Use JythonService to manage cleanup

The JythonReferenceCleaner needs to be shut down when the Context is
disposed. The JythonService provides us a dispose() hook to ensure this
happens.

To maintain the JythonReferenceCleaner, the JythonService must also be
the gateway for creating JythonScriptEngines.

Author: hinerm

src/main/java/org/scijava/plugins/scripting/jython/DefaultJythonService.java

@@ -0,0 +1,87 @@
+/*
+ * #%L
+ * JSR-223-compliant Jython scripting language plugin.
+ * %%
+ * Copyright (C) 2008 - 2016 Board of Regents of the University of
+ * Wisconsin-Madison, Broad Institute of MIT and Harvard, and Max Planck
+ * Institute of Molecular Cell Biology and Genetics.
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
+package org.scijava.plugins.scripting.jython;
+
+import javax.script.ScriptEngine;
+
+import org.scijava.log.LogService;
+import org.scijava.plugin.Parameter;
+import org.scijava.plugin.Plugin;
+import org.scijava.service.AbstractService;
+import org.scijava.service.Service;
+import org.scijava.thread.ThreadService;
+
+/**
+ * Default {@link JythonService} implementation. Maintains a
+ * {@link JythonReferenceCleaner} instance.
+ *
+ * @author Mark Hiner hinerm at gmail.com
+ */
+@Plugin(type = Service.class)
+public class DefaultJythonService extends AbstractService implements JythonService {
+
+	// -- Fields --
+
+	private JythonReferenceCleaner cleaner;
+
+	// -- Parameters --
+
+	@Parameter
+	private ThreadService threadService;
+
+	@Parameter
+	private LogService logService;
+
+	// -- JythonService methods --
+
+	@Override
+	public ScriptEngine getScriptEngine() {
+		// TODO: Consider adapting the wrapped ScriptEngineFactory's
+		// ScriptEngine.
+		final JythonScriptEngine engine = new JythonScriptEngine();
+		cleaner.queueCleanup(engine, threadService, logService);
+		return engine;
+	}
+
+	// -- Service methods --
+
+	@Override
+	public void initialize() {
+		cleaner = new JythonReferenceCleaner();
+	}
+
+	// -- Disposable methods --
+
+	@Override
+	public void dispose() {
+		cleaner.shutDown();
+	}
+}

src/main/java/org/scijava/plugins/scripting/jython/JythonReferenceCleaner.java

@@ -59,6 +59,8 @@ public class JythonReferenceCleaner {
 	private final ReferenceQueue<JythonScriptEngine> queue =
 		new ReferenceQueue<JythonScriptEngine>();
 
+	private boolean shutDown = false;
+
 	/** Queues the future cleanup operation on a separate thread, */
 	public synchronized void queueCleanup(final JythonScriptEngine engine,
 		final ThreadService threadService, final LogService log)
@@ -106,7 +108,7 @@ public void run() {
 
 								// Once we're done with our known phantom refs
 								// we can let this thread shut down
-								done = phantomReferences.size() == 0;
+								done = phantomReferences.size() == 0 || shutDown;
 							}
 
 						}
@@ -120,6 +122,10 @@ public void run() {
 		}
 	}
 
+	public void shutDown() {
+		shutDown = true;
+	}
+
 	// -- Helper classes --
 
 	/**

src/main/java/org/scijava/plugins/scripting/jython/JythonScriptLanguage.java

@@ -36,12 +36,11 @@
 import org.python.core.PyNone;
 import org.python.core.PyObject;
 import org.python.core.PyString;
-import org.scijava.log.LogService;
+import org.scijava.Context;
 import org.scijava.plugin.Parameter;
 import org.scijava.plugin.Plugin;
 import org.scijava.script.AdaptedScriptLanguage;
 import org.scijava.script.ScriptLanguage;
-import org.scijava.thread.ThreadService;
 
 /**
  * An adapter of the Jython interpreter to the SciJava scripting interface.
@@ -53,24 +52,20 @@
 @Plugin(type = ScriptLanguage.class, name = "Python")
 public class JythonScriptLanguage extends AdaptedScriptLanguage {
 
-	private JythonReferenceCleaner cleaner = new JythonReferenceCleaner();
-
-	@Parameter
-	private ThreadService threadService;
-
 	@Parameter
-	private LogService logService;
+	private Context context;
 
 	public JythonScriptLanguage() {
 		super("jython");
 	}
 
 	@Override
 	public ScriptEngine getScriptEngine() {
-		// TODO: Consider adapting the wrapped ScriptEngineFactory's ScriptEngine.
-		final JythonScriptEngine engine = new JythonScriptEngine();
-		cleaner.queueCleanup(engine, threadService, logService);
-		return engine;
+		// NB: recursive priorities can only be resolved via inter-service
+		//     dependencies. There is no way to make the ScriptService
+		//     depend on the JythonService because of the hierarchy
+		//     of components. So we have to get the JythonService indirectly.
+		return context.service(JythonService.class).getScriptEngine();
 	}
 
 	@Override

src/main/java/org/scijava/plugins/scripting/jython/JythonService.java

@@ -0,0 +1,53 @@
+/*
+ * #%L
+ * JSR-223-compliant Jython scripting language plugin.
+ * %%
+ * Copyright (C) 2008 - 2016 Board of Regents of the University of
+ * Wisconsin-Madison, Broad Institute of MIT and Harvard, and Max Planck
+ * Institute of Molecular Cell Biology and Genetics.
+ * %%
+ * Redistribution and use in source and binary forms, with or without
+ * modification, are permitted provided that the following conditions are met:
+ *
+ * 1. Redistributions of source code must retain the above copyright notice,
+ *    this list of conditions and the following disclaimer.
+ * 2. Redistributions in binary form must reproduce the above copyright notice,
+ *    this list of conditions and the following disclaimer in the documentation
+ *    and/or other materials provided with the distribution.
+ *
+ * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
+ * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
+ * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE
+ * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE
+ * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR
+ * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF
+ * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS
+ * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN
+ * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE)
+ * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE
+ * POSSIBILITY OF SUCH DAMAGE.
+ * #L%
+ */
+package org.scijava.plugins.scripting.jython;
+
+import javax.script.ScriptEngine;
+
+import org.scijava.service.SciJavaService;
+import org.scijava.service.Service;
+
+/**
+ * {@link Service} for managing contextual Jython metadata.
+ * <p>
+ * The {@link #getScriptEngine()} method should be used to access
+ * {@link JythonScriptEngine} instances, to ensure they are cleaned properly.
+ * </p>
+ *
+ * @author Mark Hiner hinerm at gmail.com
+ */
+public interface JythonService extends SciJavaService {
+
+	/**
+	 * @return Get a Jython {@link ScriptEngine} instance.
+	 */
+	ScriptEngine getScriptEngine();
+}