Issue #57 - Fixed server startup issue. Cleaned-up KnowledgeBaseModule.

owlsim-services/src/main/java/org/monarchinitiative/owlsim/services/OwlSimServiceApplication.java

@@ -15,37 +15,34 @@
  */
 package org.monarchinitiative.owlsim.services;
 
-import java.util.EnumSet;
-import java.util.Set;
-
-import javax.servlet.DispatcherType;
-import javax.servlet.FilterRegistration;
-
-import org.apache.log4j.Logger;
-import org.eclipse.jetty.servlets.CrossOriginFilter;
-import org.monarchinitiative.owlsim.services.configuration.ApplicationConfiguration;
-import org.monarchinitiative.owlsim.services.modules.EnrichmentMapModule;
-import org.monarchinitiative.owlsim.services.modules.KnowledgeBaseModule;
-import org.monarchinitiative.owlsim.services.modules.MatcherMapModule;
-import org.semanticweb.owlapi.OWLAPIParsersModule;
-import org.semanticweb.owlapi.OWLAPIServiceLoaderModule;
-
 import com.fasterxml.jackson.annotation.JsonInclude;
 import com.fasterxml.jackson.databind.SerializationFeature;
 import com.google.common.reflect.ClassPath;
 import com.google.common.reflect.ClassPath.ClassInfo;
 import com.google.inject.Guice;
 import com.google.inject.Injector;
-
 import io.dropwizard.Application;
 import io.dropwizard.assets.AssetsBundle;
 import io.dropwizard.setup.Bootstrap;
 import io.dropwizard.setup.Environment;
 import io.swagger.jaxrs.config.BeanConfig;
 import io.swagger.jaxrs.listing.ApiListingResource;
+import org.apache.log4j.Logger;
+import org.eclipse.jetty.servlets.CrossOriginFilter;
+import org.monarchinitiative.owlsim.services.configuration.ApplicationConfiguration;
+import org.monarchinitiative.owlsim.services.modules.EnrichmentMapModule;
+import org.monarchinitiative.owlsim.services.modules.KnowledgeBaseModule;
+import org.monarchinitiative.owlsim.services.modules.MatcherMapModule;
+import org.semanticweb.owlapi.OWLAPIParsersModule;
+import org.semanticweb.owlapi.OWLAPIServiceLoaderModule;
 import uk.ac.manchester.cs.owl.owlapi.OWLAPIImplModule;
 import uk.ac.manchester.cs.owl.owlapi.concurrent.Concurrency;
 
+import javax.servlet.DispatcherType;
+import javax.servlet.FilterRegistration;
+import java.util.EnumSet;
+import java.util.Set;
+
 public class OwlSimServiceApplication extends Application<ApplicationConfiguration> {
 
 	private Logger LOG = Logger.getLogger(OwlSimServiceApplication.class);
@@ -146,7 +143,7 @@ public void run(ApplicationConfiguration configuration, Environment environment)
 				new KnowledgeBaseModule(configuration.getOntologyUris(), configuration.getOntologyDataUris(),
 						configuration.getDataTsvs(), configuration.getCuries()),
 				new EnrichmentMapModule(), new MatcherMapModule());
-		LOG.info("BINDINGS =" + i.getAllBindings());
+		//removed binding info as this caused things to explode. Wasn't helpful.
 		// Add resources
 		Set<ClassInfo> resourceClasses = ClassPath.from(getClass().getClassLoader())
 				.getTopLevelClasses("org.monarchinitiative.owlsim.services.resources");

owlsim-services/src/main/java/org/monarchinitiative/owlsim/services/modules/KnowledgeBaseModule.java

@@ -1,57 +1,28 @@
 package org.monarchinitiative.owlsim.services.modules;
 
-import com.google.common.collect.ImmutableCollection;
-import com.google.common.collect.ImmutableMap;
-import com.google.common.collect.ImmutableSet;
 import com.google.inject.AbstractModule;
 import com.google.inject.Provides;
 import com.google.inject.Singleton;
-import org.apache.commons.validator.routines.UrlValidator;
-import org.jboss.logging.Logger;
+import org.apache.log4j.Logger;
 import org.monarchinitiative.owlsim.compute.classmatch.ClassMatcher;
 import org.monarchinitiative.owlsim.compute.enrich.impl.HypergeometricEnrichmentEngine;
 import org.monarchinitiative.owlsim.compute.matcher.impl.BayesianNetworkProfileMatcher;
 import org.monarchinitiative.owlsim.compute.mica.MostInformativeCommonAncestorCalculator;
 import org.monarchinitiative.owlsim.compute.mica.impl.MostInformativeCommonAncestorCalculatorImpl;
+import org.monarchinitiative.owlsim.io.OwlKnowledgeBase;
 import org.monarchinitiative.owlsim.kb.BMKnowledgeBase;
-import org.monarchinitiative.owlsim.kb.impl.BMKnowledgeBaseOWLAPIImpl;
-import org.monarchinitiative.owlsim.services.modules.bindings.IndicatesDataTsvs;
-import org.monarchinitiative.owlsim.services.modules.bindings.IndicatesOwlDataOntologies;
-import org.monarchinitiative.owlsim.services.modules.bindings.IndicatesOwlOntologies;
-import org.prefixcommons.CurieUtil;
-import org.semanticweb.elk.owlapi.ElkReasonerFactory;
-import org.semanticweb.owlapi.model.IRI;
-import org.semanticweb.owlapi.model.OWLOntology;
-import org.semanticweb.owlapi.model.OWLOntologyCreationException;
-import org.semanticweb.owlapi.model.OWLOntologyManager;
-import org.semanticweb.owlapi.reasoner.OWLReasonerFactory;
 
-import java.io.*;
 import java.util.Collection;
 import java.util.Map;
 import java.util.Set;
-import java.util.zip.GZIPInputStream;
 
-/**
- * TODO: Uncomment the OwlKnowledgeBase code and remove unecessary code once happy.
- */
 public class KnowledgeBaseModule extends AbstractModule {
 
 	Logger logger = Logger.getLogger(KnowledgeBaseModule.class);
 
-	private final ImmutableCollection<String> ontologyUris;
-	private final ImmutableCollection<String> ontologyDataUris;
-	private final ImmutableCollection<String> dataTsvs;
-	private final ImmutableMap<String, String> curies;
-	private final UrlValidator urlValdiator = UrlValidator.getInstance();
-
-//	private final BMKnowledgeBase bmKnowledgeBase;
+	private final BMKnowledgeBase bmKnowledgeBase;
 
 	public KnowledgeBaseModule(Collection<String> ontologyUris, Collection<String> ontologyDataUris, Set<String> dataTsvs, Map<String, String> curies) {
-		this.ontologyUris = new ImmutableSet.Builder<String>().addAll(ontologyUris).build();
-		this.ontologyDataUris = new ImmutableSet.Builder<String>().addAll(ontologyDataUris).build();
-		this.dataTsvs = new ImmutableSet.Builder<String>().addAll(dataTsvs).build();
-		this.curies = new ImmutableMap.Builder<String, String>().putAll(curies).build();
 
 		logger.info("Loading ontologyUris:");
 		ontologyUris.forEach(logger::info);
@@ -62,91 +33,28 @@ public KnowledgeBaseModule(Collection<String> ontologyUris, Collection<String> o
 		logger.info("Loading curies:");
 		curies.entrySet().forEach(logger::info);
 
-//		//The OwlKnowledgeBase.Loader uses the ELKReasonerFactory and Concurrency.CONCURRENT as defaults.
-//		this.bmKnowledgeBase = OwlKnowledgeBase.loader()
-//				.loadOntologies(ontologyUris)
-//				.loadDataFromOntologies(ontologyDataUris)
-//				.loadDataFromTsv(dataTsvs)
-//				.loadCuries(curies)
-//				.createKnowledgeBase();
-//
-//		logger.info("Created BMKnowledgebase");
+		//The OwlKnowledgeBase.Loader uses the ELKReasonerFactory and Concurrency.CONCURRENT as defaults.
+		this.bmKnowledgeBase = OwlKnowledgeBase.loader()
+				.loadOntologies(ontologyUris)
+				.loadDataFromOntologies(ontologyDataUris)
+				.loadDataFromTsv(dataTsvs)
+				.loadCuries(curies)
+				.createKnowledgeBase();
+
+		logger.info("Created BMKnowledgebase");
 	}
 
 	@Override
 	protected void configure() {
-		bind(BMKnowledgeBase.class).to(BMKnowledgeBaseOWLAPIImpl.class).in(Singleton.class);
-		bind(OWLReasonerFactory.class).to(ElkReasonerFactory.class);
-		bind(CurieUtil.class).toInstance(new CurieUtil(curies));
-
-		// bind(OWLOntologyManager.class).to(OWLOntologyManagerImpl.class);
-		// bind(ReadWriteLock.class).to(NoOpReadWriteLock.class);
-		// bind(OWLDataFactory.class).to(OWLDataFactoryImpl.class);
-		// bind(OWLOntologyManager.class).toInstance(OWLManager.createOWLOntologyManager());
 	}
 
-//	@Provides
-//	BMKnowledgeBase provideBMKnowledgeBaseOWLAPIImpl() {
-//		return bmKnowledgeBase;
-//	}
-
 	@Provides
-	BMKnowledgeBaseOWLAPIImpl provideBMKnowledgeBaseOWLAPIImpl(@IndicatesOwlOntologies OWLOntology owlOntology,
-			@IndicatesOwlDataOntologies OWLOntology owlDataOntology, OWLReasonerFactory rf, CurieUtil curieUtil) {
-		return new BMKnowledgeBaseOWLAPIImpl(owlOntology,owlDataOntology, rf, curieUtil);
-	}
-
-	OWLOntology loadOntology(OWLOntologyManager manager, String uri) throws OWLOntologyCreationException {
-		if (urlValdiator.isValid(uri)) {
-			return manager.loadOntology(IRI.create(uri));
-		} else {
-			File file = new File(uri);
-			return manager.loadOntologyFromOntologyDocument(file);
-		}
-	}
-
-	OWLOntology mergeOntologies(OWLOntologyManager manager, Collection<String> uris)
-			throws OWLOntologyCreationException, FileNotFoundException, IOException {
-		OWLOntology ontology = manager.createOntology();
-		for (String uri : uris) {
-			OWLOntology loadedOntology;
-			if (uri.endsWith(".gz")) {
-				GZIPInputStream gis = new GZIPInputStream(new FileInputStream(uri));
-				BufferedReader bf = new BufferedReader(new InputStreamReader(gis, "UTF-8"));
-				loadedOntology = manager.loadOntologyFromOntologyDocument(gis);
-			} else {
-				loadedOntology = loadOntology(manager, uri);
-			}
-			manager.addAxioms(ontology, loadedOntology.getAxioms());
-		}
-		return ontology;
-	}
-
-	@Provides
-	@IndicatesOwlOntologies
-	@Singleton
-	OWLOntology getOwlOntologies(OWLOntologyManager manager)
-			throws OWLOntologyCreationException, FileNotFoundException, IOException {
-		return mergeOntologies(manager, ontologyUris);
-	}
-
-	@Provides
-	@IndicatesOwlDataOntologies
 	@Singleton
-	OWLOntology getOwlDataOntologies(OWLOntologyManager manager)
-			throws OWLOntologyCreationException, FileNotFoundException, IOException {
-		return mergeOntologies(manager, ontologyDataUris);
+	BMKnowledgeBase provideBMKnowledgeBaseOWLAPIImpl() {
+		return bmKnowledgeBase;
 	}
 
 	@Provides
-	@IndicatesDataTsvs
-	@Singleton
-	OWLOntology getDataTsvs(OWLOntologyManager manager)
-			throws OWLOntologyCreationException, FileNotFoundException, IOException {
-		return mergeOntologies(manager, dataTsvs);
-	}
-	
-	@Provides
 	MostInformativeCommonAncestorCalculator getMostInformativeCommonAncestorCalculator(BMKnowledgeBase knowledgeBase) {
         return new MostInformativeCommonAncestorCalculatorImpl(knowledgeBase);
 	}