I think this corrects #335

There is a method in the GPAD sparql export that gathers model annotations such as state.  This was getting confused because, at that point in the code, the RDF for the model also contains the RDF for all the Arachne rules.  See comment in CoreMMM .

minerva-converter/src/main/java/org/geneontology/minerva/legacy/sparql/GPADSPARQLExport.java

@@ -194,6 +194,7 @@ private Map<String, String> getModelAnnotations(Model model) {
  Map<String, String> modelAnnotations = new HashMap<>();
  while (result.hasNext()) {
  QuerySolution qs = result.next();
+ //"http://therules.org" 
  if (qs.get("model_state") != null) {
  String modelState = qs.getLiteral("model_state").getLexicalForm();
  modelAnnotations.put("model-state", modelState);
@@ -202,7 +203,7 @@ private Map<String, String> getModelAnnotations(Model model) {
  String providedBy = qs.getLiteral("provided_by").getLexicalForm();
  modelAnnotations.put("assigned-by", providedBy);
  }
- break;
+ //break;
  }
  return modelAnnotations;
  }

minerva-core/src/main/java/org/geneontology/minerva/CoreMolecularModelManager.java

@@ -316,6 +316,7 @@ public WorkingMemory createInferredModel(OWLOntology abox, IRI modelId) {
  // Using model's ontology IRI so that a spurious different ontology declaration triple isn't added
  // OWLOntology schemaOntology = OWLManager.createOWLOntologyManager().createOntology(getOntology().getRBoxAxioms(Imports.INCLUDED), modelId);
  // I think the re-use of the model IRI as the IRI of the rule ontology has some weird effects on the model in question, rendering its contents inaccesible. 
+ //this influences GPAD export
  OWLOntologyManager tmp_man = OWLManager.createOWLOntologyManager();
  OWLOntology schemaOntology = tmp_man.createOntology(IRI.create("http://therules.org"));
  Set<OWLAxiom> owl_rules = getOntology().getRBoxAxioms(Imports.INCLUDED);