Fix Apache Jena in write command for GraalVM build

cli/build.gradle

@@ -18,6 +18,7 @@ dependencies {
     implementation(deps.owlapi) {
         exclude group: 'org.slf4j', module: 'slf4j-simple'
     }
+    implementation(deps.jena_core)
     implementation(deps.vavr)
     implementation(deps.picocli)
     implementation(deps.logback)

cli/src/main/java/de/atextor/owlcli/AbstractCommand.java

@@ -17,6 +17,7 @@
 
 import com.google.common.collect.ImmutableSet;
 import io.vavr.control.Try;
+import org.apache.jena.sys.JenaSystem;
 import org.semanticweb.owlapi.io.OWLParserFactory;
 import org.semanticweb.owlapi.model.OWLDataFactory;
 import org.semanticweb.owlapi.model.OWLOntology;
@@ -196,4 +197,9 @@ public Try<OWLOntology> loadOntology( final InputStream inputStream ) {
             return Try.failure( exception );
         }
     }
+
+    protected void initJena() {
+        JenaSystem.setSubsystemRegistry( new StaticJenaSubsystemRegistry() );
+        JenaSystem.init();
+    }
 }

cli/src/main/java/de/atextor/owlcli/OWLCLIWriteCommand.java

@@ -60,6 +60,8 @@ public void run() {
             .outputFormat( outputFormat )
             .inputFormat( inputFormat );
 
+        initJena();
+
         final RdfWriter writer = new RdfWriter();
 
         if ( input.toLowerCase().startsWith( "http:" ) || input.toLowerCase().startsWith( "https:" ) ) {

cli/src/main/java/de/atextor/owlcli/StaticJenaSubsystemRegistry.java

@@ -0,0 +1,70 @@
+/*
+ * This file is part of OWL-CLI.
+ * The contents of this file are subject to the LGPL License, Version 3.0.
+ * Copyright (c) 2020, Andreas Textor.
+ *
+ * This program is free software: you can redistribute it and/or modify it under the terms of the GNU Lesser General
+ * Public License as published by the Free Software Foundation, either version 3 of the License, or (at your option)
+ * any later version.
+ * This program is distributed in the hope that it will be useful, but WITHOUT ANY WARRANTY; without even the implied
+ *  warranty of MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the GNU General Public License for more
+ * details.
+ * You should have received a copy of the GNU General Public License along with this program.  If not, see http://www
+ * .gnu.org/licenses/.
+ */
+
+package de.atextor.owlcli;
+
+import org.apache.jena.sys.InitJenaCore;
+import org.apache.jena.sys.JenaSubsystemLifecycle;
+import org.apache.jena.sys.JenaSubsystemRegistry;
+
+import java.util.ArrayList;
+import java.util.List;
+
+/**
+ * This class implements Jena's internal module registry, but unlike the default implementation
+ * {@link org.apache.jena.sys.JenaSubsystemRegistryBasic}, it does not depend on the service loader
+ * mechanism, which is disabled in OWL-CLI's GraalVM build.
+ * <p>
+ * The modules list therefore must contain all classes that are mentioned in the respective
+ * META-INF/services/org.apache.jena.sys.JenaSubsystemLifcycle of the used Jena dependencies.
+ */
+public class StaticJenaSubsystemRegistry implements JenaSubsystemRegistry {
+    private final List<JenaSubsystemLifecycle> modules = List.of( new InitJenaCore() );
+
+    @Override
+    public void load() {
+        // Nothing to do
+    }
+
+    @Override
+    public void add( final JenaSubsystemLifecycle module ) {
+        // Nothing to do
+    }
+
+    @Override
+    public boolean isRegistered( final JenaSubsystemLifecycle module ) {
+        return modules.contains( module );
+    }
+
+    @Override
+    public void remove( final JenaSubsystemLifecycle module ) {
+        // Nothing to do
+    }
+
+    @Override
+    public int size() {
+        return modules.size();
+    }
+
+    @Override
+    public boolean isEmpty() {
+        return modules.isEmpty();
+    }
+
+    @Override
+    public List<JenaSubsystemLifecycle> snapshot() {
+        return new ArrayList<>( modules );
+    }
+}

cli/src/main/resources/META-INF/native-image/de.atextor/owlcli/reflect-config.json

@@ -243,6 +243,11 @@
   "allDeclaredMethods":true,
   "allPublicMethods":true
 },
+{
+  "name":"de.atextor.owlcli.OWLCLIWriteCommand",
+  "allDeclaredFields":true,
+  "allDeclaredMethods":true
+},
 {
   "name":"java.lang.Object",
   "allDeclaredFields":true,
@@ -336,6 +341,21 @@
   "name":"java.time.ZonedDateTime",
   "methods":[{"name":"parse","parameterTypes":["java.lang.CharSequence"] }]
 },
+{
+  "name":"org.apache.jena.ext.com.google.common.cache.Striped64",
+  "fields":[
+    {"name":"base", "allowUnsafeAccess":true},
+    {"name":"busy", "allowUnsafeAccess":true}
+  ]
+},
+{
+  "name":"org.apache.jena.n3.N3TurtleJenaWriter",
+  "methods":[{"name":"<init>","parameterTypes":[] }]
+},
+{
+  "name":"org.apache.jena.n3.turtle.TurtleReader",
+  "methods":[{"name":"<init>","parameterTypes":[] }]
+},
 {
   "name":"org.semanticweb.owlapi.apibinding.OWLManager$InjectorConstants",
   "fields":[

cli/src/main/resources/META-INF/native-image/de.atextor/owlcli/resource-config.json

@@ -1,8 +1,11 @@
 {
   "resources":[
+    {"pattern":"\\QMETA-INF/services/org.apache.jena.sys.JenaSubsystemLifecycle\\E"},
+    {"pattern":"\\Qorg/apache/jena/jena-properties.xml\\E"},
     {"pattern":"\\Qorg/slf4j/impl/StaticLoggerBinder.class\\E"}
   ],
   "bundles": [
-    {"name":"com.sun.org.apache.xerces.internal.impl.msg.XMLMessages"}
+    {"name":"com.sun.org.apache.xerces.internal.impl.msg.XMLMessages"},
+    {"name":"org.apache.jena.ext.xerces.impl.xpath.regex.message"}
   ]
 }