Activity
From 10/08/2005 to 11/06/2005
11/06/2005
- 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... - 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:
... - 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... - 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):
...
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 ...
11/04/2005
- 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 - 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... - 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 ... - 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...- 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... - 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... - 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... - 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...
11/03/2005
- 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 - 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... - 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. ... - 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 - 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... - 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 ...
11/02/2005
- 05:49 PM Bug #2171: Add support for missingValueCode in EML parser
- Adding dependency to null value handling bug.
- 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. - 05:46 PM Bug #2134: More advanced integration with R
- we should handle this after the 1.0.0 release.
- 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... - 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 ... - 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 ... - 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... - 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 ... - 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... - 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... - 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... - 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... - 05:09 PM Bug #2133: Need ability to update data searches
- This is related to the cache expiration bug.
- 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. ***
- 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 ... - 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. ***
- 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. ... - 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,... - 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... - 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... - 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. - 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... - 04:59 PM Bug #2117: mechanism for user to query for semantically compatible actors
- partially working, but UI needs lots of thought and work.
- 04:55 PM Bug #2112: add default data browse heirarchy
- Duplicate of bug #2031
*** This bug has been marked as a duplicate of 2031 *** - 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. ***
- 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... - 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... - 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 *** - 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... - 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... - 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.
- 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... - 04:33 PM Bug #2027: provide ability to assign checkpoints in the workflow
- Related to the provenance framework that Ilkay is developing.
- 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.
***... - 04:32 PM Bug #1340: define and implement kepler archive file format (kar)
- *** Bug 2025 has been marked as a duplicate of this bug. ***
- 12:46 PM Bug #1340: define and implement kepler archive file format (kar)
- Mostly complete. Cleaning up loose ends dealing with class loading.
- 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. ... - 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. ***
- 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"
- 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.
- 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 *** - 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 ... - 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... - 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.
- 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 ... - 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... - 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... - 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... - 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... - 01:35 PM Bug #2145: need ontology storage system
- This ontology storage system would be useful but will not make alpha8, so moving
target. - 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... - 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. - 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... - 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... - 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. - 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.
- 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... - 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 ... - 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... - 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... - 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. - 12:45 PM Bug #1882: Investigate UI Changes
- Partially complete. Need to post time estimates on the wiki.
- 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... - 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... - 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. - 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... - 12:35 PM Bug #1997: Support Getting Metadata for Darwin Core search result item
- Retargeting at kruland for alpha 8.
- 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. - 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... - 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... - 12:27 PM Bug #1751: new mailing lists: kepler-users, kepler-votes
- kepler-users and kepler-members now exist. Closing.
- 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... - 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. - 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... - 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. - 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... - 12:12 PM Bug #1885: Create new DataRelationsManager
- Obsoleted by Object Manager redesign. CLosing.
- 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 - 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 ... - 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... - 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. - 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. - 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. - 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...
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... - 02:34 PM Bug #2143: fix functionality and GUI issues with query builder
- *** Bug 2144 has been marked as a duplicate of this bug. ***
- 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 ***
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
- 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...
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... - 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 ...
10/17/2005
- 12:04 PM Bug #2231: Documentation system implementation
- Bug Also Assigned to : 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... - 12:02 PM Bug #2232: Website updates
- Nandita Mangal needs to work on it.
- 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... - 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... - 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... - 11:09 AM Bug #1908: GEON datasets wrappers
- done
- 11:09 AM Bug #1903: Wrappers to access ADN metadata
- done
- 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... - 11:08 AM Bug #1897: Remove unused geon specific components and jars
- done
- 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... - 11:06 AM Bug #2137: create a docbook format for WF documentation
- Included in the new bug.
- 10:52 AM Bug #1901: Documentation system
- Done items:
* Includes way to serialize docs for atomic and composite actors (and
directors, and utilities, etc)
... - 10:13 AM Bug #1904: Nimrod implementation and templates
- The Nimrod actors were checked into the Resurgence folder by Wibke Sudholt.
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...
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.
10/10/2005
- 03:08 PM Bug #2225 (In Progress): EML parser does not handle attribute list reference
- Currently, our eml parser in kepler couldn't handle attribute list reference.
And it couldn't handle entity referenc... - 03:03 PM Bug #2224 (Resolved): Annotation actor not working correctly from KAR file
- With the new .kar files for building the actor tree, the Annotation actor gives
a simple rectangle with dragged to t...
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