[#24] first experiment

.gitignore

@@ -6,7 +6,7 @@ target/
 ./src/test/resources/catalog-v001.xml
 *iml
 .idea
-/bin/
+**/bin/
 **/semantic.cache
 owlsim-services/js
 owlsim-services/python

owlsim-core/pom.xml

@@ -177,19 +177,19 @@
 			<version>0.7.7</version>
 		</dependency>
 		<dependency>
-			<groupId>org.apache.commons</groupId>
-			<artifactId>commons-math3</artifactId>
-			<version>3.3</version>
-		</dependency>
-		<dependency>
 		  <groupId>commons-validator</groupId>
 		  <artifactId>commons-validator</artifactId>
 		  <version>1.4.0</version>
 		</dependency>
 		<dependency>
 			<groupId>org.apache.commons</groupId>
 			<artifactId>commons-math3</artifactId>
-                        <version>3.6.1</version>
+			<version>3.6.1</version>
+		</dependency>
+		<dependency>
+		    <groupId>org.prefixcommons</groupId>
+		    <artifactId>curie-util</artifactId>
+		    <version>0.0.1</version>
 		</dependency>
 	</dependencies>
 

owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/enrich/EnrichmentMapModule.java

@@ -1,15 +1,12 @@
 package org.monarchinitiative.owlsim.compute.enrich;
 
 import java.io.IOException;
-import java.lang.reflect.Modifier;
 import java.util.HashMap;
 import java.util.Map;
 
 import org.apache.log4j.Logger;
 import org.monarchinitiative.owlsim.compute.enrich.impl.HypergeometricEnrichmentEngine;
-import org.monarchinitiative.owlsim.compute.matcher.impl.JaccardSimilarityProfileMatcher;
 
-import com.google.common.reflect.ClassPath;
 import com.google.inject.AbstractModule;
 import com.google.inject.Injector;
 import com.google.inject.Provides;

owlsim-core/src/main/java/org/monarchinitiative/owlsim/compute/matcher/impl/BayesianNetworkProfileMatcher.java

@@ -87,8 +87,8 @@
 
 	private Logger LOG = Logger.getLogger(BayesianNetworkProfileMatcher.class);
 
-	double falseNegativeRate = 0.01; // TODO - do not harcode
-	double falsePositiveRate = 0.01; // TODO - do not harcode
+	double falseNegativeRate = 0.01; // TODO - do not hardcode
+	double falsePositiveRate = 0.01; // TODO - do not hardcode
 
 	ConditionalProbabilityIndex cpi = null; // index of Pr(Node={on,off}|ParentsState)
 

owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/CURIEMapper.java

@@ -12,7 +12,7 @@
 
 	/**
 	 * @param iri
-	 * @return Shorform (aka ID, CURIE)
+	 * @return Short form (aka ID, CURIE)
 	 */
 	public String getShortForm(IRI iri);
 

owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/KnowledgeBaseModule.java

@@ -7,8 +7,8 @@
 import java.io.IOException;
 import java.io.InputStreamReader;
 import java.util.Collection;
+import java.util.Map;
 import java.util.Set;
-import java.util.concurrent.locks.ReadWriteLock;
 import java.util.zip.GZIPInputStream;
 
 import javax.inject.Singleton;
@@ -18,21 +18,16 @@
 import org.monarchinitiative.owlsim.kb.bindings.IndicatesOwlDataOntologies;
 import org.monarchinitiative.owlsim.kb.bindings.IndicatesOwlOntologies;
 import org.monarchinitiative.owlsim.kb.impl.BMKnowledgeBaseOWLAPIImpl;
+import org.prefixcommons.CurieUtil;
 import org.semanticweb.elk.owlapi.ElkReasonerFactory;
-import org.semanticweb.owlapi.apibinding.OWLManager;
-import org.semanticweb.owlapi.model.HasAxioms;
 import org.semanticweb.owlapi.model.IRI;
-import org.semanticweb.owlapi.model.OWLDataFactory;
 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 uk.ac.manchester.cs.owl.owlapi.OWLDataFactoryImpl;
-import uk.ac.manchester.cs.owl.owlapi.OWLOntologyManagerImpl;
-import uk.ac.manchester.cs.owl.owlapi.concurrent.NoOpReadWriteLock;
-
 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;
@@ -48,21 +43,25 @@
 	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();
 
 	public KnowledgeBaseModule(Collection<String> ontologyUris, 
 	        Collection<String> ontologyDataUris, 
-	        Set<String> dataTsvs) {
+	        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();
 	}
 
 	@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);