Kepler: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362015-12-03T00:33:05ZEcoinformatics Redmine
Redmine Bug #6893 (New): DateToken value inconsistenthttps://projects.ecoinformatics.org/ecoinfo/issues/68932015-12-03T00:33:05ZDaniel Crawldanielcrawl@gmail.com
<p>DateToken stores the date internally in _value and _calendar, but these fields are not kept consistent. For example, if you use ModifyDate to add 2 seconds, _value is not updated. See the attached test workflow.</p>
<p>Also, ModifyDate changes the state of the input token instead of creating a new one - I thought this was not allowed in actors.</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 #6629 (Closed): type resolution problem when using RecordAssemblerhttps://projects.ecoinformatics.org/ecoinfo/issues/66292014-12-02T00:04:25ZDaniel Crawldanielcrawl@gmail.com
<p>Using RecordAssembler can cause type resolution to fail. Attached are two models that demonstrate the problem.</p>
<p>In rec-assembler-1.xml, a type resolution error will usually, but not always, occur when you run it.</p>
<p>In rec-assembler-2.xml, the second RecordAssembler actor is replaced with an Expression actor that constructs the same record, and no type resolution error occurs.</p> Bug #6588 (New): R actor does not have error for missing outputhttps://projects.ecoinformatics.org/ecoinfo/issues/65882014-08-21T20:27:56ZDaniel Crawldanielcrawl@gmail.com
<p>If the R actor has an output port "x", but the script does not assign a value to a variable "x", then the actor should report an error. Currently, the actor successfully runs but does not write a token to the output port.</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 #6439 (Closed): Double rounding fails in some cases while evaluating Expressionshttps://projects.ecoinformatics.org/ecoinfo/issues/64392014-03-04T12:24:32ZOwsiak Michalmichal.owsiak@man.poznan.pl
<p>It seems that addition of doubles can produce values slightly different than they should to be.</p>
<p>Please take a look at attached workflow (simple_error.xml).</p>
<p>Condition that should be satisfied to escape the loop is: 1.7 > 1.5 + 0.1</p>
<p>However, loop is interrupted sooner, because of incorrect calculation of doubles. Value of "p" is set to: 1.6000000000000003</p>
<p>This, of course, makes it impossible to use doubles as check points for the loops.</p>
<p>However, it seems that casting to string and back works fine (take a look at second workflow - simple.xml)</p>
<p>Cheers</p>
<p>Michal</p> Bug #6413 (New): error when switching to DDF inside Case refinementhttps://projects.ecoinformatics.org/ecoinfo/issues/64132014-02-07T21:14:52ZDaniel Crawldanielcrawl@gmail.com
<p>I get an exception when switching from SDF to DDF inside a Case Refinement. It seems to be caused by having an unconnected input port.</p>
<p>To reproduce:</p>
<p>1. open $PTII/ptolemy/actor/lib/hoc/test/auto/Case1.xml<br />2. add a new input port to Case<br />3. run the model<br />4. open the Case actor and replace SDF in each Refinement with DDF<br />5. run the model</p>
<p>The error is:</p>
<p>java.lang.IllegalArgumentException: hasToken() requires a positive argument.<br /> at ptolemy.actor.Mailbox.hasToken(Mailbox.java:149)<br /> at ptolemy.actor.IOPort.hasToken(IOPort.java:2061)<br /> at ptolemy.domains.ddf.kernel.DDFDirector.prefire(DDFDirector.java:649)<br /> at ptolemy.actor.CompositeActor.prefire(CompositeActor.java:1665)<br /> at ptolemy.actor.lib.hoc.CaseDirector.prefire(CaseDirector.java:267)<br /> at ptolemy.actor.CompositeActor.prefire(CompositeActor.java:1665)<br /> at ptolemy.actor.CompositeActor.iterate(CompositeActor.java:1082)<br /> at ptolemy.actor.sched.StaticSchedulingDirector.fire(StaticSchedulingDirector.java:211)<br /> at ptolemy.domains.sdf.kernel.SDFDirector.fire(SDFDirector.java:492)<br /> at ptolemy.actor.CompositeActor.fire(CompositeActor.java:450)<br /> at ptolemy.actor.Manager.iterate(Manager.java:787)<br /> at ptolemy.actor.Manager.execute(Manager.java:352)<br /> at ptolemy.actor.Manager.run(Manager.java:1202)<br /> at ptolemy.actor.Manager$PtolemyRunThread.run(Manager.java:1760)</p> 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 #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 #5652 (New): Geon Scp and spa Ssh2Exec have duplicate code.https://projects.ecoinformatics.org/ecoinfo/issues/56522012-08-06T23:35:23ZChristopher Brookscxh@eecs.berkeley.edu
<p>Duplicate code detected with CPD. See</p>
<p>actors/src/org/geon/Scp.java line 295<br />actors/src/org/sdm/spa/Ssh2Exec.java line 361
# lines : 143</p> Bug #5590 (New): RExpression forces pdf if 'automatically show graphics' is checkedhttps://projects.ecoinformatics.org/ecoinfo/issues/55902012-04-26T01:34:05ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>Look into this forced format change side-effect which is confusing to a user. If you select e.g. png, and 'auto show..', you get a pdf.</p> Bug #5586 (New): Get newest version of local files in EML actorhttps://projects.ecoinformatics.org/ecoinfo/issues/55862012-04-16T18:54:00ZJing Taotao@nceas.ucsb.edu
<p>Here is an email from kepler user:</p>
<p>--------------------------------------------------------------<br />Running v2.3 on Mac OSX 10.7.3 Fairly new to Kepler.</p>
<p>I'm trying to use the EML 2 Dataset Actor to read in a local copy (in a folder on my laptop drive) of a sample metadata (.xml) file using the EML 2.1.0 schema and a simple 4-column data (.txt) file. I have checked the files using the <a class="external" href="http://knb.ecoinformatics.org/emlparser/">http://knb.ecoinformatics.org/emlparser/</a> site, and both were validated.</p>
<p>Two problems:<br />i) If I change either file the Actor doesn't keep up with the changes. It seems to revert to a cached version of the file as it was when I first specified it to the Actor (via the EML File: and Data File: fields in Configure Actor).<br />ii) I wondered about checking the "Check for latest version" checkbox. However doing this generates an error dialog with the message "null Please enter a new value:" I have to uncheck to stop the error.<br />----------------------------------------------------------------</p>
<p>So we may need a feature:<br />When the "Check for latest version" box is checked, Kepler will check local files as well.</p> Bug #5577 (New): EML 2 Dataset actor EML File and Data File parameters should accept URLshttps://projects.ecoinformatics.org/ecoinfo/issues/55772012-02-27T22:34:47ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>Corinna would like to access remote datapackages via configuring the EML 2 Dataset actor's EML File and Data File parameters to refer to remote files. I agree this would be very useful, I find it confusing that the actor can do this when instantiated as a result of a Data tab metacat search, yet you can't configure it to do so manually.</p>
<p>"that's too bad. In the documentation is says: "The datapackage can be accessed from the local file system or through any EcoGrid server that provides access to its collection of data objects. The supported data transfer protocols include http, ftp, file, ecogrid and srb." Which led me to believe I could access the data via the url. I think, it would be very useful to add that functionality, i.e. I would like to request this feature to be added. Possibly even getting the data when there is a download link provided in the EML?<br />It does get the EML file from the URL, so that works fine. It's just the data that it seems to have problems with. So, maybe it is not that far off to support that feature?"</p>