Examples with CurieMappings org.geneontology.minerva.curie.CurieMappings used on opensource projects

Example 11 with CurieMappings

use of org.geneontology.minerva.curie.CurieMappings in project minerva by geneontology.

the class BatchModelHandlerTest method init.

static void init(ParserWrapper pw) throws OWLOntologyCreationException, IOException, UnknownIdentifierException {
    final MinervaOWLGraphWrapper graph = pw.parseToOWLGraph("src/test/resources/go-lego-minimal.owl");
    final OWLObjectProperty legorelParent = StartUpTool.getRelation("http://purl.obolibrary.org/obo/LEGOREL_0000000", graph);
    assertNotNull(legorelParent);
    importantRelations = StartUpTool.getAssertedSubProperties(legorelParent, graph);
    assertFalse(importantRelations.isEmpty());
    // curie handler
    final String modelIdcurie = "gomodel";
    final String modelIdPrefix = "http://model.geneontology.org/";
    final CurieMappings localMappings = new CurieMappings.SimpleCurieMappings(Collections.singletonMap(modelIdcurie, modelIdPrefix));
    curieHandler = new MappedCurieHandler(DefaultCurieHandler.loadDefaultMappings(), localMappings);
    InferenceProviderCreator ipc = CachingInferenceProviderCreatorImpl.createElk(false, null);
    models = new UndoAwareMolecularModelManager(graph.getSourceOntology(), curieHandler, modelIdPrefix, folder.newFile().getAbsolutePath(), null, ontology_journal_file, true);
    lookupService = createTestProteins(curieHandler);
    handler = new JsonOrJsonpBatchHandler(models, "development", ipc, importantRelations, lookupService) {

        @Override
        protected String generateDateString() {
            // hook for overriding the date generation with a custom counter
            if (dateGenerator.useCounter) {
                int count = dateGenerator.counter;
                dateGenerator.counter += 1;
                return Integer.toString(count);
            }
            return super.generateDateString();
        }
    };
    JsonOrJsonpBatchHandler.VALIDATE_BEFORE_SAVE = true;
}