Examples with ExternalLookupService org.geneontology.minerva.lookup.ExternalLookupService used on opensource projects

Example 1 with ExternalLookupService

use of org.geneontology.minerva.lookup.ExternalLookupService in project minerva by geneontology.

the class ARTHandlerTest method setUpBeforeClass.

/**
 * @throws java.lang.Exception
 */
@BeforeClass
public static void setUpBeforeClass() throws Exception {
    LOGGER.info("Setup shex.");
    File shex_schema_file = new File("src/test/resources/validate.shex");
    File shex_map_file = new File("src/test/resources/validate.shapemap");
    LOGGER.info("Set up molecular model manager - loading files into a journal");
    // set curie handler
    final CurieMappings localMappings = new CurieMappings.SimpleCurieMappings(Collections.singletonMap(modelIdcurie, modelIdPrefix));
    curieHandler = new MappedCurieHandler(DefaultCurieHandler.loadDefaultMappings(), localMappings);
    String inputDB = makeBlazegraphJournal(valid_model_folder);
    OWLOntologyManager ontman = OWLManager.createOWLOntologyManager();
    // empty tbox
    tbox_ontology = ontman.createOntology(IRI.create("http://example.org/dummy"));
    models = new UndoAwareMolecularModelManager(tbox_ontology, curieHandler, modelIdPrefix, inputDB, model_save, go_lego_journal_file, true);
    models.addTaxonMetadata();
    LOGGER.info("Setup Jetty config.");
    ResourceConfig resourceConfig = new ResourceConfig();
    resourceConfig.register(GsonMessageBodyHandler.class);
    resourceConfig.register(RequireJsonpFilter.class);
    MinervaShexValidator shex = new MinervaShexValidator(shex_schema_file, shex_map_file, curieHandler, models.getGolego_repo());
    shex.setActive(true);
    // setup the config for the startup tool.
    MinervaStartUpConfig conf = new MinervaStartUpConfig();
    conf.reasonerOpt = "arachne";
    conf.shex = shex;
    conf.port = 6800;
    conf.contextString = "/";
    InferenceProviderCreator ipc = StartUpTool.createInferenceProviderCreator(conf.reasonerOpt, models, conf.shex);
    ModelARTHandler artHandler = new ModelARTHandler(models, ipc);
    // set up a handler for testing with M3BatchRequest service
    handler = new JsonOrJsonpBatchHandler(models, "development", ipc, Collections.<OWLObjectProperty>emptySet(), (ExternalLookupService) null);
    resourceConfig = resourceConfig.registerInstances(artHandler);
    // setup jetty server port, buffers and context path
    server = new Server();
    // create connector with port and custom buffer sizes
    HttpConfiguration http_config = new HttpConfiguration();
    http_config.setRequestHeaderSize(conf.requestHeaderSize);
    ServerConnector connector = new ServerConnector(server, new HttpConnectionFactory(http_config));
    connector.setPort(conf.port);
    server.addConnector(connector);
    ServletContextHandler context = new ServletContextHandler(ServletContextHandler.SESSIONS);
    context.setContextPath(conf.contextString);
    server.setHandler(context);
    ServletHolder h = new ServletHolder(new ServletContainer(resourceConfig));
    context.addServlet(h, "/*");
    // start jetty server
    LOGGER.info("Start server on port: " + conf.port + " context: " + conf.contextString);
    server.start();
}

Example 2 with ExternalLookupService

use of org.geneontology.minerva.lookup.ExternalLookupService in project minerva by geneontology.

the class ModelEditTest method init.

static void init(ParserWrapper pw) throws OWLOntologyCreationException, IOException {
    // This includes only the needed terms for the test to pass
    final OWLOntology tbox = OWLManager.createOWLOntologyManager().loadOntology(IRI.create(new File("src/test/resources/edit-test/go-lego-empty.owl")));
    // 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);
    models = new UndoAwareMolecularModelManager(tbox, curieHandler, modelIdPrefix, folder.newFile().getAbsolutePath(), null, go_lego_journal_file, true);
    InferenceProviderCreator ipc = null;
    handler = new JsonOrJsonpBatchHandler(models, "development", ipc, Collections.<OWLObjectProperty>emptySet(), (ExternalLookupService) null);
}

Example 3 with ExternalLookupService

use of org.geneontology.minerva.lookup.ExternalLookupService in project minerva by geneontology.

the class ParallelModelReasonerTest method init.

static void init(ParserWrapper pw) throws OWLOntologyCreationException, IOException {
    // FIXME need more from go-lego
    final OWLOntology tbox = OWLManager.createOWLOntologyManager().loadOntology(IRI.create(new File("src/test/resources/go-lego-minimal.owl")));
    // 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);
    models = new UndoAwareMolecularModelManager(tbox, curieHandler, modelIdPrefix, folder.newFile().getAbsolutePath(), null, go_lego_journal_file, true);
    ipc = new CountingCachingInferenceProvider(false);
    handler = new JsonOrJsonpBatchHandler(models, "development", ipc, Collections.<OWLObjectProperty>emptySet(), (ExternalLookupService) null);
// models.setPathToOWLFiles("src/test/resources/reasoner-test");
}

Example 4 with ExternalLookupService

use of org.geneontology.minerva.lookup.ExternalLookupService in project minerva by geneontology.

the class ModelReasonerTest method init.

static void init() throws OWLOntologyCreationException, IOException {
    // FIXME need more from go-lego
    final OWLOntology tbox = OWLManager.createOWLOntologyManager().loadOntology(IRI.create(new File("src/test/resources/go-lego-minimal.owl")));
    // 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);
    models = new UndoAwareMolecularModelManager(tbox, curieHandler, modelIdPrefix, folder.newFile().getAbsolutePath(), null, go_lego_journal_file, true);
    InferenceProviderCreator ipc = CachingInferenceProviderCreatorImpl.createElk(false, null);
    handler = new JsonOrJsonpBatchHandler(models, "development", ipc, Collections.<OWLObjectProperty>emptySet(), (ExternalLookupService) null);
// models.setPathToOWLFiles("src/test/resources/reasoner-test");
}

Example 5 with ExternalLookupService

use of org.geneontology.minerva.lookup.ExternalLookupService in project minerva by geneontology.

the class ModelSearchHandlerTest method setUpBeforeClass.

/**
 * @throws java.lang.Exception
 */
@BeforeClass
public static void setUpBeforeClass() throws Exception {
    LOGGER.info("Set up molecular model manager - loading files into a journal");
    // set curie handler
    String modelIdPrefix = "http://model.geneontology.org/";
    String modelIdcurie = "gomodel";
    final CurieMappings localMappings = new CurieMappings.SimpleCurieMappings(Collections.singletonMap(modelIdcurie, modelIdPrefix));
    curieHandler = new MappedCurieHandler(DefaultCurieHandler.loadDefaultMappings(), localMappings);
    String valid_model_folder = "src/test/resources/models/should_pass/";
    String model_save = "src/test/resources/models/tmp/";
    String inputDB = makeBlazegraphJournal(valid_model_folder);
    // leave tbox empty for now
    OWLOntologyManager ontman = OWLManager.createOWLOntologyManager();
    tbox_ontology = ontman.createOntology(IRI.create("http://example.org/dummy"));
    models = new UndoAwareMolecularModelManager(tbox_ontology, curieHandler, modelIdPrefix, inputDB, model_save, go_lego_journal_file, true);
    models.addTaxonMetadata();
    LOGGER.info("Setup Jetty config.");
    // Configuration: Use an already existing handler instance
    // Configuration: Use custom JSON renderer (GSON)
    ResourceConfig resourceConfig = new ResourceConfig();
    resourceConfig.register(GsonMessageBodyHandler.class);
    resourceConfig.register(RequireJsonpFilter.class);
    ModelSearchHandler searchHandler = new ModelSearchHandler(models);
    resourceConfig = resourceConfig.registerInstances(searchHandler);
    // setup jetty server port, buffers and context path
    server = new Server();
    // create connector with port and custom buffer sizes
    HttpConfiguration http_config = new HttpConfiguration();
    int requestHeaderSize = 64 * 1024;
    int requestBufferSize = 128 * 1024;
    int port = 6800;
    String contextString = "/";
    http_config.setRequestHeaderSize(requestHeaderSize);
    ServerConnector connector = new ServerConnector(server, new HttpConnectionFactory(http_config));
    connector.setPort(port);
    server.addConnector(connector);
    ServletContextHandler context = new ServletContextHandler(ServletContextHandler.SESSIONS);
    context.setContextPath(contextString);
    server.setHandler(context);
    ServletHolder h = new ServletHolder(new ServletContainer(resourceConfig));
    context.addServlet(h, "/*");
    // start jetty server
    LOGGER.info("Start server on port: " + port + " context: " + contextString);
    server.start();
    // set up a handler for testing with M3BatchRequest service
    handler = new JsonOrJsonpBatchHandler(models, "development", null, Collections.<OWLObjectProperty>emptySet(), (ExternalLookupService) null);
}