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From 03/06/2008 to 04/04/2008

04/05/2008

05:41 PM Bug #3196: Find/Change license on gpl/lgpl code
Apache-licensed code is generally redistributable in both source and binary forms (it is similar to BSD), although it... Matt Jones
05:31 PM Bug #3196: Find/Change license on gpl/lgpl code
Ok, we're looking more deeply into LGPL. Thanks, Christopher. I think we'll at least need to include the source code... Timothy McPhillips
05:01 PM Bug #2965: Ability to easily concatenate identical data structures (EMLDatasource)
I've worked with kevin to implement this in some of his workflows.
I've also packaged a custom R actor called "UnionA...
ben leinfelder

04/04/2008

03:04 PM Bug #3196: Find/Change license on gpl/lgpl code
I also thought that LGPL'd code should be acceptable.
But what about the Apache Licence, Kepler has a whole bunch o...
Dan Higgins
02:54 PM Bug #3196: Find/Change license on gpl/lgpl code
I might be confused, but I thought that LGPL code was ok to include
because it is non-viral
http://ptolemy.eecs.berke...
Christopher Brooks
02:39 PM Bug #3196: Find/Change license on gpl/lgpl code
The jar file lib/jar/cipres/jacorb.jar needs to be removed and dependencies on it satisfied some other way. The Jaco... Timothy McPhillips
02:44 PM Bug #3154: Documentation missing for DarwinCoreDataSource
added documentation to the actor moml and also added method for pulling the documentation from the actor library for ... ben leinfelder
10:06 AM Bug #3209: ecogrid SearchRegistryAction error when disconnected from network
sounds like some error catching is in order. should there be an alert using MessageHandler (attack of the pop up win... ben leinfelder
10:00 AM Bug #3209 (Resolved): ecogrid SearchRegistryAction error when disconnected from network
About 30 seconds after starting kepler with no network connection, a long error
message is displayed, starting with:...
Daniel Crawl
10:05 AM Bug #3210 (New): add netCDF support to Kepler
Many scientific data sets are represented in netcdf format (http://www.unidata.ucar.edu/software/netcdf/). Kepler sh... Matt Jones
09:17 AM Bug #3208: consolidate matlab actors
I can help on this one.
Combining the two actors seems reasonable to me.
In addition, the expression language has a ...
Christopher Brooks
09:10 AM Bug #3208 (New): consolidate matlab actors
MatlabExpression and PtMatlabExpression both execute expressions
in matlab. They should be combined such that if the...
Daniel Crawl
09:12 AM Bug #3207: consolidate command line execution actors
The Ptolemy Exec actor also has duplicate functionality.
I looked at CommandLineExec and it looked like it
really nee...
Christopher Brooks
09:03 AM Bug #3207 (Resolved): consolidate command line execution actors
Command Line Exec and External Execution have different interfaces
but perform the same basic functionality. They sh...
Daniel Crawl

04/03/2008

04:30 PM Bug #3206 (Resolved): ecogrid error message occurs when running disconnected from network
[java] ERROR (org.ecoinformatics.seek.datasource.EcogridDataCacheItem:cleanUpCache:373) Couldn't close the output str... Daniel Crawl
01:51 PM Bug #3201: Remove all links to FSM from the GUI
It looks like this works. I'll close this, but if anyone has any objections to the way this works or thinks it break... Chad Berkley
01:46 PM Bug #3200: create a 1.0.0 branch in cvs
The branch is there. See kepler-dev email for checkin instructions. Chad Berkley
01:12 PM Bug #3167: Customize documentation fails when ports added
This seems to work for me. I might have fixed it and forgotten to close this bug. reopen this bug if it fails to wo... Chad Berkley
01:08 PM Bug #3138: remove the distributed options menu item for 1.0 release
both have now been removed from the release branch. Chad Berkley
09:24 AM Bug #3205 (New): gdalTranslate actor crashes on bad format and won't work with all gdal formats
Niels Hoffman reports that the gdalTranslate actor will not work with all of the current formats supported by gdal_tr... Chad Berkley
08:00 AM Bug #3203: Add dateType
See also https://chess.eecs.berkeley.edu/bugzilla/show_bug.cgi?id=141
"Plotter should be better about displaying times"
Christopher Brooks
06:44 AM Bug #2571: position of new elements on screen
One way to do this would be to translate the coordinates
relative to the location of the mouse.
Christopher Brooks
06:41 AM Bug #3110: Can't access actors via http
I can't replicate my own bug (Can't access actors via http),
so I'm closing this.
Christopher Brooks

04/02/2008

04:32 PM Bug #3162: ptExecuteConfig.xml depends on removed basicKeplerLibrary.xml
basicKeplerLibrary is not necessary to run ptexecute and has been removed from
ptExecuteConfig.xml.
Daniel Crawl
04:15 PM Bug #3097: incorrect classpath in generated ptexecute.sh and momlexecute.sh
I added a new target to the build file: 'ant build_wfexecute_sh' creates
wfexecute.sh, which accepts -gui/-nogui and ...
Daniel Crawl
09:13 AM Bug #3097: incorrect classpath in generated ptexecute.sh and momlexecute.sh
On the 1.0 release conference call, we discussed creating one shell script to replace all of the current ones. There... Chad Berkley
03:11 PM Bug #2509: FSM & Modal Model Menu selections do not work
I hadn't realized about the State button being on the toolbar. So it seems that we can successfully create an FSM. S... Matt Jones
02:47 PM Bug #2509: FSM & Modal Model Menu selections do not work
In Ptolemy, a State does appear in the left hand palette.
This state is not present in Kepler.
However, in both Ptol...
Christopher Brooks
02:28 PM Bug #2509: FSM & Modal Model Menu selections do not work
Actually, the problem was not with the menu item itself -- the problem is that when you create an FSM model, the acto... Matt Jones
02:17 PM Bug #2509: FSM & Modal Model Menu selections do not work
File | New Workflow | FSM Model
and
File | New Workflow | Modal Model
both work for me.
I'm marking this as fixed, ...
Christopher Brooks
08:59 AM Bug #2509: FSM & Modal Model Menu selections do not work
moving to post 1.0 Chad Berkley
02:19 PM Bug #3201: Remove all links to FSM from the GUI
Ok, I've fixed bug #3022 and bug #2509.
bug #3204 is a RFE for FSM examples to be added to Kepler
Unless someone ind...
Christopher Brooks
09:38 AM Bug #3201: Remove all links to FSM from the GUI
Mainly the reason is that we don't have time to re-integrate it and figure out all of the dependencies that we've bro... Chad Berkley
09:31 AM Bug #3201: Remove all links to FSM from the GUI
I feel that Kepler should ship with FSM.
What's the reasoning behind not shipping FSM?
There is this bug:
FSM State ...
Christopher Brooks
09:00 AM Bug #3201 (Resolved): Remove all links to FSM from the GUI
We are postponing re-adding the FSM items to kepler to post-1.0. All GUI items related to FSM should be removed from... Chad Berkley
02:15 PM Bug #3204 (New): Kepler should have FSM examples
Finite State Machines are very powerful, there should
be a Kepler-specific scientific workflow that
illustrates FSMs.
Christopher Brooks
11:31 AM Bug #3022: FSM State cannot be opened from context menu
The issue here is that in Ptolemy, the transition menu choices
are "Look Inside", not "Open Actor".
See bug #2110 f...
Christopher Brooks
08:58 AM Bug #3022: FSM State cannot be opened from context menu
moving to post 1.0. Chad Berkley
11:13 AM Bug #3203 (Resolved): Add dateType
Add a date type to Kepler; being able to pass date tokens between a variety of actors would be nice. My original moti... Derik Barseghian
10:50 AM Bug #3196: Find/Change license on gpl/lgpl code
Here are the GPL'd and LGPL'd sources Sean Riddle found in the
Kepler source tree (with known authors/copyright hold...
Timothy McPhillips
08:45 AM Bug #3196 (Resolved): Find/Change license on gpl/lgpl code
We need to find any code and/or libraries that currently are using gpl or lgpl as the license and negotiate with the ... Chad Berkley
10:30 AM Bug #2531: The link from Kepler intro page to the Ptolemy quick links page is broken
This bug is ready to be closed.
It should be checked in the release branch and then closed.
Christopher Brooks
10:16 AM Bug #2531: The link from Kepler intro page to the Ptolemy quick links page is broken
This bug could be assigned to me.
I just added CCodeGenerator to this list of classes to be
excluded in:
kepler/conf...
Christopher Brooks
08:51 AM Bug #2531: The link from Kepler intro page to the Ptolemy quick links page is broken
Ilkay will take this on. We basically need to make sure that any ptII demos that are actually linked to the kepler d... Chad Berkley
09:27 AM Bug #3172: windows mouse wheel doesn't scroll canvas
This is fixed in the ptII devel branch. See:
https://chess.eecs.berkeley.edu/bugzilla/show_bug.cgi?id=73
I believe ...
Christopher Brooks
09:13 AM Bug #3172: windows mouse wheel doesn't scroll canvas
This should be fixed with the other ui bugs that are outstanding. pushing this to 1.1. Chad Berkley
09:10 AM Bug #3149: cannot add arbitrary jars when exporting archive
postponing to 1.1.0 There are numerous items that need to be worked out with this bug. How the user interacts with ... Chad Berkley
09:09 AM Bug #3130: Add an accelerator (keyboard shortcut) for opening a new blank workflow
If this bug is easily fixable, do it. If not, postpone it. Chad Berkley
09:08 AM Bug #3115: Need to check Kepler for memory leaks
We should run each of the demo workflows with a memory usage analyzer to make sure that no major leaks are found with... Chad Berkley
09:06 AM Bug #3108: ENM GARP Baseline 3-Actor GARP - Browser Display demo fails with NameDuplication: convertTo?
We should not be linking to any workflows that do not work. All html links need to be checked and if any broken work... Chad Berkley
09:04 AM Bug #3101: Inclusion of R executable for Mac and Linux ?
duplicate bug of 3126
*** This bug has been marked as a duplicate of bug 3126 ***
Chad Berkley
09:04 AM Bug #3126: add R system installation to the Mac installer
*** Bug 3101 has been marked as a duplicate of this bug. *** Chad Berkley
08:48 AM Bug #3126: add R system installation to the Mac installer
We should also try to get this to work with the NMI build. Chad Berkley
09:03 AM Bug #3074: Code library installation issues
postponing this development until after 1.0. We just don't have the time to get this done. This will be something k... Chad Berkley
09:02 AM Bug #3202 (Resolved): Remove the workflows directory from the release
Many of the workflows in this directory are broken, and although they are useful as examples, we do not want to inclu... Chad Berkley
08:57 AM Bug #3144: add link in OSX Applications folder
also need to clean up the installer for osx. make sure no windows specific files are included. Sean also agreed to ... Chad Berkley
08:54 AM Bug #3200 (Resolved): create a 1.0.0 branch in cvs
We need a branch for 1.0 targeted development so that normal dev can go on in the head. Any items that need to be in... Chad Berkley
08:52 AM Bug #3122: Get installer size down
Try to locate all extraneous items and remove them from the installer. Chad Berkley
08:50 AM Bug #3199 (Resolved): include R 2.6 in the installer
We are currently including 2.4 in the windows installer. we'd like to upgrade that to 2.6 and also see if we can get... Chad Berkley
08:49 AM Bug #3198 (Resolved): test dynamic library installations on all platforms
Make sure that the dylibs work on windows, osx and linux and that they get put in the correct place by the installer. Chad Berkley
08:41 AM Bug #3195 (Resolved): Check all documentation for 1.0 release
All of the documentation needs to be checked for accuracy and completeness before the 1.0 release, which is currently... Chad Berkley
06:22 PM Bug #3124: Automatically refresh ecogrid sources (endpoints) once per Kepler
data sources are now refreshed by a new thread that is scheduled to execute 30 seconds (configurable in config.xml) a... ben leinfelder

04/01/2008

03:39 PM Bug #3179: Distinguish "download" and "information" attribute values in eml distributlon online url
Here are solutions after the 04/01/2008 telephone conference:
1. Modify the query to exclude the eml packages which o...
Jing Tao
03:02 PM Bug #3192: behavior of documentation actor
I may have found the reason for the loss of my documentation after the first view in Windows XP. When I right-click ... Kevin Drury
03:01 PM Bug #3154: Documentation missing for DarwinCoreDataSource
-solicit information from Dave V. and Jing to flesh out documentation in the actor library
-include actor documentati...
ben leinfelder
02:49 PM Bug #3124: Automatically refresh ecogrid sources (endpoints) once per Kepler
from 1.0.0 release meeting:
-at startup, queue a thread for refreshing the endpoints after a small delay (~minute)
ben leinfelder
10:11 AM Bug #3147: Get rid of Swing componets in Ecogrid data access classes
As ben said, this bug was fixed. Jing Tao
11:58 PM Bug #3194 (New): add actors to support Sun Grid
Chirs Zhu <chris.zhu@sun.com> and others at Sun have contributed actors that allow Kepler to be used as a client for ... Matt Jones

03/31/2008

04:38 PM Bug #3192 (New): behavior of documentation actor
Hello. The documentation actor will be an important component of workflows that outlive individual analyst's involve... Kevin Drury
03:00 PM Bug #3103: Building actor documentation from within Kepler fails
This is now fixed. The documentation can be edited with the Customize function. Chad Berkley
01:36 PM Bug #3187: RExpression actor does not share focus
I think you have it inverted. the frame _won't_ be null in our Kepler case for the R actor. The code block should b... ben leinfelder
01:16 PM Bug #3187: RExpression actor does not share focus
Ok, I put the setTitle inside the if block, so this might now work.
What we have is:
if (frame == null) {
...
Christopher Brooks
11:14 AM Bug #3187: RExpression actor does not share focus
It's less than ideal to have a bunch of open text editor windows all named "Unnamed".
But I think we can handle it fo...
ben leinfelder
12:43 PM Bug #3152: Use EcoGridServicesController with EcoGridWriter actor
retargeting for after 1.0 - not a high priority. ben leinfelder
12:38 PM Bug #3147: Get rid of Swing componets in Ecogrid data access classes
I believe this is fixed. There was spot in the EML actor that was using Swing directly, but I replaced that with Mes... ben leinfelder
12:18 PM Bug #3138: remove the distributed options menu item for 1.0 release
We should also remove the DCA actor from the tree to be sure it isn't used, and check the documentation to be sure we... Matt Jones
11:24 AM Bug #3184: right-click context menu in RExpression actor
the best solution for adding a feature like code commenting would be to use an external editor.
there's apparently a ...
ben leinfelder
11:17 AM Bug #3185: Ctrl-z does not "undo" in RExpression actor
This has been added in the ptolemy base classes now. ben leinfelder
11:16 AM Bug #3186: commit RExpression code changes, but leave actor open
Rather than just double clicking on the actor, if you "Open" the actor, the expression editing window will appear. c... ben leinfelder
11:15 AM Bug #3191: Merge TextEditor changes with ptII source
closing this bug - I'm happy with the undo/redo. (thanks, cxh) ben leinfelder

03/30/2008

08:53 PM Bug #3191: Merge TextEditor changes with ptII source
Ok, I updated Query, UndoListener and TextEditor in the ptII tree and
removed these files from kepler/src/exp/ptolemy...
Christopher Brooks
08:46 PM Bug #3187: RExpression actor does not share focus
The change to TextEditorTableau is marked below
if (frame == null) {
frame = new TextEditor(title...
Christopher Brooks

03/28/2008

02:48 PM Bug #3191 (Resolved): Merge TextEditor changes with ptII source
These changes from src/exp in Kepler should be included in the ptII tree:
src/exp/ptolemy/gui
Query.java
UndoL...
ben leinfelder

03/27/2008

04:54 PM Bug #3187: RExpression actor does not share focus
Until a change is included in ptII code (specifically ptolemy.actor.gui.TextEditorTableau), only one RExpresison text... ben leinfelder
03:26 PM Bug #3187: RExpression actor does not share focus
By using the ptolemy.actor.gui.TextEditor when "Open Actor" is invoked on the RExpression we can support having multi... ben leinfelder
03:28 PM Bug #3185: Ctrl-z does not "undo" in RExpression actor
from kepler-dev email that i sent:
---
After looking at this again, I realized it could be made even more
generic b...
ben leinfelder
10:19 AM Bug #3185: Ctrl-z does not "undo" in RExpression actor
Locally, I have implemented an UndoableEditListener for the JTextArea that is used in ptolemy.gui.Query along with so... ben leinfelder
03:09 PM Bug #3186: commit RExpression code changes, but leave actor open
Proposed implementation (working locally for me):
By using the ptolemy.actor.gui.TextEditor when "Open Actor" is invo...
ben leinfelder

03/26/2008

04:01 PM Bug #3189 (New): CommandLineExec needs ability to kill spawned process
Many times when authoring/debugging a workflow, the process spawned by the command line actor runs infinitely. It wo... Chad Berkley
05:29 PM Bug #3187 (In Progress): RExpression actor does not share focus
It would be nice to be able to change the focus from an open RExpression actor to another Kepler window. Two cases t... Kevin Drury
05:18 PM Bug #3186 (Resolved): commit RExpression code changes, but leave actor open
R-script development within an RExpression actor can get pretty tedious. For example, when you add a line of code a... Kevin Drury
05:06 PM Bug #3185 (Resolved): Ctrl-z does not "undo" in RExpression actor
Ctrl-c (copy) and Ctrl-v (paste) work as expected in the RExpression actor. Is it possible to also make Ctrl-z (undo... Kevin Drury
05:02 PM Bug #3184 (Resolved): right-click context menu in RExpression actor
One thing that would make Kepler a more friendly environment for developing analyses would be the ability to highligh... Kevin Drury

03/25/2008

07:39 PM Bug #3002: Copy/Paste of a relation (diamond)
When ports and relations are created from the toolbar they now don't overlap.
This should help prevent problems with ...
Christopher Brooks

03/24/2008

10:53 AM Bug #3182: check for consistent licensing text in all source files
No, I think this is a separate item from the copyright check, even though we might do them simultaneously with a sing... Matt Jones
10:47 AM Bug #3182: check for consistent licensing text in all source files
Should this be combined with "Copyrights of subpackages need to be handled"
http://bugzilla.ecoinformatics.org/show_b...
Christopher Brooks
10:18 AM Bug #3182 (Resolved): check for consistent licensing text in all source files
Kepler is licensed under the BSD. We need to check that all code is properly licensed this way throughout the releas... Matt Jones
10:28 AM Bug #3183 (New): Return/Enter does not select default button in dialog boxes
Pressing Return/Enter does not select the default button (usually 'Commit') of dialogs. This should be the case accor... Sean Riddle

03/22/2008

11:10 AM Bug #2870: Copy/Paste of composite actors
I think I have this fixed by making changes to moml/MoMLVariableChecker.java
I've added a test case:
ptII/ptolemy/mo...
Christopher Brooks

03/21/2008

04:20 PM Bug #3056: unable to print output of Display actor
The "Print" menu choice is now enabled in Display. The change was to ptolemy/actor/gui/TextEditor.java
Getting multi...
Christopher Brooks

03/19/2008

01:58 PM Bug #3107: http links don't work: Unsupported file type or connection not supported
I'm closing this. We can revisit this problem when ptII and Kepler require Java 1.6. At that point, we can change t... Chad Berkley
01:55 PM Bug #3107: http links don't work: Unsupported file type or connection not supported
I can no longer reproduce this? I'm not sure what's up, or what changed?
I tried it on the same machine (my laptop w...
Christopher Brooks

03/18/2008

04:00 PM Bug #3179: Distinguish "download" and "information" attribute values in eml distributlon online url
Yeah. So here is my approach:
I am not exactly sure how hard the query will be implemented, but I don't think it will...
Jing Tao
03:50 PM Bug #3179: Distinguish "download" and "information" attribute values in eml distributlon online url
Whether or not the query is altered, I think Kepler will still need to handle both types of distribution urls. I'm t... ben leinfelder
03:45 PM Bug #3179: Distinguish "download" and "information" attribute values in eml distributlon online url
from Jing:
I am not exactly sure how hard the query will be implemented, but I don't
think it will be too hard. Howe...
ben leinfelder
03:40 PM Bug #3179 (Resolved): Distinguish "download" and "information" attribute values in eml distributlon online url
I agree, I don't think it does handle this, but this is a bug in my opinion. It should distinguish these URL types. ... Jing Tao
03:10 PM Bug #3135: semantic type and class params need special handling in doc window
Fixed this by adding an exclusion list to the configuration. the docviewer can now take a list of attribute names no... Chad Berkley
05:32 PM Bug #3107: http links don't work: Unsupported file type or connection not supported
I agree that ptolemy.actor.gui.BrowserLauncher is somewhat sketchy.
However, it works fine for me under Ptolemy and f...
Christopher Brooks

03/17/2008

04:47 PM Bug #3107: http links don't work: Unsupported file type or connection not supported
Chad,
The BareBoneBrowserLaunch you reference in http://www.centerkey.com/java/browser/ is already in Kepler. Che...
Dan Higgins
02:35 PM Bug #3107: http links don't work: Unsupported file type or connection not supported
This looks like a bug in the somewhat sketchy class ptolemy.actor.gui.BrowserLauncher. This class was written in 200... Chad Berkley
01:59 PM Bug #3107: http links don't work: Unsupported file type or connection not supported
I've been looking into this and it appears to be a problem on windows and linux but not OSX. The BrowserEffigy$Facto... Chad Berkley
01:33 PM Bug #3036: Need to be able to delete actors from the library
There is now a right click menu item to remove a component from the library. It removes the component from the cache... Chad Berkley

03/13/2008

11:41 AM Bug #3150: Need to add PTII Python actors back into Kepler
The Python actor(s) now operate correctly in Kepler. Several examples workflows are now in the demos/Python directory... Dan Higgins
11:57 PM Bug #3173: Improve data frame handling between RExpression actors
The R actor now uses the serialize/unserialize method described by jim for data frames and also for other complex R o... ben leinfelder

03/12/2008

10:40 AM Bug #3173: Improve data frame handling between RExpression actors
tried with my system (running R v2.4.1) and it does work.
Jim pointed out that my version of R does not use "1L" to e...
ben leinfelder
08:36 PM Bug #3173 (Resolved): Improve data frame handling between RExpression actors
The short version: true data types might not be preserved when using text file-based serialization of data frames bet... ben leinfelder

03/11/2008

04:04 PM Bug #3172 (New): windows mouse wheel doesn't scroll canvas
Kepler Version: Release Candidate 1
OS: Windows xp
I have a usb mouse. When a workflow exceeds the window size,...
Kevin Drury

03/06/2008

02:39 PM Bug #3127: workflows can open off the screen
I changed ptolemy/actor/gui/WindowPropertiesAttribute.java so that if any part of the window is off of the screen, th... Chad Berkley
 

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