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

Example 16 with MappedCurieHandler

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

the class GoCamModelTest method testRootTypesForComplements.

@Test
public void testRootTypesForComplements() throws Exception {
    String ontologyJournalFile = "/tmp/test-go-lego-blazegraph-complements.jnl";
    OWLOntologyManager man = OWLManager.createOWLOntologyManager();
    OWLOntology tboxOntology = man.loadOntologyFromOntologyDocument(new File("src/test/resources/go-basic.obo"));
    CurieHandler curieHandler = new MappedCurieHandler();
    String inputDB = "/tmp/test-blazegraph-models-complements.jnl";
    UndoAwareMolecularModelManager m3 = null;
    m3 = new UndoAwareMolecularModelManager(tboxOntology, curieHandler, "gomodel", inputDB, null, ontologyJournalFile, true);
    m3.importModelToDatabase(new File("src/test/resources/test-complement-roots.ttl"), true);
    ModelContainer mc = m3.getModel(IRI.create("http://model.geneontology.org/61f3310500000003"));
    OWLOntology gocam_via_mc = mc.getAboxOntology();
    GoCamModel g = new GoCamModel(gocam_via_mc, m3);
    assertTrue("Can get roots for classes and complements", g.ind_types.get(man.getOWLDataFactory().getOWLNamedIndividual(IRI.create("http://model.geneontology.org/61f3310500000003/61f3310500000004"))).contains("http://purl.obolibrary.org/obo/GO_0008150"));
    assertTrue("Can get roots for classes and complements", g.ind_types.get(man.getOWLDataFactory().getOWLNamedIndividual(IRI.create("http://model.geneontology.org/61f3310500000003/61f3310500000005"))).contains("http://purl.obolibrary.org/obo/GO_0008150"));
    m3.getGolego_repo().dispose();
}

Example 17 with MappedCurieHandler

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

the class GoCamModelTest method testGoModelStats.

@Test
public void testGoModelStats() throws Exception {
    OWLOntologyManager man = OWLManager.createOWLOntologyManager();
    OWLOntology tbox_ontology = man.loadOntology(IRI.create("http://purl.obolibrary.org/obo/go/extensions/go-lego.owl"));
    CurieHandler curieHandler = new MappedCurieHandler();
    String inputDB = "/tmp/test-blazegraph-models.jnl";
    // load it into a journal and launch an m3
    UndoAwareMolecularModelManager m3 = null;
    File f = new File(gocam_dir);
    if (f.isDirectory()) {
        // remove anything that existed from previous runs
        File bgdb = new File(inputDB);
        if (bgdb.exists()) {
            bgdb.delete();
        }
        // set it up with empty db
        m3 = new UndoAwareMolecularModelManager(tbox_ontology, curieHandler, "gomodel", inputDB, null, ontology_journal_file, true);
        onto_repo = m3.getGolego_repo();
        // load the db
        for (File file : f.listFiles()) {
            if (file.getName().endsWith("ttl")) {
                m3.importModelToDatabase(file, true);
            }
        }
    }
    // read it back out and check on stats
    for (IRI modelIRI : m3.getAvailableModelIds()) {
        ModelContainer mc = m3.getModel(modelIRI);
        OWLOntology gocam_via_mc = mc.getAboxOntology();
        GoCamModel g = new GoCamModel(gocam_via_mc, m3);
        // testing for an issue with the OWL blazegraph loader
        assertFalse("title not read out of M3 retrieved model " + modelIRI, (g.getTitle() == null));
        // these reactions are not counted as activities, but causal relations coming from them are counted.
        if (modelIRI.toString().contains("R-HSA-5654719")) {
            // SHC-mediated cascade:FGFR4
            assertTrue("wrong n activities " + g.getStats().n_activity_units, g.getStats().n_activity_units == 4);
            assertTrue("wrong n complete activities " + g.getStats().n_complete_activity_units, g.getStats().n_complete_activity_units == 2);
            assertTrue("wrong n unenabled activities " + g.getStats().n_no_enabler, g.getStats().n_no_enabler == 2);
            assertTrue("wrong n causal relations " + g.getStats().n_causal_in_relation_assertions, g.getStats().n_causal_in_relation_assertions == 6);
        } else if (modelIRI.toString().contains("R-HSA-201688")) {
            // WNT mediated activation of DVL
            assertTrue("wrong n activities " + g.getStats().n_activity_units, g.getStats().n_activity_units == 4);
            assertTrue("wrong n complete activities " + g.getStats().n_complete_activity_units, g.getStats().n_complete_activity_units == 3);
            assertTrue("wrong n unenabled activities " + g.getStats().n_no_enabler, g.getStats().n_no_enabler == 1);
            assertTrue("wrong n causal relations " + g.getStats().n_causal_in_relation_assertions, g.getStats().n_causal_in_relation_assertions == 3);
        } else if (modelIRI.toString().contains("R-HSA-5654733")) {
            // Negative regulation of FGFR4 signaling
            assertTrue("wrong n activities " + g.getStats().n_activity_units, g.getStats().n_activity_units == 3);
            assertTrue("wrong n complete activities " + g.getStats().n_complete_activity_units, g.getStats().n_complete_activity_units == 2);
            assertTrue("wrong n unenabled activities " + g.getStats().n_no_enabler, g.getStats().n_no_enabler == 1);
            assertTrue("wrong n causal relations " + g.getStats().n_causal_in_relation_assertions, g.getStats().n_causal_in_relation_assertions == 3);
        }
    }
}

Example 18 with MappedCurieHandler

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

the class BlazegraphMolecularModelManagerTest method createBlazegraphMolecularModelManager.

/**
 * @return the instance of BlazegraphMolecularModelManager
 * @throws Exception
 */
private BlazegraphMolecularModelManager<Void> createBlazegraphMolecularModelManager() throws Exception {
    /* A path of the temporary journal file for Blazegraph storage system */
    String journalPath = folder.newFile().getAbsolutePath();
    /* A root path of the temporary directory */
    String tempRootPath = folder.getRoot().getAbsolutePath();
    /* Delete the journal file if exists */
    FileUtils.deleteQuietly(new File(journalPath));
    OWLOntology tbox = OWLManager.createOWLOntologyManager().loadOntology(IRI.create(new File("src/test/resources/mmg/basic-tbox.omn")));
    Map<String, String> prefixes = new HashMap<>();
    prefixes.put("gomodel", "http://model.geneontology.org/");
    prefixes.put("ex", "http://example.org/");
    prefixes.put("GO", "http://purl.obolibrary.org/obo/GO_");
    CurieHandler curieHandler = new MappedCurieHandler(prefixes);
    BlazegraphMolecularModelManager<Void> m3 = new BlazegraphMolecularModelManager<>(tbox, curieHandler, "http://model.geneontology.org/", journalPath, tempRootPath, go_lego_journal_file, true);
    return m3;
}