Instantiate and execute an OPPL pattern with variable scope defined

[mariadelcarmen]

I am trying to instantiate and execute an OPPL pattern like this:

?adenoma:CLASS[subClassOf Adenoma] BEGIN ADD !item instanceOf HistopathologyReport and hasFinding some ?adenoma END;

I try to parser it with:

String patternCode = "?adenoma:CLASS[subClassOf Adenoma]\nBEGIN\nADD !item instanceOf HistopathologyReport and hasFinding some ?adenoma\nEND;"
ParserFactory factory = new ParserFactory(ontology, manager);
OPPLPatternParser parser = factory.build(new SystemErrorEcho());
PatternModel patternModel = parser.parse(patternCode);

But I get "No reasoner selected at line 1 position 14" Since I do not see a way to create org.coode.patterns.ParserFactory with a reasoner, a tried this way:

OWLReasoner reasoner=new Reasoner.ReasonerFactory().createReasoner(ontology); //Hermit reasoner     
org.coode.oppl.ParserFactory factoryOpplScript = new org.coode.oppl.ParserFactory(manager, ontology, reasoner);
ParserFactory factoryOpplPattern = new ParserFactory(ontology, manager);    
OPPLParser opplParser = factoryOpplScript.build(new SystemErrorEcho());     
OPPLScript script = opplParser.parse(patternCode);
PatternModel patternModel = factoryOpplPattern.getPatternFactory().createPatternModel(script);

But I got "Recognition exception when parsing token: BEGIN line 2 position 0 unexpected token code 83" and the result of variable script is null. It seems that I cannot parser the pattern as an OPPLScript, since it does not have a SELECT action. Then, how could I get the PatternModel for my OPPL pattern with the variable scope defined using a reasoner?

[mariadelcarmen]

Well, I changed the OPPL and OWLAPI versions I was using. Now I do not have the above problem anymore. However, I new problem showed up:

.....               
OPPLScript script = opplParser.parse(problematicPattern);
PatternModel patternModel = factoryOpplPattern.getPatternFactory().createPatternModel(script);
if (patternModel != null) {
    List<OWLAxiomChange> newAxioms = new ArrayList<OWLAxiomChange>();
    InstantiatedPatternModel ip = factoryOpplPattern.getPatternFactory().createInstantiatedPatternModel(patternModel,new QuickFailRuntimeExceptionHandler());
    for (Variable v : patternModel.getInputVariables()) {
        ip.instantiate(v, manager.getOWLDataFactory().getOWLClass(IRI.create("http://domain.owl#AdenoAdenoma")));
    }
    NonClassPatternExecutor ncpe = new NonClassPatternExecutor(ip,ontology, manager,    manager.getOntologyDocumentIRI(ontology),new QuickFailRuntimeExceptionHandler());
    newAxioms.addAll(ncpe.visit(patternModel));
...
}

I get the following exception performing ncpe.visit(patternModel):

Exception in thread "main" java.lang.ClassCastException: org.coode.oppl.ConstraintSystem cannot be cast to org.coode.patterns.PatternConstraintSystem
    at org.coode.patterns.PatternModel.getConstraintSystem(PatternModel.java:483)
    at org.coode.patterns.PatternModel$ClassPatternDetector.<init>(PatternModel.java:119)
    at org.coode.patterns.PatternModel.isClassPattern(PatternModel.java:704)
    at org.coode.patterns.InstantiatedPatternModel.isClassPattern(InstantiatedPatternModel.java:430)
    at org.coode.patterns.InstantiatedPatternModel.extractBindingNodes(InstantiatedPatternModel.java:279)
    at org.coode.patterns.PatternActionFactory.createChange(PatternActionFactory.java:111)
    at org.coode.patterns.NonClassPatternExecutor.visit(NonClassPatternExecutor.java:71)
    at test.oppl.PatternExecution.executionNotWorkingWithReasoner(PatternExecution.java:244)
    at test.oppl.PatternExecution.main(PatternExecution.java:1353)

It seems that I cannot really execute an OPPL pattern through an OPPL script.

[ignazio1977]

Thanks for the test case, I'm going to try and replicate it.

[ignazio1977]

I can replicate your issue and correct it (in the sense that I do not get exceptions) this way.

Note that there are two issues:

• you are parsing the script with an OPPLParser, but actually need a Pattern parser
• the current API for creating a PatternModelFactory does not allow for a reasoner to be set easily, as far s I can tell, so I had to create it manually here. Not ideal.

    public static void main(String[] args) throws OWLOntologyCreationException {
        String patternCode = "?adenoma:CLASS[subClassOf Adenoma]\nBEGIN\nADD !item instanceOf HistopathologyReport and hasFinding some ?adenoma\nEND;";
        OWLOntologyManager manager = OWLManager.createOWLOntologyManager();
        OWLOntology ontology = manager.createOntology();
        OWLDataFactory df = manager.getOWLDataFactory();
    // initializing the ontology to be able to parse the query
        manager.addAxiom(ontology, df.getOWLDeclarationAxiom(df.getOWLClass(IRI.create("urn:HistopathologyReport")), new HashSet<OWLAnnotation>(Arrays.asList(df.getOWLAnnotation(df.getRDFSLabel(), df.getOWLLiteral("HistopathologyReport"))))));
        OWLClass adenoma = df.getOWLClass(IRI.create("urn:Adenoma"));
        manager.addAxiom(ontology, df.getOWLDeclarationAxiom(adenoma, new HashSet<OWLAnnotation>(Arrays.asList(df.getOWLAnnotation(df.getRDFSLabel(), df.getOWLLiteral("Adenoma"))))));
        manager.addAxiom(ontology, df.getOWLDeclarationAxiom(df.getOWLObjectProperty(IRI.create("urn:hasFinding")), new HashSet<OWLAnnotation>(Arrays.asList(df.getOWLAnnotation(df.getRDFSLabel(), df.getOWLLiteral("hasFinding"))))));
    // the exact reasoner does not matter here
        OWLReasoner reasoner = new JFactFactory().createReasoner(ontology);

//bit that needs changing
        OPPLPatternParser patternParser = new OPPLPatternParser(new PatternModelFactory(ontology, manager, reasoner), new SystemErrorEcho(), new SimpleSymbolTableFactory(manager));

        OPPLScript script = patternParser.parse(patternCode);
        PatternModel patternModel = patternParser.getOPPLPatternFactory().createPatternModel(script);
        List<OWLAxiomChange> newAxioms = new ArrayList<OWLAxiomChange>();
        InstantiatedPatternModel ip = patternParser.getOPPLPatternFactory().createInstantiatedPatternModel(patternModel, new QuickFailRuntimeExceptionHandler());
        for (Variable v : patternModel.getInputVariables()) {
            ip.instantiate(v, adenoma);
        }
        NonClassPatternExecutor ncpe = new NonClassPatternExecutor(ip, ontology, manager, manager.getOntologyDocumentIRI(ontology), new QuickFailRuntimeExceptionHandler());
        newAxioms.addAll(ncpe.visit(patternModel));
    }

[mariadelcarmen]

I still had to download all the code of the libraries from github and recompile because I had some odd exceptions with those downloaded from http://sourceforge.net/projects/oppl2/files/. Now this works perfect, Thanks a lot!

[ignazio1977]

On 24 Oct 2013 10:23, "mariadelcarmen" notifications@github.com wrote:

I still had to download all the code of the libraries from github and recompile because I had some odd exceptions with those downloaded from http://sourceforge.net/projects/oppl2/files/. Now this works perfect, Thanks a lot!

Yeah we need to sort the maven build and make a release. I.

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