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| 1 | +/* |
| 2 | + * #%L |
| 3 | + * JSR-223-compliant Jython scripting language plugin. |
| 4 | + * %% |
| 5 | + * Copyright (C) 2008 - 2015 Board of Regents of the University of |
| 6 | + * Wisconsin-Madison, Broad Institute of MIT and Harvard, and Max Planck |
| 7 | + * Institute of Molecular Cell Biology and Genetics. |
| 8 | + * %% |
| 9 | + * Redistribution and use in source and binary forms, with or without |
| 10 | + * modification, are permitted provided that the following conditions are met: |
| 11 | + * |
| 12 | + * 1. Redistributions of source code must retain the above copyright notice, |
| 13 | + * this list of conditions and the following disclaimer. |
| 14 | + * 2. Redistributions in binary form must reproduce the above copyright notice, |
| 15 | + * this list of conditions and the following disclaimer in the documentation |
| 16 | + * and/or other materials provided with the distribution. |
| 17 | + * |
| 18 | + * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" |
| 19 | + * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE |
| 20 | + * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE |
| 21 | + * ARE DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDERS OR CONTRIBUTORS BE |
| 22 | + * LIABLE FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR |
| 23 | + * CONSEQUENTIAL DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF |
| 24 | + * SUBSTITUTE GOODS OR SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS |
| 25 | + * INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN |
| 26 | + * CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) |
| 27 | + * ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE, EVEN IF ADVISED OF THE |
| 28 | + * POSSIBILITY OF SUCH DAMAGE. |
| 29 | + * #L% |
| 30 | + */ |
| 31 | + |
| 32 | +package org.scijava.plugins.scripting.jython; |
| 33 | + |
| 34 | +import java.lang.ref.PhantomReference; |
| 35 | +import java.lang.ref.ReferenceQueue; |
| 36 | +import java.util.ArrayList; |
| 37 | +import java.util.LinkedList; |
| 38 | +import java.util.List; |
| 39 | + |
| 40 | +import org.python.core.PyObject; |
| 41 | +import org.python.util.PythonInterpreter; |
| 42 | +import org.scijava.log.LogService; |
| 43 | +import org.scijava.thread.ThreadService; |
| 44 | + |
| 45 | +/** |
| 46 | + * A helper class for purging dangling references within a Jython interpreter |
| 47 | + * after it executes a script. |
| 48 | + * |
| 49 | + * @author Mark Hiner |
| 50 | + */ |
| 51 | +public class JythonReferenceCleaner { |
| 52 | + |
| 53 | + // List of PhantomReferences and corresponding ReferenceQueue to |
| 54 | + // facilitate proper PhantomReference use. |
| 55 | + // See http://resources.ej-technologies.com/jprofiler/help/doc/index.html |
| 56 | + |
| 57 | + private final LinkedList<JythonEnginePhantomReference> phantomReferences = |
| 58 | + new LinkedList<JythonEnginePhantomReference>(); |
| 59 | + private final ReferenceQueue<JythonScriptEngine> queue = |
| 60 | + new ReferenceQueue<JythonScriptEngine>(); |
| 61 | + |
| 62 | + /** Queues the future cleanup operation on a separate thread, */ |
| 63 | + public synchronized void queueCleanup(final JythonScriptEngine engine, |
| 64 | + final ThreadService threadService, final LogService log) |
| 65 | + { |
| 66 | + // NB: This phantom reference is used to clean up any local variables |
| 67 | + // created by evaluation of scripts via this ScriptEngine. We need |
| 68 | + // to use PhantomReferences because the "scope" of a script extends |
| 69 | + // beyond its eval method - a consumer may still want to inspect |
| 70 | + // the state of variables after evaluation. |
| 71 | + // |
| 72 | + // By using PhantomReferences we are saying that the scope of |
| 73 | + // script evaluation equals the lifetime of the ScriptEngine. |
| 74 | + phantomReferences.add(new JythonEnginePhantomReference(engine, queue)); |
| 75 | + |
| 76 | + // NB: The use of PhantomReferences requires a paired polling thread. |
| 77 | + // We poll instead of blocking for input to avoid leaving lingering |
| 78 | + // threads that would need to be interrupted - instead only starting |
| 79 | + // threads running when there is actually a PhantomReference that |
| 80 | + // will eventually be enqueued. |
| 81 | + // |
| 82 | + // Here we check if there is already a polling thread in operation - |
| 83 | + // if not, we start a new thread. |
| 84 | + if (phantomReferences.size() == 1) { |
| 85 | + threadService.run(new Runnable() { |
| 86 | + |
| 87 | + @Override |
| 88 | + public void run() { |
| 89 | + boolean done = false; |
| 90 | + |
| 91 | + // poll the queue |
| 92 | + while (!done) { |
| 93 | + try { |
| 94 | + Thread.sleep(100); |
| 95 | + |
| 96 | + synchronized (JythonReferenceCleaner.this) { |
| 97 | + // poll the queue |
| 98 | + final JythonEnginePhantomReference ref = |
| 99 | + (JythonEnginePhantomReference) queue.poll(); |
| 100 | + |
| 101 | + // if we have a ref, clean it up |
| 102 | + if (ref != null) { |
| 103 | + ref.cleanup(); |
| 104 | + phantomReferences.remove(ref); |
| 105 | + } |
| 106 | + |
| 107 | + // Once we're done with our known phantom refs |
| 108 | + // we can let this thread shut down |
| 109 | + done = phantomReferences.size() == 0; |
| 110 | + } |
| 111 | + |
| 112 | + } |
| 113 | + catch (final Exception ex) { |
| 114 | + // log exception, continue |
| 115 | + log.error(ex); |
| 116 | + } |
| 117 | + } |
| 118 | + } |
| 119 | + }); |
| 120 | + } |
| 121 | + } |
| 122 | + |
| 123 | + // -- Helper classes -- |
| 124 | + |
| 125 | + /** |
| 126 | + * Helper class to clean up {@link PythonInterpreter} local variables when a |
| 127 | + * parent {@link JythonScriptEngine} leaves scope. |
| 128 | + */ |
| 129 | + private static class JythonEnginePhantomReference extends |
| 130 | + PhantomReference<JythonScriptEngine> |
| 131 | + { |
| 132 | + |
| 133 | + public PythonInterpreter interpreter; |
| 134 | + |
| 135 | + public JythonEnginePhantomReference(final JythonScriptEngine engine, |
| 136 | + final ReferenceQueue<JythonScriptEngine> queue) |
| 137 | + { |
| 138 | + super(engine, queue); |
| 139 | + interpreter = engine.interpreter; |
| 140 | + } |
| 141 | + |
| 142 | + public void cleanup() { |
| 143 | + final List<String> scriptLocals = new ArrayList<String>(); |
| 144 | + final PythonInterpreter interp = interpreter; |
| 145 | + if (interp == null) return; |
| 146 | + |
| 147 | + // NB: This method for cleaning up local variables was taken from: |
| 148 | + // http://python.6.x6.nabble.com/Cleaning-up-PythonInterpreter-object-td1777184.html |
| 149 | + // |
| 150 | + // Because Python is an interpreted language, when a Python script |
| 151 | + // creates new variables they stick around in a static |
| 152 | + // org.python.core.PySystemState variable (defaultSystemState) |
| 153 | + // the org.python.core.Py class. |
| 154 | + // |
| 155 | + // Thus an implicit static state is created by script evaluation, |
| 156 | + // so we must manually clean up local variables known to the |
| 157 | + // interpreter when the scope of an executed script is over. |
| 158 | + // |
| 159 | + // See original bug report for the leak that prompted this solution: |
| 160 | + // http://fiji.sc/bugzilla/show_bug.cgi?id=1203 |
| 161 | + |
| 162 | + final PyObject locals = interp.getLocals(); |
| 163 | + for (final PyObject item : locals.__iter__().asIterable()) { |
| 164 | + final String localVar = item.toString(); |
| 165 | + // Ignore __name__ and __doc__ variables, which are special |
| 166 | + // and known not to be local variables created by evaluation. |
| 167 | + if (!localVar.contains("__name__") && !localVar.contains("__doc__")) { |
| 168 | + // Build list of variables to clean |
| 169 | + scriptLocals.add(item.toString()); |
| 170 | + } |
| 171 | + } |
| 172 | + // Null out local variables |
| 173 | + for (final String string : scriptLocals) { |
| 174 | + interp.set(string, null); |
| 175 | + } |
| 176 | + } |
| 177 | + } |
| 178 | + |
| 179 | +} |
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