Kepler: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362014-03-04T12:24:32ZEcoinformatics Redmine
Redmine 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 #5508 (Resolved): Link to "Additional background information on Ptolemy" brings up empty pagehttps://projects.ecoinformatics.org/ecoinfo/issues/55082011-10-06T01:51:53ZChristopher Brookscxh@eecs.berkeley.edu
<p>Under Windows Server 2008:</p>
<p>If I do Help -> Kepler Documentation,<br />and click on<br />"background information on Ptolemy" <br />I get a blank page that has<br />jar:file:!/ptolemy/configs/ptinyKepler/intro.htm in the title.</p>
<p>I looked in the jar file and the file is there?</p>
<p>View ->Source brings up a NPE?</p>
<p>java.lang.reflect.InvocationTargetException<br /> at sun.reflect.NativeConstructorAccessorImpl.newInstance0(Native Method)<br /> at sun.reflect.NativeConstructorAccessorImpl.newInstance(Unknown Source)<br /> at sun.reflect.DelegatingConstructorAccessorImpl.newInstance(Unknown Source)<br /> at java.lang.reflect.Constructor.newInstance(Unknown Source)<br /> at ptolemy.actor.gui.TextEditorTableau$Factory.createTableau(TextEditorTableau.java:221)<br /> at ptolemy.actor.gui.TextEditorTableau$Factory.createTableau(TextEditorTableau.java:279)<br /> at ptolemy.actor.gui.TableauFrame$ViewMenuListener.actionPerformed(TableauFrame.java:1572)<br /> at org.kepler.gui.MenuMapper$1.actionPerformed(MenuMapper.java:386)<br /> at javax.swing.AbstractButton.fireActionPerformed(Unknown Source)<br /> at javax.swing.AbstractButton$Handler.actionPerformed(Unknown Source)<br /> at javax.swing.DefaultButtonModel.fireActionPerformed(Unknown Source)<br /> at javax.swing.DefaultButtonModel.setPressed(Unknown Source)<br /> at javax.swing.AbstractButton.doClick(Unknown Source)<br /> at javax.swing.plaf.basic.BasicMenuItemUI.doClick(Unknown Source)<br /> at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(Unknown Source)<br /> at java.awt.Component.processMouseEvent(Unknown Source)<br /> at javax.swing.JComponent.processMouseEvent(Unknown Source)<br /> at java.awt.Component.processEvent(Unknown Source)<br /> at java.awt.Container.processEvent(Unknown Source)<br /> at java.awt.Component.dispatchEventImpl(Unknown Source)<br /> at java.awt.Container.dispatchEventImpl(Unknown Source)<br /> at java.awt.Component.dispatchEvent(Unknown Source)<br /> at java.awt.LightweightDispatcher.retargetMouseEvent(Unknown Source)<br /> at java.awt.LightweightDispatcher.processMouseEvent(Unknown Source)<br /> at java.awt.LightweightDispatcher.dispatchEvent(Unknown Source)<br /> at java.awt.Container.dispatchEventImpl(Unknown Source)<br /> at java.awt.Window.dispatchEventImpl(Unknown Source)<br /> at java.awt.Component.dispatchEvent(Unknown Source)<br /> at java.awt.EventQueue.dispatchEventImpl(Unknown Source)<br /> at java.awt.EventQueue.access$000(Unknown Source)<br /> at java.awt.EventQueue$3.run(Unknown Source)<br /> at java.awt.EventQueue$3.run(Unknown Source)<br /> at java.security.AccessController.doPrivileged(Native Method)<br /> at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)<br /> at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)<br /> at java.awt.EventQueue$4.run(Unknown Source)<br /> at java.awt.EventQueue$4.run(Unknown Source)<br /> at java.security.AccessController.doPrivileged(Native Method)<br /> at java.security.ProtectionDomain$1.doIntersectionPrivilege(Unknown Source)<br /> at java.awt.EventQueue.dispatchEvent(Unknown Source)<br /> at java.awt.EventDispatchThread.pumpOneEventForFilters(Unknown Source)<br /> at java.awt.EventDispatchThread.pumpEventsForFilter(Unknown Source)<br /> at java.awt.EventDispatchThread.pumpEventsForHierarchy(Unknown Source)<br /> at java.awt.EventDispatchThread.pumpEvents(Unknown Source)<br /> at java.awt.EventDispatchThread.pumpEvents(Unknown Source)<br /> at java.awt.EventDispatchThread.run(Unknown Source)<br />Caused by: java.lang.NullPointerException<br /> at ptolemy.actor.gui.TextEditor.getBackground(TextEditor.java:144)<br /> at java.awt.Window.setBackground(Unknown Source)<br /> at java.awt.Frame.setBackground(Unknown Source)<br /> at ptolemy.gui.Top.access$1001(Top.java:141)<br /> at ptolemy.gui.Top$SetBackgroundRunnable.run(Top.java:1889)<br /> at ptolemy.gui.Top.deferIfNecessary(Top.java:247)<br /> at ptolemy.gui.Top.setBackground(Top.java:501)<br /> at ptolemy.actor.gui.TextEditor.setBackground(TextEditor.java:238)<br /> at javax.swing.JFrame.frameInit(Unknown Source)<br /> at javax.swing.JFrame.<init>(Unknown Source)<br /> at ptolemy.gui.Top.<init>(Top.java:162)<br /> at ptolemy.actor.gui.TableauFrame.<init>(TableauFrame.java:133)<br /> at ptolemy.actor.gui.TableauFrame.<init>(TableauFrame.java:168)<br /> at ptolemy.actor.gui.TextEditor.<init>(TextEditor.java:104)<br /> at ptolemy.actor.gui.TextEditor.<init>(TextEditor.java:91)<br /> at ptolemy.actor.gui.TextEditorTableau.<init>(TextEditorTableau.java:89)<br /> at ptolemy.actor.gui.TextEditorTableau.<init>(TextEditorTableau.java:68)<br /> ... 46 more</p>
<p>This page works on the Mac and I don't get the NPE.</p> Bug #5504 (Resolved): Kepler incorrectly uses old version of a kar file in ~KeplerData/workflows/...https://projects.ecoinformatics.org/ecoinfo/issues/55042011-10-04T22:36:41ZJing Taotao@nceas.ucsb.edu
<p>I updated the tpc01 workflow by changing an eml actor to point to knb rather than dev in my mac machine. It worked and i committed the newer version of the tpc01 kar file to the svn server.</p>
<p>I tried to run this new kar file in my linux machine. But it confused me.<br />First, i updated the kar file in project/kruger directory. Then i run the kepler-reporting-2.3 and opened the kar file staying project/kruger directory. However, it still access the data on dev. I decompressed the kar file which I opened. It shows that it points to the knb. I tried couple times and got the same result.</p>
<p>I talked with derik and we removed the core module under ~/KeplerData. But it didn't help. Derik asked if i had another copy of the kar file. I said that I had another one under ~KeplerData/workflows/MyWorkflows. And this copy was the older version. We removed this old one and it worked.</p>
<p>It seems that the old version of kar file locating at ~KeplerData/workflows/MyWorkflows affect the open of the new version.</p> Bug #5501 (Resolved): Got an java.lang.NullPointerException when click any menu after downloading...https://projects.ecoinformatics.org/ecoinfo/issues/55012011-10-03T18:21:15ZJing Taotao@nceas.ucsb.edu
<p>After decompress the linux kepler-2.3 installer, I started kepler by running ./kepler.sh.</p>
<p>Then I searched the kepler library and found a kar file windChill. I downloaded the kar file and wanted to open it. However, when i clicked file menu and got the error:<br />[null] Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException<br /> [null] at com.sun.java.swing.plaf.gtk.GTKIconFactory$MenuArrowIcon.paintIcon(GTKIconFactory.java:340)<br /> [null] at sun.swing.plaf.synth.SynthIcon.paintIcon(SynthIcon.java:104)<br /> [null] at com.jgoodies.looks.common.MinimumSizedIcon.paintIcon(MinimumSizedIcon.java:80)<br /> [null] at com.jgoodies.looks.common.MenuItemRenderer.paintMenuItem(MenuItemRenderer.java:419)<br /> [null] at com.jgoodies.looks.common.ExtBasicMenuUI.paintMenuItem(ExtBasicMenuUI.java:135)<br /> [null] at com.jgoodies.looks.plastic.PlasticMenuUI.paintMenuItem(PlasticMenuUI.java:80)<br /> [null] at javax.swing.plaf.basic.BasicMenuItemUI.paint(BasicMenuItemUI.java:471)<br /> [null] at javax.swing.plaf.basic.BasicMenuItemUI.update(BasicMenuItemUI.java:467)<br /> [null] at javax.swing.JComponent.paintComponent(JComponent.java:765)<br /> [null] at javax.swing.JComponent.paint(JComponent.java:1029)<br /> [null] at javax.swing.JComponent.paintChildren(JComponent.java:866)<br /> [null] at javax.swing.JComponent.paint(JComponent.java:1038)<br /> [null] at javax.swing.JComponent.paintChildren(JComponent.java:866)<br /> [null] at javax.swing.JComponent.paint(JComponent.java:1038)<br /> [null] at javax.swing.JComponent.paintChildren(JComponent.java:866)<br /> [null] at javax.swing.JComponent.paint(JComponent.java:1038)<br /> [null] at javax.swing.JLayeredPane.paint(JLayeredPane.java:581)<br /> [null] at javax.swing.JComponent.paintChildren(JComponent.java:866)<br /> [null] at javax.swing.JComponent.paint(JComponent.java:1038)<br /> [null] at javax.swing.JComponent.paintToOffscreen(JComponent.java:5138)<br /> [null] at javax.swing.BufferStrategyPaintManager.paint(BufferStrategyPaintManager.java:302)<br /> [null] at javax.swing.RepaintManager.paint(RepaintManager.java:1145)<br /> [null] at javax.swing.JComponent._paintImmediately(JComponent.java:5086)<br /> [null] at javax.swing.JComponent.paintImmediately(JComponent.java:4896)<br /> [null] at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:740)<br /> [null] at javax.swing.RepaintManager.paintDirtyRegions(RepaintManager.java:696)<br /> [null] at javax.swing.RepaintManager.prePaintDirtyRegions(RepaintManager.java:676)<br /> [null] at javax.swing.RepaintManager.access$700(RepaintManager.java:57)<br /> [null] at javax.swing.RepaintManager$ProcessingRunnable.run(RepaintManager.java:1550)<br /> [null] at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:226)<br /> [null] at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:647)<br /> [null] at java.awt.EventQueue.access$000(EventQueue.java:96)<br /> [null] at java.awt.EventQueue$1.run(EventQueue.java:608)<br /> [null] at java.awt.EventQueue$1.run(EventQueue.java:606)<br /> [null] at java.security.AccessController.doPrivileged(Native Method)<br /> [null] at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:105)<br /> [null] at java.awt.EventQueue.dispatchEvent(EventQueue.java:617)<br /> [null] at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:275)<br /> [null] at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:200)<br /> [null] at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:190)<br /> [null] at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:185)<br /> [null] at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:177)<br /> [null] at java.awt.EventDispatchThread.run(EventDispatchThread.java:138)</p>
<p>I doubled checked the MyWorkflow folder, and found that windChill.kar is there.</p>
<p>Then i quited the kepler and started it again. This time i can open and run the windChill.kar successfully.</p> Bug #5496 (Resolved): non-English (United State) OS locale causes File menu and button text to no...https://projects.ecoinformatics.org/ecoinfo/issues/54962011-09-20T21:55:09ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>If your locale is not set to English (United State), the Kepler File menu and certain button text will not appear. A user reports this happening on Vista, and I verified it happens on XP.<br /><a class="external" href="http://lists.nceas.ucsb.edu/kepler/pipermail/kepler-users/2011-September/002585.html">http://lists.nceas.ucsb.edu/kepler/pipermail/kepler-users/2011-September/002585.html</a></p> Bug #5473 (Resolved): 2.3.0rc1 won't start on Windows XPhttps://projects.ecoinformatics.org/ecoinfo/issues/54732011-08-16T23:42:37ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>I can't get 2.3.0 rc1 to start on Windows XP after installing using the installer.<br />The shortcuts are broken, and double-clicking on kepler.exe and module-manager.exe doesn't do anything.</p> Bug #5462 (Resolved): Can't run the kepler by ./kepler.sh after decompressing the linux installerhttps://projects.ecoinformatics.org/ecoinfo/issues/54622011-08-15T15:58:10ZJing Taotao@nceas.ucsb.edu
<p>After decompressing the linux installer(RC1), i tried to run kepler by type ./kepler.sh. But I got an error:<br />tao@pacific:~/download/kepler-2.3-rc1$ ./kepler.sh <br /> [null] Copying 1 file to /home/tao/KeplerData/kepler.modules/build-area<br /> [null] Copying 1 file to /home/tao/KeplerData/kepler.modules/build-area<br />JVM Memory = 5m 512m<br />Error: The following modules are missing: <br /> kepler-2.2.0</p>
<p>Why it looks kepler-2.2.0? It is kepler-2.3 release.</p> Bug #5461 (Resolved): Add a directory to contain all modules in linux installerhttps://projects.ecoinformatics.org/ecoinfo/issues/54612011-08-15T15:50:26ZJing Taotao@nceas.ucsb.edu
<p>In the current linux installer, the modules will be decompressed to the directory where you run the command. So I have to manually to create a directory named kepler-2.3-rc1 to contain all modules in order to manage the installation easily.</p>
<p>Can we add directory kepler-2.3-rc1 (or kepler-2.3) above the moduels in the installer? So people don't need to manually added a directory.</p>
<p>Current the structure looks like:<br />build-area/current-suite.txt<br />build-area/install-id.txt<br />build-area/lib/ant.jar<br />.......</p>
<p>kepler.jar<br />kepler.sh<br />.....<br />kepler-2.3.0/resources/system.properties/<br />kepler-2.3.0/module-info/licenses.txt<br />kepler-2.3.0/module-info/modules.txt<br />........</p>
<p>We may change to :</p>
<p>kepler-2.3/build-area/current-suite.txt<br />kepler-2.3/build-area/install-id.txt<br />kepler-2.3/build-area/lib/ant.jar<br />.......</p>
<p>kepler-2.3/kepler.jar<br />kepler-2.3/kepler.sh<br />.....<br />kepler-2.3/kepler-2.3.0/resources/system.properties/<br />kepler-2.3/kepler-2.3.0/module-info/licenses.txt<br />kepler-2.3/kepler-2.3.0/module-info/modules.txt<br />........</p> Bug #5460 (Resolved): Mac OS X: Matlab Actors fail in Kepler.apphttps://projects.ecoinformatics.org/ecoinfo/issues/54602011-08-14T18:25:13ZChristopher Brookscxh@eecs.berkeley.edu
<p>Models that use the Matlab interface fail when started under Mac OS X <br />by double clicking on Kepler.app.</p>
<p>This is a new Mac running Mac OS X 10.7.</p>
<p>I had to make some changes to Matlab interface, these should be folded<br />into the Kepler-2.3 tree.</p>
<p>The problem is that in the devel tree, <br />ant run-only was failing with:</p>
<p>ptolemy.kernel.util.IllegalActionException: .MatlabExpression.MatlabExpression: ptolemy.kernel.util.IllegalActionException: Token 0.0 is of type double<br /> in .MatlabExpression.MatlabExpression<br />Because:<br />.MatlabExpression.MatlabExpression: ptolemy.kernel.util.IllegalActionException: Token 0.0 is of type double<br /> at ptolemy.actor.AtomicActor.iterate(AtomicActor.java:500)<br /> at ptolemy.actor.sched.StaticSchedulingDirector.fire(StaticSchedulingDirector.java:188)<br /> at ptolemy.actor.CompositeActor.fire(CompositeActor.java:458)<br /> at ptolemy.actor.Manager.iterate(Manager.java:742)<br /> at ptolemy.actor.Manager.execute(Manager.java:351)<br /> at ptolemy.actor.Manager.run(Manager.java:1111)<br /> at ptolemy.actor.Manager$PtolemyRunThread.run(Manager.java:1641)<br />Caused by: ptolemy.kernel.util.IllegalActionException: .MatlabExpression.MatlabExpression: ptolemy.kernel.util.IllegalActionException: Token 0.0 is of type double<br /> at ptolemy.matlab.Expression.fire(Expression.java:436)<br /> at ptolemy.actor.AtomicActor.iterate(AtomicActor.java:461)<br /> ... 6 more<br />Caused by: ptolemy.kernel.util.IllegalActionException: .MatlabExpression.MatlabExpression: ptolemy.kernel.util.IllegalActionException: Token 0.0 is of type double<br /> at ptolemy.matlab.Expression.fire(Expression.java:436)<br /> at ptolemy.actor.AtomicActor.iterate(AtomicActor.java:461)<br /> at ptolemy.actor.sched.StaticSchedulingDirector.fire(StaticSchedulingDirector.java:188)<br /> at ptolemy.actor.CompositeActor.fire(CompositeActor.java:458)<br /> at ptolemy.actor.Manager.iterate(Manager.java:742)<br /> at ptolemy.actor.Manager.execute(Manager.java:351)<br /> at ptolemy.actor.Manager.run(Manager.java:1111)<br /> at ptolemy.actor.Manager$PtolemyRunThread.run(Manager.java:1641)</p>
<p>I fixed this in</p>
<p>New Revision: 61797</p>
<p>Modified:<br /> trunk/ptolemy/matlab/Engine.java<br /> trunk/ptolemy/matlab/Expression.java<br />Log:<br />Better error messages if time and iteration cannot be set. Properly handle DoubleToken and IntToken in Engine.put(). It is a mystery as to why this bug did appear before.</p>
<p>However, with Kepler-2.3 rc1, I'm not even getting that far.<br />When I run the SDF MatlabExpression model, I get:</p>
<p>ptolemy.kernel.util.IllegalActionException: matlabEngine.open(null) : can't find Matlab engine. Try starting Matlab by hand as an application to verify that Matlab is set up properly and the license is correct. Under Windows, try running "matlab /regserver", the Matlab C API communicates with Matlab via COM, and apparently the COM interface is not automatically registered when Matlab is installed. Under Linux and other types of UNIX, csh must be installed in /bin/csh.<br /> at ptolemy.matlab.Engine.open(Engine.java:280)<br /> at ptolemy.matlab.Engine.open(Engine.java:232)<br /> at ptolemy.matlab.Expression.preinitialize(Expression.java:303)<br /> at ptolemy.actor.Director.preinitialize(Director.java:1010)<br /> at ptolemy.actor.Director.preinitialize(Director.java:991)<br /> at ptolemy.domains.sdf.kernel.SDFDirector.preinitialize(SDFDirector.java:647)<br /> at ptolemy.actor.CompositeActor.preinitialize(CompositeActor.java:1735)<br /> at ptolemy.actor.Manager.preinitializeAndResolveTypes(Manager.java:983)<br /> at ptolemy.actor.Manager.initialize(Manager.java:643)<br /> at ptolemy.actor.Manager.execute(Manager.java:340)<br /> at ptolemy.actor.Manager.run(Manager.java:1164)<br /> at ptolemy.actor.Manager$3.run(Manager.java:1217)</p>
<p>The Console application reports:</p>
<p>8/14/11 11:17:34.240 AM [0x0-0x156156].org.kepler.build.runner.Kepler: [null] matlab: Command not found.<br />8/14/11 11:17:34.241 AM [0x0-0x156156].org.kepler.build.runner.Kepler: [null] ptmatlabEngOpen: failed!</p>
<p>However, the matlab directory is in my path, see<br /><a class="external" href="https://kepler-project.org/developers/teams/build/setting-up-mac-os-x-to-use-the-matlab-interface">https://kepler-project.org/developers/teams/build/setting-up-mac-os-x-to-use-the-matlab-interface</a></p> Bug #5446 (Resolved): View=>XML View brokenhttps://projects.ecoinformatics.org/ecoinfo/issues/54462011-08-02T22:19:36ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>Trying the View=>XML View menu gives an NPE. Seems to be broken in Vergil, as far back as 61608:</p>
<p>java.lang.NullPointerException<br /> at ptolemy.actor.gui.TextEditorTableau$Factory.createTableau(TextEditorTableau.java:281)<br /> at ptolemy.actor.gui.TableauFrame$ViewMenuListener.actionPerformed(TableauFrame.java:1540)<br /> at org.kepler.gui.MenuMapper$1.actionPerformed(MenuMapper.java:386)<br /> at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2028)<br /> at javax.swing.AbstractButton$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 com.apple.laf.ScreenMenuItem.actionPerformed(ScreenMenuItem.java:95)<br /> at java.awt.MenuItem.processActionEvent(MenuItem.java:627)<br /> at java.awt.MenuItem.processEvent(MenuItem.java:586)<br /> at java.awt.MenuComponent.dispatchEventImpl(MenuComponent.java:337)<br /> at java.awt.MenuComponent.dispatchEvent(MenuComponent.java:325)<br /> at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:682)<br /> at java.awt.EventQueue.access$000(EventQueue.java:85)<br /> at java.awt.EventQueue$1.run(EventQueue.java:638)<br /> at java.awt.EventQueue$1.run(EventQueue.java:636)<br /> at java.security.AccessController.doPrivileged(Native Method)<br /> at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)<br /> at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98)<br /> at java.awt.EventQueue$2.run(EventQueue.java:652)<br /> at java.awt.EventQueue$2.run(EventQueue.java:650)<br /> at java.security.AccessController.doPrivileged(Native Method)<br /> at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)<br /> at java.awt.EventQueue.dispatchEvent(EventQueue.java:649)<br /> at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)<br /> at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)<br /> at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)<br /> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)<br /> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)<br /> at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)</p> Bug #5442 (Resolved): View->Automate Layout doesn't work in kepler-2.3 branchhttps://projects.ecoinformatics.org/ecoinfo/issues/54422011-07-15T01:56:19ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>A bunch of ptolemy jars aren't added to the classpath when using the kepler-2.3 branch. This causes at least one problem, View->Automate Layout doesn't work.</p>
<p>If you:<br />ant change-to <del>Dsuite=kepler-2.3;<br />ant run;<br />Then use: View</del>>Automate Layout</p>
<p>You get an error:<br /> [run] java.lang.Exception: Failed to invoke layout graph dialog class "ptolemy.vergil.basic.layout.KielerLayoutAction", which was read from the configuration.<br /> [run] at ptolemy.vergil.basic.BasicGraphFrame.layoutGraph(BasicGraphFrame.java:1146)<br /> [run] at ptolemy.vergil.actor.ActorGraphFrame$LayoutAction.actionPerformed(ActorGraphFrame.java:758)<br /> [run] at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2028)<br /> [run] at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2351)<br /> [run] at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)<br /> [run] at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)<br /> [run] at javax.swing.AbstractButton.doClick(AbstractButton.java:389)<br /> [run] at com.apple.laf.ScreenMenuItem.actionPerformed(ScreenMenuItem.java:95)<br /> [run] at java.awt.MenuItem.processActionEvent(MenuItem.java:627)<br /> [run] at java.awt.MenuItem.processEvent(MenuItem.java:586)<br /> [run] at java.awt.MenuComponent.dispatchEventImpl(MenuComponent.java:337)<br /> [run] at java.awt.MenuComponent.dispatchEvent(MenuComponent.java:325)<br /> [run] at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:682)<br /> [run] at java.awt.EventQueue.access$000(EventQueue.java:85)<br /> [run] at java.awt.EventQueue$1.run(EventQueue.java:638)<br /> [run] at java.awt.EventQueue$1.run(EventQueue.java:636)<br /> [run] at java.security.AccessController.doPrivileged(Native Method)<br /> [run] at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)<br /> [run] at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98)<br /> [run] at java.awt.EventQueue$2.run(EventQueue.java:652)<br /> [run] at java.awt.EventQueue$2.run(EventQueue.java:650)<br /> [run] at java.security.AccessController.doPrivileged(Native Method)<br /> [run] at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)<br /> [run] at java.awt.EventQueue.dispatchEvent(EventQueue.java:649)<br /> [run] at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)<br /> [run] at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)<br /> [run] at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)<br /> [run] at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)<br /> [run] at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)<br /> [run] at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)<br /> [run] Caused by: java.lang.NoClassDefFoundError: de/cau/cs/kieler/core/KielerException<br /> [run] at ptolemy.vergil.basic.layout.KielerLayoutAction.doAction(KielerLayoutAction.java:139)<br /> [run] at ptolemy.vergil.basic.BasicGraphFrame.layoutGraph(BasicGraphFrame.java:1141)<br /> [run] ... 29 more<br /> [run] Caused by: java.lang.ClassNotFoundException: de.cau.cs.kieler.core.KielerException<br /> [run] at java.net.URLClassLoader$1.run(URLClassLoader.java:202)<br /> [run] at java.security.AccessController.doPrivileged(Native Method)<br /> [run] at java.net.URLClassLoader.findClass(URLClassLoader.java:190)<br /> [run] at java.lang.ClassLoader.loadClass(ClassLoader.java:306)<br /> [run] at sun.misc.Launcher$AppClassLoader.loadClass(Launcher.java:301)<br /> [run] at java.lang.ClassLoader.loadClass(ClassLoader.java:247)<br /> [run] ... 31 more</p>
<p>If you edit your kepler-2.3/module-info/modules.txt to refer to ptolemy instead of ptolemy-kepler-2.3 (either rename your ptolemy-kepler-2.3 to ptolemy, or just use your existing 'trunk' ptolemy dir), and restart kepler-2.3, Automate Layout works fine.</p>
<p>I compared the classpaths between the two ways of launching kepler described above, and when using "ptolemy-kepler-2.3", the classpath is lacking a bunch of jars, including the kieler.jar:</p>
<p>/Users/derik/dev2/kepler.modules/ptolemy/src/lib/PDFRenderer.jar:/Users/derik/dev2/kepler.modules/ptolemy/src/lib/aopalliance-license.htm:/Users/derik/dev2/kepler.modules/ptolemy/src/lib/aopalliance.jar:/Users/derik/dev2/kepler.modules/ptolemy/src/lib/bsh-2.0b4.jar:/Users/derik/dev2/kepler.modules/ptolemy/src/lib/chic.jar:/Users/derik/dev2/kepler.modules/ptolemy/src/lib/diva.jar:/Users/derik/dev2/kepler.modules/ptolemy/src/lib/guice-3.0.jar:/Users/derik/dev2/kepler.modules/ptolemy/src/lib/guice-license.htm:/Users/derik/dev2/kepler.modules/ptolemy/src/lib/jasminclasses.jar:/Users/derik/dev2/kepler.modules/ptolemy/src/lib/java_cup.jar:/Users/derik/dev2/kepler.modules/ptolemy/src/lib/javax.inject-license.htm:/Users/derik/dev2/kepler.modules/ptolemy/src/lib/javax.inject.jar:/Users/derik/dev2/kepler.modules/ptolemy/src/lib/jna.jar:/Users/derik/dev2/kepler.modules/ptolemy/src/lib/junit-4.8.2.jar:/Users/derik/dev2/kepler.modules/ptolemy/src/lib/junit-license.htm:/Users/derik/dev2/kepler.modules/ptolemy/src/lib/jython.jar:/Users/derik/dev2/kepler.modules/ptolemy/src/lib/kieler.jar:/Users/derik/dev2/kepler.modules/ptolemy/src/lib/libptmatlab.jnilib:/Users/derik/dev2/kepler.modules/ptolemy/src/lib/libptmatlab.so:/Users/derik/dev2/kepler.modules/ptolemy/src/lib/mapss.jar:/Users/derik/dev2/kepler.modules/ptolemy/src/lib/matlab.jar:/Users/derik/dev2/kepler.modules/ptolemy/src/lib/matlabLinux.jar:/Users/derik/dev2/kepler.modules/ptolemy/src/lib/matlabMacOSX.jar:/Users/derik/dev2/kepler.modules/ptolemy/src/lib/matlabSunOS.jar:/Users/derik/dev2/kepler.modules/ptolemy/src/lib/matlabWindows.jar:/Users/derik/dev2/kepler.modules/ptolemy/src/lib/naomi.jar:/Users/derik/dev2/kepler.modules/ptolemy/src/lib/ojdcheck-license.htm:/Users/derik/dev2/kepler.modules/ptolemy/src/lib/ojdcheck.jar:/Users/derik/dev2/kepler.modules/ptolemy/src/lib/polyglotclasses-1.3.2.jar:/Users/derik/dev2/kepler.modules/ptolemy/src/lib/ptCal.jar:/Users/derik/dev2/kepler.modules/ptolemy/src/lib/ptII.properties.in:/Users/derik/dev2/kepler.modules/ptolemy/src/lib/ptcolt.jar:/Users/derik/dev2/kepler.modules/ptolemy/src/lib/ptjacl.jar:/Users/derik/dev2/kepler.modules/ptolemy/src/lib/rxtxMacOSX.jar:/Users/derik/dev2/kepler.modules/ptolemy/src/lib/rxtxWindows.jar:/Users/derik/dev2/kepler.modules/ptolemy/src/lib/saxon8-dom.jar:/Users/derik/dev2/kepler.modules/ptolemy/src/lib/saxon8.jar:/Users/derik/dev2/kepler.modules/ptolemy/src/lib/sootclasses.jar:/Users/derik/dev2/kepler.modules/ptolemy/src/lib/swing-worker-1.2.jar:/Users/derik/dev2/kepler.modules/ptolemy/src/lib/swing-worker-license.htm</p> Bug #5439 (Resolved): file parameter ignores directoryhttps://projects.ecoinformatics.org/ecoinfo/issues/54392011-07-11T23:10:47ZDaniel Crawldanielcrawl@gmail.com
<p>Choosing a file /tmp/file.txt gets replaced with $KEPLER/file.txt. In Ptolemy it's replaced with $CWD/file.txt.</p> Bug #5432 (Resolved): 2.2 mac installer contains 2 copies of everythinghttps://projects.ecoinformatics.org/ecoinfo/issues/54322011-06-28T19:32:35ZDaniel Crawldanielcrawl@gmail.com
<p>There is a zip file in each module containing the contents of the module.</p>
<p>I would not create a new installer for 2.2, since it has already been released, but the next installer should not contain these duplicates.</p> Bug #5414 (Resolved): fileparameter browse has NPEhttps://projects.ecoinformatics.org/ecoinfo/issues/54142011-05-27T21:12:33ZDaniel Crawldanielcrawl@gmail.com
<p>FileParameter browse button throws an NPE on Mac. No error on linux.</p>
<pre><code>[run] Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException<br /> [run] at ptolemy.gui.Query$QueryFileChooser._actionPerformedFileDialog(Query.java:2065)<br /> [run] at ptolemy.gui.Query$QueryFileChooser.actionPerformed(Query.java:2026)<br /> [run] at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2028)<br /> [run] at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2351)<br /> [run] at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)<br /> [run] at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)<br /> [run] at javax.swing.plaf.basic.BasicButtonListener.mouseReleased(BasicButtonListener.java:236)<br /> [run] at java.awt.Component.processMouseEvent(Component.java:6374)<br /> [run] at javax.swing.JComponent.processMouseEvent(JComponent.java:3267)<br /> [run] at java.awt.Component.processEvent(Component.java:6139)<br /> [run] at java.awt.Container.processEvent(Container.java:2085)<br /> [run] at java.awt.Component.dispatchEventImpl(Component.java:4736)<br /> [run] at java.awt.Container.dispatchEventImpl(Container.java:2143)<br /> [run] at java.awt.Component.dispatchEvent(Component.java:4566)<br /> [run] at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4621)<br /> [run] at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4282)<br /> [run] at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4212)<br /> [run] at java.awt.Container.dispatchEventImpl(Container.java:2129)<br /> [run] at java.awt.Window.dispatchEventImpl(Window.java:2478)<br /> [run] at java.awt.Component.dispatchEvent(Component.java:4566)<br /> [run] at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:680)<br /> [run] at java.awt.EventQueue.access$000(EventQueue.java:86)<br /> [run] at java.awt.EventQueue$1.run(EventQueue.java:639)<br /> [run] at java.awt.EventQueue$1.run(EventQueue.java:637)<br /> [run] at java.security.AccessController.doPrivileged(Native Method)<br /> [run] at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)<br /> [run] at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98)<br /> [run] at java.awt.EventQueue$2.run(EventQueue.java:653)<br /> [run] at java.awt.EventQueue$2.run(EventQueue.java:651)<br /> [run] at java.security.AccessController.doPrivileged(Native Method)<br /> [run] at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)<br /> [run] at java.awt.EventQueue.dispatchEvent(EventQueue.java:650)<br /> [run] at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)<br /> [run] at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)<br /> [run] at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:205)<br /> [run] at java.awt.Dialog$1.run(Dialog.java:1046)<br /> [run] at java.awt.Dialog$3.run(Dialog.java:1098)<br /> [run] at java.security.AccessController.doPrivileged(Native Method)<br /> [run] at java.awt.Dialog.show(Dialog.java:1096)<br /> [run] at java.awt.Component.show(Component.java:1585)<br /> [run] at java.awt.Component.setVisible(Component.java:1537)<br /> [run] at java.awt.Window.setVisible(Window.java:842)<br /> [run] at java.awt.Dialog.setVisible(Dialog.java:986)<br /> [run] at ptolemy.gui.ComponentDialog.&lt;init&gt;(ComponentDialog.java:209)<br /> [run] at ptolemy.gui.ComponentDialog.&lt;init&gt;(ComponentDialog.java:122)<br /> [run] at ptolemy.gui.ComponentDialog.&lt;init&gt;(ComponentDialog.java:101)<br /> [run] at ptolemy.actor.gui.EditParametersDialog.&lt;init&gt;(EditParametersDialog.java:105)<br /> [run] at ptolemy.actor.gui.EditParametersDialog.&lt;init&gt;(EditParametersDialog.java:93)<br /> [run] at ptolemy.vergil.toolbox.ConfigureAction._openDialog(ConfigureAction.java:145)<br /> [run] at ptolemy.vergil.toolbox.ConfigureAction.actionPerformed(ConfigureAction.java:99)<br /> [run] at diva.canvas.interactor.ActionInteractor.mousePressed(ActionInteractor.java:74)<br /> [run] at diva.canvas.interactor.CompositeInteractor.mousePressed(CompositeInteractor.java:199)<br /> [run] at diva.canvas.interactor.SelectionInteractor.mousePressed(SelectionInteractor.java:202)<br /> [run] at diva.canvas.FigureLayer.dispatchEventUpTree(FigureLayer.java:551)<br /> [run] at diva.canvas.FigureLayer.grabPointer(FigureLayer.java:319)<br /> [run] at diva.canvas.FigureLayer.processLayerEvent(FigureLayer.java:673)<br /> [run] at diva.canvas.FigureLayer.dispatchEvent(FigureLayer.java:203)<br /> [run] at diva.canvas.CanvasPane.processLayerEvent(CanvasPane.java:280)<br /> [run] at diva.canvas.CanvasPane.dispatchEvent(CanvasPane.java:89)<br /> [run] at diva.canvas.JCanvas.internalProcessMouseEvent(JCanvas.java:518)<br /> [run] at diva.canvas.JCanvas.processMouseEvent(JCanvas.java:472)<br /> [run] at java.awt.Component.processEvent(Component.java:6139)<br /> [run] at java.awt.Container.processEvent(Container.java:2085)<br /> [run] at java.awt.Component.dispatchEventImpl(Component.java:4736)<br /> [run] at java.awt.Container.dispatchEventImpl(Container.java:2143)<br /> [run] at java.awt.Component.dispatchEvent(Component.java:4566)<br /> [run] at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4621)<br /> [run] at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4279)<br /> [run] at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4212)<br /> [run] at java.awt.Container.dispatchEventImpl(Container.java:2129)<br /> [run] at java.awt.Window.dispatchEventImpl(Window.java:2478)<br /> [run] at java.awt.Component.dispatchEvent(Component.java:4566)<br /> [run] at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:680)<br /> [run] at java.awt.EventQueue.access$000(EventQueue.java:86)<br /> [run] at java.awt.EventQueue$1.run(EventQueue.java:639)<br /> [run] at java.awt.EventQueue$1.run(EventQueue.java:637)<br /> [run] at java.security.AccessController.doPrivileged(Native Method)<br /> [run] at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)<br /> [run] at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98)<br /> [run] at java.awt.EventQueue$2.run(EventQueue.java:653)<br /> [run] at java.awt.EventQueue$2.run(EventQueue.java:651)<br /> [run] at java.security.AccessController.doPrivileged(Native Method)<br /> [run] at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87)<br /> [run] at java.awt.EventQueue.dispatchEvent(EventQueue.java:650)<br /> [run] at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)<br /> [run] at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)<br /> [run] at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)<br /> [run] at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)<br /> [run] at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)<br /> [run] at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)</code></pre> Bug #4483 (Resolved): Module dependencies in MoML fileshttps://projects.ecoinformatics.org/ecoinfo/issues/44832009-10-21T23:15:30ZAaron Aaronaschultz@nceas.ucsb.edu
<p>To reproduce: <br />Save a KAR from the WRP suite<br />change to the kepler suite<br />on startup you see the error: <br />Error encountered in: <property name="TOP Provenance Recorder" class="org.kepler.provenance.ProvenanceRecorder"><br />etc....</p>
<p>I used to think this was an issue with the startup building of the library and that dependencies in the KARs was the problem. But it turns out to be much more malicious. It is actually a dependency from the MoML file itself. Because the WRP suite has the Provenance recorder included in the moml, when the provenance module is not around the error is displayed and the workflow can not be used. So this means that any moml file generated by the WRP suite cannot be run in the Kepler suite. Unlike in Reporting where the reporting files are separate from the MoML itself and therefore the MoML can still run in the Kepler suite.</p>
<p>So the task here is to figure out how to add a dependency on the provenance module to all the workflows that are created from the WRP suite. The ability to do this I think is not built into the KAR design and I'll have to figure out how to do it.</p>