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 #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 #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> Kepler - Bug #3893 (Resolved): EML 2 Dataset not working with local datahttps://projects.ecoinformatics.org/ecoinfo/issues/38932009-03-16T22:43:51ZOliver Soongsoong@nceas.ucsb.edu
<p>Kepler 1.0.0, Java 1.6.0_11, XP 64-bit</p>
<p>I downloaded an EML/XML file and some text data tables to experiment with. The EML 2 Dataset actor is having problems running with this local data.</p>
<p>This bug may be related to <a class="issue tracker-1 status-3 priority-2 priority-default closed" title="Bug: EML 2 Dataset file path confusion (Resolved)" href="https://projects.ecoinformatics.org/ecoinfo/issues/3892">#3892</a>: <br /><a class="external" href="http://bugzilla.ecoinformatics.org/show_bug.cgi?id=3892">http://bugzilla.ecoinformatics.org/show_bug.cgi?id=3892</a></p>
<p>The URL is a zip of four files: <br />EML file: judithk.609.21.xml<br />Data file: judithk.657.1-Dailyrain1980.txt<br />problem workflow: full path.xml<br />unrelated workflow: filename only.xml</p> Kepler - Bug #3892 (Resolved): EML 2 Dataset file path confusionhttps://projects.ecoinformatics.org/ecoinfo/issues/38922009-03-16T22:39:23ZOliver Soongsoong@nceas.ucsb.edu
<p>Kepler 1.0.0, Java 1.6.0_11, XP 64-bit</p>
<p>The EML 2 Dataset actor parameters EML File and Data File look for file paths. If I open a new workflow, add the EML 2 Dataset actor, and browser to two files, their full paths are recorded in the actor. I can save this workflow and open it with no problems.</p>
<p>If I place the saved workflow in the same folder as the EML and data files, open the saved workflow, edit the EML 2 Dataset actor, and browse to the same two files, then the full paths are replaced with local paths relative to the workflow's xml file (i.e., just the filename). If I save this modified workflow and try to reopen it, I get an error:</p>
<p>Data entity : Dailyrain1992.txt, failed to be downloaded and please check the data link in metadata</p>
<p>The URL is a zip of four files: <br />EML file: judithk.609.21.xml<br />Data file: judithk.657.1-Dailyrain1980.txt<br />first workflow (no error on load): full path.xml<br />second workflow (error on load): filename only.xml</p> Kepler - Bug #3890 (Resolved): EML 2 Dataset has trouble with a certain data tablehttps://projects.ecoinformatics.org/ecoinfo/issues/38902009-03-16T20:49:59ZOliver Soongsoong@nceas.ucsb.edu
<p>Kepler 1.0.0, Java 1.6.0_11, XP 64-bit</p>
<p>Kepler has difficulty with table Dailyrain2004.txt from judithk.609.21 in KNB. The workflow at the URL is simply the EML 2 Dataset actor for that table and nothing else. The error message is not particularly helpful.</p> Kepler - Bug #3807 (Resolved): reserved symbols in record names passed to the RExpression actor g...https://projects.ecoinformatics.org/ecoinfo/issues/38072009-02-04T00:08:55ZOliver Soongsoong@nceas.ucsb.edu
<p>XP Pro x64 SP2, Java 1.6.0_11-b03, Kepler 1.0.0, R 2.8.0</p>
<p>The URL contains a bugged Kepler workflow. The data from KNB contains a column called %CC that causes an error when R is executing Kepler's RExpression initialization code. This causes Kepler to think that R is not found.</p>
<p>A frustrating workaround is to disassemble the record and reassemble it, changing the name of the offending column.</p> Kepler - 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>