Kepler: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362015-08-12T23:39:08ZEcoinformatics Redmine
Redmine Bug #6829 (Closed): ant change-to fails under Windows Server 2012 R2 with Cygwinhttps://projects.ecoinformatics.org/ecoinfo/issues/68292015-08-12T23:39:08ZChristopher Brookscxh@eecs.berkeley.edu
<p>Under Windows Server 2012 R2 with Cygwin, I ran<br /><pre>
mkdir kepler.modules
cd kepler.modules
svn co https://code.kepler-project.org/code/kepler/trunk/modules/build-area
cd build-area
</pre></p>
<p>and then ant change-to failed:</p>
<pre>
$ ant change-to -Dsuite=kepler
Buildfile: C:\Users\cxh\src\kepler.modules\build-area\build.xml
change-to:
[change-to] Copying 1 file to C:\Users\cxh\src\kepler.modules\build-area
[change-to] Retrieving modules....
[change-to]
[change-to] kepler:
[change-to] Downloading (if necessary) kepler...
[change-to] svn co -r head https://code.kepler-project.org/code/kepler/trunk/modules/kepler C:\Users\cxh\src\kep\
ler.modules\kepler
[change-to] svn: E000002: Can't make directory '/cygdrive/c/Users/cxh/src/kepler.modules/build-area/C:\Users\cxh\
\src\kepler.modules\kepler': No such file or directory
[change-to]
BUILD FAILED
C:\Users\cxh\src\kepler.modules\build-area\build.xml:104: ERROR: It appears that the command did not execute pro\
perly and exited with an exit code of: 1
Total time: 1 second
cxh@AMPERE ~/src/kepler.modules/build-area
$
</pre>
<p>I can give out accounts on ampere.eecs.berkele.edu if necessary.</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 #6467 (Closed): data tab no longer workshttps://projects.ecoinformatics.org/ecoinfo/issues/64672014-03-17T17:42:22ZDaniel Crawldanielcrawl@gmail.com
<p>Searching for "datos" in the data tab generates exceptions:</p>
<pre><code>[null] ERROR (org.ecoinformatics.seek.datasource.EcogridQueryDataCacheItem:doWork:110) The exception in query is <br /> [null] AxisFault<br /> [null] faultCode: {http://xml.apache.org/axis/}HTTP<br /> [null] faultSubcode: <br /> [null] faultString: (301)Moved Permanently<br /> [null] faultActor: <br /> [null] faultNode: <br /> [null] faultDetail: <br /> [null] {}:return code: 301<br /> [null] &lt;!DOCTYPE HTML PUBLIC &quot;-//IETF//DTD HTML 2.0//EN&quot;&gt;<br /> [null] &lt;html&gt;&lt;head&gt;<br /> [null] &lt;title&gt;301 Moved Permanently&lt;/title&gt;<br /> [null] &lt;/head&gt;&lt;body&gt;<br /> [null] &lt;h1&gt;Moved Permanently&lt;/h1&gt;<br /> [null] &lt;p&gt;The document has moved &lt;a href=&quot;<a class="external" href="https://knb.ecoinformatics.org/knb/services/QueryService&quot;&gt;here&lt;/a&gt;.&lt;/p">https://knb.ecoinformatics.org/knb/services/QueryService&amp;quot;&amp;gt;here&amp;lt;/a&amp;gt;.&amp;lt;/p</a>&gt;<br /> [null] &lt;hr&gt;<br /> [null] &lt;address&gt;Apache/2.2.14 (Ubuntu) Server at ecogrid.ecoinformatics.org Port 80&lt;/address&gt;<br /> [null] &lt;/body&gt;&lt;/html&gt;<br /> [null] <br /> [null] {http://xml.apache.org/axis/}HttpErrorCode:301<br /> [null] <br /> [null] (301)Moved Permanently<br /> [null] at org.apache.axis.transport.http.HTTPSender.readFromSocket(HTTPSender.java:744)<br /> [null] at org.apache.axis.transport.http.HTTPSender.invoke(HTTPSender.java:144)<br /> [null] at org.apache.axis.strategies.InvocationStrategy.visit(InvocationStrategy.java:32)<br /> [null] at org.apache.axis.SimpleChain.doVisiting(SimpleChain.java:118)<br /> [null] at org.apache.axis.SimpleChain.invoke(SimpleChain.java:83)<br /> [null] at org.apache.axis.client.AxisClient.invoke(AxisClient.java:165)<br /> [null] at org.apache.axis.client.Call.invokeEngine(Call.java:2784)<br /> [null] at org.apache.axis.client.Call.invoke(Call.java:2767)<br /> [null] at org.apache.axis.client.Call.invoke(Call.java:2443)<br /> [null] at org.apache.axis.client.Call.invoke(Call.java:2366)<br /> [null] at org.apache.axis.client.Call.invoke(Call.java:1812)<br /> [null] at org.ecoinformatics.ecogrid.queryservice.stub.QueryServiceStub.query(Unknown Source)<br /> [null] at org.ecoinformatics.ecogrid.queryservice.QueryServiceClient.query(Unknown Source)<br /> [null] at org.ecoinformatics.seek.datasource.EcogridQueryDataCacheItem.doWork(EcogridQueryDataCacheItem.java:101)<br /> [null] at org.kepler.objectmanager.cache.DataCacheObject.run(DataCacheObject.java:422)<br /> [null] at java.lang.Thread.run(Thread.java:695)</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 #5894 (Closed): Clone problems in NamedObjIdhttps://projects.ecoinformatics.org/ecoinfo/issues/58942013-03-19T19:07:23ZChristopher Brookscxh@eecs.berkeley.edu
<p>Checking the configuration results in messages about clone problems in NamedObjId:</p>
<p>The valueListeners java.util.Vector field<br /> in the clone of "org.kepler.moml.NamedObjId" <br /> does not point to an object distinct from the master. <br /> This may cause problems with actor oriented classes.<br /> The clone(Workspace) method should have a line like:<br /> newObject.valueListeners = (Vector)newObject<br /> /* Get the object method or null? <strong>/ valueListeners;<br />The _id org.kepler.objectmanager.lsid.KeplerLSID field<br /> in the clone of "org.kepler.moml.NamedObjId" <br /> does not point to an object distinct from the master. <br /> This may cause problems with actor oriented classes.<br /> The clone(Workspace) method should have a line like:<br /> newObject._id = (KeplerLSID)newObject<br /> /</strong> Get the object method or null? */ _id;</p>
<p>To replicate:<br />1) Start Kepler<br />2) Click on the Documentation link<br />3) Click on "Background information about Ptolemy" <br />4) Click on the Copyright link<br />5) Click on the Copyright link at the bottom (Other copyrights ...)<br />6) Click on "other" information about this configuration at the bottom<br />7) Click on "about:configuration"</p>
<p>The text above will appear.</p>
<p>The issue with cloning could be causing problems with actor oriented classes.</p>
<p>This class should have a clone(Workspace) method added.</p> Bug #5893 (Closed): During installation, Kepler takes a long time to start up under Windowshttps://projects.ecoinformatics.org/ecoinfo/issues/58932013-03-19T14:51:33ZChristopher Brookscxh@eecs.berkeley.edu
<p>With Kepler-2.4RC3 under Windows2008R2 64-bit, the user is asked if they want to start up Kepler. I chose "yes" and nothing happened, so I completed the installation.</p>
<p>Then, I started up Kepler from the menu and it took a long time (over a minute?) to start up.</p>
<p>Then, it seemed like there were two Kepler instances?</p>
<p>It seems like Kepler took a long time to start, which is why when Kepler was starting during the installation, it seemed like nothing was happening.</p> Bug #5722 (Resolved): Check for problems with sanitized RecordToken labelshttps://projects.ecoinformatics.org/ecoinfo/issues/57222012-10-02T01:33:32ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>Filing a bug so this doesn't get forgotten - I said I'd try to look into this ptII change, r64639:<br />-------<br />Sanitize RecordToken or OrderedRecordToken labels, which means that characters like spaces will be converted to underscores. This is necessary so that the string representations of RecordTokens can be reparsed by the expression language. The alternative of modifying the expression language to allow strings as labels causes conflicts in the parser.<br />-------</p>
<p>I worry this change is going to cause problems...anything that expects (e.g. checks equivalence) the data in a label to come out of a RecordToken as it went in will seemingly have a problem. It also sounds like a lossy translation.</p> Feature #5720 (Resolved): Kepler component documentation layout needs improvementhttps://projects.ecoinformatics.org/ecoinfo/issues/57202012-10-01T21:12:51ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>In-Kepler Actor documentation can be pretty frustrating to read due to GUI layout. Generally, for an actor that's been documented, the bulk of the doc information is the explanation of the actor, yet this section of the window isn't given much more space than the others. You cannot adjust individual pane/area sizes, and when you resize the entire actor doc window vertically, all the new space is given to the title pane/area, which is pointless.</p> Bug #5498 (Resolved): Issue a patch for ptolemy classpath problem in kepler-2.2https://projects.ecoinformatics.org/ecoinfo/issues/54982011-09-27T00:46:39ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>User reports eclipse problem wrt ptolemy classpath missing jars. I verified the fix is the same as for<br /><a class="external" href="http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5442">http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5442</a></p>
<p>See about issuing patch to kepler-tasks-2.2 for this bug. The build-area-2.2 tag would also have to get the update.</p>