Kepler: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362011-08-02T22:19:36ZEcoinformatics Redmine
Redmine 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 #5441 (Resolved): no 'work will be lost' warning when accepting a patch via Module Managerhttps://projects.ecoinformatics.org/ecoinfo/issues/54412011-07-13T20:04:23ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>If you check for, find, and accept an available patch via the Module Manager, kepler is restarted with no warning that any open work will be lost.</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 $CWD/file.txt.</p> Bug #5432 (Resolved): 2.2 mac installer contains 2 copies of everythinghttps://projects.ecoinformatics.org/ecoinfo/issues/54322011-06-28T19:32:35ZDaniel Crawldanielcrawl@gmail.com
<p>There is a zip file in each module containing the contents of the module.</p>
<p>I would not create a new installer for 2.2, since it has already been released, but the next installer should not contain these duplicates.</p> Bug #5430 (Resolved): problems with multiple instances of keplerhttps://projects.ecoinformatics.org/ecoinfo/issues/54302011-06-25T00:51:54ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>If you start two instances of kepler running at the same time on one machine, and quit the first instance, the second instance will begin having problems like being unable to search the Components library, unable to instantiate new components, etc. It appears the connection to the database is closed.</p> Bug #5414 (Resolved): fileparameter browse has NPEhttps://projects.ecoinformatics.org/ecoinfo/issues/54142011-05-27T21:12:33ZDaniel Crawldanielcrawl@gmail.com
<p>FileParameter browse button throws an NPE on Mac. No error on linux.</p>
<pre><code>[run] Exception in thread "AWT-EventQueue-0" java.lang.NullPointerException<br /> [run] at ptolemy.gui.Query$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 #5412 (Resolved): saving with an open plot window crasheshttps://projects.ecoinformatics.org/ecoinfo/issues/54122011-05-26T22:04:34ZDaniel Crawldanielcrawl@gmail.com
<p>If there is a plot window open, the following error occurs when saving and crashes Kepler. It also partially writes out the model file, leaving it corrupt.</p>
<pre><code>[run] java.lang.RuntimeException: Internal Error. Mark style 0 not supported.<br /> [run] at ptolemy.plot.Plot.writeFormat(Plot.java:1071)<br /> [run] at ptolemy.actor.lib.gui.PlotterBase._exportMoMLContents(PlotterBase.java:509)<br /> [run] at ptolemy.kernel.util.NamedObj.exportMoML(NamedObj.java:933)<br /> [run] at ptolemy.kernel.InstantiableNamedObj.exportMoML(InstantiableNamedObj.java:218)<br /> [run] at ptolemy.kernel.util.NamedObj.exportMoML(NamedObj.java:839)<br /> [run] at ptolemy.kernel.util.NamedObj.exportMoML(NamedObj.java:767)<br /> [run] at org.kepler.objectmanager.ActorMetadata.toString(ActorMetadata.java:1106)<br /> [run] at org.kepler.kar.KARBuilder.handleInitiatorList(KARBuilder.java:202)<br /> [run] at org.kepler.kar.KARBuilder.generateKAR(KARBuilder.java:313)<br /> [run] at org.kepler.kar.SaveKAR.saveToDisk(SaveKAR.java:154)<br /> [run] at org.kepler.gui.kar.ExportArchiveAction.actionPerformed(ExportArchiveAction.java:403)<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:683)<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$1.doIntersectionPrivilege(AccessControlContext.java:87)<br /> [run] at java.awt.EventQueue.dispatchEvent(EventQueue.java:650)<br /> [run] at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)<br /> [run] at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)<br /> [run] at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)<br /> [run] at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)<br /> [run] at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)<br /> [run] at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)</code></pre> Bug #5411 (Resolved): file->save to xml does not workhttps://projects.ecoinformatics.org/ecoinfo/issues/54112011-05-26T22:00:03ZDaniel Crawldanielcrawl@gmail.com
<p>An error occurs when saving to xml:</p>
<p>java.io.FileNotFoundException: /Users/crawl/KeplerData/Users/crawl/KeplerData/Unnamed1.xml (No such file or directory)<br /> at java.io.FileOutputStream.open(Native Method)<br /> at java.io.FileOutputStream.<init>(FileOutputStream.java:179)<br /> at java.io.FileOutputStream.<init>(FileOutputStream.java:131)<br /> at java.io.FileWriter.<init>(FileWriter.java:73)<br /> at ptolemy.actor.gui.PtolemyEffigy.writeFile(PtolemyEffigy.java:208)<br /> at ptolemy.actor.gui.PtolemyFrame._writeFile(PtolemyFrame.java:463)<br /> at ptolemy.vergil.basic.BasicGraphFrame._writeFile(BasicGraphFrame.java:2583)<br /> at ptolemy.actor.gui.TableauFrame._saveAsHelperFileDialog(TableauFrame.java:1259)<br /> at ptolemy.actor.gui.TableauFrame._saveAsHelper(TableauFrame.java:1109)<br /> at org.kepler.gui.KeplerGraphFrame._saveAs(KeplerGraphFrame.java:1462)<br /> at ptolemy.actor.gui.PtolemyFrame._saveAs(PtolemyFrame.java:368)<br /> at ptolemy.actor.gui.TableauFrame._save(TableauFrame.java:1051)<br /> at ptolemy.gui.Top$FileMenuListener.actionPerformed(Top.java:1208)<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:683)<br /> at java.awt.EventQueue.access$000(EventQueue.java:86)<br /> at java.awt.EventQueue$1.run(EventQueue.java:639)<br /> at java.awt.EventQueue$1.run(EventQueue.java:637)<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:653)<br /> at java.awt.EventQueue$2.run(EventQueue.java:651)<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:650)<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 #5402 (Resolved): Linux build at r27617 can't drag instantiate componentshttps://projects.ecoinformatics.org/ecoinfo/issues/54022011-05-12T21:22:48ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>Attempting to drag an actor out from the library gives an exception. Oddly only happening to me on linux - I tried a fresh checkout as a sanity check. Possibly related to MoML_1.dtd not being available atm: <a class="external" href="http://lists.nceas.ucsb.edu/kepler/pipermail/kepler-dev/2011-May/019529.html">http://lists.nceas.ucsb.edu/kepler/pipermail/kepler-dev/2011-May/019529.html</a></p>
<p>com.microstar.xml.XmlException: Cannot create entity without a class name. in [external stream] at line 2 and column 23<br /> at ptolemy.moml.MoMLParser._checkForNull(MoMLParser.java:3809)<br /> at ptolemy.moml.MoMLParser._createEntity(MoMLParser.java:3990)<br /> at ptolemy.moml.MoMLParser.startElement(MoMLParser.java:2510)<br /> at com.microstar.xml.XmlParser.parseElement(XmlParser.java:921)<br /> at com.microstar.xml.XmlParser.parseContent(XmlParser.java:1104)<br /> at com.microstar.xml.XmlParser.parseElement(XmlParser.java:924)<br /> at com.microstar.xml.XmlParser.parseContent(XmlParser.java:1104)<br /> at com.microstar.xml.XmlParser.parseElement(XmlParser.java:924)<br /> at com.microstar.xml.XmlParser.parseDocument(XmlParser.java:481)<br /> at com.microstar.xml.XmlParser.doParse(XmlParser.java:159)<br /> at com.microstar.xml.XmlParser.parse(XmlParser.java:132)<br /> at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1419)<br /> at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1391)<br /> at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1547)<br /> at ptolemy.moml.MoMLChangeRequest._execute(MoMLChangeRequest.java:289)<br /> at ptolemy.kernel.util.ChangeRequest.execute(ChangeRequest.java:171)<br /> at ptolemy.kernel.util.NamedObj.executeChangeRequests(NamedObj.java:735)<br /> at ptolemy.kernel.util.NamedObj.requestChange(NamedObj.java:1775)<br /> at ptolemy.actor.CompositeActor.requestChange(CompositeActor.java:1922)<br /> at ptolemy.vergil.basic.EditorDropTargetListener.drop(EditorDropTargetListener.java:365)<br /> at java.awt.dnd.DropTarget.drop(DropTarget.java:430)<br /> at sun.awt.dnd.SunDropTargetContextPeer.processDropMessage(SunDropTargetContextPeer.java:500)<br /> at sun.awt.X11.XDropTargetContextPeer.processDropMessage(XDropTargetContextPeer.java:165)<br /> at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchDropEvent(SunDropTargetContextPeer.java:812)<br /> at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchEvent(SunDropTargetContextPeer.java:736)<br /> at sun.awt.dnd.SunDropTargetEvent.dispatch(SunDropTargetEvent.java:30)<br /> at java.awt.Component.dispatchEventImpl(Component.java:4267)<br /> at java.awt.Container.dispatchEventImpl(Container.java:2116)<br /> at java.awt.Component.dispatchEvent(Component.java:4240)<br /> at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4322)<br /> at java.awt.LightweightDispatcher.processDropTargetEvent(Container.java:4057)<br /> at java.awt.LightweightDispatcher.dispatchEvent(Container.java:3911)<br /> at java.awt.Container.dispatchEventImpl(Container.java:2102)<br /> at java.awt.Window.dispatchEventImpl(Window.java:2429)<br /> at java.awt.Component.dispatchEvent(Component.java:4240)<br /> at java.awt.EventQueue.dispatchEvent(EventQueue.java:599)<br /> at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:273)<br /> at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:183)<br /> at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:173)<br /> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:168)<br /> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:160)<br /> at java.awt.EventDispatchThread.run(EventDispatchThread.java:121)</p> Bug #5254 (Resolved): provenance database connections keep growing when using Reporting suite.https://projects.ecoinformatics.org/ecoinfo/issues/52542010-12-10T01:02:15Zjianwu jianwujianwu@sdsc.edu
<p>Every time a window is open, or a workflow is saved, running, a separate db connection is gotten. but they are not released when a window is closed. It will cause memory usage goes up.</p>
<p>We guess WorkflowRunManager.disconnect() should call SQLQueryV8.disconnect() to close the connection. Currently, SQLQueryV8.disconnect() is not called by any classes.</p>
<p>If we can reuse existing connections. The performance will be better than creating and closing a new one.</p>
<p>This is one stack trace for db connection when a window is open:</p>
<p>DatabaseFactory.getConnectedDatabaseType(Map<String,String>, String) line: 154 <br />SQLQueryV8.<init>(Map<String,String>) line: 77 <br />WorkflowRunManager.connect() line: 135 <br />WorkflowRunManagerPanel.reconnect() line: 960 <br />WorkflowRunManagerPanel.resetProvenanceInfo(ProvenanceStore) line: 937 <br />WorkflowRunManagerPanel.initializeTab() line: 231 <br />TabPaneFactory.createTabPaneTabs(TableauFrame) line: 110 <br />TabManager.initializeTabs(TableauFrame) line: 87 <br />KeplerGraphFrame._initBasicGraphFrame() line: 377 <br />KeplerGraphFrame(BasicGraphFrame).<init>(NamedObj, Tableau, LibraryAttribute) line: 224 <br />KeplerGraphFrame(ExtendedGraphFrame).<init>(CompositeEntity, Tableau, LibraryAttribute) line: 95 <br />KeplerGraphFrame(ActorGraphFrame).<init>(CompositeEntity, Tableau, LibraryAttribute) line: 135 <br />KeplerGraphFrame.<init>(CompositeEntity, Tableau, LibraryAttribute) line: 180 <br />KeplerGraphTableau.<init>(PtolemyEffigy, String, LibraryAttribute) line: 164 <br />KeplerGraphTableau$Factory.createTableau(Effigy) line: 227 <br />PtolemyTableauFactory.createTableau(Effigy) line: 100 <br />TableauFactory.createTableau(Effigy) line: 127 <br />Configuration.createPrimaryTableau(Effigy) line: 569 <br />TableauFrame$1.actionPerformed(ActionEvent) line: 519</p> Bug #5232 (Resolved): unable to open KARs saved beneath absent (e.g. third party) moduleshttps://projects.ecoinformatics.org/ecoinfo/issues/52322010-10-28T21:17:27ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>This isn't an issue in 2.1, since apple-extensions is loaded by all OSes in 2.1, but on trunk apple-extensions is now only loaded by macs. Because of this, KARs saved on a mac on trunk cannot be opened by linux or windows trunk -- the module-dependency checking code requires apple-extensions to be present first.</p>
<p>On a related note, a user emailed me a kar that used 3rd party modules today, and I can't open it through normal means because Kepler wants these module dependencies satisfied first.</p>
<p>The best solution isn't clear to me yet, an additional strictness level, that doesn't require module dependencies be satisfied to attempt to open the kar? Or it may be more streamlined to simply warn and offer to attempt to open without the module dependencies satisfied on each relevant open attempt.</p> Bug #5186 (Resolved): Publish example KARs to repositoryhttps://projects.ecoinformatics.org/ecoinfo/issues/51862010-09-16T21:10:39ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>The two KARs on the kepler library were published inadvertently, and may and should be removed, because they are not good examples.</p>
<p>We should also publish some good examples (using 2.1, so they are KAR 2.1) for users to see.<br />Matt suggests:<br />REAP examples<br />SANPark examples<br />some useful components</p>
<p>Publishing a run kar that includes a nice report (sanparks?) would be good too.</p> Bug #5071 (Resolved): Improve the installer so that it is automated instead of requiring so many ...https://projects.ecoinformatics.org/ecoinfo/issues/50712010-07-01T03:48:40ZDavid Welkerwelker4kepler@gmail.com
<p>(7) Improve the installer so that it is automated instead of requiring so many manual steps. Also, develop streamlined release process so that minor releases 2.1, 2.2, etc. can be accomplished more rapidly.</p>
<p>This is critical if we want to make more frequent releases. Also, application wide resources that need to be updated with every incremental release should be stored in one module. An ideal candidate would be the Kepler suite module. That way, if a patch occurs, the splash screen and other resources can all easily be updated to reflect the patch. The splash screen should not longer be done in photoshop, but instead a method should be devised such that text indicating the version number is somehow merged with a background image.</p> 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>