Kepler: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362010-11-24T02:18:03ZEcoinformatics Redmine
Redmine Bug #5247 (Resolved): Allow user to set memory allocated to Kepler from within Keplerhttps://projects.ecoinformatics.org/ecoinfo/issues/52472010-11-24T02:18:03ZDerik Barseghianbarseghian@nceas.ucsb.edu
<p>A nice feature for advanced users would be to let them set how much memory kepler is allocated (presumably a restart would be required for the change to take place).</p>
<p>This is in part motivated by some users who have run workflows that pass large chunks of data around as tokens, and execution has stopped with an error because of heap space errors.</p> Bug #5240 (Resolved): NameDuplicationException from SequencePlotterhttps://projects.ecoinformatics.org/ecoinfo/issues/52402010-11-16T19:08:16ZDaniel Crawldanielcrawl@gmail.com
<p>Reproduce with attached workflow.</p>
<p>ptolemy.kernel.util.IllegalActionException: Error creating effigy and tableau<br /> in .plot-error.a plot<br />Because:<br />Attempt to insert object named "plot" into container named ".configuration.directory.effigy2", which already contains an object with that name.<br /> at ptolemy.actor.lib.gui.Plotter.initialize(Plotter.java:167)<br /> at ptolemy.actor.lib.gui.SequencePlotter.initialize(SequencePlotter.java:130)<br /> at ptolemy.actor.process.ProcessThread.run(ProcessThread.java:135)<br />Caused by: ptolemy.kernel.util.NameDuplicationException: Attempt to insert object named "plot" into container named ".configuration.directory.effigy2", which already contains an object with that name.<br /> at ptolemy.kernel.util.NamedList.append(NamedList.java:133)<br /> at ptolemy.kernel.CompositeEntity._addEntity(CompositeEntity.java:2080)<br /> at ptolemy.kernel.ComponentEntity.setContainer(ComponentEntity.java:518)<br /> at ptolemy.kernel.CompositeEntity.setContainer(CompositeEntity.java:1815)<br /> at ptolemy.actor.gui.Effigy.setContainer(Effigy.java:401)<br /> at ptolemy.kernel.ComponentEntity.<init>(ComponentEntity.java:106)<br /> at ptolemy.kernel.CompositeEntity.<init>(CompositeEntity.java:164)<br /> at ptolemy.actor.gui.Effigy.<init>(Effigy.java:133)<br /> at ptolemy.actor.gui.PlotEffigy.<init>(PlotEffigy.java:71)<br /> at ptolemy.actor.lib.gui.Plotter.initialize(Plotter.java:155)<br /> ... 2 more<br />Caused by: ptolemy.kernel.util.NameDuplicationException: Attempt to insert object named "plot" into container named ".configuration.directory.effigy2", which already contains an object with that name.<br /> at ptolemy.kernel.util.NamedList.append(NamedList.java:133)<br /> at ptolemy.kernel.CompositeEntity._addEntity(CompositeEntity.java:2080)<br /> at ptolemy.kernel.ComponentEntity.setContainer(ComponentEntity.java:518)<br /> at ptolemy.kernel.CompositeEntity.setContainer(CompositeEntity.java:1815)<br /> at ptolemy.actor.gui.Effigy.setContainer(Effigy.java:401)<br /> at ptolemy.kernel.ComponentEntity.<init>(ComponentEntity.java:106)<br /> at ptolemy.kernel.CompositeEntity.<init>(CompositeEntity.java:164)<br /> at ptolemy.actor.gui.Effigy.<init>(Effigy.java:133)<br /> at ptolemy.actor.gui.PlotEffigy.<init>(PlotEffigy.java:71)<br /> at ptolemy.actor.lib.gui.Plotter.initialize(Plotter.java:155)<br /> at ptolemy.actor.lib.gui.SequencePlotter.initialize(SequencePlotter.java:130)<br /> at ptolemy.actor.process.ProcessThread.run(ProcessThread.java:135)</p> Bug #5194 (Resolved): demos are difficult to findhttps://projects.ecoinformatics.org/ecoinfo/issues/51942010-09-29T15:40:45ZChristopher Brookscxh@eecs.berkeley.edu
<p>Help | Kepler Documentation says:</p>
<p>"All listed demos are in the KeplerData/workflows/module/outreach-2.X.Y/demos/getting-started"</p>
<p>That path name is difficult to find as it is long and there is a<br />"KeplerData/modules" directory that is confusing.</p>
<p>Also, if I follow the typical pattern of looking at the help file,<br />opening a demo, then closing the demo and looking at the help file,<br />I need to retraverse the confusing path hierarchy each time.</p>
<p>To replicate:<br />1. Help | Kepler Documentation<br />2. File | Open, then browse through to <br /> KeplerData/workflows/module/outreach-2.X.Y/demos/getting-started" <br />3. Open the 04-HelloWorld.kar<br />4. Run the demo and close it.<br />5. Now, look at the Kepler Documentation page and try to open the next<br /> demo. The result is I have to go through the Open dialog again.</p>
<p>This is not very usable and does not promote actually viewing the demos. <br />There should be hyperlinks in the text that opens the demos.</p> Bug #5188 (Resolved): closing workflow does not save the location change of popup display windows.https://projects.ecoinformatics.org/ecoinfo/issues/51882010-09-21T22:16:42Zjianwu jianwujianwu@sdsc.edu
<p>To find the differences:<br />1) create a test workflow with display actors<br />2a) save the workflow as a kar<br />2b) save the workflow as a moml file<br />3) open the saved workflow <br />4) run workflow to have popup display windows<br />5) move display windows to another location<br />6) close the workflow, no popup window will show for overwrite confirmation <br />7) open the workflow again and run it</p>
<p>If the workflow is saved as a moml file, the new window location will be saved and show in the new execution. But it doesn't work for kar file saving.</p> Bug #5156 (Resolved): ant run for kepler 1.0 fails after clean svn checkouthttps://projects.ecoinformatics.org/ecoinfo/issues/51562010-08-19T08:57:01ZMichal Owsiakmichalo@man.poznan.pl
<p>gamma:build-area michalo$ pwd<br />/Users/michalo/modules.dir/build-area<br />gamma:build-area michalo$ sw_vers <br />ProductName: Mac OS X<br />ProductVersion: 10.6.4<br />BuildVersion: 10F569<br />gamma:build-area michalo$ java -version<br />java version "1.6.0_20" <br />Java(TM) SE Runtime Environment (build 1.6.0_20-b02-279-10M3065)<br />Java HotSpot(TM) 64-Bit Server VM (build 16.3-b01-279, mixed mode)<br />gamma:build-area michalo$ ant -version<br />Apache Ant version 1.7.1 compiled on April 8 2010<br />gamma:build-area michalo$ pwd<br />/Users/michalo/modules.dir/build-area<br />gamma:build-area michalo$ ant run<br />Buildfile: build.xml</p>
<p>compile:<br /> [echo] Note that you may need to run "ant force-ptolemy compile" to compile ptolemy.<br /> [compile] Compiling kepler-1.0-jar-tag...<br /> [compile] Compiling loader-for-kepler-1.0...</p>
<p>run:</p>
<p>BUILD FAILED<br />java.lang.NullPointerException<br /> at org.kepler.build.Run.runSuite(Run.java:262)<br /> at org.kepler.build.Run.run(Run.java:202)<br /> at org.kepler.build.modules.ModulesTask.execute(ModulesTask.java:101)<br /> at org.apache.tools.ant.UnknownElement.execute(UnknownElement.java:288)<br /> at sun.reflect.GeneratedMethodAccessor1.invoke(Unknown Source)<br /> at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25)<br /> at java.lang.reflect.Method.invoke(Method.java:597)<br /> at org.apache.tools.ant.dispatch.DispatchUtils.execute(DispatchUtils.java:106)<br /> at org.apache.tools.ant.Task.perform(Task.java:348)<br /> at org.apache.tools.ant.Target.execute(Target.java:357)<br /> at org.apache.tools.ant.Target.performTasks(Target.java:385)<br /> at org.apache.tools.ant.Project.executeSortedTargets(Project.java:1337)<br /> at org.apache.tools.ant.Project.executeTarget(Project.java:1306)<br /> at org.apache.tools.ant.helper.DefaultExecutor.executeTargets(DefaultExecutor.java:41)<br /> at org.apache.tools.ant.Project.executeTargets(Project.java:1189)<br /> at org.apache.tools.ant.Main.runBuild(Main.java:758)<br /> at org.apache.tools.ant.Main.startAnt(Main.java:217)<br /> at org.apache.tools.ant.launch.Launcher.run(Launcher.java:257)<br /> at org.apache.tools.ant.launch.Launcher.main(Launcher.java:104)</p>
<p>Total time: 0 seconds</p> Bug #5142 (Resolved): comma improperly inserted in kar filename rather than a period (.)https://projects.ecoinformatics.org/ecoinfo/issues/51422010-08-11T23:56:58ZMatt Jonesjones@nceas.ucsb.edu
<p>When KAR files are saved, with a name such as "foo.kar", then show up incorrectly in the kepler component pane with a comma in the name rather than the period (e.g., it becomes "foo,kar". KAR files should be saved with the normal period as the extension separator in the filename, and should display this way as well.</p> Bug #5072 (Resolved): Move the R module out of Kepler/CORE entirely.https://projects.ecoinformatics.org/ecoinfo/issues/50722010-07-01T03:49:08ZDavid Welkerwelker4kepler@gmail.com
<p>(8) Move the R module out of Kepler/CORE entirely. Set up the module manager to handle the R installation process when a suite including the R module is downloaded without requiring the user to handle installation manually. Move getting-started workflows that use the R actor out of Kepler/CORE into the r module.</p>
<p>The R module does not add anything to Kepler unless R is installed. Also, often the exact version of R that is required matters. A mini-installer would be able to ensure that the user downloads a compatible version of R for use with Kepler.</p> Bug #5052 (Resolved): default file open directory of Kepler 2.0https://projects.ecoinformatics.org/ecoinfo/issues/50522010-06-17T00:38:51Zjianwu jianwujianwu@sdsc.edu
<p>If I remember correctly, the default directory for 'File-->Open File...' menu item is getting-started directory in Kepler 1.0. In Kepler 2.0 RC 5, the default directory is KeplerData and the getting-started directory is at KeplerData/workflows/module/outreach-2.0.0/demos/getting-started. It might be inconvenient to find this directory, especially for novice.</p>
<p>The discussion about it on IRC is as follows:<br /><jianwu> but why it has such a name, and it is not the default dir for 'file opening'<br /><jianwu> If I remember correctly, the file open will go to the getting-started directory by default.<br /><jianwu> for Keplre 1.0<br /><jianwu> In Kepler 2.0, this directory will take people a long time to find it.<br /><jianwu> what do you think, davidwelker?<br /><davidwelker> hmm<br /><davidwelker> I think we could change it<br /><davidwelker> who knows how to change it quickly?<br /><davidwelker> I agree this is less convenient. But I am not going to delay the release for it<br /><davidwelker> Oh wait...<br /><jianwu> not sure. may chad know the situation of Kepler 1.0 and how to do it?<br /><davidwelker> I don't know if we should use getting-started anymore as the defult<br /><davidwelker> what if outreach is patched and goes to outreach-2.0.1<br /><davidwelker> then you code might break<br /><davidwelker> that is sort of fragile<br /><davidwelker> yeah, lets just leave it<br /><davidwelker> I agree it is a little less convenient<br /><davidwelker> But it is fine for now<br /><davidwelker> I want to do a Kepler 2.1 in the not too distant future<br /><davidwelker> and we can fix stuff like this<br /><jianwu> hmm<br /><davidwelker> you feel strongly about this =)<br /><davidwelker> if you feel really strongly, we can move it up<br /><davidwelker> but the issue is tricky. We have to find where the default is set<br /><davidwelker> and then that person has to detect not outreach<br /><davidwelker> but the latest outreach<br /><davidwelker> and then go from there to demos/getting-started<br /><jianwu> you can set it acordding to property("outreach.workflowdir")<br /><davidwelker> I am not sure how exactly to do that in code right off the top of my head<br /><davidwelker> right<br /><jianwu> not like outreach-2.0.1 or outreach-2.0.0 <br /><davidwelker> you want to change it?<br /><davidwelker> I agree<br /><davidwelker> that is right<br /><davidwelker> I remember now<br /><davidwelker> derik made that<br /><davidwelker> so, if you want to put this out before 2.0, do you think you can hunt down where the default is and change it?<br /><davidwelker> if you don't have time, it would be fine to do it post 2.0<br /><davidwelker> I am not even sure that getting-started is where we want it to always open files<br /><davidwelker> that seems great for checking out demos<br /><jianwu> I can try. I'll fire a bug firstly about the issue.<br /><davidwelker> but what about their own work?<br /><davidwelker> If you are working on your own stuff, you want to open your own workflow<br /><davidwelker> so, should the default really be getting-started?<br /><jianwu> it's true. <br /><jianwu> so it should be configurable?<br /><davidwelker> yeah<br /><davidwelker> I think it should be configurable<br /><davidwelker> but, I think KeplerData would probably be good for now, actually<br /><jianwu> ok. good discussion. I'll fire an enhancement bug and see what other guys say about it.<br /><davidwelker> perfect<br /><derik_> just catching up here<br /><derik_> i think Open dialog opens whereever you last opened from<br /><davidwelker> yeah<br /><jianwu> yes<br /><davidwelker> it definitely does htat<br /><davidwelker> cause if I open one workflow from getting-started<br /><davidwelker> then it opens from there without me having to navigate to it<br /><derik_> ok...maybe that wasn't relevant to what you guys are discussing :)<br /><davidwelker> so, where should it start the first time?<br /><davidwelker> actually derik, it is relevant<br /><davidwelker> it puts it in context<br /><derik_> ok, hmm<br /><davidwelker> we are just talking about where it should open the first time<br /><davidwelker> so, getting-started is not a bad choice<br /><jianwu> I agree<br /><davidwelker> since if you are working on your own stuff, well, it is going to open near there anyway<br /><davidwelker> I will leave decision to whoever has an opinion. =) I can go either way<br /><derik_> yeah getting-started would be a good choice for first time open. it would be a bad choice for first time save (not sure if they're one and the same or not)<br /><davidwelker> good point derik_<br /><davidwelker> I don't think getting-started would be a good choice for first time save</p> Bug #5020 (Resolved): 2.0-RC3 installer: R Kepler Module is not optionalhttps://projects.ecoinformatics.org/ecoinfo/issues/50202010-05-20T17:28:08ZChristopher Brookscxh@eecs.berkeley.edu
<p>When installing Kepler-2.0-RC3, I'm presented with<br />two choices:<br />Kepler<br />R Kepler Module</p>
<p>Both are required, I can't uncheck "R Kepler Module",<br />so why bother with this window?</p> Bug #4926 (Resolved): Examine Kepler for duplicated Ptolemy codehttps://projects.ecoinformatics.org/ecoinfo/issues/49262010-04-02T23:14:46ZChristopher Brookscxh@eecs.berkeley.edu
<p>There are a few files in Kepler that have Edward listed as an author.<br />I suspect that some of these are duplicated code from the Ptolemy II tree.</p>
<p>In the 2.0 release, I searched all the java files for Edward's name and<br />came up with this list:</p>
<p>bash-3.2$ find . -name "*.java" > /tmp/kj<br />bash-3.2$ cat /tmp/kj | grep -v ptolemy-8.0 | xargs grep "Edward A. Lee" <br />./actors-2.0/src/org/sdm/spa/CommandLineExec.java: * Contributor: Edward A. Lee<br />./actors-2.0/src/org/sdm/spa/gui/ShellInterpreter.java: * @author Edward A. Lee<br />./actors-2.0/src/org/sdm/spa/gui/ShellTextArea.java: * @author John Reekie, Christopher Hylands, Edward A. Lee<br />./actors-2.0/src/org/sdm/spa/gui/UserInteractiveShell.java: * This actor code is adopted from InteractiveShell.java by Edward A. Lee<br />./ecogrid-2.0/src/ptolemy/vergil/tree/PTree.java: @author Steve Neuendorffer and Edward A. Lee<br />./gui-2.0/src/org/kepler/gui/frame/CaseGraphFrame.java: @author Edward A. Lee<br />./gui-2.0/src/org/kepler/gui/frame/CaseGraphTableau.java: @author Edward A. Lee<br />./gui-2.0/src/org/kepler/gui/frame/KeplerGraphTableau.java: @author Based on GraphTableau by Steve Neuendorffer and Edward A. Lee<br />./gui-2.0/src/org/kepler/gui/frame/MultiCompositeGraphFrame.java: @author Edward A. Lee, Daniel Crawl<br />./gui-2.0/src/org/kepler/gui/frame/MultiCompositeTableau.java: @author Edward A. Lee, Daniel Crawl<br />./gui-2.0/src/org/kepler/gui/KeplerIconLoader.java: * @author Christopher Brooks, contributor: Edward A. Lee<br />./gui-2.0/src/org/kepler/gui/KeplerXMLIcon.java: * @author Steve Neuendorffer, John Reekie, Contributor: Edward A. Lee<br />./util-2.0/src/util/LineReader.java: * @author Edward A. Lee, Yuhong Xiong<br />bash-3.2$</p>
<p>Sean Riddle is in the process of fixing the PTree duplication.</p>
<p>To close this bug, each of the files should be examined and ideally, the<br />original class in Ptolemy be modified and the copy be removed or made much smaller.</p>
<p>In addition, to close this bug, if Edward is not listed in the history for the<br />file, then he should be removed as an author and added as a contributor.</p> Bug #4903 (Resolved): Text in attributes not rendered properlyhttps://projects.ecoinformatics.org/ecoinfo/issues/49032010-03-24T19:30:58ZChristopher Brookscxh@eecs.berkeley.edu
<p>In a version of Kepler checked out from the svn tree, I did:<br /> Tools->Instantiate Attribute<br />and entered<br /> ptolemy.vergil.actor.lib.MonitorReceiverContents<br />and that created an attribute.</p>
<p>However, the attribute does not have the text<br />MonitorReceiverContents<br />visible</p>
<p>If I instantiate a ptolemy.actor.gui.ModelRepaintController<br />in the same manner, then the same problem occurs.</p>
<p>Dragging in a Documentation attribute has the same problem<br />1. In Search Components, enter "Documentation" <br />2. In the Search Results, under Actors-2_0, drag the<br /> Documentation attribute into the graph pane<br />3. Note that the text is not visible.</p>
<p>This occurs in the Kepler-2.0.0 Beta 1 installer and in <br />the devel tree.</p> Bug #4711 (Resolved): Problem with L.H. actor tree: ActorName,karhttps://projects.ecoinformatics.org/ecoinfo/issues/47112010-01-29T16:41:18ZChristopher Brookscxh@eecs.berkeley.edu
<p>In a clean checkout under Windows, I'm now seeing the<br />kar files listed in the left hand actor tree.</p>
<p>I see<br />-Actors<br /> -ANOVA,kar<br /> ANOVA</p>
<p>I would expect to see<br />+Actors<br /> ANOVA</p>
<p>It would be nice to not display the ANOVA,kar nodes for kar files that<br />only contain actors.</p> Bug #4068 (Resolved): File Menu should display 5 most recently used workflowshttps://projects.ecoinformatics.org/ecoinfo/issues/40682009-05-14T22:53:55ZBertram Ludaescherludaesch@ucdavis.edu
<p>The 'File' menu in Kepler does not show the most recently opened workflows.<br />It would be important to have a "Recent Files" (really: "Recent Workflows") list that shows say the last 5 or so workflows that have been open.</p>
<p>Related: "Open File" should probably be "Open Workflow" in Kepler!?</p>
<p>Also related: <br />Should the Open File/Workflow operation should remember the last directory used!?</p>
<p>Bertram</p> Bug #3997 (Resolved): Supporting display actor conversion for command line execution.https://projects.ecoinformatics.org/ecoinfo/issues/39972009-04-20T21:20:53Zjianwu jianwujianwu@sdsc.edu
<p>When executing workflow for batch mode, users may want the display actors in the workflow can be converted automatically. We can enable it by adding one more option: "-displayRevert path/to/put/diplay/files". We can use the jar of Hydrant to filter the display actors to the corresponding file writing actors before workflow execution. This is already implemented in Kepler Web service and CAMERA project. Tristan also said his jar can be updated and re-distributed.</p> Bug #2335 (Resolved): MENUS: Top-Level Menu - dynamic addition of menu itemshttps://projects.ecoinformatics.org/ecoinfo/issues/23352006-01-18T22:12:20ZMatthew Brookebrooke@nceas.ucsb.edu
<p>Need to look at dynamic addition of menu items to Window menu and MRU File menu.<br />Need to keep a pointer to these for future use (actually, already have pointer<br />in keplerMenuMap)</p>