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

Example 11 with MappedCurieHandler

use of org.geneontology.minerva.curie.MappedCurieHandler 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 12 with MappedCurieHandler

use of org.geneontology.minerva.curie.MappedCurieHandler 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);
}

Example 13 with MappedCurieHandler

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

the class TaxonHandlerTest 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";
    curieHandler = new MappedCurieHandler();
    String valid_model_folder = "src/test/resources/models/should_pass/";
    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"));
    UndoAwareMolecularModelManager models = new UndoAwareMolecularModelManager(tbox_ontology, curieHandler, modelIdPrefix, inputDB, null, 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);
    taxonHandler = new TaxonHandler(models);
    resourceConfig = resourceConfig.registerInstances(taxonHandler);
    // 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();
}

Example 14 with MappedCurieHandler

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

the class StartUpTool method main.

public static void main(String[] args) throws Exception {
    Opts opts = new Opts(args);
    MinervaStartUpConfig conf = new MinervaStartUpConfig();
    while (opts.hasArgs()) {
        if (opts.nextEq("-g|--graph")) {
            conf.ontology = opts.nextOpt();
        } else if (opts.nextEq("-c|--catalog")) {
            conf.catalog = opts.nextOpt();
        } else if (opts.nextEq("-f|--journal-file")) {
            conf.journalFile = opts.nextOpt();
        } else if (opts.nextEq("--export-folder")) {
            conf.exportFolder = opts.nextOpt();
        } else if (opts.nextEq("--model-id-prefix")) {
            conf.modelIdPrefix = opts.nextOpt();
        } else if (opts.nextEq("--model-id-curie")) {
            conf.modelIdcurie = opts.nextOpt();
        } else if (opts.nextEq("-p|--protein-folder")) {
            System.err.println("specific protein ontologies are no longer supported");
            System.exit(-1);
        } else if (opts.nextEq("--gaf-folder")) {
            System.err.println("--gaf-folder is not longer supported");
            System.exit(-1);
        } else if (opts.nextEq("--context-prefix")) {
            conf.contextPrefix = opts.nextOpt();
        } else if (opts.nextEq("--port")) {
            conf.port = Integer.parseInt(opts.nextOpt());
        } else if (opts.nextEq("-i|--import|--additional-import")) {
            System.err.println("-i|--import|--additional-import is no longer supported, all imports are expected to be in the source ontology '-g|--graph'");
            System.exit(-1);
        } else if (opts.nextEq("--obsolete-import")) {
            System.err.println("--obsolete-import is no longer supported");
            System.exit(-1);
        } else if (opts.nextEq("--set-relevant-relations")) {
            System.err.println("--set-relevant-relations is no longer supported, use '--set-important-relation-parent' instead");
            System.exit(-1);
        } else if (opts.nextEq("--add-relevant-relations")) {
            System.err.println("--add-relevant-relations is no longer supported, use '--set-important-relation-parent' instead");
            System.exit(-1);
        } else if (opts.nextEq("--add-relevant-relation")) {
            System.err.println("--add-relevant-relation is no longer supported, use '--set-important-relation-parent' instead");
            System.exit(-1);
        } else if (opts.nextEq("--set-important-relation-parent")) {
            conf.importantRelationParent = opts.nextOpt();
        } else if (opts.nextEq("--skip-class-id-validation")) {
            conf.checkLiteralIds = false;
        } else if (opts.nextEq("--golr-cache-size")) {
            String sizeString = opts.nextOpt();
            conf.golrCacheSize = Integer.parseInt(sizeString);
        } else // --golr-labels http://noctua-golr.berkeleybop.org/
        if (opts.nextEq("--golr-labels")) {
            conf.golrUrl = opts.nextOpt();
        } else if (opts.nextEq("--monarch-labels")) {
            conf.monarchUrl = opts.nextOpt();
        } else if (opts.nextEq("--golr-seed")) {
            conf.golrSeedUrl = opts.nextOpt();
        } else if (opts.nextEq("--no-reasoning|--no-reasoner")) {
            conf.reasonerOpt = null;
        } else if (opts.nextEq("--slme-hermit")) {
            conf.reasonerOpt = "slme-hermit";
        } else if (opts.nextEq("--slme-elk")) {
            conf.reasonerOpt = "slme-elk";
        } else if (opts.nextEq("--elk")) {
            conf.reasonerOpt = "elk";
        } else if (opts.nextEq("--arachne")) {
            conf.reasonerOpt = "arachne";
        } else if (opts.nextEq("--use-request-logging|--request-logging")) {
            conf.useRequestLogging = true;
        } else if (opts.nextEq("--use-golr-url-logging|--golr-url-logging")) {
            conf.useGolrUrlLogging = true;
        } else if (opts.nextEq("--prefix-mappings")) {
            conf.prefixesFile = opts.nextOpt();
        } else if (opts.nextEq("--sparql-endpoint-timeout")) {
            conf.sparqlEndpointTimeout = Integer.parseInt(opts.nextOpt());
        } else if (opts.nextEq("--ontojournal")) {
            conf.pathToOntologyJournal = opts.nextOpt();
        } else {
            break;
        }
    }
    if (conf.pathToOntologyJournal == null) {
        System.err.println("No blazegraph journal containing tbox ontology provided. exit.");
        System.exit(-1);
    }
    if (conf.ontology == null) {
        System.err.println("No ontology graph available");
        System.exit(-1);
    }
    if (conf.journalFile == null) {
        System.err.println("No journal file available");
        System.exit(-1);
    }
    // if (conf.golrUrl == null) {
    // conf.golrUrl = "http://noctua-golr.berkeleybop.org/";
    // System.err.println("No GOLR service configured.  This is required, please add e.g. --golr-labels http://noctua-golr.berkeleybop.org/ to start up parameters ");
    // //System.exit(-1);
    // }
    conf.contextString = "/";
    if (conf.contextPrefix != null) {
        conf.contextString = "/" + conf.contextPrefix;
    }
    // set curie handler
    final CurieMappings mappings;
    if (conf.prefixesFile != null) {
        mappings = DefaultCurieHandler.loadMappingsFromFile(new File(conf.prefixesFile));
    } else {
        mappings = DefaultCurieHandler.loadDefaultMappings();
    }
    CurieMappings localMappings = new CurieMappings.SimpleCurieMappings(Collections.singletonMap(conf.modelIdcurie, conf.modelIdPrefix));
    conf.curieHandler = new MappedCurieHandler(mappings, localMappings);
    // wrap the Golr service with a cache
    // get rid of external look ups altogether.
    // if (conf.golrUrl != null) {
    // conf.lookupService = new GolrExternalLookupService(conf.golrUrl, conf.curieHandler, conf.useGolrUrlLogging);
    // LOGGER.info("Setting up Golr cache with size: "+conf.golrCacheSize+" duration: "+
    // conf.golrCacheDuration+" "+conf.golrCacheDurationUnit+
    // " use url logging: "+conf.useGolrUrlLogging);
    // conf.lookupService = new CachingExternalLookupService(conf.lookupService, conf.golrCacheSize, conf.golrCacheDuration, conf.golrCacheDurationUnit);
    // }
    // if (conf.monarchUrl != null) {
    // conf.lookupService = new MonarchExternalLookupService(conf.monarchUrl, conf.curieHandler, conf.useGolrUrlLogging);
    // LOGGER.info("Setting up Monarch Golr cache with size: "+conf.golrCacheSize+" duration: "+
    // conf.golrCacheDuration+" "+conf.golrCacheDurationUnit+
    // " use url logging: "+conf.useGolrUrlLogging);
    // conf.lookupService = new CachingExternalLookupService(conf.lookupService, conf.golrCacheSize, conf.golrCacheDuration, conf.golrCacheDurationUnit);
    // }
    // TODO maybe make these command line parameters
    URL shex_schema_url = new URL(conf.shexFileUrl);
    File shex_schema_file = new File("./target/shex-schema.shex");
    org.apache.commons.io.FileUtils.copyURLToFile(shex_schema_url, shex_schema_file);
    URL shex_map_url = new URL(conf.goshapemapFileUrl);
    File shex_map_file = new File("./target/go-cam-shapes.shapeMap");
    org.apache.commons.io.FileUtils.copyURLToFile(shex_map_url, shex_map_file);
    // reasoner set in next phase after ontologies loaded
    conf.shex = new MinervaShexValidator(shex_schema_file, shex_map_file, conf.curieHandler, null);
    Server server = startUp(conf);
    try {
        server.join();
    } finally {
        server.stop();
        server.destroy();
    }
}

Example 15 with MappedCurieHandler

use of org.geneontology.minerva.curie.MappedCurieHandler 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;
}