AtomGraph · namedgraph · Jun 5, 2026 · Mar 15, 2026 · Mar 15, 2026 · Mar 15, 2026
diff --git a/.github/workflows/http-tests.yml b/.github/workflows/http-tests.yml
@@ -8,11 +8,16 @@ jobs:
     runs-on: ubuntu-latest
     env:
       ASF_ARCHIVE: https://archive.apache.org/dist/
-      JENA_VERSION: 4.7.0
+      JENA_VERSION: 6.1.0
       BASE_URI: https://localhost:4443/
     steps:
       - name: Install Linux packages
         run: sudo apt-get update && sudo apt-get install -qq raptor2-utils && sudo apt-get install curl
+      - name: Set up Java 21
+        uses: actions/setup-java@v4
+        with:
+          distribution: 'temurin'
+          java-version: '21'
       - name: Download Jena
         run: curl -sS --fail "${{ env.ASF_ARCHIVE }}jena/binaries/apache-jena-${{ env.JENA_VERSION }}.tar.gz" -o "${{ runner.temp }}/jena.tar.gz"
       - name: Unpack Jena
@@ -49,6 +54,12 @@ jobs:
         run: ./run.sh "$PWD/ssl/owner/cert.pem" "${{ secrets.HTTP_TEST_OWNER_CERT_PASSWORD }}" "$PWD/ssl/secretary/cert.pem" "${{ secrets.HTTP_TEST_SECRETARY_CERT_PASSWORD }}"
         shell: bash
         working-directory: http-tests
+      - name: Dump container logs on failure
+        if: failure()
+        run: docker compose --env-file ./http-tests/.env logs --no-color
+      - name: Dump Tomcat logs from linkeddatahub container on failure
+        if: failure()
+        run: docker compose --env-file ./http-tests/.env exec -T linkeddatahub sh -c 'for f in /usr/local/tomcat/logs/*; do echo "=== $f ==="; cat "$f"; done' || true
       - name: Stop Docker containers and remove volumes
         run: docker compose --env-file ./http-tests/.env down -v
       - name: Remove Docker containers

diff --git a/Dockerfile b/Dockerfile
@@ -1,8 +1,8 @@
-FROM maven:3.8.4-openjdk-17 AS maven
+FROM maven:3.9-eclipse-temurin-21 AS maven
 
 # download and extract Jena
 
-ARG JENA_VERSION=4.7.0
+ARG JENA_VERSION=6.1.0
 
 ARG JENA_TAR_URL="https://archive.apache.org/dist/jena/binaries/apache-jena-${JENA_VERSION}.tar.gz"
 
@@ -22,7 +22,7 @@ RUN mvn -Pstandalone clean install
 
 # ==============================
 
-FROM atomgraph/letsencrypt-tomcat:10.1.46
+FROM atomgraph/letsencrypt-tomcat:10.1.52
 
 LABEL maintainer="martynas@atomgraph.com"
 

diff --git a/docker-compose.yml b/docker-compose.yml
@@ -20,7 +20,7 @@ volumes:
   varnish_end_user_cache:
 services:
   nginx:
-    image: nginx:1.23.3
+    image: nginx:1.31.1
     mem_limit: 128m
     configs:
       - source: nginx_conf
@@ -105,7 +105,7 @@ services:
       - ./config/dataspaces.trig:/var/linkeddatahub/datasets/dataspaces.trig
       - ./config/system.trig:/var/linkeddatahub/datasets/system.trig
   fuseki-admin:
-    image: atomgraph/fuseki:4.7.0
+    image: atomgraph/fuseki:6.1.0
     user: root # otherwise fuseki user does not have permissions to the mounted folder which is owner by root
     expose:
       - 3030
@@ -114,7 +114,7 @@ services:
       - ./fuseki/admin:/fuseki/databases
     command: [ "--config", "/fuseki/config.ttl" ]
   fuseki-end-user:
-    image: atomgraph/fuseki:4.7.0
+    image: atomgraph/fuseki:6.1.0
     user: root # otherwise the fuseki user does not have permissions to the mounted folder which is owner by root
     expose:
       - 3030
@@ -123,7 +123,7 @@ services:
       - ./fuseki/end-user:/fuseki/databases
     command: [ "--config", "/fuseki/config.ttl" ]
   varnish-frontend:
-    image: varnish:7.3.0
+    image: varnish:7.7.3
     user: root # otherwise varnish user does not have permissions to the mounted folder which is owner by root
     configs:
       - source: varnish-frontend_vcl
@@ -136,7 +136,7 @@ services:
     entrypoint: varnishd
     command: [ "-F", "-f", "/etc/varnish/default.vcl", "-a", "http=:6060,HTTP", "-a", "proxy=:8443,PROXY", "-p", "feature=+http2", "-s", "file,/var/lib/varnish/storage.bin,3G", "-t", "86400" ] # -F: foreground, -f: config, -a: listeners, -p: http2, -s: storage, -t: TTL
   varnish-admin:
-    image: varnish:7.3.0
+    image: varnish:7.7.3
     user: root # otherwise the varnish user does not have permissions to the mounted folder which is owner by root
     configs:
       - source: varnish-admin_vcl
@@ -147,7 +147,7 @@ services:
     entrypoint: varnishd
     command: [ "-F", "-f", "/etc/varnish/default.vcl", "-a", "http=:80,HTTP", "-a", "proxy=:8443,PROXY", "-p", "feature=+http2", "-s", "malloc,1G", "-t", "86400", "-p", "timeout_idle=60s" ] # -F: foreground, -f: config, -a: listeners, -p: http2 + idle timeout, -s: storage, -t: TTL
   varnish-end-user:
-    image: varnish:7.3.0
+    image: varnish:7.7.3
     user: root # otherwise varnish user does not have permissions to the mounted folder which is owner by root
     configs:
       - source: varnish-end-user_vcl

diff --git a/platform/entrypoint.sh b/platform/entrypoint.sh
@@ -1,5 +1,7 @@
 #!/usr/bin/env bash
 set -e
+set -x  # DEBUG: trace every command (revert before merge)
+exec 2>&1  # DEBUG: merge stderr into stdout so the trace lands in docker logs
 
 # set timezone
 

diff --git a/pom.xml b/pom.xml
@@ -86,28 +86,28 @@
         <dependency>
             <groupId>jakarta.servlet</groupId>
             <artifactId>jakarta.servlet-api</artifactId>
-            <version>5.0.0</version>
+            <version>6.0.0</version>
             <scope>provided</scope>
         </dependency>
         <dependency>
             <groupId>org.glassfish.jersey.connectors</groupId>
             <artifactId>jersey-apache-connector</artifactId>
-            <version>3.1.0</version>
+            <version>3.1.11</version>
         </dependency>
         <dependency>
             <groupId>org.glassfish.jersey.media</groupId>
             <artifactId>jersey-media-multipart</artifactId>
-            <version>3.1.0</version>
+            <version>3.1.11</version>
         </dependency>
         <dependency>
             <groupId>org.glassfish.jersey.media</groupId>
             <artifactId>jersey-media-json-processing</artifactId>
-            <version>3.1.0</version>
+            <version>3.1.11</version>
         </dependency>
         <dependency>
             <groupId>com.sun.mail</groupId>
             <artifactId>jakarta.mail</artifactId>
-            <version>2.0.1</version>
+            <version>2.0.2</version>
         </dependency>
         <dependency>
             <groupId>com.google.guava</groupId>
@@ -117,7 +117,7 @@
         <dependency>
             <groupId>com.atomgraph.etl.csv</groupId>
             <artifactId>csv2rdf</artifactId>
-            <version>2.1.11</version>
+            <version>2.2.0</version>
             <exclusions>
                 <!-- exclude SL4J from CSV2RDF - we already got another coming from Core. Otherwise we get https://www.slf4j.org/codes.html#multiple_bindings -->
                 <exclusion>
@@ -129,57 +129,67 @@
         <dependency>
             <groupId>org.apache.jena</groupId>
             <artifactId>jena-shacl</artifactId>
-            <version>4.7.0</version>
+            <version>6.1.0</version>
+        </dependency>
+        <dependency>
+            <groupId>org.apache.jena</groupId>
+            <artifactId>jena-arq</artifactId>
+            <version>6.1.0</version>
+        </dependency>
+        <dependency>
+            <groupId>com.github.jsonld-java</groupId>
+            <artifactId>jsonld-java</artifactId>
+            <version>0.13.4</version>
         </dependency>
         <dependency>
             <groupId>${project.groupId}</groupId>
             <artifactId>twirl</artifactId>
-            <version>1.0.33</version>
+            <version>1.1.0</version>
         </dependency>
         <dependency>
             <groupId>${project.groupId}</groupId>
             <artifactId>client</artifactId>
-            <version>4.2.11</version>
+            <version>4.3.0</version>
             <classifier>classes</classifier>
         </dependency>
         <dependency>
             <groupId>${project.groupId}</groupId>
             <artifactId>client</artifactId>
-            <version>4.2.11</version>
+            <version>4.3.0</version>
             <type>war</type>
         </dependency>
         <!-- required by jsonld-java - version same as Jersey's HTTP Client -->
         <dependency>
             <groupId>org.apache.httpcomponents</groupId>
             <artifactId>httpclient-cache</artifactId>
-            <version>4.5.13</version>
+            <version>4.5.14</version>
         </dependency>
         <dependency>
             <groupId>com.auth0</groupId>
             <artifactId>java-jwt</artifactId>
-            <version>3.19.3</version>
+            <version>3.19.4</version>
         </dependency>
         <dependency>
             <groupId>net.jodah</groupId>
             <artifactId>expiringmap</artifactId>
-            <version>0.5.10</version>
+            <version>0.5.11</version>
         </dependency>
         <dependency>
             <groupId>org.jsoup</groupId>
             <artifactId>jsoup</artifactId>
-            <version>1.15.3</version>
+            <version>1.22.1</version>
         </dependency>
         <dependency>
             <!-- comes with atomgraph/letsencrypt-tomcat -->
             <groupId>org.apache.tomcat</groupId>
             <artifactId>tomcat-coyote</artifactId>
-            <version>10.1.2</version>
+            <version>10.1.52</version>
             <type>jar</type>
         </dependency>
         <dependency>
-            <groupId>junit</groupId>
-            <artifactId>junit</artifactId>
-            <version>4.13.2</version>
+            <groupId>org.junit.jupiter</groupId>
+            <artifactId>junit-jupiter</artifactId>
+            <version>5.11.4</version>
             <scope>test</scope>
         </dependency>
         <dependency>
@@ -188,6 +198,12 @@
             <version>5.12.0</version>
             <scope>test</scope>
         </dependency>
+        <dependency>
+            <groupId>org.mockito</groupId>
+            <artifactId>mockito-junit-jupiter</artifactId>
+            <version>5.12.0</version>
+            <scope>test</scope>
+        </dependency>
     </dependencies>
 
     <build>
@@ -216,21 +232,26 @@
         </pluginManagement>
 
         <plugins>
+            <plugin>
+                <groupId>org.apache.maven.plugins</groupId>
+                <artifactId>maven-surefire-plugin</artifactId>
+                <version>3.5.2</version>
+            </plugin>
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-release-plugin</artifactId>
-                <version>2.5.3</version>
+                <version>3.3.1</version>
                 <configuration>
                     <releaseProfiles>release</releaseProfiles>
                 </configuration>
             </plugin>
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-compiler-plugin</artifactId>
-                <version>3.10.1</version>
+                <version>3.14.1</version>
                 <configuration>
-                    <source>17</source>
-                    <target>17</target>
+                    <source>21</source>
+                    <target>21</target>
                     <!-- ignore warnings about internal Java APIs which we use for WebIDCertGen -->
                     <compilerArgs>
                         <arg>-XDignore.symbol.file</arg>
@@ -243,7 +264,7 @@
             <plugin>
                 <groupId>org.sonatype.central</groupId>
                 <artifactId>central-publishing-maven-plugin</artifactId>
-                <version>0.9.0</version>
+                <version>0.10.0</version>
                 <extensions>true</extensions>
                 <configuration>
                     <publishingServerId>central-portal-snapshots</publishingServerId>
@@ -254,7 +275,7 @@
             <plugin>
                 <groupId>org.codehaus.mojo</groupId>
                 <artifactId>exec-maven-plugin</artifactId>
-                <version>3.0.0</version>
+                <version>3.6.3</version>
                 <executions>
                     <execution>
                         <id>find-xsl-files</id>
@@ -287,7 +308,7 @@
             <plugin>
                 <groupId>org.honton.chas</groupId>
                 <artifactId>readfiles-maven-plugin</artifactId>
-                <version>0.0.1</version>
+                <version>0.1.0</version>
                 <executions>
                     <execution>
                         <id>read-comma-separated-xsl-file-list</id>
@@ -338,7 +359,7 @@
             <plugin>
                 <groupId>com.github.eirslett</groupId>
                 <artifactId>frontend-maven-plugin</artifactId>
-                <version>1.15.1</version>
+                <version>1.15.4</version>
                 <configuration>
                     <nodeVersion>v22.16.0</nodeVersion>
                     <npmVersion>11.4.2</npmVersion>
@@ -366,7 +387,7 @@
             <plugin>
                 <groupId>org.apache.maven.plugins</groupId>
                 <artifactId>maven-war-plugin</artifactId>
-                <version>3.3.2</version>
+                <version>3.5.1</version>
                 <configuration>
                     <warName>${build.warName}</warName>
                     <webappDirectory>${project.build.directory}/${build.warName}</webappDirectory>
@@ -432,7 +453,7 @@
                     <plugin>
                         <groupId>org.apache.maven.plugins</groupId>
                         <artifactId>maven-source-plugin</artifactId>
-                        <version>3.2.1</version>
+                        <version>3.4.0</version>
                         <executions>
                             <execution>
                                 <id>attach-sources</id>
@@ -445,7 +466,7 @@
                     <plugin>
                         <groupId>org.apache.maven.plugins</groupId>
                         <artifactId>maven-javadoc-plugin</artifactId>
-                        <version>3.2.0</version>
+                        <version>3.12.0</version>
                         <executions>
                             <execution>
                                 <id>attach-javadocs</id>

diff --git a/src/main/java/com/atomgraph/linkeddatahub/client/SesameProtocolClient.java b/src/main/java/com/atomgraph/linkeddatahub/client/SesameProtocolClient.java
@@ -123,7 +123,7 @@ public static MultivaluedMap<String, String> solutionMapToMultivaluedMap(QuerySo
         {
             String varName = it.next();
             RDFNode node = qsm.get(varName);
-            params.add("$" + varName, NodeFmtLib.str(node.asNode()));
+            params.add("$" + varName, NodeFmtLib.strNT(node.asNode()));
         }
 
         return params;

diff --git a/src/main/java/com/atomgraph/linkeddatahub/resource/Namespace.java b/src/main/java/com/atomgraph/linkeddatahub/resource/Namespace.java
@@ -46,15 +46,13 @@
 import jakarta.ws.rs.core.Response.Status;
 import jakarta.ws.rs.core.SecurityContext;
 import jakarta.ws.rs.core.UriInfo;
-import org.apache.jena.iri.IRI;
-import org.apache.jena.iri.IRIFactory;
+import org.apache.jena.irix.IRIx;
 import org.apache.jena.ontology.Ontology;
 import org.apache.jena.query.DatasetFactory;
 import org.apache.jena.query.Query;
 import org.apache.jena.query.QueryFactory;
 import org.apache.jena.rdf.model.Model;
 import org.apache.jena.rdf.model.ModelFactory;
-import org.apache.jena.riot.system.Checker;
 import org.apache.jena.update.UpdateRequest;
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
@@ -182,15 +180,12 @@ public Response post(UpdateRequest update, @QueryParam(USING_GRAPH_URI) List<URI
      * @param classIRIStr URI string
      * @return IRI
      */
-    public static IRI checkURI(String classIRIStr)
+    public static IRIx checkURI(String classIRIStr)
     {
         if (classIRIStr == null) throw new IllegalArgumentException("URI String cannot be null");
 
-        IRI classIRI = IRIFactory.iriImplementation().create(classIRIStr);
-        // throws Exceptions on bad URIs:
-        Checker.iriViolations(classIRI);
-
-        return classIRI;
+        // IRIx.create() validates and throws IRIException on bad URIs
+        return IRIx.create(classIRIStr);
     }
 
     /**

diff --git a/src/main/java/com/atomgraph/linkeddatahub/server/filter/request/OntologyFilter.java b/src/main/java/com/atomgraph/linkeddatahub/server/filter/request/OntologyFilter.java
@@ -173,7 +173,7 @@ public Ontology getOntology(Application app, String uri)
                     URI ontologyURI = URI.create(uri);
                     // remove fragment and normalize
                     URI ontDocURI = new URI(ontologyURI.getScheme(), ontologyURI.getSchemeSpecificPart(), null).normalize();
-                    Model baseModel = fileManager.loadModel(uri, ontDocURI.toString(), null);
+                    Model baseModel = fileManager.loadModel(ontDocURI.toString());
                     OntModel ontModel = ModelFactory.createOntologyModel(ontModelSpec, baseModel);
                     ontModel.getDocumentManager().addModel(uri, ontModel, true);
                 }