Ecoinformatics Redmine

12/11/2009

04:17 PM Morpho Bug #4625: authenticate against KNB, switch source to DEV, and still have access

soong.28.5 should be on DEV but not KNB. The data tables in it should only be accessible by kruger-tpc and jing. Se... Oliver Soong

09:07 AM Morpho Bug #4625: authenticate against KNB, switch source to DEV, and still have access

I thought about that, so I temporarily wiped my .morpho folder, but it didn't make a difference. Oliver Soong

12/10/2009

06:27 PM Kepler 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

06:07 PM Morpho Bug #4625: authenticate against KNB, switch source to DEV, and still have access

This might not be a morpho bug, now that I think about it. Maybe this should go against metacat and its authentication? Oliver Soong

06:07 PM Morpho Bug #4625 (Resolved): authenticate against KNB, switch source to DEV, and still have access

I have packages that exist on DEV but not KNB. I start Morpho r4682 with KNB set as the metacat source and authentic... Oliver Soong

05:44 PM Morpho Bug #4624 (New): local/network status icons sometimes (inconsistently) incorrect

A package that only exists remotely gets a network icon but no local icon. After a sync from remote->local, some pac... Oliver Soong

05:26 PM Morpho Bug #4623 (Resolved): docid conflict box needs a button or something

I created a package (.1 revision), synced local->remote (.2 revision?), then edited the local EML to produce a docid ... Oliver Soong

05:25 PM Morpho Bug #4622: local copies of zip "data tables" corrupt

This seems to cascade into exporting when local data are present as well. With no local data, exporting seems to wor... Oliver Soong

04:52 PM Morpho Bug #4622 (Resolved): local copies of zip "data tables" corrupt

The example is soong.37.2 on the dev metacat (search for soong). The data package contains zip files as "data tables... Oliver Soong

12/08/2009

08:52 PM Metacat Bug #4612: EML file content out of sync with metacat

Yeah, I should have been clearer. I'm pretty sure I did something wrong with the actor in Kepler, but I wanted to ra... Oliver Soong

04:46 PM Metacat Bug #4612 (Rejected): EML file content out of sync with metacat

This is on dev.nceas.ucsb.edu. Search for soong_test. There should be 2 entries for "soong_test 1". One has ID soo... Oliver Soong

06:21 PM Kepler 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

06:20 PM Kepler 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

05:43 PM Kepler 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

04:31 PM Metacat Bug #4611 (New): searching for soong_test seems to return entries with "soong test" as well as soong_test

I'm not sure if this is a "feature" or not. It surprised me. Searching for "soong test" only returns the expected e... Oliver Soong

04:28 PM Metacat Bug #4610 (New): trying to register a dataset when logged in asks for another authentication

I log into KNB, then go to Register your dataset online, and it says I must register. The register dataset page seem... Oliver Soong

04:23 PM Metacat Bug #4609 (New): when viewed with saved credentials, KNB homepage shows blank entries

I sign into the KNB, then close the window (but not the browser). The cookie persists, so when I go back to the KNB ... Oliver Soong

04:03 PM Kepler 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

03:50 PM Kepler 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

12:20 PM Kepler 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 Kepler 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

12:17 PM Kepler 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 Kepler 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

12/03/2009

05:34 PM Kepler 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

03:24 PM Kepler 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 Kepler 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 Kepler 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 Kepler Bug #4598: particular workflow triggers "QueryException: No tokens found for execution"

The error says reporting 2 lines down. Oliver Soong

04:50 PM Kepler 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

04:54 PM Kepler 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

12/01/2009

03:08 PM Kepler Bug #4592: ROML lost when saving KAR a second time

The workaround I suggested sometimes seems to trigger bug 4571, so it might be safest to restart Kepler after saving ... Oliver Soong

02:42 PM Kepler Bug #4592: ROML lost when saving KAR a second time

The error occurs on the second File->Save Archive as long as the KAR is not closed and re-opened between.
New workfl... Oliver Soong

02:16 PM Kepler Bug #4592: ROML lost when saving KAR a second time

*** Bug 4593 has been marked as a duplicate of this bug. *** Oliver Soong

02:14 PM Kepler Bug #4592: ROML lost when saving KAR a second time

Overwriting turns out not to be necessary. Simply File->Save Archive again. Oliver Soong

01:56 PM Kepler Bug #4592 (Resolved): ROML lost when saving KAR a second time

Create a workflow and report. File->Save Archive. The KAR should contain the ROML. File->Save Archive again, overw... Oliver Soong

02:16 PM Kepler Bug #4593: ROML lost when saving workflow with a composite actor to KAR after saving XML after saving to KAR

I think the trigger here is the second Save Archive, and this now seems to be a duplicate of the (newly modified) bug... Oliver Soong

02:08 PM Kepler Bug #4593 (Resolved): ROML lost when saving workflow with a composite actor to KAR after saving XML after saving to KAR

I haven't isolated exactly what the trigger is, but I think this is the bug I've been trying to track down for a coup... Oliver Soong

11:05 AM Kepler Bug #4591 (New): ImageJ creating folders based on file paths from prior executions saved in the MOML

Not a hugely important bug and unlikely to cause any actual problems, but a bug nonetheless.
If I generate a workf... Oliver Soong

10:36 AM Kepler Bug #4569: viewing report before executing sometimes generates persistent blank report

The last comment wasn't terribly specific.
1. Create a workflow, File->Save (say test.xml), and run it. I believe t... Oliver Soong

11/22/2009

12:57 PM Kepler Bug #4572 (Resolved): ROML lost when reported ports are in composite actors

Starting from a clean-cache:
1. Create a KAR containing a composite actor and a report:
a. SDF (iterations = 1... Oliver Soong

12:09 PM Kepler Bug #4571 (Resolved): report "lost" from KAR

In the process of tracking down another bug, I came across some odd behavior. I'm not sure what the exact trigger is... Oliver Soong

11:41 AM Kepler Bug #4569: viewing report before executing sometimes generates persistent blank report

It's the File->Save Archive (KAR) that triggers this. After the save, when the archive has been reloaded, changing t... Oliver Soong

11:37 AM Kepler Bug #4562: report seems to exist in MOML workflows when kar of same name exists in a local repository

So what happens if I want to have 2 reports for the same workflow? If I want to generate a new report for a workflow... Oliver Soong

11/20/2009

05:23 PM Kepler Bug #4570 (Resolved): dangling file handle for KARs

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 ... Oliver Soong

05:14 PM Kepler Bug #4569 (Resolved): viewing report before executing sometimes generates persistent blank report

I unfortunately can't figure out how to replicate this yet. It occurred with the latest tpc01 report archive, althou... Oliver Soong

04:44 PM Kepler Bug #4568 (Resolved): must have some way to view full path to port in report

Bug 4471 got rid of the report TOC. Somewhere along the line, tooltips for the report items disappeared. I now have... Oliver Soong

01:17 PM Kepler Bug #4567 (Resolved): NPE viewing LSID of non-workflow entries in local repositories

If I have a local repository with KAR files in it and I attempt to "View LSID" on any entry that is not a MOML, I get... Oliver Soong

01:15 PM Kepler Bug #4559: local repositories not showing up in components tree

I think this bug is partly due to bug 4512, partly due to the new hiding empty repositories "feature", partly due to ... Oliver Soong

12:31 PM Kepler Bug #4559: local repositories not showing up in components tree

I'll see if I can make this happen with a simpler case. There have been unusual errors with this workflow in the pas... Oliver Soong

11:40 AM Kepler Bug #4507: report designer losing content when there are too many items

I'm not currently planning on exceeding 95 items, so there's less urgency for a more involved fix. On the other hand... Oliver Soong

11/19/2009

08:12 PM Kepler Bug #4507: report designer losing content when there are too many items

I see the problem as described at r21780, but at r21788, the number of actors is pushed up to around 95 or so. The p... Oliver Soong

06:45 PM Kepler Bug #4507: report designer losing content when there are too many items

I'm at r21647 for report\src\org\kepler\reporting\gui\ReportDesignerPanel.java. I saw you just committed 2 updates, ... Oliver Soong

05:41 PM Kepler Bug #4507: report designer losing content when there are too many items

Beyond 5 items, I can no longer add to the bottom of the report designer. There doesn't seem to be any space, and an... Oliver Soong

04:36 PM Kepler Bug #4507: report designer losing content when there are too many items

I just tried r21780 on OS X here in the vis lab and lost ROML content at 10 items. Something isn't matching here... Oliver Soong

02:52 PM Kepler Bug #4507: report designer losing content when there are too many items

This doesn't quite seem to be fully fixed. I'm no longer losing report items from the test case, but add 15 items to... Oliver Soong

08:08 PM Kepler Bug #4564: Model Reference throws error with workflows in the same folder, but still functions

What boggles my mind is the tpc09-plant-dynamics-woody.xml workflow uses a VisualModelReference actor that generally ... Oliver Soong

07:34 PM Kepler Bug #4564: Model Reference throws error with workflows in the same folder, but still functions

I take back that bit about ../tmp/referred.xml working. I think I just got confused. An error seems to be thrown fo... Oliver Soong

07:11 PM Kepler Bug #4564 (New): Model Reference throws error with workflows in the same folder, but still functions

If I have a referring model (referring.xml) and a referred model (referred.xml) in the same folder, I have difficulty... Oliver Soong

07:55 PM Kepler Bug #4565: clean wrp checkout has no actors

Missed a clean-cache step from the previous checkout. Oliver Soong

07:15 PM Kepler Bug #4565 (Resolved): clean wrp checkout has no actors

I just did a clean checkout, and the Components, Projects, and Statistics branches are completely missing. The Actor... Oliver Soong

05:45 PM Kepler Bug #4563: components search seems to be broken

If you follow the instructions in comment 5 for bug 4559, you'll get a Kepler instance with the report archive and ru... Oliver Soong

05:37 PM Kepler Bug #4563: components search seems to be broken

Hm, something got buggered somewhere along the way, but I'm not sure exactly what. A clean-cache fixed it, but now I... Oliver Soong

05:19 PM Kepler Bug #4563 (Resolved): components search seems to be broken

It no longer seems to return anything. Oliver Soong

03:59 PM Kepler Bug #4559: local repositories not showing up in components tree

This is slightly more complicated. I restarted Kepler again, and now both KARs show up in the components tree.
So s... Oliver Soong

03:47 PM Kepler Bug #4559: local repositories not showing up in components tree

I deleted the run archive from the repository and restarted Kepler, but the report archive (MOML and ROML only) still... Oliver Soong

03:40 PM Kepler Bug #4559: local repositories not showing up in components tree

Well, I'm now seeing the described behavior at r21780, but I'm missing a KAR. I've got one that's just the MOML and ... Oliver Soong

02:25 PM Kepler Bug #4559 (Resolved): local repositories not showing up in components tree

Summary says it all. I'm at r21772, and the default workflows repository isn't in the components tree. Adding repos... Oliver Soong

02:49 PM Kepler Bug #4562 (Resolved): report seems to exist in MOML workflows when kar of same name exists in a local repository

Create a workflow, save it with some basename (e.g., test.xml), then create a report and save it with the same basena... Oliver Soong

02:35 PM Kepler Bug #4561 (New): icon overlays not showing up for actors in the components tree

RExpression used to have the little R icon show up in the components tree (it was an easy way to find the RExpression... Oliver Soong

02:27 PM Kepler Bug #4560 (Resolved): can't remove local repositories

This may be related to bug 4559, but attempting to remove local repositories from the components sources list gives a... Oliver Soong

11/13/2009

04:56 PM Kepler Bug #4549 (In Progress): String Replace actor "remembers" previous execution values

1. Build a workflow with an SDF director (set iterations to 1), an RExpression (turn off graphics output), and a Disp... Oliver Soong

03:11 PM Kepler Bug #4548 (Resolved): string tokens with newlines print the escape sequences

This was first noticed when viewing an RExpression's "output" port. The output port emits a string token containing ... Oliver Soong

03:06 PM Kepler Bug #4547 (Resolved): documentation for file parameter includes an error

The documentation for the file parameter includes at the top:
Error evaluating DocAttribute parameter: ptolemy.ke... Oliver Soong

03:04 PM Kepler Bug #4545: String To Image Converter seems broken

I misread the documentation. Oliver Soong

02:44 PM Kepler Bug #4545 (Resolved): String To Image Converter seems broken

If I pass the an image file as a string ("C:/tmp/image.png") to the String To Image Converter actor, it seems not to ... Oliver Soong