Ecoinformatics Redmine: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362010-02-06T02:19:48ZEcoinformatics Redmine
Redmine Kepler - Bug #4764 (New): ProvenanceRecorder.changeExecuted slow after workflow runhttps://projects.ecoinformatics.org/ecoinfo/issues/47642010-02-06T02:19:48ZOliver Soongsoong@nceas.ucsb.edu
<p>If I run any of the tpc workflows (e.g., tpc09), any subsequent changes to Kepler (say changing workflow parameters) cause Java to peg one of my CPU cores. This includes canceling changes to RExpression. I've seen this behavior on Windows XP and 7. While I haven't seen it under linux or OS X, I haven't tested those as extensively. I have tried small test workflows, and haven't seen a particularly noticeable slowdown, so it may be related to the size of the workflow run. I have to restart Kepler to get things back up to speed, and it's bad enough that I'm actually restarting Kepler after every run.</p>
<p>I'm not sure it's a memory thing. java.exe is about maxed out on memory (~0.5 GB) in the Task Manager, but the Check System Settings window says I have 46% free. I was watching jstat, and changes don't seem to trigger a flurry of garbage collection.</p> Kepler - Bug #4655 (Resolved): data packages are suddenly unusablehttps://projects.ecoinformatics.org/ecoinfo/issues/46552010-01-08T02:23:01ZOliver Soongsoong@nceas.ucsb.edu
<p>For some reason, EML 2 Dataset actors are not outputting any tokens for most output formats. The data exists at .kepler/cache/cachedata, as expected. If I set the EML 2 Dataset Data Output Format to As ColumnBased Record, then I get an error message, "The data cloumn (sic) didn't match head column". If I set the EML 2 Dataset Data Output Format to "As All Cache File Names", then things seem to work as expected. All other output formats don't seem to work.</p>
<p>Things were definitely working as of Dec. 8 and possibly Dec. 10.</p> Kepler - Bug #4633 (Resolved): LSID conflictshttps://projects.ecoinformatics.org/ecoinfo/issues/46332009-12-15T01:04:31ZOliver Soongsoong@nceas.ucsb.edu
<p>Create a workflow and save a KAR (KAR1). Note the LSID. Change the workflow in some recognizable fashion and save a KAR (KAR2). The LSID bumps as expected. Close the workflow and open KAR1. Make a different change (so it's obviously not the workflow in KAR2) and save the KAR (KAR3). Notice that when the workflow reopens, it looks like KAR2 because it is KAR2 down to the MOML in KAR3.</p>
<p>I'm observing this at r22183 right now.</p> Kepler - Bug #4632 (Resolved): problems when loading a KAR, changing the workflow, then re-saving...https://projects.ecoinformatics.org/ecoinfo/issues/46322009-12-14T23:07:12ZOliver Soongsoong@nceas.ucsb.edu
<p>Create a workflow and report and save the KAR. Next, change the workflow (i.e., bump the MOML LSID), save the KAR (overwrite or not doesn't seem to matter), and run it. The report should be blank. Sometimes, the ROML still exists in the KAR, so closing and re-opening works fine. In this case, the run archive contains the correct workflow_ROML.xml entry and a different ROML.#.xml that doesn't match the workflow_ROML.xml entry. Other times, the ROML seems to be lost from the KAR, in which case the run archive has no workflow_ROML.xml entry and a blank ROML.#.xml.</p> Kepler - Bug #4608 (Resolved): ROML in KAR files not being shown at allhttps://projects.ecoinformatics.org/ecoinfo/issues/46082009-12-08T20:10:55ZOliver Soongsoong@nceas.ucsb.edu
<p>ROML in KAR files is not being loaded. This happens regardless of the LSID in the workflow and ROML matching the InstanceAuthNamespace. This happens regardless of opening from a local repository or not.</p>
<p>This is happening at 22117, but I think I also saw it at 22111. I'm guessing it has something to do with 22083, although I can't be sure.</p> Kepler - Bug #4569 (Resolved): viewing report before executing sometimes generates persistent bla...https://projects.ecoinformatics.org/ecoinfo/issues/45692009-11-21T01:14:11ZOliver Soongsoong@nceas.ucsb.edu
<p>I unfortunately can't figure out how to replicate this yet. It occurred with the latest tpc01 report archive, although I'm not certain it's truly specific to this KAR. After debugging the workflow and building the report, I found that opening the archive and viewing the report would not trigger a message saying the workflow needed to be run first. Executing the workflow would then generate a single blank page with no title or any content, but with a time and date stamp at the bottom. I have attached the run archive with that output in it.</p>
<p>A clean-cache made the problem go away, but I can't replicate it, so I can't be sure what went wrong or that it won't happen again.</p> Kepler - Bug #4559 (Resolved): local repositories not showing up in components treehttps://projects.ecoinformatics.org/ecoinfo/issues/45592009-11-19T22:25:52ZOliver Soongsoong@nceas.ucsb.edu
<p>Summary says it all. I'm at r21772, and the default workflows repository isn't in the components tree. Adding repositories doesn't do anything. I'm not even getting prompts to sign into KNB or DEV to cache data.</p> Kepler - Bug #4527 (Resolved): reports cannot be loaded when InstanceAuthNamespace changeshttps://projects.ecoinformatics.org/ecoinfo/issues/45272009-11-04T03:39:51ZOliver Soongsoong@nceas.ucsb.edu
<p>Generate a report and save the KAR. Close Kepler, clean-all, delete the configuration folder, LastObjectID, and .ptolemy-compiled (I think that's almost everything that Kepler generates). Run Kepler again, and open the KAR. The report layout should be there. Now close Kepler and delete only InstanceAuthNamespace. Run Kepler again and open the KAR. The report should not be there.</p>
<p>This makes it hard to transport a KAR file to another computer or even another build of Kepler.</p> Kepler - Bug #4521 (Resolved): KNB data error checking is overly aggressivehttps://projects.ecoinformatics.org/ecoinfo/issues/45212009-11-04T01:03:36ZOliver Soongsoong@nceas.ucsb.edu
<p>On r21314, I can no longer access the Kruger data. I believe this is due to some overly aggressive error checking on the data. The data packages (which are not directly under my control) have thrown errors on the console. I think this is due to negative numbers and zeroes in columns that are nominally whole numbers. In the past, there were non-fatal, but this is now major problem.</p>
<p>This change happened somewhere between r21218 and r21310.</p>
<p>The error message is specifically "Unable to parse the MetaData: Error parsing the eml package: Exception in DataTypeResolver"</p> Kepler - Bug #4507 (Resolved): report designer losing content when there are too many itemshttps://projects.ecoinformatics.org/ecoinfo/issues/45072009-10-27T23:25:05ZOliver Soongsoong@nceas.ucsb.edu
<p>If I have a lot of items in the report designer, the scroll bar seems to be too short for the content. Eventually, there are figures that are above and below the scrollable area and are not accessible. They still show up in reports, though.</p> Kepler - Bug #4409 (Resolved): View Documentation for an actor works oncehttps://projects.ecoinformatics.org/ecoinfo/issues/44092009-09-24T18:00:46ZOliver Soongsoong@nceas.ucsb.edu
<p>I can view the documentation for an actor in the actor library once. After that, I can no longer drag actors onto the canvas and I can no longer view any more documentation.</p>
<p>I just updated and this is observed on linux and XP.</p>
<p>Restarting Kepler seems to at least reset this.</p> Kepler - 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> Kepler - Bug #4358 (New): variable setter seems to lock Kepler in the wrapping up stage of a work...https://projects.ecoinformatics.org/ecoinfo/issues/43582009-08-31T22:15:15ZOliver Soongsoong@nceas.ucsb.edu
<p>Running the attached workflow seems to cause Kepler to freeze at Wrapping Up. I'm not sure if I just need to wait (for a really long time) or whether there's some other issue.</p> Kepler - 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> Kepler - Bug #3901 (Resolved): unescaped & in <entity name="a & b"> on line 4https://projects.ecoinformatics.org/ecoinfo/issues/39012009-03-18T02:08:48ZOliver Soongsoong@nceas.ucsb.edu
<p>XP Pro x64 SP2, Java 1.6.0_11, Kepler 1.0.0 from kepler-project.org</p>
<p>If a workflow is saved with an & in the file name, even though the file name is valid in the file system, Kepler throws an exception because the name attribute is unescaped in the outermost TypedCompositeActor entity. If Kepler is trying to re-open the workflow similar to how a save as is handled, then it's choking while attempting to parse the file. The & should be escaped as & in the name attribute, I think.</p>