Kepler: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362010-03-05T22:14:10ZEcoinformatics Redmine
Redmine Bug #4872 (Resolved): listen to director throws errorhttps://projects.ecoinformatics.org/ecoinfo/issues/48722010-03-05T22:14:10ZOliver Soongsoong@nceas.ucsb.edu
<p>Add an SDF Director and the Tools->Listen to Director. An error pops up on the console:</p>
<p>Error creating action for class: org.kepler.gui.RunWithFeedbackChkBoxAction : null<br />Error creating action for class: org.kepler.gui.RunWithFeedbackChkBoxAction</p>
<p>I'm not sure if this causes problems or not.</p> Bug #4869 (In Progress): changes made to workflows during dialogs before committing (Edit Paramet...https://projects.ecoinformatics.org/ecoinfo/issues/48692010-03-04T19:04:24ZOliver Soongsoong@nceas.ucsb.edu
<p>When I make changes to an actor through the dialog, it seems like the changes are made to the workflow immediately, before the "Commit" button is clicked.</p>
<p>For example, create a workflow with an EML 2 Dataset actor. Make sure Kepler has not already authenticated with KNB. Now edit the EML 2 Dataset actor to reference a data package that requires authentication. The KNB login window will immediately pop up, even though no changes have been committed. Dismiss the window in some way. Now click the Help button and close the help window. The dialog will have disappeared. Open the actor dialog again, and the change will be there.</p>
<p>I should point out that the "Cancel" button does seem to work, but I suspect (based on debugging comments and comments in code) that this acts by reverting the changes already made.</p>
<p>I've seen this for sure on EML 2 Dataset and RExpression, since changes to one trigger visual feedback and I've mucked around in the code of the other. I suspect this is a general problem, though, and it may be a result of the underlying ptolemy design.</p> Bug #4846 (Resolved): error opening kar from local repositoryhttps://projects.ecoinformatics.org/ecoinfo/issues/48462010-02-25T22:50:11ZOliver Soongsoong@nceas.ucsb.edu
<p>This is with wrp at r23202. I deleted .kepler and KeplerData. I create a trivial workflow (default SDF and RExpression) and save it as a KAR in the default local repository. On restarting Kepler, the KAR and local repository are not listed in the components pane. If I go into Sources and manually trigger a re-build of the component library, I can see the KAR, but nothing happens when I attempt to open it (right-click menu) except an error in the console:</p>
<p>org.kepler.objectmanager.cache.CacheException: Exception occurred while deserializing object<br /> at org.kepler.objectmanager.cache.CacheManager.getObject(CacheManager.java:529)<br /> at org.kepler.kar.handlers.ActorMetadataKAREntryHandler.open(ActorMetadataKAREntryHandler.java:206)<br /> at org.kepler.kar.KARFile.open(KARFile.java:889)<br /> at org.kepler.kar.KARFile.openKARContents(KARFile.java:665)<br /> at org.kepler.gui.kar.OpenArchiveAction.openKAR(OpenArchiveAction.java:162)<br /> at org.kepler.gui.kar.OpenArchiveAction.actionPerformed(OpenArchiveAction.java:143)<br /> at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:1995)<br /> at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2318)<br /> at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:387)<br /> at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:242)<br /> at javax.swing.AbstractButton.doClick(AbstractButton.java:357)<br /> at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:1223)<br /> at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:1264)<br /> at java.awt.Component.processMouseEvent(Component.java:6263)<br /> at javax.swing.JComponent.processMouseEvent(JComponent.java:3255)<br /> at java.awt.Component.processEvent(Component.java:6028)<br /> at java.awt.Container.processEvent(Container.java:2041)<br /> at java.awt.Component.dispatchEventImpl(Component.java:4630)<br /> at java.awt.Container.dispatchEventImpl(Container.java:2099)<br /> at java.awt.Component.dispatchEvent(Component.java:4460)<br /> at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4574)<br /> at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4238)<br /> at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4168)<br /> at java.awt.Container.dispatchEventImpl(Container.java:2085)<br /> at java.awt.Window.dispatchEventImpl(Window.java:2475)<br /> at java.awt.Component.dispatchEvent(Component.java:4460)<br /> at java.awt.EventQueue.dispatchEvent(EventQueue.java:599)<br /> at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269)<br /> at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)<br /> at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174)<br /> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169)<br /> at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161)<br /> at java.awt.EventDispatchThread.run(EventDispatchThread.java:122)<br />Caused by: java.io.IOException: Error in ActorCacheObject(ReadExternal): null<br /> at org.kepler.objectmanager.cache.ActorCacheObject.readExternal(ActorCacheObject.java:250)<br /> at java.io.ObjectInputStream.readExternalData(ObjectInputStream.java:1792)<br /> at java.io.ObjectInputStream.readOrdinaryObject(ObjectInputStream.java:1751)<br /> at java.io.ObjectInputStream.readObject0(ObjectInputStream.java:1329)<br /> at java.io.ObjectInputStream.readObject(ObjectInputStream.java:351)<br /> at org.kepler.objectmanager.cache.CacheManager.getObject(CacheManager.java:517)<br /> ... 32 more</p> Bug #4801 (In Progress): out of memoryhttps://projects.ecoinformatics.org/ecoinfo/issues/48012010-02-17T22:13:10ZOliver Soongsoong@nceas.ucsb.edu
<p>ERROR: RecordingException: Unable to query data table: out of memory</p>
<p>I opened tpc01, ran it, closed it, opened tpc03-herbs, ran it, closed it, opened tpc03-large-herbivores, ran it, closed it, opened tpc03-woody, ran it, closed it, opened tpc09, ran it, and hit the above out of memory error. I have 68 runs in the wrm, but 63 of them are various iterations of the small test workflow for bug 4789. I also have those 5 Kruger KARs in a local repository and all the data for them is cached. I can start Kepler and run any of those workflows by themselves. I started Kepler with an ant run, so the jvm should have a 512MB memory max.</p>
<p>Kruger workflows: <a class="external" href="https://code.ecoinformatics.org/code/kruger/trunk/workflows">https://code.ecoinformatics.org/code/kruger/trunk/workflows</a><br />Kruger: r439<br />Kepler: wrp r23080</p>
<p>It may be worth looking at bug 4642.</p> Bug #4660 (Resolved): Clicking in a section header highlights all the text.https://projects.ecoinformatics.org/ecoinfo/issues/46602010-01-12T19:16:05ZOliver Soongsoong@nceas.ucsb.edu
<p>I have a section header with some text in it and I want to change that text. If I click on it, it highlights all of the text. If I click on it again, it highlights all of the text again. There seems to be no way to move the editing cursor to a specific location with the mouse. I can use the keyboard arrow keys, but this behavior of the section header is different from the text item and the label parts of the dynamic items.</p> Bug #4642 (New): memory usage & slowdownshttps://projects.ecoinformatics.org/ecoinfo/issues/46422009-12-19T03:45:53ZOliver Soongsoong@nceas.ucsb.edu
<p>I just hit a big slowdown caused by OOM problems. This bug is mostly a place to put down some of the stuff I found out. I used jmap to produce histograms when Kepler was crawling and immediately after a fresh restart. When Kepler was slow, there was a single workflow open with 4 actors and the Check System Settings window. The fresh Kepler retained the wrm and cache content, but discarded the 4 actors and all the accumulated memory leaking cruft.</p>
<p>A few things jump out at me, and I'd say I'm pretty uninformed. I've formatted as Object: stale #, fresh #.</p>
<p>org.kepler.util.WorkflowRun: 39206, 29<br />javax.swing.JMenuItem: 3411, 96<br />java.util.HashMap: 689643, 22885<br />org.kepler.objectmanager.lsid.KeplerLSID: 120115, 1339<br />java.util.LinkedList: 95565, 4468<br />ptolemy.kernel.util.Location: 1837, 45</p>
<p>Interestingly enough, I have 28 wrm entries. I think something's up with the wrm, but also a lot of GUI objects seem to be hanging around as well, so there may be other things going on as well.</p>
<p>And on a side note, jps -> jmap -> jhat produces some pretty cool results.</p> Bug #4613 (New): EML 2 Dataset automatically updating to latest package doesn't trigger "workflow...https://projects.ecoinformatics.org/ecoinfo/issues/46132009-12-09T01:43:12ZOliver Soongsoong@nceas.ucsb.edu
<p>I have a saved workflow that uses judithk.40.47 in an EML 2 Dataset actor. It also has "Check for latest version" checked. The LSID is urn:lsid:gamma.msi.ucsb.edu/OpenAuth/:965:34:50. judithk.40 is currently at judithk.40.48. When I open Kepler, it prompts to update the actor to use the latest version. When closing Kepler, it doesn't prompt to save changes. If I let Kepler update the workflow to use judithk.40.48 and save, the LSID is not updated.</p> Bug #4548 (Resolved): string tokens with newlines print the escape sequenceshttps://projects.ecoinformatics.org/ecoinfo/issues/45482009-11-13T23:11:17ZOliver Soongsoong@nceas.ucsb.edu
<p>This was first noticed when viewing an RExpression's "output" port. The output port emits a string token containing a section of the RExpression's stdout stream, with newlines encoded in the relevant OS's format. The report will then display literal "\n" or "\r\n" in the report, rather than the appropriate newlines.</p>
<p>While much of reporting ignores newlines (text boxes, for example), it might be useful to respect them here, since the RExpression output is less useful without them.</p> Bug #4533 (In Progress): printing from the report viewer prints the workflow editor contenthttps://projects.ecoinformatics.org/ecoinfo/issues/45332009-11-05T18:16:49ZOliver Soongsoong@nceas.ucsb.edu
<p>I didn't entirely expect this to work, but File->Print from the report viewer prints the workflow content, not the report. It would be nice to either make it work (!) or to disable the entry from the menu while in the report designer and viewer modes.</p> Bug #4526 (Resolved): multi-line entries can be put into text items in reports, but they are disp...https://projects.ecoinformatics.org/ecoinfo/issues/45262009-11-04T02:59:57ZOliver Soongsoong@nceas.ucsb.edu
<p>I'm not sure if this is a bug or an enhancement request. I guess it depends on what the intention was. Are text boxes supposed to be a single "line" like <P></P> in HTML, or are they supposed to be more powerful?</p>
<p>I can live with either way, but the interface should be consistent, and it would be nice to know what I'm supposed to be doing.</p> Bug #4524 (Resolved): no prompt to save a changed reporthttps://projects.ecoinformatics.org/ecoinfo/issues/45242009-11-04T02:34:45ZOliver Soongsoong@nceas.ucsb.edu
<p>If I change the report, don't save, and close the window, I get no prompt to save it.</p> Bug #4480 (In Progress): can't view more than one of workflow editor, report designer, and report...https://projects.ecoinformatics.org/ecoinfo/issues/44802009-10-17T04:47:18ZOliver Soongsoong@nceas.ucsb.edu
<p>It's a little frustrating to have to constantly find that little menu in the upper right hand corner and flip between the workflow editor, report designer, and report viewer, especially when I have more than enough screen real estate. If I open a composite actor, I get a new window. Maybe the report designer and viewer could open in similar new windows? It might also help resolve the problem of there being different "reports" for a workflow and for its composite actors.</p>
<p>I'm thinking of report designer and report viewer buttons. They each bring the appropriate window for that workflow into focus, opening/creating it if necessary. That's just my own thought, and any way to view things side by side should help.</p> Bug #4361 (New): Workflow Run Manager column "Workflow Name" can be confusinghttps://projects.ecoinformatics.org/ecoinfo/issues/43612009-08-31T23:41:54ZOliver Soongsoong@nceas.ucsb.edu
<p>This is a general problem with workflow naming that seems to come up here. Consider two of the attachments to <a class="external" href="http://bugzilla.ecoinformatics.org/show_bug.cgi?id=4359">http://bugzilla.ecoinformatics.org/show_bug.cgi?id=4359</a>, CalledModel.xml and CalledModelCopy.xml. The files are identical, and differ only in filename. If I open both, Kepler will display the different filenames in the window title. If I run both, though, they show up in the Workflow Run Manager with the same name.</p>
<p>The problem is that there is the filename and there is the workflow name saved in the XML. I'm not sure how significant a problem this might be in practice, but I know I tend to rename files on my computer a lot.</p> Bug #4357 (Resolved): Workflow Run Manager does not mark last failed execution redhttps://projects.ecoinformatics.org/ecoinfo/issues/43572009-08-31T21:41:30ZOliver Soongsoong@nceas.ucsb.edu
<p>The workflow run manager is supposed to highlight failed executions in red. If I run a workflow and it fails, though, it is not highlighted. If I run it again, then the first failure is highlighted but not the second. If I run it again, then the first two are highlighted, but not the third. If I close and re-open Kepler, all failures are highlighted. It seems that highlighting is not updated after an execution.</p> Bug #3801 (Resolved): open dialog, common places pane has white box instead of texthttps://projects.ecoinformatics.org/ecoinfo/issues/38012009-01-29T23:58:59ZOliver Soongsoong@nceas.ucsb.edu
<p>XP Pro x64 SP2, Java 1.6.0_11, Kepler 1.0.0 from kepler-project.org.</p>
<p>When I go to File->Open File..., the common places pane on the left has five icons and five white boxes where the icon labels are supposed to be.</p>
<p>Image at the URL.</p>