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From 10/11/2005 to 11/09/2005

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

11/05/2005

02:41 PM Bug #2248 (Resolved): Need to merge corresponding mutable and immutable subclasses of DomainObject
In alpha7, complex, domain-specific objects passed between actors in
collection-oriented workflows were implemented ...
Timothy McPhillips
11:19 PM Bug #2247: TRACKING: Popup Dialog Changes
This will also enable the removal of several soon-to-be-redundant options from
the right-click context menus
Matthew Brooke
11:15 PM Bug #2247 (In Progress): TRACKING: Popup Dialog Changes
Collect dialogs together in tabbed versions, per laura's designs.
dialog(s) in Kepler source quicker/easier; dialogs...
Matthew Brooke
11:14 PM Bug #2108: changes to simple search
1-3 done. Also added code to render the source and advanced search buttons when
we have the backend functionality to ...
Matthew Brooke
11:06 PM Bug #2246: TOOLBAR: status on opening workflows and blank frames

also need to go thru' all new toolbar icons and check colors are to spec;
graphic designer got mis-matches on some o...
Matthew Brooke
10:58 PM Bug #2246 (In Progress): TOOLBAR: status on opening workflows and blank frames
-- should be easy - replace existing gif images with Laura's new ones, and add
code to incorporate new icons for rol...
Matthew Brooke
10:56 PM Bug #2245 (In Progress): TRACKING: Batik SVG Rendering - remaining tasks
tasks remaining before Batik SVG rendering is ready for primetime:
1) ASSIGNING ICONS
Icons can be assigned in ac...
Matthew Brooke

11/04/2005

11:47 AM Bug #2243: bug in inverse distance interpolation in Grid Rescaling actor
Bug fixed with logic change in code for IDW interpolation. Smoothing near
NO_DATA edges could probably be improved, b...
Dan Higgins
09:22 AM Bug #2243 (Resolved): bug in inverse distance interpolation in Grid Rescaling actor
An attempt to smooth the IDW interpolation near NO_DATA edges of a grid has
resulted in errors in interpolation (tha...
Dan Higgins
08:19 PM Bug #2235: Search text-field only 1 character wide on Mac OS X
fixed by fixing part of bug #2108 - textfield is now on its own line, so no
buttons to squash it up
Matthew Brooke
05:13 PM Bug #2241: {de-}serialize semantic annotations to and from EML
I would like to contribute to this discussion/design/code. Another issue
concerns "flipping" between different outpu...
Shawn Bowers

11/03/2005

12:18 PM Bug #2242 (Resolved): move metacat ecogrid service to new host
Current metacat ecogrid node is hosted on ecoinfo2. This needs to be moved to
the new metacat on knb.msi.ucsb.edu. ...
Matt Jones
12:04 PM Bug #2056: Port labels appear 'twice' when DataSource actor added
As of 11/3/2005, this problem still occurs for me on a windows OS
Dan Higgins
Dan Higgins
09:40 AM Bug #1909: generalize cache manager to provide support for very large data files
Java GIS actors have capability for handling very large files (i.e. no need for
very large grids to be in RAM, althou...
Dan Higgins
09:37 AM Bug #1913: Problem running workflow after it is saved
Kepler code has changed greatly since this bug was entered and bug can no longer
be replicated. Removed as no longer ...
Dan Higgins
05:49 PM Bug #2171: Add support for missingValueCode in EML parser
Adding dependency to null value handling bug. Matt Jones
05:46 PM Bug #2134: More advanced integration with R
we should handle this after the 1.0.0 release. Matt Jones
05:43 PM Bug #2241: {de-}serialize semantic annotations to and from EML
We may also want to consider what information from EML should be exposed as
annotations on the EML data source. Much...
Matt Jones
05:42 PM Bug #2241 (In Progress): {de-}serialize semantic annotations to and from EML
EML200DataSource actors can currently be annotated on the canvas with semantic
annotations. This essentially marks ...
Matt Jones
05:37 PM Bug #2240 (Resolved): add support for null values to data passing among ports
Currently ptolemy and kepler do not support passing null values (sometimes
called missing values) among ports, even ...
Matt Jones
05:19 PM Bug #2233: Name duplication exception with KAR files
Or alternatively detect the name collision and rename one of the files when it
is imported. There is nothing special...
Matt Jones
05:17 PM Bug #2239: Second copy of datasource fails on reload of workflow
This could either be a cache/object manager problem, or a problem in the data
source actors (eg EML200DataSource) or ...
Matt Jones
05:15 PM Bug #2150: 'Edit Custom Icon' menu item doesn't work
Probably should remove it as we are moving to custom SVG icons for everything.
Maybe we should allow the user to choo...
Matt Jones
05:14 PM Bug #2146: Design and implement authentication system for kepler
Decided to use GAMA and X.509 GSI proxy certificates. Design is on the wiki here:
http://kepler-project.org/Wiki.js...
Matt Jones
05:12 PM Bug #2139: mollusc -> R -> plot WF for examples and documentation uses
The mollus workflow that uses GCE mollusc data and then plots it in R could be
expanded to be a bit more realistic, a...
Matt Jones
05:09 PM Bug #2133: Need ability to update data searches
This is related to the cache expiration bug. Matt Jones
05:08 PM Bug #2031: browse/filter for data and data nodes on the ecogrid and local
*** Bug 2124 has been marked as a duplicate of this bug. *** Matt Jones
04:56 PM Bug #2031: browse/filter for data and data nodes on the ecogrid and local
text from bug #2112:
In the data tab/pane, add/display a default dat browse heirarchy (similar to
component browse ...
Matt Jones
04:55 PM Bug #2031: browse/filter for data and data nodes on the ecogrid and local
*** Bug 2112 has been marked as a duplicate of this bug. *** Matt Jones
04:41 PM Bug #2031: browse/filter for data and data nodes on the ecogrid and local
Request not specificed in enough detail. EcoGrid nodes can already be obtained
via searching in the Sources dialog. ...
Matt Jones
05:08 PM Bug #2124: provide mechanism for user to see available nodes on ecogrid
Already possible through the data sources tab. Beyond this sort of a node
listing we can really only do data browse,...
Matt Jones
05:06 PM Bug #2123: need a way to uniquely identify actor in a workflow and locate it
How this would work is not clear. Is the ID the LSID? If so, it may not be the
best to expose. Also, we need to di...
Matt Jones
05:03 PM Bug #2121: add features to support structural incompatibility
Portions of this are already implemented (e.g., validation), although i don't
think the transformation stuff will nec...
Matt Jones
05:02 PM Bug #2120: add visual indicators for non-annotated ports
This may clutter the interface. Need some proposals to evaluate for how to do
this before we decide to do it.
Matt Jones
05:00 PM Bug #2118: allow users to create units based on units in current ontology
Also need to consider how to link EML-defined units from the EML unit dictionary
to the ontological units and the pto...
Matt Jones
04:59 PM Bug #2117: mechanism for user to query for semantically compatible actors
partially working, but UI needs lots of thought and work. Matt Jones
04:55 PM Bug #2112: add default data browse heirarchy
Duplicate of bug #2031
*** This bug has been marked as a duplicate of 2031 ***
Matt Jones
04:52 PM Bug #2028: provide ability to easily visualize data at various places in workflow
*** Bug 2111 has been marked as a duplicate of this bug. *** Matt Jones
04:51 PM Bug #2028: provide ability to easily visualize data at various places in workflow
Additional info from bug #2111, which is a duplicate of this one.
Add "view data" capability (and menu item) for dat...
Matt Jones
04:36 PM Bug #2028: provide ability to easily visualize data at various places in workflow
The data source actors (EMLDataSource, DiGIRDataSource, ADNDataSOurce, etc,
should all have the capability to pull up...
Matt Jones
04:52 PM Bug #2111: Add "view data" capability for data sources
Text added to earlier bug report.
*** This bug has been marked as a duplicate of 2028 ***
Matt Jones
04:47 PM Bug #2105: add taxon concept search for data
Partially complete. Rob Gales has several TOS actors in place. Need to
integrate these with the left hand data sear...
Matt Jones
04:45 PM Bug #2089: Problem with docs source code with Java 1.5
Need to remove the taglet dependencies fromthe tree as we decided not to use
this functionality and instead but the c...
Matt Jones
04:43 PM Bug #2035: use checkboxes and radio buttons correctly
I'm pretty sure this works now. Need to test and close the bug if so. Matt Jones
04:38 PM Bug #2029: consider guided analysis wizard
Its really not clear if this is possible in the general case. We may be able to
do something for specific cases. Bu...
Matt Jones
04:33 PM Bug #2027: provide ability to assign checkpoints in the workflow
Related to the provenance framework that Ilkay is developing. Matt Jones
04:32 PM Bug #1340: define and implement kepler archive file format (kar)
*** Bug 2025 has been marked as a duplicate of this bug. *** Matt Jones
04:32 PM Bug #2025: provide workflow and results in some publishable format
This is the kepler archive format. It is partially working. Marking this bug
as a duplicate of that bug #1340.
***...
Matt Jones
04:31 PM Bug #2014: Disallow editing of the schema for data
Data source schemas are immuatable, so editing shouldbe disabled. However, its
not clear what is meant by this bug. ...
Matt Jones
04:21 PM Bug #1906: Add reset/cancel button(s) for search in actor panel
*** Bug 2010 has been marked as a duplicate of this bug. *** Matt Jones
04:21 PM Bug #2010: Provide Clear/Reset for Search
Dupliace of bug#1906. Fixed as "Stop' in data pane.
*** This bug has been marked as a duplicate of 1906 ***
Matt Jones

11/02/2005

01:54 PM Bug #1923: Develop ontologies; engage KR group
Madin hired in postdoc KR position to lead the charge on this ontology
development. Aim for at least an initial set ...
Matt Jones
01:51 PM Bug #1922: Develop strategies for GUI extenstions for the semantics stuff
Its not clear that there are any deliverables for this bug. It is more a
meta-level design bug. Maybe bowers can cl...
Matt Jones
01:48 PM Bug #1921: Define the Kepler GUI components required for semantic mediation in Kepler
This is an overall tracking bug for kepler semantic UI issues. Matt Jones
01:47 PM Bug #1919: choose language for semantic annotations in kepler archives
Probably complete. Need bowers to document the choices and verify that it
works, provide developer documentation in ...
Matt Jones
01:45 PM Bug #1918: Search based on the semantic annotation of an actor's port
prototype partially working but needs significant work on integrating with the
kepler UI so that the search can be co...
Matt Jones
01:43 PM Bug #1917: Design and implement workflow semantic type check.
Possibly complete except for UI redesign issues. Check with bowers and test.
Create a new bug for the UI redesign t...
Matt Jones
01:41 PM Bug #1915: Define a published interface for a semantic search service
Not clear on status of this. Originally intended to allow both Kepler and
non-kepler uses of the semantic search ser...
Matt Jones
01:40 PM Bug #2234: creating KAR file loses port semantic annotations
THis probably involves cloning more than just annotaitons -- need to verify that
the clone in both directions puts al...
Matt Jones
01:35 PM Bug #2145: need ontology storage system
This ontology storage system would be useful but will not make alpha8, so moving
target.
Matt Jones
01:32 PM Bug #2143: fix functionality and GUI issues with query builder
Query builder needs to be simplified and tested, making sure that all advertised
features work reliably for the alpha...
Matt Jones
01:31 PM Bug #2142: new schema for data sources
Not clear why this is needed. Moving to the post-1.0.0 target until the need
and approach can be clarified.
Matt Jones
01:30 PM Bug #2141: resultset cache expiration problem
This has still not been resolved. Reassigning to kruland. Cache expiration
policies should be settable for each type...
Matt Jones
01:28 PM Bug #1906: Add reset/cancel button(s) for search in actor panel
Cancel Button is already implemented. But it renamed as "Stop" Jing Tao
11:52 AM Bug #1906: Add reset/cancel button(s) for search in actor panel
Fixed at alpha5 release. Will not add cancle button at this time. Closing bug. Matt Jones
01:25 PM Bug #2230: EML actor doesn't handle footer line in data file
Once footer lines are supported, test and close this bug. This is needed for
some of the data files inthe SEEK biodi...
Matt Jones
01:24 PM Bug #2225: EML parser does not handle attribute list reference
I believe the parser has been fixed to now properly follow references in EML.
Test and close this bug if true.
Matt Jones
01:22 PM Bug #2171: Add support for missingValueCode in EML parser
This also depends on being able to handle the NULL values as well, which will be
entered as a separate bug.
Matt Jones
01:21 PM Bug #2056: Port labels appear 'twice' when DataSource actor added
Seems to be fixed. Test and close the bug if no sign of it. Matt Jones
01:01 PM Bug #1909: generalize cache manager to provide support for very large data files
This needs to be added as general support in the cache manager. Data files can
frequently be tens to hundreds of meg...
Matt Jones
01:00 PM Bug #2239 (Resolved): Second copy of datasource fails on reload of workflow
If there are 2 copies of an eml datasource in a workflow, then one will fail to
open (stays red) when a saved versio...
Dan Higgins
12:57 PM Bug #1899: Implementation of grid-enabling kepler
Its not clear whether grid-execution can be implemented by alpha8 -- probably
not. So I'm leaving it in the list for ...
Matt Jones
12:55 PM Bug #1891: writedesign for staged implementation of grid-enabled kepler
Several ideas have been proposed and fleshed out on the wiki. Need to
consolidate and decide on a course for impleme...
Matt Jones
12:51 PM Bug #1895: remote actor repository
Initial experimentation with using EcoGrid for remote repository is successful.
Need to try to deploy at least one E...
Matt Jones
12:48 PM Bug #1548: consolidating data access user interfaces
put/get should be implemented for 1.0.0, but the fully unified data access
interface will not be, so changing milestone.
Matt Jones
12:46 PM Bug #1340: define and implement kepler archive file format (kar)
Mostly complete. Cleaning up loose ends dealing with class loading. Matt Jones
12:45 PM Bug #1882: Investigate UI Changes
Partially complete. Need to post time estimates on the wiki. Matt Jones
12:43 PM Bug #1888: changes to data access system to incorporate geon data
At least some GEON data is now accessible. Need to refactor for the new changes
to the EcoGrid web service interface...
Matt Jones
12:42 PM Bug #1851: save atomic and composite actors in the new actor library
The mechanism for saving actors in the library has now changed. However, the
problem with saving composite actors is...
Matt Jones
12:38 PM Bug #1587: Define and implement EcoGrid "dataQuery" method
Still need these data queries, but will be done after the 1.0.0 release is
finalized.
Matt Jones
12:37 PM Bug #1334: need installer for kepler
Final installer for 1.0.0 should resolve size issues, partially by excluding
many actors that might be distributed th...
Matt Jones
12:35 PM Bug #1997: Support Getting Metadata for Darwin Core search result item
Retargeting at kruland for alpha 8. Matt Jones
12:34 PM Bug #1913: Problem running workflow after it is saved
Not nearly enogh details to replicate this problem. Postponing until details to
replicate are posted here.
Matt Jones
12:33 PM Bug #1898: Redesign the web service harvester and create design documentation
The web service harvester should probably become part of the left hand pane to
allow for a user to choose a UDDI (etc...
Matt Jones
12:31 PM Bug #1872: kepler possibly not picking up changes as entered
Need to be able to replicate this before it can be fixed. Will try to replicate
during the test period before the be...
Matt Jones
12:27 PM Bug #1751: new mailing lists: kepler-users, kepler-votes
kepler-users and kepler-members now exist. Closing. Matt Jones
12:25 PM Bug #1883: Add LSID to Cache Manager
This is mostly accomplished. The object manager uses LSIDs to identifiy cache
items. Some refactoring is being cons...
Matt Jones
12:22 PM Bug #1839: adding new port sometimes causes canvas to resize
This is probably a ptolemy layout issue. We should deal with it if we can, but
it shouldn't hold up the 1.0.0 release.
Matt Jones
12:21 PM Bug #1750: Allow KAR files to include jar/class files
We have now decided to only include initial actor loading in this feature.
Reloading, and version and class name con...
Matt Jones
12:18 PM Bug #1655: DIALOGS: Implement New UI for Sources Dialog (was "integrate ecogrid registry into kepler ecogrid client")
Need to rework registry dialogs according to Laura's redesign. Base
functionality works as far as I know.
Matt Jones
12:16 PM Bug #2043: create suite of common statistical actors using R
Lets attempt to get at least a handful of R statistical actors created that can
be reused. Madin can probably handle...
Matt Jones
12:12 PM Bug #1885: Create new DataRelationsManager
Obsoleted by Object Manager redesign. CLosing. Matt Jones
12:09 PM Bug #1881: Add intermediate pane to Query Builder
Need to work out overall how to restructure the Query Builder. See related
problems reported in bug #2143
Matt Jones
12:06 PM Bug #1836: data search and access problems via ecogrid
This bug is related to Bug # 2174 in SEEK Bugzilla which describes details of
problems with mutliple datasources.
A ...
Dan Higgins
11:48 AM Bug #1836: data search and access problems via ecogrid
Initial fixes introduced using the Factory method to fix some of these issues.
Need to verify that they work, and ada...
Matt Jones
12:04 PM Bug #1338: find GIS system for inclusion in kepler
Java, GRASS and GDAL actors have been incorporated for common GIS functions.
CLosing bug.
Matt Jones
11:53 AM Bug #1907: New ports don't draw when added dynamically
This bug has been fised by use of a MomlChangeRequest to force the redraw.
Closing bug.
Matt Jones
11:50 AM Bug #1893: Investigate Collapsing Data and Actor Tabs
Decision was to not collapse these tabs because the distinction was a valuable
one to target scientists.
Matt Jones
11:33 AM Bug #1914: Implement the 'most recently used' concept for workflows and actors
Some software presents a list of 'recently opened' documents. That list is added
to (usually the File menu) so that i...
Dan Higgins

11/01/2005

02:35 PM Bug #2143: fix functionality and GUI issues with query builder
Issues submitted by Efrat Frank regarding Query Builder in Kepler.
--------------------
1. No conversion available f...
Matt Jones
02:34 PM Bug #2143: fix functionality and GUI issues with query builder
*** Bug 2144 has been marked as a duplicate of this bug. *** Matt Jones
02:34 PM Bug #2144: fix functionality and GUI issues with query builder
Duplicate, mistakenly entered.
*** This bug has been marked as a duplicate of 2143 ***
Matt Jones

10/25/2005

03:48 PM Bug #2235: Search text-field only 1 character wide on Mac OS X
Screenshot showing the truncated search text field on OS X Matthew Brooke
03:41 PM Bug #2235 (Resolved): Search text-field only 1 character wide on Mac OS X
On the left-hand side of the Kelper UI, the text field in which the user types
search terms is only 1 character wide...
Matthew Brooke

10/19/2005

03:37 PM Bug #2234 (Resolved): creating KAR file loses port semantic annotations
I created an R actor on the canvas, annotated it and its ports with terms from
the ontologies, and then saved the ac...
Matt Jones
03:07 PM Bug #2233 (Resolved): Name duplication exception with KAR files
The new kar system throws a name duplication exception when two kars
implemented by (perhaps completely) different ...
Efrat Jaeger

10/17/2005

12:04 PM Bug #2231: Documentation system implementation
Bug Also Assigned to : Nandita Mangal Nandita Mangal
10:58 AM Bug #2231 (Resolved): Documentation system implementation
-- How-to manuals chapters for specific computational tasks (patterns of use)
(for example, how to do iteration in a...
Ilkay Altintas
12:02 PM Bug #2232: Website updates
Nandita Mangal needs to work on it. Nandita Mangal
11:03 AM Bug #2232 (Resolved): Website updates
-- The webpages have a few different links to installation manuals. We need to
incorporate these under one unique te...
Ilkay Altintas
11:15 AM Bug #1888: changes to data access system to incorporate geon data
Need to cache the db schema.
Still need to decide within the GEON project what to do with Web services
components.
M...
Efrat Jaeger
11:10 AM Bug #1898: Redesign the web service harvester and create design documentation
We need to discuss next week what harvesting web services mean for Kepler in the
new kar-based architecture. Then thi...
Ilkay Altintas
11:09 AM Bug #1908: GEON datasets wrappers
done Efrat Jaeger
11:09 AM Bug #1903: Wrappers to access ADN metadata
done Efrat Jaeger
11:08 AM Bug #1892: Design an interface to optionally log inputs, parameters and intermediate results
This was included in the provenance framework. The desig is at
http://kepler-project.org/Wiki.jsp?page=KeplerProvenan...
Ilkay Altintas
11:08 AM Bug #1897: Remove unused geon specific components and jars
done Efrat Jaeger
11:06 AM Bug #1890: Add query builder to generic db actor
Query builder is now available through the the generic db query actor.
Still need to find out how to to access MS Acc...
Efrat Jaeger
11:06 AM Bug #2137: create a docbook format for WF documentation
Included in the new bug. Ilkay Altintas
10:52 AM Bug #1901: Documentation system
Done items:
* Includes way to serialize docs for atomic and composite actors (and
directors, and utilities, etc)
...
Ilkay Altintas
10:13 AM Bug #1904: Nimrod implementation and templates
The Nimrod actors were checked into the Resurgence folder by Wibke Sudholt. Ilkay Altintas

10/13/2005

10:45 AM Bug #2230 (In Progress): EML actor doesn't handle footer line in data file
Currently our delimiter reader only handle head line number and doesn't handle
foot line in data file. We need to su...
Jing Tao

10/11/2005

09:37 AM Bug #2224: Annotation actor not working correctly from KAR file
fixed configuration information for Annotation and Documentation actors to
correct values.
Dan Higgins
 

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