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From 11/06/2005 to 12/05/2005

12/05/2005

10:41 AM Bug #2304: RExpression accepts only limited input size.
Some further examination indicates that the problem indicate that the problem is
in 'R' rather than the RExpression c...
Dan Higgins

12/02/2005

08:59 AM Bug #2307 (In Progress): Mac OSX code missing for several JNI actors
We have compiled libraries (in CVS) for GARP and some GIS tools (e.g. GDAL) for
Windows and Linux OSs, but we do not...
Dan Higgins

12/01/2005

09:26 AM Bug #2109: make double-click open composite actor
yes, my professional assessment is that double-clicking to open a composite
actor is still preferred over the altern...
Laura Downey
09:16 AM Bug #2109: make double-click open composite actor
My feeling is that it is far better to have double click on composites open the
composite, and double click on atomic...
Matt Jones
08:51 AM Bug #2109: make double-click open composite actor
The natural inclination when "drilling down" in graphical heirarchical systems
is to double click on the object you ...
Laura Downey
09:24 AM Bug #2273: Problem with Hydro1K Flow Accumulation data
This looks like a GDAL problem - see comments below from Dave Vieglais
Hi Dan,
from gdal-1.3.1/frmts/raw/ehdrdatase...
Dan Higgins
08:02 PM Bug #2304: RExpression accepts only limited input size.
I think I may have limited the size of the string used to pass data from Kepler
to R. (I will check the code.)
It may...
Dan Higgins

11/30/2005

03:13 PM Bug #2304 (Resolved): RExpression accepts only limited input size.
The R expression actor accepts only a very limited size of input. For example,
a vector x <- 1:20000 with 20000 elem...
Lareo Lareo
02:44 PM Bug #2109: make double-click open composite actor
I have to take issue with the goal of this 'bug'. On atomic actors, a
double-click just displays the 'Edit parameters...
Dan Higgins
10:09 AM Bug #2273: Problem with Hydro1K Flow Accumulation data
This appears to be a GDAL problem. GDAL tries to read the data in a 32 bit bil
file as a 32 bit float when it is (app...
Dan Higgins

11/29/2005

01:58 PM Bug #2302 (In Progress): Problem unzipping hierarchical data
When EML Datasources point to zipped data files, the data is supposed to be
automatically unzipped when downloaded. ...
Dan Higgins
12:37 PM Bug #2300 (Resolved): migrate to new web services-only ecogrid client in Kepler
Kepler currently uses the version of the EcoGrid client based on Grid service
APIs. THat client will be changed to ...
Matt Jones
08:56 AM Bug #2290: EML2 Data Source problem with higgins.5087.3 - 'BaselineLayers'
This was really not a bug, but rather a mistake in my understanding. Read access
has to be given to TESTUSER for obje...
Dan Higgins

11/28/2005

01:09 PM Bug #2290 (Resolved): EML2 Data Source problem with higgins.5087.3 - 'BaselineLayers'
To reproduce this bug, do a datasearch for 'BaselineLayers'. This shold give the
knb package 'higgins.5087.3'. The d...
Dan Higgins

11/23/2005

06:30 AM Bug #2266: SVG - Assigning Icons
per my IRC conversation with matt, mappings should use LSIDs as keys instead of
(or perhaps in addition to?) classnam...
Matthew Brooke
04:12 PM Bug #2266: SVG - Assigning Icons
added code to:
kepler/src/exp/ptolemy/actor/Director.java and
kepler/src/exp/ptolemy/kernel/ComponentEntity.java
t...
Matthew Brooke
04:11 PM Bug #2286 (Resolved): SVG - reduce svg file size
SVG icons in kepler-docs/dev/usability/graphics/svg are mostly ~500MB in size.
Most of this is unneeded stuff that I...
Matthew Brooke

11/17/2005

03:40 PM Bug #2281 (Resolved): Duplicated and incorrect search results in actor searching
The three actors "ENM PCP","ESRI Shapefile Displayer" and "GML Displayer" are
desinged to be GISOutputActor in the ...
jianting zhang
12:34 PM Bug #2246: TOOLBAR: status on opening workflows and blank frames
There are four icons for each toolbar button. Per Laura, these represent the
four states:
Normal (unpressed)
Rollove...
Matthew Brooke

11/16/2005

12:08 PM Bug #2278: Fix cache file name clash
Fixed in v1.5 of org.kepler.objectmanager.cache.DataCacheObject. Kevin Ruland
10:21 AM Bug #2278 (Resolved): Fix cache file name clash
The cache file naming system relies on system date (to millisecond). On faster
systems this can cause naming clashes.
Kevin Ruland
10:18 AM Bug #2277 (Resolved): Simplify Kar loading
For first release, simplify the kar loading process to operate on moml documents
only. Each moml file will describe...
Kevin Ruland
10:05 AM Bug #2275: Replace the DataCacheManager
This will also require us changing all of the ecogrid classes to use the new system. Chad Berkley
10:03 AM Bug #2275 (Resolved): Replace the DataCacheManager
The DataCacheManager does some funky things and needs to be refactored to make
the API simpler and enable native use...
Chad Berkley
09:56 AM Bug #2233: Name duplication exception with KAR files
This is not a kepler bug. This is a restriction of PTII. Each actor is also a
NamedObj. Names in PTII MUST be unique.
Chad Berkley
09:55 AM Bug #1924: Refactor actor and data display and search code
This is being addressed both with the TreeIndex class and the new ObjectCache.
the ObjectCache includes callbacks so...
Chad Berkley
09:49 AM Bug #1909: generalize cache manager to provide support for very large data files
This should be implemented in the extension of CacheObject that deals with data
files.
Chad Berkley
09:48 AM Bug #1883: Add LSID to Cache Manager
the objectcache will replace the datacachemanager as the main caching system in
kepler. the objectcache relies compl...
Chad Berkley
09:39 AM Bug #1340: define and implement kepler archive file format (kar)
The kar format has been specified and kar files are currently being used to load
actors into kepler. it was recently...
Chad Berkley
09:37 AM Bug #1750: Allow KAR files to include jar/class files
we decided to wait on this until after the next release. Chad Berkley

11/15/2005

08:43 AM Bug #2273 (Resolved): Problem with Hydro1K Flow Accumulation data
Hydro1K Flow Accumulation data is somehow not getting processed correctly. It
should range from small numbers to num...
Dan Higgins

11/12/2005

06:07 PM Bug #2150: 'Edit Custom Icon' menu item doesn't work
Removed New->Icon Editor from File menu. Still need to remove 'Edit Custom Icon'
item from popup menu
Matthew Brooke

11/11/2005

02:30 PM Bug #1882: Investigate UI Changes
see wiki page:
http://kepler-project.org/Wiki.jsp?page=UIImplementation
These examples all have their own bug entri...
Matthew Brooke
02:28 PM Bug #2271 (In Progress): Changing the Color Scheme
TRANSFERRED FROM Bug #1882
------- Additional Comment #2 From Matthew Brooke 2005-11-08 15:56 -------
re: Chan...
Matthew Brooke
02:21 PM Bug #2270 (In Progress): TRACKING: Localization and Improvement of User-Visible Messaging Strings
There are several bugs that pertain to changing the various messaging strings
that the user sees (general UI text, l...
Matthew Brooke
12:08 PM Bug #2245: TRACKING: Batik SVG Rendering - remaining tasks
Have assigned the above to separate bugs, as follows:
1) ASSIGNING ICONS - Bug #2266
2) MEMORY USAGE - Bug #2267
3 &...
Matthew Brooke
12:05 PM Bug #2269 (Resolved): SVG - Small Icon (Actor Library Thumbnail)
getIcon() method in XMLIcon works, but its success seems to be linked to the odd
tree refreshing behavior described ...
Matthew Brooke
12:01 PM Bug #2268: SVG - Backward Compatibility
Another back-compat issue:
In EML simple example plot, text at bottom is rendered using SVG, and it does
not wrap, bu...
Matthew Brooke
11:59 AM Bug #2268 (Resolved): SVG - Backward Compatibility
- Need to add code so old SVG icons are translated to have their origin at the
top-left corner. They are currently c...
Matthew Brooke
11:56 AM Bug #2267: SVG - Memory Usage
This is partly exacerbated by the current large size of the actor SVG icons.
After hand-editiing the director icon, a...
Matthew Brooke
11:53 AM Bug #2267 (Resolved): SVG - Memory Usage
Currently, if Batik has to display more than about 150 SVG icons, it causes a
JVM crash with an OutOfMemoryError. T...
Matthew Brooke
11:49 AM Bug #2266 (Resolved): SVG - Assigning Icons
Icons can be assigned in actor moml, or can be assigned in the actor's java
code. Assigning in moml means icons will...
Matthew Brooke
04:07 PM Bug #2265 (New): Simple Kepler features movie to be displayed at the 1st time installation
Build up of a small movie or a slide show that walks to user through the basic
features of Kepler. The suggestion is...
Ilkay Altintas

11/10/2005

02:41 PM Bug #2264 (In Progress): DIALOGS: Implement New "Semantic Annotation" Dialog
Implement New "Semantic Annotation" Dialog:
http://kepler-project.org/Wiki.jsp?page=SemanticAnnotationDialogs
Matthew Brooke
02:39 PM Bug #2263 (In Progress): DIALOGS: Implement New "Search Ecogrid for Data Sources" Dialog
Implement New "Search Ecogrid for Data Sources" Dialog:
http://kepler-project.org/Wiki.jsp?page=SearchDialogs
Matthew Brooke
02:38 PM Bug #2262 (In Progress): DIALOGS: Implement New "Search Ecogrid for Component Sources" Dialog
Implement New "Search Ecogrid for Component Sources" Dialog:
(can't find this dialog on wiki. Can see only the "Se...
Matthew Brooke
02:37 PM Bug #2029: consider guided analysis wizard
Further suggestions to improve the "new workflow" menu action as per conference
call on Nov 10, 2005:
1. "New Workfl...
Ferdinando Villa
02:33 PM Bug #2261 (New): DIALOGS: Implement New "Advanced Search for Data" Dialog
Implement New "Advanced Search for Data" Dialog. See:
http://kepler-project.org/Wiki.jsp?page=SearchDialogs
Matthew Brooke
02:32 PM Bug #2260 (In Progress): DIALOGS: Implement New "Advanced Search for Components" Dialog
Implement New "Advanced Search for Components" Dialog. See:
http://kepler-project.org/Wiki.jsp?page=SearchDialogs
Matthew Brooke
02:27 PM Bug #1655: DIALOGS: Implement New UI for Sources Dialog (was "integrate ecogrid registry into kepler ecogrid client")
The "sources" button on the search panel under the "Components" tab (the tab
formerly known as "Actors") will also br...
Matthew Brooke
02:23 PM Bug #2247: TRACKING: Popup Dialog Changes
added depenencies for tracking Matthew Brooke
02:21 PM Bug #2259 (In Progress): DIALOGS: Implement New Actor Dialog
Implement New Actor Dialog, per Laura's design. See:
http://kepler-project.org/Wiki.jsp?page=WorkflowDirectorAndActo...
Matthew Brooke
02:20 PM Bug #2258 (In Progress): DIALOGS: Implement New Director Dialog
Implement New Director Dialog, per Laura's design. See:
http://kepler-project.org/Wiki.jsp?page=WorkflowDirectorAndA...
Matthew Brooke
02:19 PM Bug #2257 (In Progress): DIALOGS: Implement New Workflow Dialog
Implement New Workflow Dialog, per Laura's design. See:
http://kepler-project.org/Wiki.jsp?page=WorkflowDirectorAndA...
Matthew Brooke
10:19 AM Bug #1911: Provide real-time feedback/animation for workflow progress as a default
*** Bug 2008 has been marked as a duplicate of this bug. *** Matthew Brooke
10:18 AM Bug #2008: Provide real-time feedback for workflow progress as a default
same as bug#1911
*** This bug has been marked as a duplicate of 1911 ***
Matthew Brooke

11/09/2005

02:48 PM Bug #1340: define and implement kepler archive file format (kar)
reclassified to core Matthew Brooke
12:58 PM Bug #1882: Investigate UI Changes
Applications can indeed have a different color set and still look okay on a
desktop -- it just needs to be done righ...
Laura Downey
10:52 AM Bug #1882: Investigate UI Changes
My rationale for making this suggestion is as follows:
1) It would actually involve be *less* effort to make this wo...
Matthew Brooke
09:54 AM Bug #1882: Investigate UI Changes
Well then my take is this. Having one application on a Mac desktop that
doesn't have the striped look is not going ...
Laura Downey
09:00 AM Bug #1882: Investigate UI Changes
Unfortunately, that is not how it would work. The panels and window backgrounds
in the UI either get the native OS lo...
Matthew Brooke
08:26 AM Bug #1882: Investigate UI Changes
There is no proposal to change the "feel" of any system components of various
operating systems. The proposal is to...
Laura Downey

11/08/2005

03:56 PM Bug #1882: Investigate UI Changes
re: Changing the color scheme:
Do we really want to override the default system look & feel for background
colors? I...
Matthew Brooke
12:42 PM Bug #2253: ENM Workflows errors on newer, faster computer
Found the problem in the RExpression actor (after 2 1/2 days of looking!).
Needed to add another _read statement befo...
Dan Higgins
09:49 AM Bug #2256 (Resolved): Actor selection problem inside some Composites
This is a strange one!
How to observe the problem:
1) Open the GARP_Single_Species_BestRuleSet.xml workflow (#19 in...
Dan Higgins
09:29 AM Bug #2255 (Resolved): Simple Composite Actor cannot be dragged onto display
The simple, empty 'Composite Actor' does not appear in the actor tree because it
has been 'commented out' in the act...
Dan Higgins
05:29 PM Bug #1655: DIALOGS: Implement New UI for Sources Dialog (was "integrate ecogrid registry into kepler ecogrid client")
search panel now now uses same visual component as actor search panel. dialog
still to redo
Matthew Brooke

11/07/2005

10:27 AM Bug #2254 (Resolved): Order of actors in list changes with every new launch of Kepler
The order of actors in the actor list changes every time Kepler is launched!
This is confusing if one actually brows...
Dan Higgins
09:32 AM Bug #2253 (Resolved): ENM Workflows errors on newer, faster computer
Errors are occurring in 'SingleSpecies_BestRuleSet_Aug2005 ENM workflow on new,
faster computer (Optiiplex GX620 - 3...
Dan Higgins
06:33 PM Bug #2252 (Resolved): Need to add actors for aligning mulitiple DNA or protein sequences
We need to wrap the ClustalW and Gblocks programs in collection-oriented actors.
The aligned sequences output by th...
Timothy McPhillips
06:23 PM Bug #2251 (In Progress): Need to document how to use Kepler for phylogenetics
We need to write documentation for users of the phylogenetics actors in Kepler.
This documentation should include:
...
Timothy McPhillips
06:11 PM Bug #2250 (In Progress): Need documentation for collection-oriented workflow approach
We need to write documentation describing:
1. How the framework supporting collection-oriented workflows works.
2...
Timothy McPhillips
05:59 PM Bug #2249 (In Progress): Need to support a useful subset of PHYLIP (PHYlogeny Inference Package)
At present, actors wrap the following PHYLIP programs (but do not yet support
all features of these programs):
...
Timothy McPhillips
 

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