Merge branch 'hotfix-1.1.22'

pom.xml

@@ -5,15 +5,15 @@
 	<name>baseCode</name>
 	<groupId>baseCode</groupId>
 	<artifactId>baseCode</artifactId>
-	<version>1.1.21</version>
+	<version>1.1.22</version>
 	<inceptionYear>2003</inceptionYear>
 	<description>
 		<![CDATA[Data structures, math and statistics tools, and utilities that are often needed across projects.]]>
 	</description>
-	<url>https://github.com/pavlidisLab/basecode</url>
+	<url>https://github.com/PavlidisLab/baseCode</url>
 	<organization>
-		<name>UBC Michael Smith Laboratories</name>
-		<url>http://www.msl.ubc.ca/</url>
+		<name>Pavlidis Lab</name>
+		<url>https://pavlab.msl.ubc.ca/</url>
 	</organization>
 	<packaging>jar</packaging>
 	<issueManagement>
@@ -27,7 +27,7 @@
 	<licenses>
 		<license>
 			<name>The Apache Software License, Version 2.0</name>
-			<url>http://www.apache.org/licenses/LICENSE-2.0.txt</url>
+			<url>https://www.apache.org/licenses/LICENSE-2.0.txt</url>
 			<distribution>repo</distribution>
 		</license>
 	</licenses>
@@ -81,7 +81,7 @@
 		<dependency>
 			<groupId>commons-io</groupId>
 			<artifactId>commons-io</artifactId>
-			<version>2.15.1</version>
+			<version>2.16.1</version>
 		</dependency>
 		<dependency>
 			<groupId>org.apache.commons</groupId>
@@ -144,45 +144,7 @@
 		<dependency>
 			<groupId>org.apache.jena</groupId>
 			<artifactId>jena-core</artifactId>
-			<version>2.7.4</version>
-			<exclusions>
-				<exclusion>
-					<groupId>log4j</groupId>
-					<artifactId>log4j</artifactId>
-				</exclusion>
-				<exclusion>
-					<groupId>org.slf4j</groupId>
-					<artifactId>slf4j-log4j12</artifactId>
-				</exclusion>
-			</exclusions>
-		</dependency>
-		<!-- Be careful with versions of lucene -->
-		<!-- jena-text uses lucene 4.x.. Not ready for this. -->
-		<!-- <dependency> <groupId>org.apache.jena</groupId> <artifactId>jena-text</artifactId> <version>1.0.0-SNAPSHOT</version>
-			</dependency> -->
-		<dependency>
-			<groupId>org.apache.jena</groupId>
-			<artifactId>jena-larq</artifactId>
-			<version>1.0.0-incubating</version>
-			<exclusions>
-				<exclusion>
-					<groupId>log4j</groupId>
-					<artifactId>log4j</artifactId>
-				</exclusion>
-				<exclusion>
-					<groupId>org.slf4j</groupId>
-					<artifactId>slf4j-log4j12</artifactId>
-				</exclusion>
-				<exclusion>
-					<artifactId>icu4j</artifactId>
-					<groupId>com.ibm.icu</groupId>
-				</exclusion>
-			</exclusions>
-		</dependency>
-		<dependency>
-			<groupId>org.apache.jena</groupId>
-			<artifactId>jena-arq</artifactId>
-			<version>2.9.4</version> <!-- latest release is 2.10.1, but not compatible with larq? -->
+			<version>2.13.0</version>
 			<exclusions>
 				<exclusion>
 					<groupId>log4j</groupId>
@@ -264,16 +226,28 @@
 			<version>4.11.0</version>
 			<scope>test</scope>
 		</dependency>
+		<dependency>
+			<groupId>org.assertj</groupId>
+			<artifactId>assertj-core</artifactId>
+			<version>3.25.3</version>
+			<scope>test</scope>
+		</dependency>
+		<dependency>
+			<groupId>org.apache.logging.log4j</groupId>
+			<artifactId>log4j-api</artifactId>
+			<version>2.23.1</version>
+			<scope>test</scope>
+		</dependency>
 		<dependency>
 			<groupId>org.apache.logging.log4j</groupId>
 			<artifactId>log4j-core</artifactId>
-			<version>2.21.1</version>
+			<version>2.23.1</version>
 			<scope>test</scope>
 		</dependency>
 		<dependency>
 			<groupId>org.apache.logging.log4j</groupId>
 			<artifactId>log4j-slf4j-impl</artifactId>
-			<version>2.21.1</version>
+			<version>2.23.1</version>
 			<scope>test</scope>
 		</dependency>
 	</dependencies>
@@ -341,7 +315,7 @@
 			<plugin>
 				<groupId>com.amashchenko.maven.plugin</groupId>
 				<artifactId>gitflow-maven-plugin</artifactId>
-				<version>1.16.0</version>
+				<version>1.21.0</version>
 				<configuration>
 					<!-- Do not push to remote -->
 					<pushRemote>false</pushRemote>
@@ -444,7 +418,7 @@
 			<plugin>
 				<groupId>org.apache.maven.plugins</groupId>
 				<artifactId>maven-project-info-reports-plugin</artifactId>
-				<version>3.1.2</version>
+				<version>3.2.2</version>
 				<reportSets>
 					<reportSet>
 						<reports>

src/ontology.properties → src/basecode.properties

@@ -37,4 +37,7 @@ url.fmaOntology=http://purl.obolibrary.org/obo/fma.owl
 
 ontology.index.dir=
 ontology.cache.dir=
-ncbo.api.key=
+ncbo.api.key=
+
+rserve.start.command=
+rlibpath=

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

@@ -25,37 +25,25 @@
 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
  */
 abstract class AbstractOntologyResource implements OntologyResource {
 
     protected static final Logger log = LoggerFactory.getLogger( AbstractOntologyResource.class );
 
-    private static final Comparator<OntologyResource> comparator = Comparator
-            .comparing( OntologyResource::getScore, nullsLast( reverseOrder() ) )
-            .thenComparing( OntologyResource::getUri, nullsLast( naturalOrder() ) );
-
     private final OntResource res;
-    @Nullable
-    private final Double score;
 
     private String _label;
     private boolean _isLabelNull = false;
 
-    protected AbstractOntologyResource( OntResource resource ) {
-        this.res = resource;
-        this.score = null;
-    }
+    private String _label;
+    private boolean _isLabelNull = false;
 
-    public AbstractOntologyResource( OntResource resource, double score ) {
+    protected AbstractOntologyResource( OntResource resource ) {
         this.res = resource;
-        this.score = score;
     }
 
     @Override
@@ -97,17 +85,6 @@ 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( this, other, comparator );
-    }
-
     @Override
     public boolean equals( Object obj ) {
         if ( this == obj ) return true;