Examples with MinervaOWLGraphWrapper org.geneontology.minerva.MinervaOWLGraphWrapper used on opensource projects

Example 1 with MinervaOWLGraphWrapper

use of org.geneontology.minerva.MinervaOWLGraphWrapper in project minerva by geneontology.

the class M3ExpressionParserTest method init.

static void init(ParserWrapper pw) throws OWLOntologyCreationException, IOException {
    /* File file = new File("src/test/resources/go-lego-module.omn.gz").getCanonicalFile(); */
    File file = new File("src/test/resources/go-lego-module-compact.omn.gz").getCanonicalFile();
    graph = new MinervaOWLGraphWrapper(pw.parseOWL(IRI.create(file)));
}

Example 2 with MinervaOWLGraphWrapper

use of org.geneontology.minerva.MinervaOWLGraphWrapper in project minerva by geneontology.

the class MolecularModelJsonRendererTest method testSimpleClassExpression.

private void testSimpleClassExpression(OWLClassExpression ce, String expectedJsonType) throws Exception {
    // setup test model/ontology
    OWLOntology o = m.createOntology();
    OWLImportsDeclaration importDeclaration = f.getOWLImportsDeclaration(g.getSourceOntology().getOntologyID().getOntologyIRI().get());
    m.applyChange(new AddImport(o, importDeclaration));
    // create indivdual with a ce type
    final IRI i1IRI = IRI.generateDocumentIRI();
    final OWLNamedIndividual ni1 = f.getOWLNamedIndividual(i1IRI);
    // declare individual
    m.addAxiom(o, f.getOWLDeclarationAxiom(ni1));
    // declare type
    m.addAxiom(o, f.getOWLClassAssertionAxiom(ce, ni1));
    MolecularModelJsonRenderer r = new MolecularModelJsonRenderer(null, o, null, curieHandler);
    JsonOwlIndividual jsonOwlIndividualOriginal = r.renderObject(ni1);
    String json = MolecularModelJsonRenderer.renderToJson(jsonOwlIndividualOriginal, true);
    assertTrue(json, json.contains("\"type\": \"" + expectedJsonType + "\""));
    JsonOwlIndividual jsonOwlIndividualParse = MolecularModelJsonRenderer.parseFromJson(json, JsonOwlIndividual.class);
    assertNotNull(jsonOwlIndividualParse);
    assertEquals(jsonOwlIndividualOriginal, jsonOwlIndividualParse);
    Set<OWLClassExpression> ces = TestJsonOwlObjectParser.parse(new MinervaOWLGraphWrapper(o), jsonOwlIndividualParse.type);
    assertEquals(1, ces.size());
    assertEquals(ce, ces.iterator().next());
}

Example 3 with MinervaOWLGraphWrapper

use of org.geneontology.minerva.MinervaOWLGraphWrapper in project minerva by geneontology.

the class FindTaxonTool method getEntityTaxon.

public String getEntityTaxon(String curie, OWLOntology model) throws UnknownIdentifierException {
    if (curie == null || curie.isEmpty()) {
        return null;
    }
    OWLDataFactory df = model.getOWLOntologyManager().getOWLDataFactory();
    OWLClass cls = df.getOWLClass(curieHandler.getIRI(curie));
    String taxon = getEntityTaxon(cls, model);
    if (taxon == null) {
        MinervaOWLGraphWrapper g = new MinervaOWLGraphWrapper(model);
        cls = g.getOWLClassByIdentifier(curie);
        if (cls != null) {
            taxon = getEntityTaxon(cls, model);
        }
        IOUtils.closeQuietly(g);
    }
    return taxon;
}

Example 4 with MinervaOWLGraphWrapper

use of org.geneontology.minerva.MinervaOWLGraphWrapper in project minerva by geneontology.

the class MolecularModelJsonRenderer method renderEvidences.

public static List<JsonEvidenceInfo> renderEvidences(OWLOntologyManager manager, CurieHandler curieHandler) throws OWLException, IOException {
    // TODO remove the hard coded ECO dependencies
    OntologyMapperPair<EcoMapper> pair;
    synchronized (ecoMutex) {
        if (eco == null) {
            eco = EcoMapperFactory.createEcoMapper(manager);
        }
        pair = eco;
    }
    final MinervaOWLGraphWrapper graph = pair.getGraph();
    final EcoMapper mapper = pair.getMapper();
    Set<OWLClass> ecoClasses = graph.getAllOWLClasses();
    Map<OWLClass, String> codesForEcoClasses = mapper.getCodesForEcoClasses();
    List<JsonEvidenceInfo> relList = new ArrayList<JsonEvidenceInfo>();
    for (OWLClass ecoClass : ecoClasses) {
        if (ecoClass.isBuiltIn()) {
            continue;
        }
        JsonEvidenceInfo json = new JsonEvidenceInfo();
        json.id = curieHandler.getCuri(ecoClass);
        json.label = graph.getLabel(ecoClass);
        String code = codesForEcoClasses.get(ecoClass);
        if (code != null) {
            json.code = code;
        }
        relList.add(json);
    }
    return relList;
}

Example 5 with MinervaOWLGraphWrapper

use of org.geneontology.minerva.MinervaOWLGraphWrapper in project minerva by geneontology.

the class MolecularModelJsonRenderer method renderProperties.

public static Pair<List<JsonRelationInfo>, List<JsonRelationInfo>> renderProperties(MolecularModelManager<?> mmm, Set<OWLObjectProperty> importantRelations, CurieHandler curieHandler) throws OWLOntologyCreationException {
    /* [{
         *   id: {String}
         *   label: {String}
         *   relevant: {boolean} // flag to indicate if this is a relation to be used in the model
         *   ?color: {String} // TODO in the future?
         *   ?glyph: {String} // TODO in the future?
         * }]
         */
    // retrieve (or load) all ontologies
    // put in a new wrapper
    MinervaOWLGraphWrapper wrapper = new MinervaOWLGraphWrapper(mmm.getOntology());
    Collection<IRI> imports = mmm.getImports();
    OWLOntologyManager manager = wrapper.getManager();
    for (IRI iri : imports) {
        OWLOntology ontology = manager.getOntology(iri);
        if (ontology == null) {
            // only try to load it, if it isn't already loaded
            try {
                ontology = manager.loadOntology(iri);
            } catch (OWLOntologyDocumentAlreadyExistsException e) {
                IRI existing = e.getOntologyDocumentIRI();
                ontology = manager.getOntology(existing);
            } catch (OWLOntologyAlreadyExistsException e) {
                OWLOntologyID id = e.getOntologyID();
                ontology = manager.getOntology(id);
            }
        }
        if (ontology == null) {
            LOG.warn("Could not find an ontology for IRI: " + iri);
        } else {
            wrapper.addSupportOntology(ontology);
        }
    }
    // get all properties from all loaded ontologies
    Set<OWLObjectProperty> properties = new HashSet<OWLObjectProperty>();
    Set<OWLDataProperty> dataProperties = new HashSet<OWLDataProperty>();
    Set<OWLOntology> allOntologies = wrapper.getAllOntologies();
    for (OWLOntology o : allOntologies) {
        properties.addAll(o.getObjectPropertiesInSignature());
        dataProperties.addAll(o.getDataPropertiesInSignature());
    }
    // sort properties
    List<OWLObjectProperty> propertyList = new ArrayList<OWLObjectProperty>(properties);
    List<OWLDataProperty> dataPropertyList = new ArrayList<OWLDataProperty>(dataProperties);
    Collections.sort(propertyList);
    Collections.sort(dataPropertyList);
    // retrieve id and label for all properties
    List<JsonRelationInfo> relList = new ArrayList<JsonRelationInfo>();
    for (OWLObjectProperty p : propertyList) {
        if (p.isBuiltIn()) {
            // skip owl:topObjectProperty
            continue;
        }
        JsonRelationInfo json = new JsonRelationInfo();
        json.id = curieHandler.getCuri(p);
        json.label = wrapper.getLabel(p);
        if (importantRelations != null && (importantRelations.contains(p))) {
            json.relevant = true;
        } else {
            json.relevant = false;
        }
        relList.add(json);
    }
    // retrieve id and label for all data properties
    List<JsonRelationInfo> dataList = new ArrayList<JsonRelationInfo>();
    for (OWLDataProperty p : dataPropertyList) {
        if (p.isBuiltIn()) {
            continue;
        }
        JsonRelationInfo json = new JsonRelationInfo();
        json.id = curieHandler.getCuri(p);
        json.label = wrapper.getLabel(p);
        dataList.add(json);
    }
    IOUtils.closeQuietly(wrapper);
    return Pair.of(relList, dataList);
}