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minor update - now assumes pre-merged tbox ontology #320

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May 24, 2020
Merged

minor update - now assumes pre-merged tbox ontology #320

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22 changes: 4 additions & 18 deletions minerva-cli/src/main/java/org/geneontology/minerva/cli/CommandLineInterface.java
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Original file line number Diff line number Diff line change
Expand Up @@ -748,25 +748,11 @@ public static void validateGoCams(String input, String basicOutputFile, String e
}else {
LOGGER.info("no catalog, resolving all ontology uris directly");
}
for(OWLOntologyIRIMapper m : ontman.getIRIMappers()) {
IRI neo_iri = m.getDocumentIRI(IRI.create("http://purl.obolibrary.org/obo/go/noctua/neo.owl"));
LOGGER.info("neo mapped iri: "+neo_iri);
OWLOntology neo_test = ontman.loadOntology(neo_iri);
LOGGER.info("neo axioms "+neo_test.getAxiomCount());

IRI gp_iri = m.getDocumentIRI(IRI.create("http://purl.obolibrary.org/obo/go/extensions/go-plus.owl"));
LOGGER.info("go plus mapped iri: "+gp_iri);
//OWLOntology go_test = ontman.loadOntology(gp_iri);
//LOGGER.info("go axioms "+go_test.getAxiomCount());

IRI the_iri = m.getDocumentIRI(IRI.create(ontologyIRI));
LOGGER.info("lego mapped iri: "+the_iri);
}
LOGGER.info("loading tbox ontologies");
OWLOntology tbox_ontology = ontman.loadOntology(IRI.create(ontologyIRI));
LOGGER.info("tbox ontologies loaded: "+tbox_ontology.getAxiomCount());
tbox_ontology = StartUpTool.forceMergeImports(tbox_ontology, tbox_ontology.getImports());
LOGGER.info("ontology axioms merged loaded: "+tbox_ontology.getAxiomCount());
LOGGER.info("tbox ontology axioms loaded: "+tbox_ontology.getAxiomCount());
//should not be necessary using pre-merged ontology
//tbox_ontology = StartUpTool.forceMergeImports(tbox_ontology, tbox_ontology.getImports());
//LOGGER.info("ontology axioms merged loaded: "+tbox_ontology.getAxiomCount());

if(input.endsWith(".jnl")) {
inputDB = input;
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