Ecoinformatics Redmine: Issueshttps://projects.ecoinformatics.org/ecoinfo/https://projects.ecoinformatics.org/ecoinfo/ecoinfo/favicon.ico?14691340362010-02-06T02:52:36ZEcoinformatics Redmine
Redmine Kepler - Bug #4767 (Resolved): error instantiating actor with port types from KARhttps://projects.ecoinformatics.org/ecoinfo/issues/47672010-02-06T02:52:36ZOliver Soongsoong@nceas.ucsb.edu
<p>Create an Expression actor, give it an input port of type boolean, save it as a KAR into a local repository, then try and drag it onto the canvas. I get an error:</p>
<p>ptolemy.kernel.util.IllegalActionException: TypeAttribute can only be contained by instances of TypedIOPort.<br /> in .Expression.kepler:input and ._type</p> 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 #4630 (Resolved): creating and changing relations don't trigger LSID bumphttps://projects.ecoinformatics.org/ecoinfo/issues/46302009-12-14T22:28:16ZOliver Soongsoong@nceas.ucsb.edu
<p>Make a workflow with at least 3 ports and only 2 connected. Check the LSID. Now move a relation from one port to another. The LSID is the same.</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 #4570 (Resolved): dangling file handle for KARshttps://projects.ecoinformatics.org/ecoinfo/issues/45702009-11-21T01:23:46ZOliver Soongsoong@nceas.ucsb.edu
<p>I'm not a 100% certain this is the cause, but on Windows, if I open a KAR file then close it, Kepler doesn't seem to release the file handle, which prevents me from deleting the KAR. I seem to recall having problems overwriting KAR files in the past, so this is somewhat problematic. Obviously, closing Kepler releases the file handle.</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 #4529 (Resolved): NPE while saving KAR crashes Keplerhttps://projects.ecoinformatics.org/ecoinfo/issues/45292009-11-04T06:19:39ZOliver Soongsoong@nceas.ucsb.edu
<p>While exploring another bug, I encountered this NPE, and it entirely killed Kepler. This happened after saving a workflow into a local repository. I don't know specifically how to replicate it, though.</p>
<p>done writing KAR file to C:\Documents and Settings\visitor\Desktop\kepler\workflows\test1.kar<br />java.lang.NullPointerException<br /> at org.kepler.kar.handlers.ActorMetadataKAREntryHandler.open(ActorMetadataKAREntryHandler.java:217)<br />[...]<br />ERROR (org.kepler.kar.handlers.ActorMetadataKAREntryHandler:open:235) error opening the workflow: null<br /> at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184)</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 #4512 (Resolved): missing entries with multiple copies of the same KAR file in a sin...https://projects.ecoinformatics.org/ecoinfo/issues/45122009-10-28T22:43:23ZOliver Soongsoong@nceas.ucsb.edu
<p>Things don't seem to work right if I have multiple copies of the same KAR file in a single local repository. I think this is related to only one entry for an LSID being allowed in a repository.</p>
<p>If I make a file system copy of the KAR file, only one copy (the oldest?) will show up in Kepler, which could be reasonable if potentially confusing and inconvenient. I presume this is because the KAR files have identical LSIDs.</p>
<p>However, if I open the KAR in Kepler and Save Archive to create a copy, that copy will show up in Kepler, will appear to be empty (lacking XML and ROML entries), but can be opened. The original remains as before. I think this is because the KAR files have different LSIDs, but the XML and ROML files have the same.</p>
<p>Maybe this is as intended, but it's certainly confusing because the KARs look empty and the folder/KAR listing does not accurately reflect the file system structure.</p> Kepler - Bug #4510 (Resolved): can't add local repository if its name begins with the name of ano...https://projects.ecoinformatics.org/ecoinfo/issues/45102009-10-28T19:24:57ZOliver Soongsoong@nceas.ucsb.edu
<p>If I've added C:\Documents and Settings\soong\Desktop\kruger as a local repository, I can't add C:\Documents and Settings\soong\Desktop\kruger2. It complains that one is a subdirectory of the other, even though they are not.</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>