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 #5564 (Resolved): dragging sdf director to the canvas causes exceptionhttps://projects.ecoinformatics.org/ecoinfo/issues/55642011-12-07T00:08:19ZJing Taotao@nceas.ucsb.edu
<p>I searched sdf director and got it on the left panel. Then I tried to drag it to the canvas, but i got the exception:<br />com.microstar.xml.XmlException: Cannot create entity without a class name. in [external stream] at line 2 and column 22<br /> at ptolemy.moml.MoMLParser._checkForNull(MoMLParser.java:3992)<br /> at ptolemy.moml.MoMLParser._createEntity(MoMLParser.java:4173)<br /> at ptolemy.moml.MoMLParser.startElement(MoMLParser.java:2694)<br /> at com.microstar.xml.XmlParser.parseElement(XmlParser.java:922)<br /> at com.microstar.xml.XmlParser.parseContent(XmlParser.java:1105)<br /> at com.microstar.xml.XmlParser.parseElement(XmlParser.java:925)<br /> at com.microstar.xml.XmlParser.parseContent(XmlParser.java:1105)<br /> at com.microstar.xml.XmlParser.parseElement(XmlParser.java:925)<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:1538)<br /> at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1510)<br /> at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1666)<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:738)<br /> at ptolemy.kernel.util.NamedObj.requestChange(NamedObj.java:1778)<br /> at ptolemy.actor.CompositeActor.requestChange(CompositeActor.java:1922)<br /> at ptolemy.vergil.basic.EditorDropTargetListener.drop(EditorDropTargetListener.java:369)<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:4270)<br /> at java.awt.Container.dispatchEventImpl(Container.java:2116)<br /> at java.awt.Component.dispatchEvent(Component.java:4243)<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:2440)<br /> at java.awt.Component.dispatchEvent(Component.java:4243)<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 #5549 (Resolved): Help=>Modules Documentation not working in ubuntuhttps://projects.ecoinformatics.org/ecoinfo/issues/55492011-11-21T23:30:42ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>If you click on e.g. reporting from Modules Documentation, you get an error that isn't helpful.<br />It's coming from module-manager ActiveModulesDocumentationPanel, which is not finding a browser to use to open the file.</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 #5494 (Resolved): existence of remote 2.2 patches can cause 2.3 to fail to start 2.2 on first...https://projects.ecoinformatics.org/ecoinfo/issues/54942011-09-20T00:32:14ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>Now two patches to 2.2 exist: loader-2.1.1 and module-manager-gui-2.2.1.<br />If you launch 2.3.0 from the 2.3 app and attempt to use it to switch back to kepler-2.2, if you have not previously downloaded the patches mentioned above from within 2.2, 2.2 will fail to start on this initial attempt. The error on console is:<br />9/19/11 4:34:20 PM [0x0-0xfdafda].org.kepler.build.runner.Kepler<sup><a href="#fn38570">38570</a></sup> [null] Error: The following modules are missing: <br />9/19/11 4:34:20 PM [0x0-0xfdafda].org.kepler.build.runner.Kepler<sup><a href="#fn38570">38570</a></sup> [null] loader-2.1.1<br />9/19/11 4:34:20 PM [0x0-0xfdafda].org.kepler.build.runner.Kepler<sup><a href="#fn38570">38570</a></sup> [null] module-manager-gui-2.2.1</p>
<p>A subsequent start up of the 2.3 app does what was supposed to happen the first time: start 2.2, immediately prompting you to download the two available patches.</p>
<p>During the Module Manager restart process something seems to have knowledge of remote patches and mistakenly assumes they've been downloaded.</p> Bug #5488 (Resolved): domain/username/password in command line hadn't been parsed in kepler when ...https://projects.ecoinformatics.org/ecoinfo/issues/54882011-09-08T23:56:39ZJing Taotao@nceas.ucsb.edu
<p>When I used the command line to run a workflow which would access some private data, i found the domain/username/password arguments in command line were not used. So the execution failed since kepler thought the public user wanted to access those data.</p>
<p>The reason is the authentication path was done earlier than the path which parsed the domain/username/password in KeplerConfigurationApplication class. I changed the order and the bug was fixed.</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 #5455 (Resolved): Documentation for 2.3.0https://projects.ecoinformatics.org/ecoinfo/issues/54552011-08-12T01:38:38ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>Documentation needs to be done for the 2.3.0 release. <br />The getting-started-guide needs updating, at the very least to mention that Java 1.6 is now required. This should have been done for 2.2.0.<br />The UserManual, at the very least, needs a new date on title page.<br />I think the Actor Reference and Guide to ENM can again go unchanged as we've done for the last two releases.</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$1.doIntersectionPrivilege(AccessControlContext.java:87)<br /> [run] at java.awt.EventQueue.dispatchEvent(EventQueue.java:650)<br /> [run] at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296)<br /> [run] at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211)<br /> [run] at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201)<br /> [run] at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196)<br /> [run] at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188)<br /> [run] at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)</code></pre> Bug #5411 (Resolved): file->save to xml does not workhttps://projects.ecoinformatics.org/ecoinfo/issues/54112011-05-26T22:00:03ZDaniel Crawldanielcrawl@gmail.com
<p>An error occurs when saving to xml:</p>
<p>java.io.FileNotFoundException: /Users/crawl/KeplerData/Users/crawl/KeplerData/Unnamed1.xml (No such file or directory)<br /> at java.io.FileOutputStream.open(Native Method)<br /> at java.io.FileOutputStream.<init>(FileOutputStream.java:179)<br /> at java.io.FileOutputStream.<init>(FileOutputStream.java:131)<br /> at java.io.FileWriter.<init>(FileWriter.java:73)<br /> at ptolemy.actor.gui.PtolemyEffigy.writeFile(PtolemyEffigy.java:208)<br /> at ptolemy.actor.gui.PtolemyFrame._writeFile(PtolemyFrame.java:463)<br /> at ptolemy.vergil.basic.BasicGraphFrame._writeFile(BasicGraphFrame.java:2583)<br /> at ptolemy.actor.gui.TableauFrame._saveAsHelperFileDialog(TableauFrame.java:1259)<br /> at ptolemy.actor.gui.TableauFrame._saveAsHelper(TableauFrame.java:1109)<br /> at org.kepler.gui.KeplerGraphFrame._saveAs(KeplerGraphFrame.java:1462)<br /> at ptolemy.actor.gui.PtolemyFrame._saveAs(PtolemyFrame.java:368)<br /> at ptolemy.actor.gui.TableauFrame._save(TableauFrame.java:1051)<br /> at ptolemy.gui.Top$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 #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>