:about="http://protege.stanford.edu/plugins/owl/owl-library/koala.owl#Animal">
        <rdfs:subClassOf>
            <owl:Restriction>
                <owl:onProperty rdf:resource="http://protege.stanford.edu/plugins/owl/owl-library/koala.owl#hasHabitat"/>
                <owl:minCardinality rdf:datatype="http://www.w3.org/2001/XMLSchema#nonNegativeInteger">1</owl:minCardinality>
            </owl:Restriction>
        </rdfs:subClassOf>
    </owl:Class>

L70 treats <owl:Restriction> as a blank node. Here is the screenshot of debugging

@ismriv could you take a look at this?