Update to virt_jena3 and jena 3.10.0

.gitignore

@@ -6,6 +6,7 @@
 target/
 out
 *~
+.vscode/
 .settings/
 .project
 .classpath

Dockerfile

@@ -9,6 +9,7 @@ RUN mkdir $BUILD_DIR && \
 WORKDIR $BUILD_DIR/lodestar/
 
 ADD ./config-docker/lode.properties web-ui/src/main/resources/lode.properties
+ADD ./config-docker/log4j.xml web-ui/src/main/resoures/log4j.xml
 
 RUN mvn clean package && \
   cp web-ui/target/lodestar.war $CATALINA_HOME/webapps/ && \

lode-core-api/pom.xml

@@ -4,7 +4,7 @@
     <parent>
         <artifactId>ebi-lode</artifactId>
         <groupId>ebi-lode</groupId>
-        <version>1.4.1</version>
+        <version>1.4.1001-SNAPSHOT</version>
     </parent>
     <modelVersion>4.0.0</modelVersion>
     <artifactId>lode-core-api</artifactId>
@@ -26,10 +26,17 @@
         <dependency>
             <groupId>org.apache.jena</groupId>
             <artifactId>apache-jena-libs</artifactId>
-            <version>2.12.0</version>
+            <version>${jena.version}</version>
             <type>pom</type>
         </dependency>
 
+        <!-- override version of commons-compress in Jena -->
+        <dependency>
+            <groupId>org.apache.commons</groupId>
+            <artifactId>commons-compress</artifactId>
+            <version>1.21</version>
+        </dependency>
+
         <dependency>
             <groupId>org.springframework</groupId>
             <artifactId>spring-context</artifactId>
@@ -39,65 +46,58 @@
         <dependency>
             <groupId>org.json</groupId>
             <artifactId>json</artifactId>
-            <version>20090211</version>
+            <version>20211205</version>
         </dependency>
 
         <!-- Override Jena dependencies on versions of httpclient and jackson with CVEs -->
         <dependency>
             <groupId>org.apache.httpcomponents</groupId>
             <artifactId>httpclient</artifactId>
-            <version>4.5.2</version>
+            <version>4.5.13</version>
         </dependency>
 
         <dependency>
             <groupId>com.github.jsonld-java</groupId>
             <artifactId>jsonld-java</artifactId>
-            <version>0.8.3</version>
+            <version>0.13.4</version>
+        </dependency>
+
+        <dependency>
+            <groupId>org.apache.thrift</groupId>
+            <artifactId>libthrift</artifactId>
+            <version>0.15.0</version>
         </dependency>
 
         <dependency>
             <groupId>com.fasterxml.jackson.core</groupId>
             <artifactId>jackson-core</artifactId>
-            <version>2.8.4</version>
         </dependency>
 
         <dependency>
             <groupId>com.fasterxml.jackson.core</groupId>
             <artifactId>jackson-databind</artifactId>
-            <version>2.8.4</version>
         </dependency>
 
-        <!--
         <dependency>
             <groupId>org.codehaus.jackson</groupId>
             <artifactId>jackson-mapper-asl</artifactId>
-            <version>1.9.13</version>
         </dependency>
 
         <dependency>
             <groupId>org.codehaus.jackson</groupId>
             <artifactId>jackson-core-asl</artifactId>
-            <version>1.9.13</version>
         </dependency>
-        -->
-
+
         <dependency>
             <groupId>commons-logging</groupId>
             <artifactId>commons-logging</artifactId>
-            <version>1.1.1</version>
+            <version>1.2</version>
         </dependency>
 
         <dependency>
             <groupId>org.apache.commons</groupId>
             <artifactId>commons-lang3</artifactId>
-            <version>3.1</version>
-        </dependency>
-
-        <!-- jackson json mapping library, describes mappings from java to json for model objects -->
-        <dependency>
-            <groupId>org.codehaus.jackson</groupId>
-            <artifactId>jackson-mapper-asl</artifactId>
-            <version>1.5.3</version>
+            <version>3.12.0</version>
         </dependency>
     </dependencies>
 

lode-core-api/src/main/java/uk/ac/ebi/fgpt/lode/exception/LodeException.java

@@ -6,6 +6,8 @@
  * Functional Genomics Group EMBL-EBI
  */
 public class LodeException extends Exception {
+    private static final long serialVersionUID = 1L;
+
     public LodeException() {
         super();
     }

lode-core-api/src/main/java/uk/ac/ebi/fgpt/lode/impl/JenaExploreService.java

@@ -1,28 +1,40 @@
 package uk.ac.ebi.fgpt.lode.impl;
 
-import com.hp.hpl.jena.graph.Graph;
-import com.hp.hpl.jena.graph.Node;
-import com.hp.hpl.jena.graph.Triple;
-import com.hp.hpl.jena.query.*;
-import com.hp.hpl.jena.rdf.model.*;
-import com.hp.hpl.jena.rdf.model.impl.ResourceImpl;
-import com.hp.hpl.jena.sparql.syntax.ElementTriplesBlock;
-import com.hp.hpl.jena.sparql.syntax.ElementUnion;
+import java.net.URI;
+import java.util.Collection;
+import java.util.Collections;
+import java.util.HashSet;
+import java.util.LinkedHashMap;
+import java.util.Map;
+import java.util.Set;
+
+import org.apache.jena.graph.Graph;
+import org.apache.jena.graph.NodeFactory;
+import org.apache.jena.graph.Triple;
+import org.apache.jena.query.Query;
+import org.apache.jena.query.QueryExecution;
+import org.apache.jena.query.QuerySolution;
+import org.apache.jena.query.QuerySolutionMap;
+import org.apache.jena.query.ResultSet;
+import org.apache.jena.rdf.model.Literal;
+import org.apache.jena.rdf.model.RDFNode;
+import org.apache.jena.rdf.model.Resource;
+import org.apache.jena.rdf.model.impl.ResourceImpl;
+import org.apache.jena.sparql.syntax.ElementTriplesBlock;
+import org.apache.jena.sparql.syntax.ElementUnion;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Autowired;
 import org.springframework.beans.factory.annotation.Value;
+
 import uk.ac.ebi.fgpt.lode.exception.LodeException;
-import uk.ac.ebi.fgpt.lode.service.JenaQueryExecutionService;
 import uk.ac.ebi.fgpt.lode.model.LabeledResource;
 import uk.ac.ebi.fgpt.lode.model.RelatedResourceDescription;
 import uk.ac.ebi.fgpt.lode.model.ShortResourceDescription;
 import uk.ac.ebi.fgpt.lode.service.ExploreService;
+import uk.ac.ebi.fgpt.lode.service.JenaQueryExecutionService;
 import uk.ac.ebi.fgpt.lode.utils.SparqlQueryReader;
 
-import java.net.URI;
-import java.util.*;
-
 /**
  * @author Simon Jupp
  * @date 03/05/2013
@@ -105,11 +117,13 @@ public void setQueryReader(SparqlQueryReader queryReader) {
         this.queryReader = queryReader;
     }
 
+    @Override
     public Collection<RelatedResourceDescription> getRelatedResourceByProperty(URI resourceUri, Set<URI> propertyUris, Set<URI> excludeTypes, boolean ignoreBnodes) throws LodeException {
         String query = getQueryReader().getSparqlQuery("PREFIX") + "\n\n" + getQueryReader().getSparqlQuery("RELATEDTO.PROPERTIES.QUERY");
         return getRelatedResourceByProperty(resourceUri, query, propertyUris, excludeTypes, ignoreBnodes, false);
     }
 
+    @Override
     public Collection<RelatedResourceDescription> getRelatedToObjects(URI resourceUri, Set<URI> excludePropertyUris, Set<URI> excludeTypes, boolean ignoreBnodes) throws LodeException {
 
         Set<URI> allRelatedProps = new HashSet<URI>();
@@ -123,6 +137,7 @@ public Collection<RelatedResourceDescription> getRelatedToObjects(URI resourceUr
 
     }
 
+    @Override
     public Collection<RelatedResourceDescription> getRelatedFromSubjects(URI resourceUri, Set<URI> excludePropertyUris, Set<URI> excludeTypes, boolean ignoreBnodes) throws LodeException {
 
         Set<URI> allRelatedProps = new HashSet<URI>();
@@ -135,6 +150,7 @@ public Collection<RelatedResourceDescription> getRelatedFromSubjects(URI resourc
         return getRelatedResourceByProperty(resourceUri, query, allRelatedProps, excludeTypes, ignoreBnodes, false);
     }
 
+    @Override
     public Collection<RelatedResourceDescription> getTypes(URI resourceUri, Set<URI> excludeTypes, boolean ignoreBnodes) throws LodeException {
 
         String query = getQueryReader().getSparqlQuery("PREFIX") + "\n\n" + getQueryReader().getSparqlQuery("TYPES.QUERY");
@@ -150,7 +166,7 @@ public Collection<RelatedResourceDescription> getTypes(URI resourceUri, Set<URI>
         try {
             ResultSet results = endpoint.execSelect();
             while (results.hasNext()) {
-                QuerySolution solution = (QuerySolution) results.next();
+                QuerySolution solution = results.next();
                 Resource res = solution.getResource("resource");
                 if (res.isAnon()) {
                     continue;
@@ -178,6 +194,7 @@ public Collection<RelatedResourceDescription> getTypes(URI resourceUri, Set<URI>
         return Collections.singleton(resources);
     }
 
+    @Override
     public Collection<RelatedResourceDescription> getAllTypes(URI resourceUri, Set<URI> excludeTypes, boolean ignoreBnodes) throws LodeException {
 
         String query = getQueryReader().getSparqlQuery("PREFIX") + "\n\n" + getQueryReader().getSparqlQuery("ALLTYPES.QUERY");
@@ -193,7 +210,7 @@ public Collection<RelatedResourceDescription> getAllTypes(URI resourceUri, Set<U
         try {
             ResultSet results = endpoint.execSelect();
             while (results.hasNext()) {
-                QuerySolution solution = (QuerySolution) results.next();
+                QuerySolution solution = results.next();
                 Resource res = solution.getResource("resource");
                 if (res.isAnon()) {
                     continue;
@@ -221,6 +238,7 @@ public Collection<RelatedResourceDescription> getAllTypes(URI resourceUri, Set<U
         return Collections.singleton(resources);
     }
 
+    @Override
     public ShortResourceDescription getShortResourceDescription(URI resourceUri, Set<URI> labelUris, Set<URI> descriptionUris) throws LodeException {
         Graph g = getQueryExecutionService().getDefaultGraph();
         ShortResourceDescription description1 = getShortResourceDescription(g, resourceUri, labelUris, descriptionUris);
@@ -251,13 +269,19 @@ private ShortResourceDescription getShortResourceDescription(Graph g, URI resour
         ElementUnion union = new ElementUnion();
         for (URI l : labelUris) {
             ElementTriplesBlock labelPattern = new ElementTriplesBlock();
-            labelPattern.addTriple(new Triple(resourceNode.asNode(), new ResourceImpl(l.toString()).asNode(), Node.createVariable("label")));
+            labelPattern.addTriple(new Triple(
+                    resourceNode.asNode(),
+                    new ResourceImpl(l.toString()).asNode(),
+                    NodeFactory.createVariable("label")));
             union.addElement(labelPattern);
         }
 
         for (URI d : descriptionUris) {
             ElementTriplesBlock descriptionPattern = new ElementTriplesBlock();
-            descriptionPattern.addTriple(new Triple(resourceNode.asNode(), new ResourceImpl(d.toString()).asNode(), Node.createVariable("description")));
+            descriptionPattern.addTriple(new Triple(
+                    resourceNode.asNode(),
+                    new ResourceImpl(d.toString()).asNode(),
+                    NodeFactory.createVariable("description")));
             union.addElement(descriptionPattern);
         }
 
@@ -270,7 +294,7 @@ private ShortResourceDescription getShortResourceDescription(Graph g, URI resour
             ResultSet results = endpoint.execSelect();
 
             while (results.hasNext()) {
-                QuerySolution solution = (QuerySolution) results.next();
+                QuerySolution solution = results.next();
 
                 Literal labelNode = solution.getLiteral("label");
                 if (label == null && labelNode !=null) {
@@ -295,6 +319,7 @@ private ShortResourceDescription getShortResourceDescription(Graph g, URI resour
         return new ShortResourceDescription(resourceUri.toString(), label, description, dataset);
     }
 
+    @Override
     public Collection<String> getResourceDepiction(URI subject, URI depictRelation) {
 
         String query = getQueryReader().getSparqlQuery("PREFIX") + "\n\n" + getQueryReader().getSparqlQuery("DEPICT.QUERY");
@@ -312,7 +337,7 @@ public Collection<String> getResourceDepiction(URI subject, URI depictRelation)
             ResultSet results = endpoint.execSelect();
 
             while (results.hasNext()) {
-                QuerySolution solution = (QuerySolution) results.next();
+                QuerySolution solution = results.next();
 
                 Resource propertyNode = solution.getResource("img");
                 if (propertyNode != null) {
@@ -350,7 +375,7 @@ private Set<String> getRelatedProperties (URI resource, String binding) {
             ResultSet results = endpoint.execSelect();
 
             while (results.hasNext()) {
-                QuerySolution solution = (QuerySolution) results.next();
+                QuerySolution solution = results.next();
 
                 Resource propertyNode = solution.getResource("property");
                 if (propertyNode != null) {
@@ -387,7 +412,7 @@ private Collection<RelatedResourceDescription> getRelatedResourceByProperty(URI
             ResultSet results = endpoint.execSelect();
 
             while (results.hasNext()) {
-                QuerySolution solution = (QuerySolution) results.next();
+                QuerySolution solution = results.next();
                 String resource = null;
                 String resourceLabel = null;
                 String resourceType = null;

lode-core-api/src/main/java/uk/ac/ebi/fgpt/lode/impl/JenaHttpExecutorService.java

@@ -1,11 +1,15 @@
 package uk.ac.ebi.fgpt.lode.impl;
 
-import com.hp.hpl.jena.graph.Graph;
-import com.hp.hpl.jena.query.*;
-import com.hp.hpl.jena.sparql.engine.http.QueryEngineHTTP;
+import org.apache.jena.graph.Graph;
+import org.apache.jena.query.ParameterizedSparqlString;
+import org.apache.jena.query.Query;
+import org.apache.jena.query.QueryExecution;
+import org.apache.jena.query.QuerySolutionMap;
+import org.apache.jena.sparql.engine.http.QueryEngineHTTP;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 import org.springframework.beans.factory.annotation.Value;
+
 import uk.ac.ebi.fgpt.lode.exception.LodeException;
 import uk.ac.ebi.fgpt.lode.service.JenaQueryExecutionService;
 
@@ -62,11 +66,13 @@ public static boolean isNullOrEmpty(Object o) {
         return "".equals(o);
     }
 
+    @Override
     public Graph getDefaultGraph() {
         return null;
 
     }
 
+    @Override
     public Graph getNamedGraph(String graphName) {
         return null;
     }