Don't use SharedSecrets, but instead directly call a private constructor

This solves the problem that SharedSecrets is found in different
packages across different Java versions, e.g.
- jdk.internal.access.SharedSecrets in OpenJDK 12+
- jdk.internal.misc.SharedSecrets in OpenJDK <12
- sun.misc.SharedSecrets in Oracle JDK 8

wrappers/java/src/main/java/org/ensembl/hive/RunWrapper.java

@@ -23,8 +23,6 @@
 import org.slf4j.Logger;
 import org.slf4j.LoggerFactory;
 
-import jdk.internal.access.SharedSecrets;
-
 import org.ensembl.hive.Utils;
 
 /**
@@ -70,10 +68,11 @@ public static void main(String[] args) throws Exception {
 
 		BaseRunnable runnable = Utils.findRunnable(args[0]);
 
-        FileDescriptor inputDescriptor = new FileDescriptor();
-        SharedSecrets.getJavaIOFileDescriptorAccess().set(inputDescriptor, Integer.parseInt(args[1]));
-        FileDescriptor outputDescriptor = new FileDescriptor();
-        SharedSecrets.getJavaIOFileDescriptorAccess().set(outputDescriptor, Integer.parseInt(args[2]));
+		Constructor<FileDescriptor> fdctor = FileDescriptor.class.getDeclaredConstructor(Integer.TYPE);
+		fdctor.setAccessible(true);
+		FileDescriptor inputDescriptor = fdctor.newInstance(Integer.parseInt(args[1]));
+		FileDescriptor outputDescriptor = fdctor.newInstance(Integer.parseInt(args[2]));
+		fdctor.setAccessible(false);
         runnable.setFileDescriptors(inputDescriptor, outputDescriptor);
 
 		runnable.processLifeCycle();

wrappers/java/wrapper

@@ -73,7 +73,7 @@ elif [ "$action" == "run" ]; then
 		exit 1
 	fi
 
-	exec java -cp "$jar" --add-exports java.base/jdk.internal.access=ALL-UNNAMED org.ensembl.hive.RunWrapper "$module" "$fd_in" "$fd_out" "$debug"
+	exec java -cp "$jar" --add-opens java.base/java.io=ALL-UNNAMED org.ensembl.hive.RunWrapper "$module" "$fd_in" "$fd_out" "$debug"
 
 else
 	echo "Command-line error: No mode provided"