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From 12/07/2009 to 01/05/2010

01/06/2010

04:08 PM Bug #4161: Develop kepler workflow execution engine
stylesheet issue on the Metacat side of things -- now fixed. ben leinfelder

01/05/2010

03:09 PM Bug #4648 (Resolved): Create classes to find and display any available documentation for installed modules or suites.
Create classes to find and display the available documentation for installed modules or suites. debi staggs
03:06 PM Bug #4647 (Resolved): Write documentation for Reporting in the style of Kepler Docs
Write the user documentation for the WRP suite, using the same style as the rest of the Kepler documentation. debi staggs
11:40 AM Bug #4161: Develop kepler workflow execution engine
script-based execution still works. There's a slight problem on the Metacat side for the first MOML DTD...but that's ... ben leinfelder
11:31 AM Bug #4538: problems with KARs that contain tags from default ontologies
(In reply to comment #2)
> this looks wrong:
> <property name="semanticType" class="org.kepler.sms.SemanticType"
> va...
Sean Riddle
10:09 AM Bug #4538: problems with KARs that contain tags from default ontologies
this looks wrong:
<property name="semanticType" class="org.kepler.sms.SemanticType"
value="urn:lsid:lsid.ecoinformati...
ben leinfelder
10:05 AM Bug #4453: tags don't show up in snow leopard (10.6)
this is working for me on snow leopard ben leinfelder
10:04 AM Bug #4480: can't view more than one of workflow editor, report designer, and report viewer at a time
retargeting to post-2/wrp ben leinfelder
09:43 AM Bug #4618: First export of a run doesn't yield KAR with ROML
in the name of upcoming code freeze, I'm thinking this can be closed. ben leinfelder

01/04/2010

02:47 PM Bug #4516: Module Manager needs ability to install modules needed by KARs
I added a karEntryHandler for modules.txt files. I'm going to add a method to the module manager sot hat the entryHa... Chad Berkley

01/03/2010

12:26 PM Bug #4547: documentation for file parameter includes an error
Viewing the documentation for FileParameter works fine in the ptII tree,
but fails in Kepler, probably because of som...
Christopher Brooks

12/29/2009

11:45 AM Bug #4603: Make limited changes to tagging in preparation for initial release
Fixed as of r22287. Sean Riddle
07:59 AM Bug #4547: documentation for file parameter includes an error
Parsing the description is throwing an error - perhaps it's trying to substitute values or $ID?
Snippet from the File...
ben leinfelder

12/27/2009

11:14 AM Bug #4547: documentation for file parameter includes an error
also in StringParameter.
It's not in the actor moml...so it must be in the action that is displaying the documentation
ben leinfelder
11:10 AM Bug #4522: Folder not found in library index
just tried this (r22284) and it seems to be working. ben leinfelder
10:48 AM Bug #4439: reporting displays output for a different actor
More testing makes this look related to provenace:
I create a simple [runnable] workflow so that I can execute it to ...
ben leinfelder
09:51 AM Bug #4618: First export of a run doesn't yield KAR with ROML
Would you just bump the run revision (entityId)? But then wouldn't that mean it's a different "run" rather than the s... ben leinfelder
09:23 AM Bug #4171: dragging actor to canvas then back to component tree area gives NPE
er, close ben leinfelder
09:23 AM Bug #4171: dragging actor to canvas then back to component tree area gives NPE
removed PTree override in reporting. all better now! ben leinfelder
08:56 AM Bug #4171: dragging actor to canvas then back to component tree area gives NPE
there's a PTree override in the reporting module...but I don't see it being referenced in that module. Looking into r... ben leinfelder

12/24/2009

01:27 PM Bug #4467: WRP - restarting/reopening Kepler throws error
I'm closing this since I can't ever get it to happen for me and there's been so much change since it was entered that... ben leinfelder
01:23 PM Bug #4534: add extra space before section headers when BREAK_BEFORE is false
added some padding above the section header text ben leinfelder
01:16 PM Bug #4480: can't view more than one of workflow editor, report designer, and report viewer at a time
we've changed it a bit: two views - the "reporting" view has 2 tabs: layout and instance. but you do still have to sw... ben leinfelder
01:13 PM Bug #4614: right click -> Open on an existing run adds an entry to the wrm
i don't see this happening in my build as of today (12-24-2009) ben leinfelder
01:09 PM Bug #4600: Changing workflow & running causes "execution history not found" message to appear in report viewer
I've not gotten this error. I had seen the blank report error from before.
With the latest fix, this should not be ha...
ben leinfelder
01:07 PM Bug #4599: changing Expression and running problematic workflow generates blank report
okay - now when the LSID is changed, the layout manager listens for the change event and reassociates the layout with... ben leinfelder
11:13 AM Bug #4638: ant clean-all no longer works
just tried it at r22278 and it works ben leinfelder

12/19/2009

07:45 PM Bug #4642 (New): memory usage & slowdowns
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 o... Oliver Soong

12/18/2009

03:18 PM Bug #4639 (New): add support for -Drev to ant change-to
Doesn't happen very often, but I often am not checking out the head revision, and so it would be nice if ant change-t... Oliver Soong
01:54 PM Bug #4630: creating and changing relations don't trigger LSID bump
For now I've allowed manually bumping the LSID revision and Object ID from the LSID Viewer panel so there's at least ... Aaron Aaron
12:19 PM Bug #4599: changing Expression and running problematic workflow generates blank report
Until this gets fixed, a workaround is to give the workflow an LSID from the local Kepler install. Basically, delete... Oliver Soong
12:09 PM Bug #4632: problems when loading a KAR, changing the workflow, then re-saving the KAR
This actually looks great right now. It seems to clear all the test cases. Oliver Soong
11:34 AM Bug #4638: ant clean-all no longer works
It works at r22253. Oliver Soong
11:33 AM Bug #4638 (Resolved): ant clean-all no longer works
This is with modules\build-area at r22254. ant clean-all and ant clean-cache both fail:
build-area\build.xml:4: ...
Oliver Soong
08:01 PM Bug #4633: LSID conflicts
The logic for querying a new namespace from an Authority in the event that the recorded object IDs and revisions have... Aaron Aaron
06:47 PM Bug #4514: Files are being saved in the Kepler installation directory
InstanceAuthNamespace now gets saved into the persistent Kepler core module directory. LastObjectID file is no longe... Aaron Aaron

12/16/2009

11:09 AM Bug #4619: WorkflowRuns not showing inside KARs in library
r22211 fixes problem in comment#5. Derik Barseghian
10:57 AM Bug #4630: creating and changing relations don't trigger LSID bump
retargeting to 2.0 ben leinfelder
10:40 AM Bug #4571: report "lost" from KAR
Tried to "loose" the ROML - it just won't go away! Closing... ben leinfelder
07:32 PM Bug #4633: LSID conflicts
LSIDGeneration and LSID Revision updates are now being recorded. The LSID_GENERATOR table still needs to be moved to... Aaron Aaron

12/15/2009

03:25 PM Bug #4578: tracking bug for changes to .kepler
I have removed the use of the AuthNamespace from the .kepler directory structure.
The cache directory is now
~/.kep...
Aaron Aaron
12:15 PM Bug #4587: Assure a clean cache when module configuration changes
I'll work on getting this working. Chad Berkley
11:45 AM Bug #4338: need to review usability and gui of module manager
I tried the MM again from a clean build. I was able to change-to the kepler-1.0.0 suite, however there are some prob... Chad Berkley
08:49 AM Bug #4473: Add WRM to bottom of report viewer for navigation
I'm really liking this the more I interact with it.
I even like how you can "open" a row in a new window if you do wa...
ben leinfelder
05:41 PM Bug #4473: Add WRM to bottom of report viewer for navigation
WRM has been moved to the Report Designer view, which now contains the report designer and the instance viewer in dif... Derik Barseghian
08:47 AM Bug #4468: Report Viewer - message to run workflow first
Since we're not refreshing the viewer when you switch views (now a tab) the only time it comes up is when you use the... ben leinfelder
11:21 PM Bug #4632: problems when loading a KAR, changing the workflow, then re-saving the KAR
I've at least addressed some of this in r22198.
I concentrated on editing wf/layout->saving kar->editing->saving.... ...
ben leinfelder
07:44 PM Bug #4632: problems when loading a KAR, changing the workflow, then re-saving the KAR
I think I can hopefully clarify the example and maybe help show why this is incredibly confusing:
1. New workflow, ...
Oliver Soong
05:46 PM Bug #4632: problems when loading a KAR, changing the workflow, then re-saving the KAR
I should also point out that bug 4571 shows up in cases 4 and 5.
4. Saved KAR, Change MOML, File->Save Archive, clos...
Oliver Soong
04:50 PM Bug #4632: problems when loading a KAR, changing the workflow, then re-saving the KAR
This is observed on both r22183 and r22155. Still trying to find a build that won't lose my data... Oliver Soong
11:18 PM Bug #4571: report "lost" from KAR
I believe r22198 will eliminate this problem. You should be able to open different KARs with different versions of th... ben leinfelder
08:37 PM Bug #4630: creating and changing relations don't trigger LSID bump
Creating relations also does not trigger an LSID bump. For some reason, deleting them does. Oliver Soong
08:33 PM Bug #4633: LSID conflicts
This still seems to occur if I'm not using local repositories.
The crux of the problem is nobody is tracking used re...
Oliver Soong
06:09 PM Bug #4633: LSID conflicts
Fixed, lsid updating now recognizes if it is the highest revision in the cache or not. If it isn't then it becomes o... Aaron Aaron
05:04 PM Bug #4633 (Resolved): LSID conflicts
Create a workflow and save a KAR (KAR1). Note the LSID. Change the workflow in some recognizable fashion and save a... Oliver Soong
08:19 PM Bug #4634 (Resolved): run archive causes NPE when building local repository
Start Kepler from a clean-cache. I'm at r22183. Move the example to the default workflows folder and re"Build" the ... Oliver Soong
07:38 PM Bug #4563: components search seems to be broken
This no longer seems to occur. Oliver Soong
07:29 PM Bug #4596: selecting text entry box of report item moves activation highlight but does not update properties window
I think this got fixed, but never re-closed. Oliver Soong
06:40 PM Bug #4619: WorkflowRuns not showing inside KARs in library
r22184 has re-broken this. KARFile now warns:
WARN (org.kepler.kar.KARFile:cache:838) KAREntry was not recognized: W...
Derik Barseghian
05:57 PM Bug #4615: pdfs missing from run archives
This got fixed somewhere along the line (before r22183). Oliver Soong
05:35 PM Bug #4505: NPE from Semantic Search
The error has changed to:
java.lang.ClassCastException: org.kepler.objectmanager.cache.ReportLayoutCacheObject
at o...
Derik Barseghian
05:32 PM Bug #4607: Workflow Run Manager - opening kar no longer adds run-row
This has been fixed. Derik Barseghian
05:32 PM Bug #4590: Workflow Run Manager - Export Archive can give error
This was fixed awhile ago. Derik Barseghian

12/14/2009

03:59 PM Bug #4605: Semantic Annotation NPE
Turns out it was just unable to find the icon, which was crashing the whole thing (not good). Fixed now. Aaron Aaron
03:01 PM Bug #4605: Semantic Annotation NPE
Somehow OntoClassSelectionJPanel is not in the classpath at runtime... It gets used from ActorSemanticTypeEditorPane... Aaron Aaron
03:58 PM Bug #4538: problems with KARs that contain tags from default ontologies
The problem in comment #1 was fixed some time ago.
Things seem to be working fine, but I notice the way the tags are...
Derik Barseghian
03:51 PM Bug #4632: problems when loading a KAR, changing the workflow, then re-saving the KAR
Regarding the part about the ROML being lost (second described symptom), it reminds me a lot of bug 4592, but I think... Oliver Soong
03:07 PM Bug #4632 (Resolved): problems when loading a KAR, changing the workflow, then re-saving the KAR
Create a workflow and report and save the KAR. Next, change the workflow (i.e., bump the MOML LSID), save the KAR (o... Oliver Soong
03:10 PM Bug #4338: need to review usability and gui of module manager
turns out it changed my modules.txt to this:
berkley@Slickrock build-area$ more modules.txt
ssh-1.0.0
Chad Berkley
03:10 PM Bug #4338: need to review usability and gui of module manager
I've reviewed the module manager and these are the things I've noticed:
* the window opens too small on OSX. It sho...
Chad Berkley
02:40 PM Bug #4631 (Resolved): Could use some way to change the "workflow name" stored in a KAR
Right now, if I want to change the "workflow name", I would have to export the MOML and recreate the report. It woul... Oliver Soong
02:28 PM Bug #4630 (Resolved): creating and changing relations don't trigger LSID bump
Make a workflow with at least 3 ports and only 2 connected. Check the LSID. Now move a relation from one port to an... Oliver Soong
01:48 PM Bug #4629 (Resolved): Undo doesn't roll LSID revision
When undoing changes in a workflow the LSID of the workflow does not get incremented. Aaron Aaron
01:48 PM Bug #4599: changing Expression and running problematic workflow generates blank report
Still happening at r22183. There might be more to it than the provenance recorder? Oliver Soong
01:24 PM Bug #4468: Report Viewer - message to run workflow first
I think this got killed with some recent commit. I'm at r22183. Oliver Soong
01:22 PM Bug #4569: viewing report before executing sometimes generates persistent blank report
This seems to have been "fixed" somewhere along the way. At the very least, it's not showing up at r22183. I'm not ... Oliver Soong

12/11/2009

08:49 AM Bug #4619: WorkflowRuns not showing inside KARs in library
While unit tests would probably minimize this wheel spinning, I think it's non-trivial to develop them. Most of the i... ben leinfelder
10:27 PM Bug #4619: WorkflowRuns not showing inside KARs in library
Derik -- it sounds to me like you need to develop a set of unit tests that exercise this functionality, in this case ... Matt Jones
07:08 PM Bug #4619: WorkflowRuns not showing inside KARs in library
partially fixed in r22162. You can now export the same run to different kars, and the run momls will show up in the t... Derik Barseghian
06:30 PM Bug #4626: NPE when saying "yes" to adding a semantic type while saving a KAR
duplicate of 4605, although it looks like the error msg may have changed since I reported. Derik Barseghian
06:27 PM Bug #4626 (Resolved): NPE when saying "yes" to adding a semantic type while saving a KAR
I'm at r22155. File->Save Archive (KAR) and answer yes to adding a semantic type. I'm getting an NPE.
Exception ...
Oliver Soong

12/10/2009

07:12 PM Bug #4619: WorkflowRuns not showing inside KARs in library
Leaving off here for now: problem is related to fact that insertEntryIntoCache fails when trying to insert WorkflowRu... Derik Barseghian
06:21 PM Bug #4619 (Resolved): WorkflowRuns not showing inside KARs in library
WorkflowsRuns that are inside kars haven't been showing up in the component library for awhile now beneath an expande... Derik Barseghian
06:16 PM Bug #4618: First export of a run doesn't yield KAR with ROML
r22150 should fix this, but I want to test it a bit more.
One oddity currently is that if you export a run, export it...
Derik Barseghian

12/09/2009

03:45 PM Bug #4614: right click -> Open on an existing run adds an entry to the wrm
r22148 should fix this. I want to test it a bit more before closing though.
Also, I've changed the duration column b...
Derik Barseghian
07:32 PM Bug #4614: right click -> Open on an existing run adds an entry to the wrm
Definitely wrong. It should only insert a new row if the one that's being opened has been deleted from the WRM. Bug h... Derik Barseghian
06:20 PM Bug #4614 (Resolved): right click -> Open on an existing run adds an entry to the wrm
I run a workflow, then right click on its run record and select open. When the new window opens, there is another en... Oliver Soong
03:44 PM Bug #4618 (Resolved): First export of a run doesn't yield KAR with ROML
I've introduce a bug in r22148:
For the case where no report is made: the first export of a run doesn't put a ROML...
Derik Barseghian
06:54 PM Bug #4577: integrate, and separate from save/export, the code for Uploading
oh, I like that - then the gui code never needs to "know" all the different kinds of metadata entry types, just that ... ben leinfelder
06:40 PM Bug #4577: integrate, and separate from save/export, the code for Uploading
A user can now create different types of KARs from within Kepler, and upload them to the repository via context menu ... Derik Barseghian
06:21 PM Bug #4615 (Resolved): pdfs missing from run archives
It's looking like PDFs are no longer found in run archives like they used to be. I'm at r22136. Oliver Soong
06:05 PM Bug #4613: EML 2 Dataset automatically updating to latest package doesn't trigger "workflow change"
It's odd that it does work for, say, the RExpression actor and the "Automatically display graphics" checkbox.
I'm not...
ben leinfelder
05:43 PM Bug #4613 (New): EML 2 Dataset automatically updating to latest package doesn't trigger "workflow change"
I have a saved workflow that uses judithk.40.47 in an EML 2 Dataset actor. It also has "Check for latest version" ch... Oliver Soong
04:03 PM Bug #4599: changing Expression and running problematic workflow generates blank report
Not quite fixed. I still get the blank report. I'm at r22136. Oliver Soong

12/08/2009

03:50 PM Bug #4600: Changing workflow & running causes "execution history not found" message to appear in report viewer
This still happens even after bug 4599 was fixed. Oliver Soong
03:21 PM Bug #4608: ROML in KAR files not being shown at all
This was a problem of the EntryHandlers being deleted from the configuration during conversion to the new Configurati... Aaron Aaron
01:33 PM Bug #4608: ROML in KAR files not being shown at all
I'm going to look into this. ROMLs, RIOs, and WorkflowRuns aren't being put into KARs anymore (at the filesystem leve... Derik Barseghian
01:25 PM Bug #4608: ROML in KAR files not being shown at all
Nevermind, it's actually not in the manifest. Checking into it. debi staggs
01:23 PM Bug #4608: ROML in KAR files not being shown at all
Do you mean that it is not showing up in the Library ? debi staggs
12:17 PM Bug #4608: ROML in KAR files not being shown at all
Oh, and to clarify, 22083 was supposed to fix bug 4512 and 22117 was supposed to fix 4601. Oliver Soong
12:10 PM Bug #4608 (Resolved): ROML in KAR files not being shown at all
ROML in KAR files is not being loaded. This happens regardless of the LSID in the workflow and ROML matching the Ins... Oliver Soong
02:20 PM Bug #4605: Semantic Annotation NPE
I guess since we don't have Tagging in the vanilla Kepler suite, we still need to warn the user if they haven't seman... Derik Barseghian
01:59 PM Bug #4535: exception when initiating the kars of a module whose name include a period.
I am unable to reproduce this bug. This code has changed substantially since this bug was entered. I'm closing it n... Chad Berkley
12:32 PM Bug #4597: adding new configuration properties before/after a certain exiting configuration property.
Added a method addPropertyAtIndex which allows the user to add a property anywhere into an existing ordering of neste... Chad Berkley
12:20 PM Bug #4559: local repositories not showing up in components tree
I think the missing reports are part of a larger problem, which I've filed separately as bug 4608. The other problem... Oliver Soong
10:27 AM Bug #4559: local repositories not showing up in components tree
Fixing bug 4512 solves part of the problem, but some others remain and there are some new ones. I'm still following ... Oliver Soong
10:51 AM Bug #4601: New LSID not propagating to provenance
Fixed. Daniel Crawl
10:51 AM Bug #4599: changing Expression and running problematic workflow generates blank report
Fixed. Daniel Crawl
04:24 PM Bug #4607 (Resolved): Workflow Run Manager - opening kar no longer adds run-row
If you export a run archive to a kar, delete the run row in WRM, and then open this KAR, the run used to be added as ... Derik Barseghian
04:11 PM Bug #4606: Workflow Run Manager - using CAPS in tags search doesn't work
Fixed in r22105. Tags column now behaves like the other columns that use text: it's case insensitive. If people want ... Derik Barseghian

12/07/2009

03:57 PM Bug #4606 (Resolved): Workflow Run Manager - using CAPS in tags search doesn't work
If you tag a run with e.g. Absence, and then use the WRM to search the tags column for "Ab", you don't get any result... Derik Barseghian
03:50 PM Bug #4605 (Resolved): Semantic Annotation NPE
If you File=> Save Achive (KAR), and say yes to semantically annotate it, you get an NPE:
Exception in thread "AWT...
Derik Barseghian
11:43 AM Bug #4336: Merge the old configuration systems
Closing... Chad Berkley
11:42 AM Bug #4336: Merge the old configuration systems
All ptolemy configuration.xml files (that I know about) in kepler (except for the main one in common) have now been r... Chad Berkley
11:03 AM Bug #4604 (In Progress): Make aesthetic changes to tagging interface
Make certain interface enhancements to tagging that are deemed not important enough to block 2.0 or the wrp release w... Sean Riddle
10:58 AM Bug #4603 (Resolved): Make limited changes to tagging in preparation for initial release
Make changes that are either easily done or essential before an initial public release through the new module manager... Sean Riddle
10:31 AM Bug #4513: On the PC the paint transparency for buttons doesn't redraw correctly
This has been corrected. debi staggs
10:30 AM Bug #4402: When a report item is deleted clear the properties window
This has been fixed. debi staggs
 

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