Merge branch 'hotfix-1.1.15'

Author: arteymix

pom.xml

@@ -5,7 +5,7 @@
 	<name>baseCode</name>
 	<groupId>baseCode</groupId>
 	<artifactId>baseCode</artifactId>
-	<version>1.1.14</version>
+	<version>1.1.15</version>
 	<inceptionYear>2003</inceptionYear>
 	<description>
 		<![CDATA[Data structures, math and statistics tools, and utilities that are often needed across projects.]]>
@@ -231,6 +231,13 @@
 			<version>5.7.1</version>
 		</dependency>
 
+		<!-- Development tools -->
+		<dependency>
+			<groupId>com.google.code.findbugs</groupId>
+			<artifactId>jsr305</artifactId>
+			<version>3.0.2</version>
+		</dependency>
+
 		<!-- Testing utilities -->
 		<dependency>
 			<groupId>junit</groupId>

src/ontology.properties

@@ -30,7 +30,7 @@ url.uberonOntology=http://purl.obolibrary.org/obo/uberon.owl
 
 # as recommended at https://www.ebi.ac.uk/efo/ (this has changed several times)
 url.efOntology=https://www.ebi.ac.uk/efo/efo.owl
-url.obiOntology=http://svn.code.sf.net/p/obi/code/releases/2016-10-11/obi.owl
+url.obiOntology=http://purl.obolibrary.org/obo/obi.owl
 
 
 # no longer actively used.

src/ubic/basecode/ontology/jena/AbstractOntologyMemoryBackedService.java

@@ -16,6 +16,9 @@
 
 import com.hp.hpl.jena.ontology.OntModel;
 
+import javax.annotation.Nullable;
+import java.io.InputStream;
+
 /**
  * This class has some stuff that's specific to in-memory ontologies. Unlike database backed ontologies we don't use a
  * pool keeping only one instance of model in memory.
@@ -25,7 +28,12 @@
 public abstract class AbstractOntologyMemoryBackedService extends AbstractOntologyService {
 
     @Override
-    protected synchronized OntModel loadModel() {
+    protected OntModel loadModel() {
         return OntologyLoader.loadMemoryModel( this.getOntologyUrl(), this.getOntologyName() );
     }
+
+    @Override
+    protected OntModel loadModelFromStream( InputStream is ) {
+        return OntologyLoader.loadMemoryModel( is, this.getOntologyUrl() );
+    }
 }

src/ubic/basecode/ontology/jena/AbstractOntologyResource.java

@@ -19,15 +19,17 @@
 package ubic.basecode.ontology.jena;
 
 import com.hp.hpl.jena.ontology.OntResource;
-import com.hp.hpl.jena.rdf.model.Resource;
 import com.hp.hpl.jena.vocabulary.OWL2;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import ubic.basecode.ontology.model.OntologyResource;
 
+import javax.annotation.Nullable;
 import java.util.Comparator;
 import java.util.Objects;
 
+import static java.util.Comparator.*;
+
 /**
  * @author pavlidis
  */
@@ -37,10 +39,22 @@ public abstract class AbstractOntologyResource implements OntologyResource {
 
     private static final long serialVersionUID = 1L;
 
+    private static final Comparator<OntologyResource> comparator = Comparator
+            .comparing( OntologyResource::getScore, nullsLast( reverseOrder() ) )
+            .thenComparing( OntologyResource::getUri, nullsLast( naturalOrder() ) );
+
     private transient final OntResource res;
+    @Nullable
+    private final Double score;
 
     protected AbstractOntologyResource( OntResource resource ) {
         this.res = resource;
+        this.score = null;
+    }
+
+    public AbstractOntologyResource( OntResource resource, double score ) {
+        this.res = resource;
+        this.score = score;
     }
 
     @Override
@@ -67,9 +81,15 @@ public boolean isObsolete() {
         return res.hasLiteral( OWL2.deprecated, true );
     }
 
+    @Override
+    @Nullable
+    public Double getScore() {
+        return score;
+    }
+
     @Override
     public int compareTo( OntologyResource other ) {
-        return Objects.compare( getUri(), other.getUri(), Comparator.nullsLast( Comparator.naturalOrder() ) );
+        return Objects.compare( this, other, comparator );
     }
 
     @Override