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From 12/13/2009 to 01/11/2010

01/12/2010

05:49 PM Bug #4659: Importing run gives a ClassCastException
I don't think it's related, but I'll keep that in mind when I look into this.
To replicate:
- change-to and launch ...
Derik Barseghian

01/11/2010

01:44 PM Bug #4659: Importing run gives a ClassCastException
The could be from my fix to bug #4547
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=4547
The change is that Doc...
Christopher Brooks
12:29 PM Bug #4659 (Resolved): Importing run gives a ClassCastException
If you try to Open Archive a KAR containing a workflow run that needs to be added to provenance, you get a ClassCastE... Derik Barseghian
12:26 PM Bug #4516: Module Manager needs ability to install modules needed by KARs
I changed this around a bunch so it is now done in the GUI instead of on kepler startup. When a module-dependencies:... Chad Berkley
08:39 AM Bug #4439: reporting displays output for a different actor
I'm thinking you'd still want the report to render if al but one reference were valid, right? Maybe just a warning th... ben leinfelder
08:36 AM Bug #4439: reporting displays output for a different actor
Why not just check that everything mentioned in the ROML exists just before you create the report (i.e., after execut... Oliver Soong
10:24 PM Bug #4439: reporting displays output for a different actor
i suppose we could be listening for the MOML change request that deletes actors/ports/parameters that are referenced ... ben leinfelder
12:39 AM Bug #4652: clicking rows in the wrm no longer updates the report designer/viewer
no difference, I simply missed checking in part of the fix initially Derik Barseghian
10:21 PM Bug #4652: clicking rows in the wrm no longer updates the report designer/viewer
what was the difference for linux? ben leinfelder
11:03 PM Bug #4547: documentation for file parameter includes an error
Fixed. Changed DocAttribute.description from a StringParameter to a StringAttribute so that Kepler does not report er... Christopher Brooks

01/09/2010

06:42 PM Bug #4652: clicking rows in the wrm no longer updates the report designer/viewer
fixed in r22437. Derik Barseghian
06:27 PM Bug #4652: clicking rows in the wrm no longer updates the report designer/viewer
r22436 fixed this on my mac build, but it's not working on linux... Derik Barseghian

01/08/2010

03:32 PM Bug #4439: reporting displays output for a different actor
I've updated provenance to handle these types of renames.
It might be nice if reporting displayed an error or warnin...
Daniel Crawl
02:16 PM Bug #4311: Build system appears to lock if there is a conflict upon update
I'm not clear why option 2 is so complicated. Just pass stdin, stdout, and stderr from svn to ant. I don't expect a... Oliver Soong
01:49 PM Bug #4311: Build system appears to lock if there is a conflict upon update
If an error is printed, I'd be fine with it. Right now, it appears to hang and does not give any further output. Chad Berkley
01:41 PM Bug #4311: Build system appears to lock if there is a conflict upon update
A couple of things. First, there are two alternative things we could mean by "fixing" this issue: (1) Print out the e... David Welker
12:45 PM Bug #4311: Build system appears to lock if there is a conflict upon update
I still don't think it really affects the user experience, but it's happened to me enough times to be annoying so I c... Chad Berkley
12:38 PM Bug #4311: Build system appears to lock if there is a conflict upon update
I was curious what the basis of your opinion that this should be done before 2.0 is? This is functionality to make li... David Welker
10:15 AM Bug #4311: Build system appears to lock if there is a conflict upon update
This bug has happened to me exactly the way that Oliver has described on many occasions. It should be fixed prior to... Chad Berkley
09:52 AM Bug #4311: Build system appears to lock if there is a conflict upon update
The problem is that it never fails to complete. Normally on a conflict, svn outputs some information and blocks for ... Oliver Soong
08:12 PM Bug #4311: Build system appears to lock if there is a conflict upon update
Are you saying that when the update failed to complete, it did not say why? That is unusual. Can you reproduce this e... David Welker
07:57 PM Bug #4311: Build system appears to lock if there is a conflict upon update
I'm not so sure it's a good idea to ignore this. This happened to Mark, Regetz, and me. None of us had made any loc... Oliver Soong
07:24 PM Bug #4311: Build system appears to lock if there is a conflict upon update
The solution to this problem is not in the build system. You should do the update manually if you have made changes. David Welker
01:46 PM Bug #4653: error message says "data cloumn"
search. replace. done. ben leinfelder
05:13 PM Bug #4653 (Resolved): error message says "data cloumn"
The data cloumn didn't match head column Oliver Soong
01:37 PM Bug #4655: data packages are suddenly unusable
dan fixed it ben leinfelder
12:39 PM Bug #4655: data packages are suddenly unusable
the cached data files are set as a data source for HSQL tables (SET TEXT....SOURCE) - but the path to the hsqldb was ... ben leinfelder
06:23 PM Bug #4655 (Resolved): data packages are suddenly unusable
For some reason, EML 2 Dataset actors are not outputting any tokens for most output formats. The data exists at .kep... Oliver Soong
12:53 PM Bug #4516: Module Manager needs ability to install modules needed by KARs
tagged my current work here: https://code.kepler-project.org/code/kepler/tags/berkley-20100108-checkpoint-kar_can_dow... Chad Berkley
12:49 PM Bug #4516: Module Manager needs ability to install modules needed by KARs
There should always be user input when downloading new modules. Imagine that you are running the Kepler suite, then ... Aaron Aaron
12:40 PM Bug #4516: Module Manager needs ability to install modules needed by KARs
Couple more issues here:
* I should have used the MANIFEST/dependsOnModule attribute instead of including a modules....
Chad Berkley
12:19 PM Bug #4516: Module Manager needs ability to install modules needed by KARs
How does appending modules to modules.txt ensure the same environment that an actor was running in?
This is going to...
David Welker
11:59 AM Bug #4516: Module Manager needs ability to install modules needed by KARs
The active modules.txt file is now appended with any information from the kar's modules.txt file. Note that this cou... Chad Berkley
10:58 AM Bug #4516: Module Manager needs ability to install modules needed by KARs
Kar files can now include a modules.txt file which will be processed by the ModuleDownloader. Any modules/suites in ... Chad Berkley
11:02 AM Bug #4656 (Resolved): Build system needs javadocs
The build system is lacking a lot of documentation. Javadocs should be added for (at least) all public methods and c... Chad Berkley
10:19 AM Bug #4108: Do more extenstive testing before designating a revision of Ptolemy as stable
I don't think this bug should be closed. I'm changing it to be a lower priority but reopening it. I think that ther... Chad Berkley
07:22 PM Bug #4108: Do more extenstive testing before designating a revision of Ptolemy as stable
Additional testing before designating a version of Ptolemy as "stable" is unnecessary. Closing this bug. David Welker
07:59 PM Bug #4388: remove the ptII module
There is no good way to remove the ptII suite without changes to the ptolemy module. This is not currently in the car... David Welker
07:52 PM Bug #4281: ant update produces message about running svn cleanup
I agree that this bug should be closed. "ant update" is a convenience method which allows one to avoid having to run ... David Welker
07:47 PM Bug #4280: ant task fails under Windows
Again, "ant task" is a convenience short cut for:
ant -f kepler-tasks.xml
Therefore, I do not intend on devoting an...
David Welker
07:44 PM Bug #4264: ant task fails if there are java compilation errors
"ant task" is a convenience method. It never needs to be invoked.
If "ant task" fails, the solution is to type:
ant...
David Welker
07:40 PM Bug #4260: Add a test suite for the build system
I think this is overkill and not a good use of resources. Problems in the build system tend to be detected immediatel... David Welker
07:21 PM Bug #4202: typos in modules.txt are ignored
The contents of modules.txt is now verified. Missing/mispelled modules now cause an error message to appear. David Welker
07:18 PM Bug #4353: Update publishing to allow for patches.
This is now implemented. David Welker
07:14 PM Bug #4351: ant netbans fails due to missing file
This bug no longer occurs. David Welker
07:12 PM Bug #4286: Changes to the GUI before 2.0
There are only minor changes left before 2.0. This bug is no longer needed. David Welker
07:03 PM Bug #4082: New user guide section on modules/module manager
Please assign bugs to welker4kepler@gmail.com when assigning bugs to me only.
I have documented module manager funct...
David Welker
07:00 PM Bug #4382: Remove switching between kepler and ptolemy
It is no longer possible to launch Ptolemy from the Kepler module manager. This reinforces the separateness of the tw... David Welker
06:58 PM Bug #4650: module manager tries to download already downloaded modules
Modules that are retrieved are not removed from the available modules pane. Instead, they are added to the "Downloade... David Welker
06:09 PM Bug #4654: searching KNB through Kepler returns many console errors and caching fails
It's looking like I managed to completely screw up my cache. A clean-cache fixed things.
Basically, I was signing i...
Oliver Soong
05:44 PM Bug #4654 (Resolved): searching KNB through Kepler returns many console errors and caching fails
This is at r22407 under linux. Things seem to work, but the cache content is all blank (files are all of size 0). Oliver Soong
04:55 PM Bug #4652 (Resolved): clicking rows in the wrm no longer updates the report designer/viewer
If I have multiple entries in the wrm and I click on different rows, the report designer and viewer no longer automat... Oliver Soong

01/07/2010

11:20 AM Bug #4650 (Resolved): module manager tries to download already downloaded modules
After downloading a module, that module should be removed from the "available modules" list. If a user tries to down... Chad Berkley
10:01 AM Bug #4516: Module Manager needs ability to install modules needed by KARs
I've now split the module manager into two modules. module-manager now has basic classes for downloading modules. m... Chad Berkley

01/06/2010

11:36 AM Bug #4161: Develop kepler workflow execution engine
installed on my local system - did a roundtrip:
-upload workflow+report
-schedule
-wait
-view PDF report when complet...
ben leinfelder
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
 

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