Few improvements and refactor for ontologies

Remove jena-arq and jena-larq dependencies by reimplementing the
indexing of statements.

Update jena to 2.13.0.

Wrap search results in a OntologySearchResult class so that we don't
have to add an optional score field in the OntologyResource interface.

Add capabilities for excluding words from stemming.

Author: arteymix

pom.xml

@@ -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>
@@ -264,6 +226,11 @@
 			<version>4.11.0</version>
 			<scope>test</scope>
 		</dependency>
+		<dependency>
+			<groupId>org.assertj</groupId>
+			<artifactId>assertj-core</artifactId>
+			<version>3.25.3</version>
+		</dependency>
 		<dependency>
 			<groupId>org.apache.logging.log4j</groupId>
 			<artifactId>log4j-core</artifactId>

src/ontology.properties src/basecode.propertiessrc/ontology.properties renamed to src/basecode.properties

@@ -25,37 +25,22 @@
 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;
-    }
-
-    public AbstractOntologyResource( OntResource resource, double score ) {
-        this.res = resource;
-        this.score = score;
     }
 
     @Override
@@ -97,17 +82,6 @@ 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;