[#24] need some cleaning

owlsim-core/src/main/java/org/monarchinitiative/owlsim/kb/impl/BMKnowledgeBaseOWLAPIImpl.java

@@ -142,9 +142,9 @@ public BMKnowledgeBaseOWLAPIImpl(@IndicatesOwlOntologies OWLOntology owlOntology
     }
   }
 
-  public static BMKnowledgeBase create(OWLOntology owlOntology, OWLReasonerFactory rf) {
-    return new BMKnowledgeBaseOWLAPIImpl(owlOntology, null, rf,
-        new CurieUtil(new HashMap<String, String>())); // TODO CURIE support?
+  public static BMKnowledgeBase create(OWLOntology owlOntology, OWLReasonerFactory rf,
+      CurieUtil curieUtil) {
+    return new BMKnowledgeBaseOWLAPIImpl(owlOntology, null, rf, curieUtil);
   }
 
   /**
@@ -154,9 +154,8 @@ public static BMKnowledgeBase create(OWLOntology owlOntology, OWLReasonerFactory
    * @return
    */
   public static BMKnowledgeBase create(OWLOntology owlOntology, OWLOntology owlDataOntology,
-      OWLReasonerFactory rf) {
-    return new BMKnowledgeBaseOWLAPIImpl(owlOntology, owlDataOntology, rf,
-        new CurieUtil(new HashMap<String, String>())); // TODO CURIE support?
+      OWLReasonerFactory rf, CurieUtil curieUtil) {
+    return new BMKnowledgeBaseOWLAPIImpl(owlOntology, owlDataOntology, rf, curieUtil);
   }
 
 
@@ -174,9 +173,8 @@ public void setKbMetdata(KBMetadata kbMetdata) {
 
 
   private String getShortForm(IRI iri) {
-    LOG.info("getShortForm: " + iri.toString());
-    //return curieUtil.getCurie(iri.toString()).or(iri.toString());
-    return curieMapper.getShortForm(iri);
+    // TODO not great to have a mix of IRI and CURIE
+    return curieUtil.getCurie(iri.toString()).or(iri.toString());
   }
 
   private void populateLabelsFromOntology(LabelMapper labelMapper, OWLOntology ontology) {
@@ -393,8 +391,7 @@ private void setPropertyValues(OWLOntology ont, OWLNamedIndividual i) {
           if (obj instanceof OWLLiteral) {
             addPropertyValue(pvm, pid, ((OWLLiteral) obj).getLiteral());
           } else if (obj instanceof OWLNamedIndividual) {
-            addPropertyValue(pvm, pid,
-                getShortForm(((OWLNamedIndividual) obj).getIRI()));
+            addPropertyValue(pvm, pid, getShortForm(((OWLNamedIndividual) obj).getIRI()));
 
           }
 
@@ -404,8 +401,7 @@ private void setPropertyValues(OWLOntology ont, OWLNamedIndividual i) {
           if (obj instanceof OWLLiteral) {
             addPropertyValue(pvm, pid, ((OWLLiteral) obj).getLiteral());
           } else if (obj instanceof OWLNamedIndividual) {
-            addPropertyValue(pvm, pid,
-                getShortForm(((OWLNamedIndividual) obj).getIRI()));
+            addPropertyValue(pvm, pid, getShortForm(((OWLNamedIndividual) obj).getIRI()));
 
           }
 
@@ -995,12 +991,14 @@ protected String getIdentifier(OWLNamedObject obj) {
   }
 
   /**
-   * @param id
+   * @param id CURIE-style
    * @return OWLAPI Class object
    */
   protected OWLClass getOWLClass(String id) {
     Preconditions.checkNotNull(id);
-    return getOWLClass(IRI.create(id));
+    // TODO not great to have a mix of IRI and CURIE
+    String iri = curieUtil.getIri(id).or(id);
+    return getOWLClass(IRI.create(iri));
   }
 
   /**
@@ -1020,12 +1018,14 @@ protected OWLNamedIndividual getOWLNamedIndividual(IRI iri) {
   }
 
   /**
-   * @param id
+   * @param id CURIE-style
    * @return OWLAPI Class object
    */
   public OWLNamedIndividual getOWLNamedIndividual(String id) {
     Preconditions.checkNotNull(id);
-    return getOWLNamedIndividual(IRI.create(id));
+    // TODO not great to have a mix of IRI and CURIE
+    String iri = curieUtil.getIri(id).or(id);
+    return getOWLNamedIndividual(IRI.create(iri));
   }
 
   public Attribute getAttribute(String id) {

owlsim-core/src/test/java/org/monarchinitiative/owlsim/compute/eval/data/MakeBackgroundDataTest.java

@@ -1,5 +1,7 @@
 package org.monarchinitiative.owlsim.compute.eval.data;
 
+import java.util.HashMap;
+
 import org.apache.commons.math3.stat.descriptive.SummaryStatistics;
 import org.apache.log4j.Logger;
 import org.junit.Assert;
@@ -8,6 +10,7 @@
 import org.monarchinitiative.owlsim.eval.data.BackgroundData;
 import org.monarchinitiative.owlsim.kb.BMKnowledgeBase;
 import org.monarchinitiative.owlsim.kb.impl.BMKnowledgeBaseOWLAPIImpl;
+import org.prefixcommons.CurieUtil;
 import org.semanticweb.elk.owlapi.ElkReasonerFactory;
 import org.semanticweb.owlapi.model.OWLOntology;
 import org.semanticweb.owlapi.model.OWLOntologyCreationException;
@@ -59,7 +62,7 @@ private void create(int numClasses, int avgParents, int numIndividuals) throws O
 		OWLOntology ontology = 
 				RandomOntologyMaker.create(numClasses, avgParents).addRandomIndividuals(numIndividuals).getOntology();
 		OWLReasonerFactory rf = new ElkReasonerFactory();
-		kb = BMKnowledgeBaseOWLAPIImpl.create(ontology, rf);
+		kb = BMKnowledgeBaseOWLAPIImpl.create(ontology, rf, new CurieUtil(new HashMap<String, String>()));
 	}
 	
 }

owlsim-core/src/test/java/org/monarchinitiative/owlsim/compute/eval/data/SimulatedDataTest.java

@@ -1,5 +1,6 @@
 package org.monarchinitiative.owlsim.compute.eval.data;
 
+import java.util.HashMap;
 import java.util.HashSet;
 import java.util.Map;
 import java.util.Set;
@@ -24,6 +25,7 @@
 import org.monarchinitiative.owlsim.kb.impl.BMKnowledgeBaseOWLAPIImpl;
 import org.monarchinitiative.owlsim.kb.impl.CURIEMapperImpl;
 import org.monarchinitiative.owlsim.kb.impl.LabelMapperImpl;
+import org.prefixcommons.CurieUtil;
 import org.semanticweb.elk.owlapi.ElkReasonerFactory;
 import org.semanticweb.owlapi.model.OWLOntology;
 import org.semanticweb.owlapi.model.OWLOntologyCreationException;
@@ -420,7 +422,7 @@ private void create(int numClasses, int avgParents, int numIndividuals) throws O
 		OWLOntology ontology = 
 				RandomOntologyMaker.create(numClasses, avgParents).addRandomIndividuals(numIndividuals).getOntology();
 		OWLReasonerFactory rf = new ElkReasonerFactory();
-		kb = BMKnowledgeBaseOWLAPIImpl.create(ontology, rf);
+		kb = BMKnowledgeBaseOWLAPIImpl.create(ontology, rf, new CurieUtil(new HashMap<String, String>()));
 	}
 	
 }

owlsim-core/src/test/java/org/monarchinitiative/owlsim/compute/matcher/perf/AbstractProfileMatcherPerfIT.java

@@ -1,10 +1,13 @@
 package org.monarchinitiative.owlsim.compute.matcher.perf;
 
 import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
 
+import javax.inject.Inject;
+
 import org.apache.log4j.Logger;
 import org.junit.Test;
 import org.monarchinitiative.owlsim.compute.matcher.ProfileMatcher;
@@ -16,6 +19,7 @@
 import org.monarchinitiative.owlsim.model.match.MatchSet;
 import org.monarchinitiative.owlsim.model.match.ProfileQuery;
 import org.monarchinitiative.owlsim.model.match.impl.ProfileQueryImpl;
+import org.prefixcommons.CurieUtil;
 import org.semanticweb.elk.owlapi.ElkReasonerFactory;
 import org.semanticweb.owlapi.model.OWLOntology;
 import org.semanticweb.owlapi.model.OWLOntologyCreationException;
@@ -96,7 +100,7 @@ private void create(int numClasses, int avgParents, int numIndividuals) throws O
 		OWLOntology ontology = 
 				RandomOntologyMaker.create(numClasses, avgParents).addRandomIndividuals(numIndividuals).getOntology();
 		OWLReasonerFactory rf = new ElkReasonerFactory();
-		kb = BMKnowledgeBaseOWLAPIImpl.create(ontology, rf);
+		kb = BMKnowledgeBaseOWLAPIImpl.create(ontology, rf, new CurieUtil(new HashMap<String, String>()));
 
 		profileMatcher = createProfileMatcher(kb);
 	}

owlsim-core/src/test/java/org/monarchinitiative/owlsim/compute/mica/MICAStoreBench.java

@@ -1,11 +1,16 @@
 package org.monarchinitiative.owlsim.compute.mica;
 
+import java.util.HashMap;
+
+import javax.inject.Inject;
+
 import org.apache.log4j.Logger;
 import org.monarchinitiative.owlsim.compute.mica.impl.MICAStoreImpl;
 import org.monarchinitiative.owlsim.compute.mica.impl.NoRootException;
 import org.monarchinitiative.owlsim.eval.RandomOntologyMaker;
 import org.monarchinitiative.owlsim.kb.BMKnowledgeBase;
 import org.monarchinitiative.owlsim.kb.impl.BMKnowledgeBaseOWLAPIImpl;
+import org.prefixcommons.CurieUtil;
 import org.semanticweb.elk.owlapi.ElkReasonerFactory;
 import org.semanticweb.owlapi.model.OWLOntology;
 import org.semanticweb.owlapi.model.OWLOntologyCreationException;
@@ -28,7 +33,6 @@
 	private Logger LOG = Logger.getLogger(MICAStoreBench.class);
 	protected boolean writeToStdout = false;
 
-
 	public static class Benchmark1 {
 		void timeNanoTime(int reps) {
 			for (int i = 0; i < reps; i++) {
@@ -55,7 +59,7 @@ private void create(int numClasses, int avgParents, int numIndividuals) throws O
 		OWLOntology ontology = 
 				RandomOntologyMaker.create(numClasses, avgParents).addRandomIndividuals(numIndividuals).getOntology();
 		OWLReasonerFactory rf = new ElkReasonerFactory();
-		kb = BMKnowledgeBaseOWLAPIImpl.create(ontology, rf);
+		kb = BMKnowledgeBaseOWLAPIImpl.create(ontology, rf, new CurieUtil(new HashMap<String, String>()));
 		LOG.info("creating MICAStore");
 		MICAStore micaStore = new MICAStoreImpl(kb);
 		LOG.info("created MICAStore");

owlsim-core/src/test/java/org/monarchinitiative/owlsim/compute/mica/perf/MICAStorePerfIT.java

@@ -1,6 +1,7 @@
 package org.monarchinitiative.owlsim.compute.mica.perf;
 
 import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.List;
 
 import org.apache.log4j.Logger;
@@ -14,6 +15,7 @@
 import org.monarchinitiative.owlsim.io.JSONWriter;
 import org.monarchinitiative.owlsim.kb.BMKnowledgeBase;
 import org.monarchinitiative.owlsim.kb.impl.BMKnowledgeBaseOWLAPIImpl;
+import org.prefixcommons.CurieUtil;
 import org.semanticweb.elk.owlapi.ElkReasonerFactory;
 import org.semanticweb.owlapi.model.OWLOntology;
 import org.semanticweb.owlapi.model.OWLOntologyCreationException;
@@ -82,7 +84,7 @@ private MICARun create(int numClasses, int avgParents, int numIndividuals) throw
 		OWLOntology ontology = 
 				RandomOntologyMaker.create(numClasses, avgParents).addRandomIndividuals(numIndividuals).getOntology();
 		OWLReasonerFactory rf = new ElkReasonerFactory();
-		kb = BMKnowledgeBaseOWLAPIImpl.create(ontology, rf);
+		kb = BMKnowledgeBaseOWLAPIImpl.create(ontology, rf, new CurieUtil(new HashMap<String, String>()));
 		kbsc = new KBStatsCalculator(kb);
 		LOG.info("creating MICAStore");
 		long t1 = System.currentTimeMillis();

owlsim-core/src/test/java/org/monarchinitiative/owlsim/compute/stats/CoAnnotationStatsTest.java

@@ -1,11 +1,14 @@
 package org.monarchinitiative.owlsim.compute.stats;
 
+import java.util.HashMap;
+
 import org.apache.log4j.Logger;
 import org.junit.Test;
 import org.monarchinitiative.owlsim.compute.mica.impl.NoRootException;
 import org.monarchinitiative.owlsim.eval.RandomOntologyMaker;
 import org.monarchinitiative.owlsim.kb.BMKnowledgeBase;
 import org.monarchinitiative.owlsim.kb.impl.BMKnowledgeBaseOWLAPIImpl;
+import org.prefixcommons.CurieUtil;
 import org.semanticweb.elk.owlapi.ElkReasonerFactory;
 import org.semanticweb.owlapi.model.OWLOntology;
 import org.semanticweb.owlapi.model.OWLOntologyCreationException;
@@ -50,7 +53,7 @@ private void create(int numClasses, int avgParents, int numIndividuals,
 				.addRandomIndividuals(numIndividuals, avgClassesPerIndividual)
 				.getOntology();
 		OWLReasonerFactory rf = new ElkReasonerFactory();
-		kb = BMKnowledgeBaseOWLAPIImpl.create(ontology, rf);
+		kb = BMKnowledgeBaseOWLAPIImpl.create(ontology, rf, new CurieUtil(new HashMap<String, String>()));
 		LOG.info("Knowledge base ready ...");
 	}
 

owlsim-core/src/test/java/org/monarchinitiative/owlsim/compute/stats/ICDistributionTest.java

@@ -1,6 +1,7 @@
 package org.monarchinitiative.owlsim.compute.stats;
 
 import java.util.Arrays;
+import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Random;
@@ -9,11 +10,11 @@
 import org.apache.commons.math3.stat.descriptive.DescriptiveStatistics;
 import org.apache.log4j.Logger;
 import org.junit.Assert;
-import org.junit.Test;
 import org.monarchinitiative.owlsim.compute.mica.impl.NoRootException;
 import org.monarchinitiative.owlsim.eval.RandomOntologyMaker;
 import org.monarchinitiative.owlsim.kb.BMKnowledgeBase;
 import org.monarchinitiative.owlsim.kb.impl.BMKnowledgeBaseOWLAPIImpl;
+import org.prefixcommons.CurieUtil;
 import org.semanticweb.elk.owlapi.ElkReasonerFactory;
 import org.semanticweb.owlapi.model.OWLOntology;
 import org.semanticweb.owlapi.model.OWLOntologyCreationException;
@@ -241,7 +242,7 @@ private void create(int numClasses, int avgParents, int numIndividuals, int avgC
 		this.ontology = 
 				RandomOntologyMaker.create(numClasses, avgParents).addRandomIndividuals(numIndividuals, avgClassesPerIndividual).getOntology();
 		OWLReasonerFactory rf = new ElkReasonerFactory();
-		kb = BMKnowledgeBaseOWLAPIImpl.create(ontology, rf);
+		kb = BMKnowledgeBaseOWLAPIImpl.create(ontology, rf, new CurieUtil(new HashMap<String, String>()));
 		icc = new ICStatsCalculator(kb);
 		LOG.info("creating ICStoreSummary");
 		icc.calculateICSummary();

owlsim-core/src/test/java/org/monarchinitiative/owlsim/compute/stats/ICStorePerfTest.java

@@ -1,6 +1,7 @@
 package org.monarchinitiative.owlsim.compute.stats;
 
 import java.util.ArrayList;
+import java.util.HashMap;
 import java.util.HashSet;
 import java.util.List;
 import java.util.Set;
@@ -12,6 +13,7 @@
 import org.monarchinitiative.owlsim.io.JSONWriter;
 import org.monarchinitiative.owlsim.kb.BMKnowledgeBase;
 import org.monarchinitiative.owlsim.kb.impl.BMKnowledgeBaseOWLAPIImpl;
+import org.prefixcommons.CurieUtil;
 import org.semanticweb.elk.owlapi.ElkReasonerFactory;
 import org.semanticweb.owlapi.model.OWLOntology;
 import org.semanticweb.owlapi.model.OWLOntologyCreationException;
@@ -83,7 +85,7 @@ private ICRun create(int numClasses, int avgParents, int numIndividuals, int avg
 				RandomOntologyMaker.create(numClasses, avgParents).addRandomIndividuals(numIndividuals, avgClassesPerIndividual).getOntology();
 
 		OWLReasonerFactory rf = new ElkReasonerFactory();
-		kb = BMKnowledgeBaseOWLAPIImpl.create(ontology, rf);
+		kb = BMKnowledgeBaseOWLAPIImpl.create(ontology, rf, new CurieUtil(new HashMap<String, String>()));
 		icc = new ICStatsCalculator(kb);
 		LOG.info("creating ICStoreSummary");
 		long t1 = System.currentTimeMillis();

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

@@ -101,8 +101,6 @@ public void run(ApplicationConfiguration configuration, Environment environment)
         configureSwagger(environment);
         configureJackson(environment);
         
-        System.out.println(configuration.getCuries());
-        
         Concurrency concurrency = Concurrency.CONCURRENT;
         LOG.info("Creating injector...");
         Injector i = Guice.createInjector(

owlsim-services/src/main/java/org/monarchinitiative/owlsim/services/resources/AncestorResource.java

@@ -1,18 +1,3 @@
-/**
- * Copyright (C) 2014 The OwlSim authors
- *
- * Licensed under the Apache License, Version 2.0 (the "License");
- * you may not use this file except in compliance with the License.
- * You may obtain a copy of the License at
- *
- *         http://www.apache.org/licenses/LICENSE-2.0
- *
- * Unless required by applicable law or agreed to in writing, software
- * distributed under the License is distributed on an "AS IS" BASIS,
- * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
- * See the License for the specific language governing permissions and
- * limitations under the License.
- */
 package org.monarchinitiative.owlsim.services.resources;
 
 import java.util.Set;
@@ -33,7 +18,6 @@
 import org.monarchinitiative.owlsim.kb.BMKnowledgeBase;
 import org.monarchinitiative.owlsim.kb.filter.UnknownFilterException;
 import org.monarchinitiative.owlsim.model.match.MatchSet;
-import org.prefixcommons.CurieUtil;
 
 import com.codahale.metrics.annotation.Timed;
 import com.googlecode.javaewah.EWAHCompressedBitmap;
@@ -54,9 +38,6 @@
   @Inject
   BMKnowledgeBase knowledgeBase;
 
-  @Inject
-  CurieUtil curieUtil;
-
   @GET
   @Path("/ancestors")
   @Timed
@@ -71,10 +52,7 @@
       @ApiParam(value = "cutoff limit", required = false) @QueryParam("limit") Integer limit)
       throws UnknownFilterException, IncoherentStateException {
 
-
-    Set<String> resolvedClassIds =
-        classIds.stream().map(id -> curieUtil.getIri(id).or(id)).collect(Collectors.toSet());
-    EWAHCompressedBitmap superBM = knowledgeBase.getSuperClassesBM(resolvedClassIds);
+    EWAHCompressedBitmap superBM = knowledgeBase.getSuperClassesBM(classIds);
     return knowledgeBase.getClassIds(superBM);
   }
 
@@ -92,14 +70,8 @@ public ClassInformationContentPair getMatches(
       @ApiParam(value = "cutoff limit", required = false) @QueryParam("limit") Integer limit)
       throws UnknownFilterException, IncoherentStateException {
 
-
-    Set<String> resolvedClassIds1 =
-        classIds1.stream().map(id -> curieUtil.getIri(id).or(id)).collect(Collectors.toSet());
-    Set<String> resolvedClassIds2 =
-        classIds2.stream().map(id -> curieUtil.getIri(id).or(id)).collect(Collectors.toSet());
-
     ClassInformationContentPair mica =
-        micaCalculator.getMostInformativeCommonAncestorWithIC(resolvedClassIds1, resolvedClassIds2);
+        micaCalculator.getMostInformativeCommonAncestorWithIC(classIds1, classIds2);
     return mica;
   }