Address deprecations

apps/openliberty/src/main/java/org/trellisldp/openliberty/WebApplication.java

@@ -20,7 +20,6 @@
 
 import jakarta.annotation.PostConstruct;
 import jakarta.enterprise.context.ApplicationScoped;
-import jakarta.inject.Inject;
 import jakarta.ws.rs.ApplicationPath;
 import jakarta.ws.rs.core.Application;
 
@@ -32,26 +31,17 @@
 /**
  * Web Application wrapper.
  */
-@ApplicationPath("/")
+@ApplicationPath("trellis")
 @ApplicationScoped
 public class WebApplication extends Application {
 
-    @Inject
-    private TrellisHttpResource httpResource;
-
-    @Inject
-    private TrellisHttpFilter httpFilter;
-
-    @Inject
-    private CacheControlFilter cacheFilter;
-
     @PostConstruct
     void init() {
         printBanner("Trellis Triplestore Application", "org/trellisldp/app/banner.txt");
     }
 
     @Override
-    public Set<Object> getSingletons() {
-        return new HashSet<>(asList(httpResource, httpFilter, cacheFilter));
+    public Set<Class<?>> getClasses() {
+        return new HashSet<>(asList(TrellisHttpResource.class, TrellisHttpFilter.class, CacheControlFilter.class));
     }
 }

apps/openliberty/src/test/java/org/trellisldp/openliberty/TrellisApplicationIT.java

@@ -21,29 +21,22 @@
 
 import jakarta.ws.rs.client.Client;
 
-import org.junit.jupiter.api.DisplayName;
-import org.junit.jupiter.api.Nested;
 import org.junit.jupiter.api.TestInstance;
 import org.trellisldp.test.AbstractApplicationLdpTests;
 
 @TestInstance(PER_CLASS)
-class TrellisApplicationIT {
+class TrellisApplicationIT extends AbstractApplicationLdpTests {
 
     private final Client CLIENT = newBuilder().build();
     private final String TRELLIS_URL = "http://localhost:" + getInteger("trellis.port", 9080) + "/trellis/";
 
-    @Nested
-    @DisplayName("Trellis LDP Tests")
-    class LdpTests extends AbstractApplicationLdpTests {
-
-        @Override
-        public Client getClient() {
-            return TrellisApplicationIT.this.CLIENT;
-        }
+    @Override
+    public Client getClient() {
+        return this.CLIENT;
+    }
 
-        @Override
-        public String getBaseURL() {
-            return TrellisApplicationIT.this.TRELLIS_URL;
-        }
+    @Override
+    public String getBaseURL() {
+        return this.TRELLIS_URL;
     }
 }

trellis-api/src/main/resources/META-INF/beans.xml

@@ -1,5 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<beans xmlns="http://xmlns.jcp.org/xml/ns/javaee" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-  xsi:schemaLocation="http://xmlns.jcp.org/xml/ns/javaee http://xmlns.jcp.org/xml/ns/javaee/beans_1_1.xsd" version="1.1"
-  bean-discovery-mode="annotated">
+<beans xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+    xmlns="https://jakarta.ee/xml/ns/jakartaee"
+    xsi:schemaLocation="https://jakarta.ee/xml/ns/jakartaee https://jakarta.ee/xml/ns/jakartaee/beans_4_0.xsd"
+    version="4.0"
+    bean-discovery-mode="annotated">
 </beans>

trellis-app/src/main/resources/META-INF/beans.xml

@@ -1,6 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<beans xmlns="http://xmlns.jcp.org/xml/ns/javaee" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-  xsi:schemaLocation="http://xmlns.jcp.org/xml/ns/javaee http://xmlns.jcp.org/xml/ns/javaee/beans_1_1.xsd" version="1.1"
-  bean-discovery-mode="annotated">
+<beans xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+    xmlns="https://jakarta.ee/xml/ns/jakartaee"
+    xsi:schemaLocation="https://jakarta.ee/xml/ns/jakartaee https://jakarta.ee/xml/ns/jakartaee/beans_4_0.xsd"
+    version="4.0"
+    bean-discovery-mode="annotated">
 </beans>
-

trellis-audit/src/main/resources/META-INF/beans.xml

@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<beans xmlns="http://xmlns.jcp.org/xml/ns/javaee"
-       xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-       xsi:schemaLocation="http://xmlns.jcp.org/xml/ns/javaee
-                           http://xmlns.jcp.org/xml/ns/javaee/beans_1_1.xsd"
-       version="1.1" bean-discovery-mode="annotated">
+<beans xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+    xmlns="https://jakarta.ee/xml/ns/jakartaee"
+    xsi:schemaLocation="https://jakarta.ee/xml/ns/jakartaee https://jakarta.ee/xml/ns/jakartaee/beans_4_0.xsd"
+    version="4.0"
+    bean-discovery-mode="annotated">
 </beans>

trellis-cdi/src/main/resources/META-INF/beans.xml

@@ -1,6 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<beans xmlns="http://xmlns.jcp.org/xml/ns/javaee" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-  xsi:schemaLocation="http://xmlns.jcp.org/xml/ns/javaee http://xmlns.jcp.org/xml/ns/javaee/beans_1_1.xsd" version="1.1"
-  bean-discovery-mode="annotated">
+<beans xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+    xmlns="https://jakarta.ee/xml/ns/jakartaee"
+    xsi:schemaLocation="https://jakarta.ee/xml/ns/jakartaee https://jakarta.ee/xml/ns/jakartaee/beans_4_0.xsd"
+    version="4.0"
+    bean-discovery-mode="annotated">
 </beans>
-

trellis-common/src/main/resources/META-INF/beans.xml

@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<beans xmlns="http://xmlns.jcp.org/xml/ns/javaee"
-       xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-       xsi:schemaLocation="http://xmlns.jcp.org/xml/ns/javaee
-                           http://xmlns.jcp.org/xml/ns/javaee/beans_1_1.xsd"
-       version="1.1" bean-discovery-mode="annotated">
+<beans xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+    xmlns="https://jakarta.ee/xml/ns/jakartaee"
+    xsi:schemaLocation="https://jakarta.ee/xml/ns/jakartaee https://jakarta.ee/xml/ns/jakartaee/beans_4_0.xsd"
+    version="4.0"
+    bean-discovery-mode="annotated">
 </beans>

trellis-constraint/src/main/resources/META-INF/beans.xml

@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<beans xmlns="http://xmlns.jcp.org/xml/ns/javaee"
-       xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-       xsi:schemaLocation="http://xmlns.jcp.org/xml/ns/javaee
-                           http://xmlns.jcp.org/xml/ns/javaee/beans_1_1.xsd"
-       version="1.1" bean-discovery-mode="annotated">
+<beans xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+    xmlns="https://jakarta.ee/xml/ns/jakartaee"
+    xsi:schemaLocation="https://jakarta.ee/xml/ns/jakartaee https://jakarta.ee/xml/ns/jakartaee/beans_4_0.xsd"
+    version="4.0"
+    bean-discovery-mode="annotated">
 </beans>

trellis-file/src/main/resources/META-INF/beans.xml

@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<beans xmlns="http://xmlns.jcp.org/xml/ns/javaee"
-       xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-       xsi:schemaLocation="http://xmlns.jcp.org/xml/ns/javaee
-                           http://xmlns.jcp.org/xml/ns/javaee/beans_1_1.xsd"
-       version="1.1" bean-discovery-mode="annotated">
+<beans xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+    xmlns="https://jakarta.ee/xml/ns/jakartaee"
+    xsi:schemaLocation="https://jakarta.ee/xml/ns/jakartaee https://jakarta.ee/xml/ns/jakartaee/beans_4_0.xsd"
+    version="4.0"
+    bean-discovery-mode="annotated">
 </beans>

trellis-http/src/main/java/org/trellisldp/http/WebApplicationExceptionMapper.java

@@ -0,0 +1,37 @@
+/*
+ * Copyright (c) Aaron Coburn and individual contributors
+ *
+ * Licensed under the Apache License, Version 2.0 (the "License");
+ * you may not use this file except in compliance with the License.
+ * You may obtain a copy of the License at
+ *
+ *     http://www.apache.org/licenses/LICENSE-2.0
+ *
+ * Unless required by applicable law or agreed to in writing, software
+ * distributed under the License is distributed on an "AS IS" BASIS,
+ * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ * See the License for the specific language governing permissions and
+ * limitations under the License.
+ */
+package org.trellisldp.http;
+
+import jakarta.ws.rs.WebApplicationException;
+import jakarta.ws.rs.core.Response;
+import jakarta.ws.rs.ext.ExceptionMapper;
+import jakarta.ws.rs.ext.Provider;
+
+import org.slf4j.Logger;
+import org.slf4j.LoggerFactory;
+
+@Provider
+public class WebApplicationExceptionMapper implements ExceptionMapper<WebApplicationException> {
+
+    private static final Logger LOGGER = LoggerFactory.getLogger(WebApplicationExceptionMapper.class);
+
+    @Override
+    public Response toResponse(final WebApplicationException err) {
+        LOGGER.debug("Unhandled web application exception", err);
+
+        return err.getResponse();
+    }
+}

trellis-http/src/main/resources/META-INF/beans.xml

@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<beans xmlns="http://xmlns.jcp.org/xml/ns/javaee"
-       xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-       xsi:schemaLocation="http://xmlns.jcp.org/xml/ns/javaee
-                           http://xmlns.jcp.org/xml/ns/javaee/beans_1_1.xsd"
-       version="1.1" bean-discovery-mode="annotated">
+<beans xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+    xmlns="https://jakarta.ee/xml/ns/jakartaee"
+    xsi:schemaLocation="https://jakarta.ee/xml/ns/jakartaee https://jakarta.ee/xml/ns/jakartaee/beans_4_0.xsd"
+    version="4.0"
+    bean-discovery-mode="annotated">
 </beans>

trellis-jdbc/src/main/resources/META-INF/beans.xml

@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<beans xmlns="http://xmlns.jcp.org/xml/ns/javaee"
-       xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-       xsi:schemaLocation="http://xmlns.jcp.org/xml/ns/javaee
-                           http://xmlns.jcp.org/xml/ns/javaee/beans_1_1.xsd"
-       version="1.1" bean-discovery-mode="annotated">
+<beans xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+    xmlns="https://jakarta.ee/xml/ns/jakartaee"
+    xsi:schemaLocation="https://jakarta.ee/xml/ns/jakartaee https://jakarta.ee/xml/ns/jakartaee/beans_4_0.xsd"
+    version="4.0"
+    bean-discovery-mode="annotated">
 </beans>

trellis-jena/pom.xml

@@ -61,6 +61,10 @@
       <groupId>org.apache.jena</groupId>
       <artifactId>jena-commonsrdf</artifactId>
     </dependency>
+    <dependency>
+      <groupId>org.eclipse.parsson</groupId>
+      <artifactId>parsson</artifactId>
+    </dependency>
     <dependency>
       <groupId>commons-io</groupId>
       <artifactId>commons-io</artifactId>

trellis-jena/src/main/java/module-info.java

@@ -28,9 +28,12 @@
     requires jakarta.cdi;
     requires jakarta.inject;
     requires jakarta.annotation;
+    requires jakarta.json;
     requires microprofile.config.api;
     requires org.slf4j;
 
+    opens org.trellisldp.jena to org.apache.jena.arq;
+
     provides org.trellisldp.api.IOService
         with org.trellisldp.jena.JenaIOService;
 }

trellis-jena/src/main/java/org/trellisldp/jena/JenaIOService.java

@@ -21,7 +21,7 @@
 import static org.apache.commons.rdf.api.RDFSyntax.NTRIPLES;
 import static org.apache.commons.rdf.api.RDFSyntax.RDFA;
 import static org.apache.commons.rdf.api.RDFSyntax.TURTLE;
-import static org.apache.jena.graph.Factory.createDefaultGraph;
+import static org.apache.jena.graph.GraphMemFactory.createDefaultGraph;
 import static org.apache.jena.riot.Lang.JSONLD;
 import static org.apache.jena.riot.RDFFormat.JSONLD10_COMPACT_FLAT;
 import static org.apache.jena.riot.RDFFormat.JSONLD10_EXPAND_FLAT;

trellis-jena/src/main/resources/META-INF/beans.xml

@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<beans xmlns="http://xmlns.jcp.org/xml/ns/javaee"
-       xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-       xsi:schemaLocation="http://xmlns.jcp.org/xml/ns/javaee
-                           http://xmlns.jcp.org/xml/ns/javaee/beans_1_1.xsd"
-       version="1.1" bean-discovery-mode="annotated">
+<beans xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+    xmlns="https://jakarta.ee/xml/ns/jakartaee"
+    xsi:schemaLocation="https://jakarta.ee/xml/ns/jakartaee https://jakarta.ee/xml/ns/jakartaee/beans_4_0.xsd"
+    version="4.0"
+    bean-discovery-mode="annotated">
 </beans>

trellis-jena/src/test/java/org/trellisldp/jena/JenaIOServiceTest.java

@@ -23,7 +23,7 @@
 import static org.apache.commons.rdf.api.RDFSyntax.RDFXML;
 import static org.apache.commons.rdf.api.RDFSyntax.TURTLE;
 import static org.apache.jena.commonsrdf.JenaCommonsRDF.fromJena;
-import static org.apache.jena.graph.Factory.createDefaultGraph;
+import static org.apache.jena.graph.GraphMemFactory.createDefaultGraph;
 import static org.apache.jena.graph.NodeFactory.createBlankNode;
 import static org.apache.jena.graph.NodeFactory.createLiteral;
 import static org.apache.jena.graph.NodeFactory.createURI;

trellis-jwt/src/main/resources/META-INF/beans.xml

@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<beans xmlns="http://xmlns.jcp.org/xml/ns/javaee"
-       xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-       xsi:schemaLocation="http://xmlns.jcp.org/xml/ns/javaee
-                           http://xmlns.jcp.org/xml/ns/javaee/beans_1_1.xsd"
-       version="1.1" bean-discovery-mode="annotated">
+<beans xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+    xmlns="https://jakarta.ee/xml/ns/jakartaee"
+    xsi:schemaLocation="https://jakarta.ee/xml/ns/jakartaee https://jakarta.ee/xml/ns/jakartaee/beans_4_0.xsd"
+    version="4.0"
+    bean-discovery-mode="annotated">
 </beans>

trellis-namespace/src/main/resources/META-INF/beans.xml

@@ -1,6 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<beans xmlns="http://xmlns.jcp.org/xml/ns/javaee" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-  xsi:schemaLocation="http://xmlns.jcp.org/xml/ns/javaee http://xmlns.jcp.org/xml/ns/javaee/beans_1_1.xsd" version="1.1"
-  bean-discovery-mode="annotated">
-
-</beans>
+<beans xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+    xmlns="https://jakarta.ee/xml/ns/jakartaee"
+    xsi:schemaLocation="https://jakarta.ee/xml/ns/jakartaee https://jakarta.ee/xml/ns/jakartaee/beans_4_0.xsd"
+    version="4.0"
+    bean-discovery-mode="annotated">
+</beans>

trellis-notification-jackson/src/main/resources/META-INF/beans.xml

@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<beans xmlns="http://xmlns.jcp.org/xml/ns/javaee"
-       xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-       xsi:schemaLocation="http://xmlns.jcp.org/xml/ns/javaee
-                           http://xmlns.jcp.org/xml/ns/javaee/beans_1_1.xsd"
-       version="1.1" bean-discovery-mode="annotated">
+<beans xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+    xmlns="https://jakarta.ee/xml/ns/jakartaee"
+    xsi:schemaLocation="https://jakarta.ee/xml/ns/jakartaee https://jakarta.ee/xml/ns/jakartaee/beans_4_0.xsd"
+    version="4.0"
+    bean-discovery-mode="annotated">
 </beans>

trellis-notification-jsonb/src/main/resources/META-INF/beans.xml

@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<beans xmlns="http://xmlns.jcp.org/xml/ns/javaee"
-       xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-       xsi:schemaLocation="http://xmlns.jcp.org/xml/ns/javaee
-                           http://xmlns.jcp.org/xml/ns/javaee/beans_1_1.xsd"
-       version="1.1" bean-discovery-mode="annotated">
+<beans xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+    xmlns="https://jakarta.ee/xml/ns/jakartaee"
+    xsi:schemaLocation="https://jakarta.ee/xml/ns/jakartaee https://jakarta.ee/xml/ns/jakartaee/beans_4_0.xsd"
+    version="4.0"
+    bean-discovery-mode="annotated">
 </beans>

trellis-parent/pom.xml

@@ -48,6 +48,8 @@
     <snakeyaml.version>2.2</snakeyaml.version>
     <jaxb.version>4.0.3</jaxb.version>
     <quarkus.version>3.4.2</quarkus.version>
+    <glassfish.json.version>2.0.1</glassfish.json.version>
+    <parsson.version>1.1.3</parsson.version>
 
     <!-- testing -->
     <awaitility.version>4.2.0</awaitility.version>
@@ -242,6 +244,16 @@
         <artifactId>mutiny-reactive-streams-operators</artifactId>
         <version>${smallrye.reactive.operators.version}</version>
       </dependency>
+      <dependency>
+        <groupId>org.glassfish</groupId>
+        <artifactId>jakarta.json</artifactId>
+        <version>${glassfish.json.version}</version>
+      </dependency>
+      <dependency>
+        <groupId>org.eclipse.parsson</groupId>
+        <artifactId>parsson</artifactId>
+        <version>${parsson.version}</version>
+      </dependency>
 
       <!-- testing -->
       <dependency>

trellis-rdfa/src/main/resources/META-INF/beans.xml

@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<beans xmlns="http://xmlns.jcp.org/xml/ns/javaee"
-       xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-       xsi:schemaLocation="http://xmlns.jcp.org/xml/ns/javaee
-                           http://xmlns.jcp.org/xml/ns/javaee/beans_1_1.xsd"
-       version="1.1" bean-discovery-mode="annotated">
+<beans xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+    xmlns="https://jakarta.ee/xml/ns/jakartaee"
+    xsi:schemaLocation="https://jakarta.ee/xml/ns/jakartaee https://jakarta.ee/xml/ns/jakartaee/beans_4_0.xsd"
+    version="4.0"
+    bean-discovery-mode="annotated">
 </beans>

trellis-reactive/src/main/resources/META-INF/beans.xml

@@ -1,7 +1,7 @@
 <?xml version="1.0" encoding="UTF-8"?>
-<beans xmlns="http://xmlns.jcp.org/xml/ns/javaee"
-       xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
-       xsi:schemaLocation="http://xmlns.jcp.org/xml/ns/javaee
-                           http://xmlns.jcp.org/xml/ns/javaee/beans_1_1.xsd"
-       version="1.1" bean-discovery-mode="annotated">
+<beans xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
+    xmlns="https://jakarta.ee/xml/ns/jakartaee"
+    xsi:schemaLocation="https://jakarta.ee/xml/ns/jakartaee https://jakarta.ee/xml/ns/jakartaee/beans_4_0.xsd"
+    version="4.0"
+    bean-discovery-mode="annotated">
 </beans>