Kepler

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

12/18/2009

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

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

12/17/2009

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

12/15/2009

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

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

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

12/14/2009

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

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

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

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

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

05:41 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

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

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

03:10 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

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

12/10/2009

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

12/09/2009

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

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

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

12/08/2009

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

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

10:51 AM Bug #4599: changing Expression and running problematic workflow generates blank report

Fixed. Daniel Crawl

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

12/07/2009

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

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

12/05/2009

01:19 PM Bug #4512: missing entries with multiple copies of the same KAR file in a single repository

The primary key used for the KARS_CACHED table has been changed to be the full File path for the KAR. So you can now... Aaron Aaron

12/04/2009

02:18 PM Bug #4336: Merge the old configuration systems

Also still need to convert the reporting module. I also missed one property in the ptolemy config. "tabPaneFactory" ... Chad Berkley

01:42 PM Bug #4336: Merge the old configuration systems

removing the 4597 dependency because that doesn't really depend on the configuration conversion. Chad Berkley

01:41 PM Bug #4336: Merge the old configuration systems

All of the kepler specific factory properties have now been removed from the configuration.xml file. I still need to... Chad Berkley

12/03/2009

10:18 PM Bug #4601 (Resolved): New LSID not propagating to provenance

This came up as a reporting bug, but that's a symptom if something larger. I'm not sure exactly where the system brea... ben leinfelder

10:11 PM Bug #4599: changing Expression and running problematic workflow generates blank report

Here's the scenario:
1. KAR/Workflow from another Kepler installation is opened - you can run it once and everything ... ben leinfelder

04:54 PM Bug #4599 (Resolved): changing Expression and running problematic workflow generates blank report

This uses the same workflow in Bug 4598. Open the workflow and change the "Figure Number" Expression from 1 to 12. ... Oliver Soong

05:34 PM Bug #4596: selecting text entry box of report item moves activation highlight but does not update properties window

I should point out this also affects section headers and dynamic report items. Basically, it's anything with a text ... Oliver Soong

04:20 PM Bug #4596: selecting text entry box of report item moves activation highlight but does not update properties window

This is now fixed. Clicking in the text entry area updates the properties window. debi staggs

03:24 PM Bug #4596 (Resolved): selecting text entry box of report item moves activation highlight but does not update properties window

Create 2 text items with different attributes. Click in the text entry area of the non-highlighted one. It will now... Oliver Soong

05:21 PM Bug #4600 (Resolved): Changing workflow & running causes "execution history not found" message to appear in report viewer

This uses the example workflow in bug 4598.
Run the workflow. Change "Figure Number" to 12 and run again. Now vi... Oliver Soong

05:15 PM Bug #4598: particular workflow triggers "QueryException: No tokens found for execution"

Ben and I have decided this is actually a symptom of bug 4436. Oliver Soong

05:08 PM Bug #4598: particular workflow triggers "QueryException: No tokens found for execution"

The error says reporting 2 lines down. Oliver Soong

04:50 PM Bug #4598 (Resolved): particular workflow triggers "QueryException: No tokens found for execution"

I've tried this on several Windows machines and 1 linux. When I run the workflow, I get this error:
org.kepler.p... Oliver Soong

04:33 PM Bug #4597 (Resolved): adding new configuration properties before/after a certain exiting configuration property.

Different modules may have their own menu items. To realize it, the module should be able to add configuration proper... jianwu jianwu

02:47 PM Bug #4595 (Resolved): ViewPane selection does not work with toolbar tear-off

When the toolbar is detached from the KeplerFrame the view selection drop down does not trigger view changes in the w... ben leinfelder

10:38 AM Bug #4582: reporting/module-info/module.properties

This was just an old file, that had no current use as far as we can tell. It has now been deleted. debi staggs

12/02/2009

06:03 PM Bug #4514: Files are being saved in the Kepler installation directory

configuration/ has been moved.
I think we just need to deal with / come to a consensus on InstanceAuthNamespace and ... Derik Barseghian

05:37 PM Bug #4578: tracking bug for changes to .kepler

.kepler now has cache and persistent areas like:
.kepler/cache/gamma.msi.ucsb.edu.OpenAuth.1278/modules/actors (etc)... Derik Barseghian

04:39 PM Bug #4579: Remove all references to specific module names from the code.

Modules can now be referenced by a stem name which is the base name before a version, for instance "common" refers to... Chad Berkley

01:11 PM Bug #4463: Grey out component names in the component library that can not be dragged to the canvas

My current thinking is to just assign appropriate icons to objects so people know what they are. Then a WorkflowRun ... Aaron Aaron

01:09 PM Bug #4380: Removing LocalRepository does not remove actors from Ontologies

Removing local repositories still causes problems, the components are not being removed from the library Aaron Aaron

01:03 PM Bug #4449: exception when dragging workflow

I'm not seeing this... closing for now Aaron Aaron

01:00 PM Bug #4150: Save in Library broken

Works now Aaron Aaron

12:23 PM Bug #4409: View Documentation for an actor works once

Should be OK now. Aaron Aaron

11:45 AM Bug #4512: missing entries with multiple copies of the same KAR file in a single repository

I should clarify the first statement in my previous comment.
Two different KARs (i.e. each KAR has a different KAR L... Aaron Aaron

11:41 AM Bug #4512: missing entries with multiple copies of the same KAR file in a single repository

With the new Library changes, having two different KARS with the same LSIDs works fine now.
As for having multiple i... Aaron Aaron

10:51 AM Bug #4582: reporting/module-info/module.properties

I think this is here from waaay back when we did the 'ant make-module' target. I don't know why it is here, either.
C... ben leinfelder

10:04 AM Bug #4336: Merge the old configuration systems

All .properties files have now been removed from kepler and their contents merged into the configuration manager. St... Chad Berkley