Kepler: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362017-05-18T20:10:09ZEcoinformatics Redmine
Redmine Bug #7191 (Resolved): memory leak in CompositeActor for actor firing listenershttps://projects.ecoinformatics.org/ecoinfo/issues/71912017-05-18T20:10:09ZDaniel Crawldanielcrawl@gmail.com
<p>List of actor firing listeners needs to be null before cloning. I'm attaching a patch.</p> Bug #7190 (Resolved): memory leak due to hierarchy listeners when cloninghttps://projects.ecoinformatics.org/ecoinfo/issues/71902017-05-12T00:09:00ZDaniel Crawldanielcrawl@gmail.com
<p>When a model is cloned, some NamedObjs in the new model have hierarchy listeners from the original model, which prevents the new model from being garbage collected.</p>
<p>In the usecase I'm debugging, the toplevel Composites in both the original and new models are added as hierarchy listeners to PortParameters, but only the toplevel in the new model should be added. The original toplevel is added since clone() and setContainer() are called for the PortParameter before its container actor has been moved to the new toplevel.</p>
<p>I don't know the best approach to fix this. Making the listeners weak references would fix the memory leaks, but wrong listeners would still receive hierarchy change events.</p> Bug #7019 (Resolved): cloning problems in NamedObj and AtomicActorhttps://projects.ecoinformatics.org/ecoinfo/issues/70192016-05-03T18:57:04ZDaniel Crawldanielcrawl@gmail.com
<p>I'm attaching a patch to fix cloning issues in NamedObj.java:</p>
<p>// Since _debugListeners is null, _debugging should be<br />// false to avoid error message in _debug()</p>
<p>and AtomicActor.java:</p>
<p>// When super.clone() is called below, attributes that are<br />// contained in this actor are also cloned, which includes<br />// calling methods on these attributes such as setContainer().<br />// These methods may add themselves to the firing listeners<br />// or initializables lists in the newObject clone, so we do<br />// not want to clear these lists in newObject after super.clone().<br />// Instead, save this instance's lists here and restore them after<br />// call super.clone().</p> Bug #6928 (Resolved): Check Kepler for the Apache commons deserialization problems, consider remo...https://projects.ecoinformatics.org/ecoinfo/issues/69282016-01-04T21:21:00ZChristopher Brookscxh@eecs.berkeley.edu
<p>I recently had a Windows machine that was successfully attacked because it was running an old version of Jenkins that was susceptible to an attack via Apache Commons Java deserialization. The email from campus stated:</p>
<blockquote>
<p>"The snort alarms concern an apparent remote attack against a "serious vulnerability in Apache Commons, a library that contains a widely used set of Java components maintained by the Apache Software Foundation, puts thousands of Java applications and servers at risk of remote code execution attacks. The library is used by default in multiple Java application servers and other products including Oracle WebLogic, IBM WebSphere, JBoss, Jenkins and OpenNMS."</p>
</blockquote>
<blockquote>
<p>"Please see"</p>
</blockquote>
<blockquote>
<p><a class="external" href="http://foxglovesecurity.com/2015/11/06/what-do-weblogic-websphere-jboss-jenkins-opennms-and-your-application-have-in-common-this-vulnerability/">http://foxglovesecurity.com/2015/11/06/what-do-weblogic-websphere-jboss-jenkins-opennms-and-your-application-have-in-common-this-vulnerability/</a></p>
</blockquote>
<blockquote>
<p><a class="external" href="http://www.oracle.com/technetwork/topics/security/alert-cve-2015-4852-2763333.html">http://www.oracle.com/technetwork/topics/security/alert-cve-2015-4852-2763333.html</a></p>
</blockquote>
<blockquote>
<p><a class="external" href="https://blogs.apache.org/foundation/entry/apache_commons_statement_to_widespread">https://blogs.apache.org/foundation/entry/apache_commons_statement_to_widespread</a></p>
</blockquote>
<p>It looks like Kepler includes the library in question:<br /><pre>
bash-3.2$ find . -name "*.jar" | xargs grep -Rl InvokerTransformer
./configuration-manager/lib/jar/commons-collections-3.2.1.jar
</pre></p>
<p>commons-collections-3.2.1.jar contains classes in packages starting with org.apache.commons.collections</p>
<p>However, I believe that the Kepler *.java files are not directly using those classes, below are classes in org.apache.commons that are imported. Note that we are not importing classes from org.apache.commons.collections:</p>
<pre>
bash-3.2$ find . -name "*.java" | xargs grep org.apache.commons | grep import | tr -d '\r' | awk '{print $NF}' | sort | uniq -c | sort -nr
235 org.apache.commons.logging.LogFactory;
235 org.apache.commons.logging.Log;
3 org.apache.commons.io.IOUtils;
3 org.apache.commons.configuration.XMLConfiguration;
2 org.apache.commons.net.ftp.FTP;
2 org.apache.commons.lang.StringEscapeUtils;
2 org.apache.commons.io.FileUtils;
2 org.apache.commons.httpclient.methods.multipart.StringPart;
2 org.apache.commons.httpclient.methods.multipart.Part;
2 org.apache.commons.httpclient.methods.multipart.FilePart;
2 org.apache.commons.httpclient.methods.MultipartPostMethod;
2 org.apache.commons.httpclient.methods.GetMethod;
2 org.apache.commons.httpclient.HttpException;
2 org.apache.commons.httpclient.HttpClient;
2 org.apache.commons.configuration.ConfigurationException;
1 org.apache.commons.lang.time.DateUtils;
1 org.apache.commons.lang.exception.ExceptionUtils;
1 org.apache.commons.io.FilenameUtils;
1 org.apache.commons.configuration.tree.ConfigurationNode;
1 org.apache.commons.configuration.PropertiesConfiguration;
1 org.apache.commons.configuration.HierarchicalConfiguration;
bash-3.2$
</pre>
<p>However, there could be dependencies between jar files used by Kepler and commons-collections-3.2.1.jar.</p>
<p><a class="external" href="https://www.kb.cert.org/vuls/id/576313">https://www.kb.cert.org/vuls/id/576313</a> suggests upgrading to Apache Commons Collections version 3.2.2</p>
<p>However, perhaps we can remove this class?</p>
<p>The log is below:<br /><pre>
bash-3.2$ svn log ./configuration-manager/lib/jar/commons-collections-3.2.1.jar
------------------------------------------------------------------------
r24000 | berkley | 2010-04-27 17:12:36 -0700 (Tue, 27 Apr 2010) | 1 line
changing keywords and eol-style on the repository
------------------------------------------------------------------------
r20925 | berkley | 2009-10-07 15:06:24 -0700 (Wed, 07 Oct 2009) | 1 line
writing tests to show the capabilities of commons and yaml and to compare them
------------------------------------------------------------------------
bash-3.2$
</pre></p> Bug #6834 (Resolved): kepler data can icon displayed incorrectlyhttps://projects.ecoinformatics.org/ecoinfo/issues/68342015-08-25T22:56:03ZDaniel Crawldanielcrawl@gmail.com
<p>The "data can" icon used by DataTurbine and several other Kepler actors is displayed incorrectly. This appears to have been started with Ptolemy r73168 (r73163-73167 do not compile).</p> Bug #6681 (Resolved): unnecessary warnings when removing parametershttps://projects.ecoinformatics.org/ecoinfo/issues/66812015-03-02T22:03:52ZDaniel Crawldanielcrawl@gmail.com
<p>When a parameter is removed that is referenced by something else, a warning is displayed to the user (in Variable.setContainer()). However, there are situations where the reference should be ignored. For example, the Kepler provenance recorder has a reference to all the parameters in the workflow. Another example is PtolemyQuery in attachParameter().</p>
<p>Attached is a patch to avoid these unnecessary warnings.</p> Bug #6676 (Resolved): External Execution actors generates exception for empty directoryhttps://projects.ecoinformatics.org/ecoinfo/issues/66762015-02-27T21:36:46ZDaniel Crawldanielcrawl@gmail.com
<p>If the directory parameter is empty for the External Execution actor, a NullPointerException is generated:</p>
<p>java.lang.NullPointerException<br /> at ptolemy.actor.lib.Exec._exec(Exec.java:516)<br /> at ptolemy.actor.lib.Exec.fire(Exec.java:337)<br /> at ptolemy.actor.AtomicActor.iterate(AtomicActor.java:496)</p>
<p>It would be better to default to user.dir or throw an exception saying directory must be specified.</p> Bug #6615 (Resolved): apple-extensions does not compile with java 8https://projects.ecoinformatics.org/ecoinfo/issues/66152014-11-02T21:28:46ZDaniel Crawldanielcrawl@gmail.com
<p>The apple-extensions module does not compile with java 8 because the package com.apple.eawt is no longer on the default classpath. Prior to java 8, these classes were in ui.jar, but are now in rt.jar, which is not used by javac. I tried explicitly adding rt.jar to the classpath, but javac still fails.</p>
<p>A workaround is to comment out this module from the Kepler suite.</p> Bug #6578 (Resolved): cannot hide director LocalClockhttps://projects.ecoinformatics.org/ecoinfo/issues/65782014-07-09T23:25:21ZDaniel Crawldanielcrawl@gmail.com
<p>I'd like to hide the "localClock" parameter in the edit parameters dialog for our DDPDirector. The problem is that LocalClock.setVisibility() overrides the base class and does nothing.</p> Bug #6577 (Resolved): infinite loop resolving port widthhttps://projects.ecoinformatics.org/ecoinfo/issues/65772014-07-09T23:06:53ZDaniel Crawldanielcrawl@gmail.com
<p>There are several actors whose output port is set to multiport. When this port is connected to a multiport input port, an error occurs when the workflow executes saying that the default port width could not be determined. The error message says that one way to fix this is call setDefaultPortWidth(1). This works if the output port is connected to only one port, but if the output port is connected to more ports, an infinite loop occurs during preinitialize(). I'm attaching an example workflow.</p> Bug #6572 (Resolved): An error is thrown when opening MatlabExpression.xml in common/workflows/de...https://projects.ecoinformatics.org/ecoinfo/issues/65722014-06-16T22:27:47Zjianwu jianwujianwu@sdsc.edu
<p>I got the following errors. The main reason is that $name is in the documentation of the actor explaining the expression parameter. If I edit the xml changing from $name to be $$name, the workflow can be opened correctly.</p>
<p>The same workflow works fine with Kepler 2.4. Not sure which changes in Kepler trunk cause this problem.</p>
<p>ptolemy.kernel.util.IllegalActionException: Error evaluating expression: <br />The parameter that is evaluated to produce the output. Typically, this parameter <br />evaluates an expression involving the inputs. To refer to parameters in scope <br />within the expression, use $name or ${name}, where "name" is the name of the <br />parameter.</p>
<pre><code>in .MatlabExpression.MatlabExpression.&lt;Unnamed Object&gt;.expression (parameter)<br />Because:<br />The ID name is undefined.<br /> in .MatlabExpression.MatlabExpression.&lt;Unnamed Object&gt;.expression (parameter)<br />Because:<br />Error evaluating expression: <br />The parameter that is evaluated to produce the output. Typically, this parameter <br />evaluates an expression involving the inputs. To refer to parameters in scope <br />within the expression, use $name or ${name}, where "name" is the name of the <br />parameter.</code></pre>
<pre><code>in .MatlabExpression.MatlabExpression.&lt;Unnamed Object&gt;.expression (parameter)<br />Because:<br />The ID name is undefined.<br /> at ptolemy.data.expr.Variable.validate(Variable.java:1507)<br /> at ptolemy.moml.MoMLParser.endDocument(MoMLParser.java:816)<br /> at com.microstar.xml.XmlParser.doParse(XmlParser.java:162)<br /> at com.microstar.xml.XmlParser.parse(XmlParser.java:132)<br /> at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1571)<br /> at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1507)<br /> at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1451)<br /> at ptolemy.moml.MoMLParser.parseFile(MoMLParser.java:1735)<br /> at org.kepler.gui.component.OpenCompositeAction.actionPerformed(OpenCompositeAction.java:147)<br /> at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2028)<br /> at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2351)<br /> at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)<br /> at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)<br /> at javax.swing.AbstractButton.doClick(AbstractButton.java:389)<br /> at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:809)<br /> at com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:137)<br /> at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:850)<br /> at java.awt.Component.processMouseEvent(Component.java:6414)<br /> at javax.swing.JComponent.processMouseEvent(JComponent.java:3275)<br /> at java.awt.Component.processEvent(Component.java:6179)<br /> at java.awt.Container.processEvent(Container.java:2084)<br /> at java.awt.Component.dispatchEventImpl(Component.java:4776)<br /> at java.awt.Container.dispatchEventImpl(Container.java:2142)<br /> at java.awt.Component.dispatchEvent(Component.java:4604)<br /> at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4618)<br /> at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4279)<br /> at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4209)<br /> at java.awt.Container.dispatchEventImpl(Container.java:2128)<br /> at java.awt.Window.dispatchEventImpl(Window.java:2492)<br /> at java.awt.Component.dispatchEvent(Component.java:4604)<br /> at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:717)<br /> at java.awt.EventQueue.access$400(EventQueue.java:82)<br /> at java.awt.EventQueue$2.run(EventQueue.java:676)<br /> at java.awt.EventQueue$2.run(EventQueue.java:674)<br /> at java.security.AccessController.doPrivileged(Native Method)<br /> at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86)<br /> at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:97)<br /> at java.awt.EventQueue$3.run(EventQueue.java:690)<br /> at java.awt.EventQueue$3.run(EventQueue.java:688)<br /> at java.security.AccessController.doPrivileged(Native Method)<br /> at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86)<br /> at java.awt.EventQueue.dispatchEvent(EventQueue.java:687)<br /> at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)<br /> at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)<br /> at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)<br /> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)<br /> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)<br /> at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)<br />Caused by: ptolemy.kernel.util.IllegalActionException: Error evaluating expression: <br />The parameter that is evaluated to produce the output. Typically, this parameter <br />evaluates an expression involving the inputs. To refer to parameters in scope <br />within the expression, use $name or ${name}, where "name" is the name of the <br />parameter.</code></pre>
<pre><code>in .MatlabExpression.MatlabExpression.&lt;Unnamed Object&gt;.expression (parameter)<br />Because:<br />The ID name is undefined.<br /> at ptolemy.data.expr.Variable._evaluate(Variable.java:1771)<br /> at ptolemy.data.expr.Variable._propagate(Variable.java:1848)<br /> at ptolemy.data.expr.Variable.validate(Variable.java:1484)<br /> ... 47 more<br />Caused by: ptolemy.data.expr.UndefinedConstantOrIdentifierException: The ID name is undefined.<br /> at ptolemy.data.expr.ParseTreeEvaluator.visitLeafNode(ParseTreeEvaluator.java:723)<br /> at ptolemy.data.expr.ASTPtLeafNode.visit(ASTPtLeafNode.java:125)<br /> at ptolemy.data.expr.ParseTreeEvaluator._evaluateChild(ParseTreeEvaluator.java:1360)<br /> at ptolemy.data.expr.ParseTreeEvaluator._evaluateAllChildren(ParseTreeEvaluator.java:1314)<br /> at ptolemy.data.expr.ParseTreeEvaluator.visitSumNode(ParseTreeEvaluator.java:1166)<br /> at ptolemy.data.expr.ASTPtSumNode.visit(ASTPtSumNode.java:129)<br /> at ptolemy.data.expr.ParseTreeEvaluator.evaluateParseTree(ParseTreeEvaluator.java:105)<br /> at ptolemy.data.expr.Variable._evaluate(Variable.java:1753)<br /> ... 49 more<br />Caused by: ptolemy.kernel.util.IllegalActionException: Error evaluating expression: <br />The parameter that is evaluated to produce the output. Typically, this parameter <br />evaluates an expression involving the inputs. To refer to parameters in scope <br />within the expression, use $name or ${name}, where "name" is the name of the <br />parameter.</code></pre>
<pre><code>in .MatlabExpression.MatlabExpression.&lt;Unnamed Object&gt;.expression (parameter)<br />Because:<br />The ID name is undefined.<br /> at ptolemy.data.expr.Variable._evaluate(Variable.java:1771)<br /> at ptolemy.data.expr.Variable._propagate(Variable.java:1848)<br /> at ptolemy.data.expr.Variable.validate(Variable.java:1484)<br /> at ptolemy.moml.MoMLParser.endDocument(MoMLParser.java:816)<br /> at com.microstar.xml.XmlParser.doParse(XmlParser.java:162)<br /> at com.microstar.xml.XmlParser.parse(XmlParser.java:132)<br /> at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1571)<br /> at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1507)<br /> at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1451)<br /> at ptolemy.moml.MoMLParser.parseFile(MoMLParser.java:1735)<br /> at org.kepler.gui.component.OpenCompositeAction.actionPerformed(OpenCompositeAction.java:147)<br /> at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2028)<br /> at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2351)<br /> at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)<br /> at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)<br /> at javax.swing.AbstractButton.doClick(AbstractButton.java:389)<br /> at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:809)<br /> at com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:137)<br /> at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:850)<br /> at java.awt.Component.processMouseEvent(Component.java:6414)<br /> at javax.swing.JComponent.processMouseEvent(JComponent.java:3275)<br /> at java.awt.Component.processEvent(Component.java:6179)<br /> at java.awt.Container.processEvent(Container.java:2084)<br /> at java.awt.Component.dispatchEventImpl(Component.java:4776)<br /> at java.awt.Container.dispatchEventImpl(Container.java:2142)<br /> at java.awt.Component.dispatchEvent(Component.java:4604)<br /> at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4618)<br /> at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4279)<br /> at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4209)<br /> at java.awt.Container.dispatchEventImpl(Container.java:2128)<br /> at java.awt.Window.dispatchEventImpl(Window.java:2492)<br /> at java.awt.Component.dispatchEvent(Component.java:4604)<br /> at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:717)<br /> at java.awt.EventQueue.access$400(EventQueue.java:82)<br /> at java.awt.EventQueue$2.run(EventQueue.java:676)<br /> at java.awt.EventQueue$2.run(EventQueue.java:674)<br /> at java.security.AccessController.doPrivileged(Native Method)<br /> at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86)<br /> at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:97)<br /> at java.awt.EventQueue$3.run(EventQueue.java:690)<br /> at java.awt.EventQueue$3.run(EventQueue.java:688)<br /> at java.security.AccessController.doPrivileged(Native Method)<br /> at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86)<br /> at java.awt.EventQueue.dispatchEvent(EventQueue.java:687)<br /> at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)<br /> at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)<br /> at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)<br /> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)<br /> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)<br /> at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)<br />Caused by: ptolemy.data.expr.UndefinedConstantOrIdentifierException: The ID name is undefined.<br /> at ptolemy.data.expr.ParseTreeEvaluator.visitLeafNode(ParseTreeEvaluator.java:723)<br /> at ptolemy.data.expr.ASTPtLeafNode.visit(ASTPtLeafNode.java:125)<br /> at ptolemy.data.expr.ParseTreeEvaluator._evaluateChild(ParseTreeEvaluator.java:1360)<br /> at ptolemy.data.expr.ParseTreeEvaluator._evaluateAllChildren(ParseTreeEvaluator.java:1314)<br /> at ptolemy.data.expr.ParseTreeEvaluator.visitSumNode(ParseTreeEvaluator.java:1166)<br /> at ptolemy.data.expr.ASTPtSumNode.visit(ASTPtSumNode.java:129)<br /> at ptolemy.data.expr.ParseTreeEvaluator.evaluateParseTree(ParseTreeEvaluator.java:105)<br /> at ptolemy.data.expr.Variable._evaluate(Variable.java:1753)<br /> ... 49 more<br />Caused by: ptolemy.data.expr.UndefinedConstantOrIdentifierException: The ID name is undefined.<br /> at ptolemy.data.expr.ParseTreeEvaluator.visitLeafNode(ParseTreeEvaluator.java:723)<br /> at ptolemy.data.expr.ASTPtLeafNode.visit(ASTPtLeafNode.java:125)<br /> at ptolemy.data.expr.ParseTreeEvaluator._evaluateChild(ParseTreeEvaluator.java:1360)<br /> at ptolemy.data.expr.ParseTreeEvaluator._evaluateAllChildren(ParseTreeEvaluator.java:1314)<br /> at ptolemy.data.expr.ParseTreeEvaluator.visitSumNode(ParseTreeEvaluator.java:1166)<br /> at ptolemy.data.expr.ASTPtSumNode.visit(ASTPtSumNode.java:129)<br /> at ptolemy.data.expr.ParseTreeEvaluator.evaluateParseTree(ParseTreeEvaluator.java:105)<br /> at ptolemy.data.expr.Variable._evaluate(Variable.java:1753)<br /> at ptolemy.data.expr.Variable._propagate(Variable.java:1848)<br /> at ptolemy.data.expr.Variable.validate(Variable.java:1484)<br /> at ptolemy.moml.MoMLParser.endDocument(MoMLParser.java:816)<br /> at com.microstar.xml.XmlParser.doParse(XmlParser.java:162)<br /> at com.microstar.xml.XmlParser.parse(XmlParser.java:132)<br /> at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1571)<br /> at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1507)<br /> at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1451)<br /> at ptolemy.moml.MoMLParser.parseFile(MoMLParser.java:1735)<br /> at org.kepler.gui.component.OpenCompositeAction.actionPerformed(OpenCompositeAction.java:147)<br /> at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2028)<br /> at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2351)<br /> at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)<br /> at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)<br /> at javax.swing.AbstractButton.doClick(AbstractButton.java:389)<br /> at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:809)<br /> at com.apple.laf.AquaMenuItemUI.doClick(AquaMenuItemUI.java:137)<br /> at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:850)<br /> at java.awt.Component.processMouseEvent(Component.java:6414)<br /> at javax.swing.JComponent.processMouseEvent(JComponent.java:3275)<br /> at java.awt.Component.processEvent(Component.java:6179)<br /> at java.awt.Container.processEvent(Container.java:2084)<br /> at java.awt.Component.dispatchEventImpl(Component.java:4776)<br /> at java.awt.Container.dispatchEventImpl(Container.java:2142)<br /> at java.awt.Component.dispatchEvent(Component.java:4604)<br /> at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4618)<br /> at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4279)<br /> at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4209)<br /> at java.awt.Container.dispatchEventImpl(Container.java:2128)<br /> at java.awt.Window.dispatchEventImpl(Window.java:2492)<br /> at java.awt.Component.dispatchEvent(Component.java:4604)<br /> at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:717)<br /> at java.awt.EventQueue.access$400(EventQueue.java:82)<br /> at java.awt.EventQueue$2.run(EventQueue.java:676)<br /> at java.awt.EventQueue$2.run(EventQueue.java:674)<br /> at java.security.AccessController.doPrivileged(Native Method)<br /> at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86)<br /> at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:97)<br /> at java.awt.EventQueue$3.run(EventQueue.java:690)<br /> at java.awt.EventQueue$3.run(EventQueue.java:688)<br /> at java.security.AccessController.doPrivileged(Native Method)<br /> at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86)<br /> at java.awt.EventQueue.dispatchEvent(EventQueue.java:687)<br /> at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)<br /> at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)<br /> at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)<br /> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)<br /> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)<br /> at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)</code></pre> Bug #6386 (Resolved): cannot drop second matlab actor on canvashttps://projects.ecoinformatics.org/ecoinfo/issues/63862014-01-16T01:22:25ZDaniel Crawldanielcrawl@gmail.com
<p>I get an error when I drop a second matlab actor on the canvas:</p>
<pre><code>[run] Error inside GetMomlFromLSID.getMoml(): Failed to set _iteration to 1: ptolemy.kernel.util.NameDuplicationException: Attempt to insert object named "iteration" into a container that already contains an object with that name.<br /> [run] Error creating alternateGetMoml!</code></pre>
<p>This doesn't occur in Vergil.</p>
<p>A workaround is to copy and paste the actor.</p> Bug #6371 (Resolved): Documentation: missing content in section 1.1.1 Featureshttps://projects.ecoinformatics.org/ecoinfo/issues/63712014-01-13T18:00:39Zben leinfelderleinfelder@nceas.ucsb.edu
<p>From the NCEAS help system:<br />-----------------<br />In the User's Manual, on page 11, just above the title 1.1.2 Architecture, the sentence ends in "...using a Seman" that's an odd end, and I suspect part of a sentence disappeared. Could you please verify and correct if necessary? Thanks in advance, Koen</p> Bug #6233 (Resolved): DirectoryListing NPE https://projects.ecoinformatics.org/ecoinfo/issues/62332013-11-21T01:22:08ZDaniel Crawldanielcrawl@gmail.com
<p>The DirectoryListing actor has an NPE:</p>
<p>java.lang.NullPointerException<br /> at ptolemy.util.RecursiveFileFilter.accept(RecursiveFileFilter.java:141)<br /> at java.io.File.list(File.java:1027)<br /> at ptolemy.util.RecursiveFileFilter.listFiles(RecursiveFileFilter.java:252)<br /> at ptolemy.actor.lib.io.DirectoryListing.fire(DirectoryListing.java:270)<br /> at ptolemy.actor.AtomicActor.iterate(AtomicActor.java:465)</p>
<p>I'm attaching an example model that demonstrates the problem in Vergil.</p> Bug #6165 (Resolved): The names of instances of the Stop actor do not display in Mac OSX.https://projects.ecoinformatics.org/ecoinfo/issues/61652013-10-22T00:48:43ZChristopher Brookscxh@eecs.berkeley.edu
<p>On Kepler-users, Kenneth Jones wrote:</p>
<blockquote>
<p>The names of instances of the Stop actor do not display in Mac OSX. Let me know if you need more info.</p>
</blockquote>
<p>Indeed, dragging in the Stop Actor results in icons without instance names</p>