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From 05/24/2009 to 06/22/2009

06/23/2009

06:13 PM Bug #4138: Workflow Run Manager - search cell edit focus isn't lost appropriately
This was partially fixed with r19403. Cell editors that extend DefaultCellEditor still have the problem. Derik Barseghian
05:46 PM Bug #4174: Actor library not building correctly
Not sure if the problem is still "actor library not building correctly" but I'm not seeing components in the tree in ... Derik Barseghian
05:37 PM Bug #4179: ant jar does not include configs/
Here is the code from line 106:
dirs.add( module.getTargetClasses() );
dirs.add( module.getSrc() );
...
Jing Tao
05:34 PM Bug #4179 (Resolved): ant jar does not include configs/
The jars produced by 'ant jar' do not include any of the files in configs/. Daniel Crawl
05:19 PM Bug #4170: Ensure reporting/provenance do not rely on any GUI classes
as far as reporting is concerned, this is done. need to make sure the -nogui ("withcache") run is working. ben leinfelder

06/22/2009

04:31 PM Bug #4122: File -> Save As does not assign new LSID
Save as now assigns a new LSID. Aaron Aaron
04:21 PM Bug #3996: Report Model - [de]serialize Items of Interest
closing this - not needed since we are using the Outline viewer as a source for items of interest ben leinfelder
03:58 PM Bug #3994: Report Designer - use "workflow outline" rather than Items of Interest
now the top portion of the ItemsOfInterestPanel [re]uses the workflow outline view of the workflow contents. you can ... ben leinfelder
03:44 PM Bug #4149: Workflow Run Manager - Export Runs feature
The problem in comment #2 was fixed some time ago. Derik Barseghian
01:42 PM Bug #4170: Ensure reporting/provenance do not rely on any GUI classes
ReportingListener is now added to the MOML model by the Initializer if not already present.
Once the model is saved (...
ben leinfelder
12:23 PM Bug #4178 (Resolved): error handling with MoMLCommandLineApplication
It would be nice if MoMLCommandLineApplication called Manager.run() instead of execute() so that any execution listen... Daniel Crawl

06/20/2009

09:39 PM Bug #3994: Report Designer - use "workflow outline" rather than Items of Interest
This is now a viable source for ports AND parameters.
I'd like to use it as the sole source for Dynamic Report Items.
ben leinfelder
08:17 PM Bug #3994: Report Designer - use "workflow outline" rather than Items of Interest
I've modified the designer panel to allow it to accept dragged objects (NamedObjs) from the outline view.
This is a m...
ben leinfelder
09:27 PM Bug #4177: WRP - look up Parameter values from Provenance
added a method to provenance to look up the type (port/parameter/etc).
using that to decide where/how to retrieve the...
ben leinfelder
08:31 PM Bug #4177 (Resolved): WRP - look up Parameter values from Provenance
Turns out Parameter values are stored differently than the tokens that are passed among actors.
Will need to augment...
ben leinfelder
07:24 PM Bug #2493: actor repository tracking bug
this isn't just for Actors - this is for Workflows. Just want to make sure we're all keeping that in mind.
The same "...
ben leinfelder
05:57 PM Bug #4036: WRM - connect to configurable provenance store
the config dialog is not being shown now - so we don't really need to worry too much about this [for SANParks].
I'm g...
ben leinfelder
05:54 PM Bug #4164: Associated Data - wf_exec_id behavior
I'm unable to get this bug to occur today...but Dan was seeing it today. Derik Barseghian
05:02 PM Bug #4164: Associated Data - wf_exec_id behavior
Examples showing weird behavior of selects on associated_data table Derik Barseghian
05:54 PM Bug #4176 (Resolved): Report Designer - opening KAR omits title
When I:
-design a report layout and "Export to KAR"
-close Kepler
-run Kepler
-open the kar "Open KAR"
I get mos...
ben leinfelder

06/19/2009

04:56 PM Bug #3992: Report Designer - finalize Report item properties
augmented the style sheet (XSLT) to handle some Item Properties:
handle:
-new subclasses of StaticReportItem (HR)
-It...
ben leinfelder
03:53 PM Bug #3992: Report Designer - finalize Report item properties
all static report items currently have: HEIGHT and WIDTH properties.
HR Items have only WIDTH.
more to come...
ben leinfelder
03:52 PM Bug #3992: Report Designer - finalize Report item properties
doing some work on this ben leinfelder
12:42 PM Bug #4160: EML - Dynamic data retrieval
Jim has this working in the riverflow tpc.
And I've recently made the "check for latest" feature of EML work as it ne...
ben leinfelder
05:15 PM Bug #4160: EML - Dynamic data retrieval
looks like we got this going in terms of getting the existing tables.
next up: check for latest revision!
ben leinfelder
12:41 PM Bug #3672: Open/Save Workflow as KAR Archive
related to other bug that is slightly reporting-specific.
same functionality, however
ben leinfelder
12:18 PM Bug #3999: WRP - create event-driven states for Kepler
using this to update the Report Viewer when the view is selected. Also alerts the Report View TOC of a report instanc... ben leinfelder
12:15 PM Bug #4172: Use DEV server for registry in the WRP suite
WRP is pointing to dev for:
registry
authentication
repository
ben leinfelder
12:07 PM Bug #4175: EML - Verify check latest revision
tested with the attached workflow - i'm happy with this. ben leinfelder
12:05 PM Bug #4175: EML - Verify check latest revision
NOTE: in order for this to function properly, it must be run in the WRP suite of kepler that currently points to the ... ben leinfelder
12:02 PM Bug #4175: EML - Verify check latest revision
When the EML actor initializes, it will check for the latest and get the latest if the checkbox is selected.
When a W...
ben leinfelder
09:13 AM Bug #4175 (Resolved): EML - Verify check latest revision
Need to make sure this is working correctly when a WF is [re]opened and run.
It needs to pull in any new (or deleted...
ben leinfelder
09:34 AM Bug #4174: Actor library not building correctly
It has been verified that this fix worked and the Components are showing up again in the actor library. Aaron Aaron
11:36 PM Bug #4174: Actor library not building correctly
It seems that the tagging module is overriding the ontologies. It just so happens that the kepler-component.owl file... Aaron Aaron
09:19 PM Bug #4174 (Resolved): Actor library not building correctly
Many of the actors are not appearing in the actor library when using the WRP suite. No visible errors are given... Aaron Aaron
06:11 PM Bug #4122: File -> Save As does not assign new LSID
We need this to be fixed for the SANParks release...I think this will be pretty confusing for the user. Derik Barseghian
05:11 PM Bug #4151: exported RIO and ROML doc run-pairs have same KeplerLSID
I've prepended the workflow name to the ROML.xml entry that is generated.
While it's non-unique, perhaps it's the fir...
ben leinfelder

06/18/2009

04:58 PM Bug #4151: exported RIO and ROML doc run-pairs have same KeplerLSID
Okay - that makes more sense: same kar entry name (ROML.xml) but different LSIDs
That'll definitely need to be addres...
ben leinfelder
11:57 AM Bug #4151: exported RIO and ROML doc run-pairs have same KeplerLSID
I thought that too; not aware of any changes to that code.
I think this problem only occurs when you're trying to ex...
Derik Barseghian
11:50 AM Bug #4151: exported RIO and ROML doc run-pairs have same KeplerLSID
i thought we made it so that if they had the same LSID and the same name, we'd only include the last one that was add... ben leinfelder
11:23 AM Bug #4151: exported RIO and ROML doc run-pairs have same KeplerLSID
This breaks the ability to export more than one run, since each run will have a ROML.xml, and an error about duplicat... Derik Barseghian
08:58 AM Bug #4151: exported RIO and ROML doc run-pairs have same KeplerLSID
for the time being, both ROMLs will be included. ben leinfelder
01:54 PM Bug #4172: Use DEV server for registry in the WRP suite
http://dev.nceas.ucsb.edu/registry/services/RegistryService is now providing services that point to DEV (not producti... ben leinfelder
01:28 PM Bug #4172: Use DEV server for registry in the WRP suite
The servers are set up and ready to go.
I'm currently updating the registry entries so that we point to the correct ...
ben leinfelder
01:26 PM Bug #4172 (Resolved): Use DEV server for registry in the WRP suite
For testing and training it will be very useful to have dev.nceas.ucsb.edu and kepler-dev.nceas.ucsb.edu set up as ou... ben leinfelder
01:16 PM Bug #4171: dragging actor to canvas then back to component tree area gives NPE
It looks like this bug is specific to the wrp suite; I don't get it in the kepler trunk or the workflow-run-manager m... Derik Barseghian
01:00 PM Bug #4171: dragging actor to canvas then back to component tree area gives NPE
I can't reproduce this in Ptolemy or Kepler on the Mac under Java 1.5.0_19.
What platform and version of Java are you...
Christopher Brooks
12:03 PM Bug #4171 (Resolved): dragging actor to canvas then back to component tree area gives NPE
I'm getting an NPE when I drag a component out to canvas, don't drop, and then drag it back over the component tree a... Derik Barseghian
12:22 PM Bug #4164: Associated Data - wf_exec_id behavior
I'm looking into this... Derik Barseghian
06:36 PM Bug #4164: Associated Data - wf_exec_id behavior
I'm still seeing this in wrp, even after a full clean. It seems to consistently begin happening on the third instance... Derik Barseghian
11:38 AM Bug #4020: WRP - create WorkflowRun object to encapsulate provenance/report instances
So to have an example all in one place, this is what an example workflow-run moml metadata doc. If everyone (e.g. mik... Derik Barseghian
11:11 AM Bug #4161: Develop kepler workflow execution engine
In the client-side GUI version of Kepler we open/run workflows and reports like so:
1-Open KAR (contains the workflow...
ben leinfelder
09:08 AM Bug #4161: Develop kepler workflow execution engine
After discussion with Jing and Derik yesterday:
1-we need to make sure we have a server-side version of Kepler that i...
ben leinfelder
10:56 AM Bug #2493: actor repository tracking bug
I started working on this yesterday. I found major problems with how lsids are assigned when uploading to the reposi... Chad Berkley
07:00 PM Bug #2493: actor repository tracking bug
I'm starting to upload KARs, sets of metadata docs that point at them (workflows and workflow runs) and sets of acces... Derik Barseghian
10:41 AM Bug #4169: Build "server-side" installation of Kepler
Jing and I are working on figuring out how to deploy kepler for the webservice. The jars for kepler can easily be cr... Chad Berkley
10:18 AM Bug #4169 (Resolved): Build "server-side" installation of Kepler
Sounds like the Kepler webservice uses a snapshot (jar?) of Kepler to execute workflows via the webservice.
For sanp...
ben leinfelder
10:40 AM Bug #4021: KAREntry Handler
We have the following KAREntryHandlers:
-ActorMetadata (for workflows/momls)
-ReportLayout (for ROML)
-ReportInstance...
ben leinfelder
10:28 AM Bug #4170 (Resolved): Ensure reporting/provenance do not rely on any GUI classes
I'm not entirely sure how much of the "GUI" code is ever called when we execute a workflow fromthe command line. But ... ben leinfelder
09:49 AM Bug #4168 (New): User documentation creates bloat in workflows
Currently, the user documentation is copied into every actor instance as the actor is drug to the canvas. The proble... Chad Berkley
09:11 AM Bug #4163: erroneous hsql database creation
retargeting - be good if this was resolved.
I'm also thinking we should change the default provenance store to use th...
ben leinfelder
08:38 AM Bug #4160: EML - Dynamic data retrieval
testing this new output format with R actor downstream - looks promising, but deferring to Jim's R expertise to get t... ben leinfelder
07:10 PM Bug #3898: update .kepler instead of removing it between versions
Progress on this bug. The InstanceAuthNamespace is kept at the project root. A configuration directory is now creat... Aaron Aaron

06/17/2009

12:37 PM Bug #4160: EML - Dynamic data retrieval
new data output format emits information about each datatable (including the pointer to the cache file).
This allows ...
ben leinfelder

06/16/2009

04:10 PM Bug #4164: Associated Data - wf_exec_id behavior
Also once it starts happening, it seems to happen every time, even new kepler instances. Derik Barseghian
04:07 PM Bug #4164: Associated Data - wf_exec_id behavior
This is what I did, twice, to the same effect, but if it's a race condition I wouldn't be surprised if it was just co... Derik Barseghian
03:53 PM Bug #4164: Associated Data - wf_exec_id behavior
I'm seeing this issue again, reopening. Derik Barseghian
12:13 PM Bug #4164: Associated Data - wf_exec_id behavior
i'm not finding this as a problem - changed a bunch of stuff with how files are written and it seems to be happy now.... ben leinfelder
07:44 PM Bug #4164 (Resolved): Associated Data - wf_exec_id behavior
Derik and I are running into a rather odd problem when querying the ASSOCIATED_DATA table for records. It appears tha... ben leinfelder
03:25 PM Bug #4161: Develop kepler workflow execution engine
Here is matt's comment:
<matt> hey jing
<matt> i saw your bugzilla note about retrieving KAR files by LSID
<jing> hi,...
Jing Tao
03:11 PM Bug #4161: Develop kepler workflow execution engine
Of course, adding metacatID is a short term solution. Jing Tao
03:09 PM Bug #4161: Develop kepler workflow execution engine
In execute(workflowID) method, we need to get the kar file from metacat first.
To my understanding. The workflowID w...
Jing Tao
06:38 PM Bug #4163: erroneous hsql database creation
I should also mention that I also see the same four files where I would expect to see them, in C:\Documents and Setti... Aaron Aaron
06:34 PM Bug #4163 (Resolved): erroneous hsql database creation
When I run the wrp suite on my windows machine a new directory appears inside of the wrp module directory called "Doc... Aaron Aaron

06/15/2009

04:23 PM Bug #4147: Error message with selectable text
It turns out that this fix causes the dialogs to be very wide because
the JTextArea is one line, whereas JLabel wraps...
Christopher Brooks
04:15 PM Bug #3801: open dialog, common places pane has white box instead of text
Assigning this to myself. Christopher Brooks
04:15 PM Bug #3801: open dialog, common places pane has white box instead of text
I'm reopening this bug, there are problems with the code under:
* Windows Server 2003 via Windows Remote Desktop. Ja...
Christopher Brooks
03:53 PM Bug #4162 (New): using the alt key makes menus appear in strange places on OSX
if you do alt-F or alt-E on the mac, the menu shows up on the application window instead of coming down from the menu... Chad Berkley
03:15 PM Bug #4103: Add the capability of creating SECTIONS in the report.
Yes, you are correct, it was identified as a high priority for the first release. In addition, this bug is being work... debi staggs
01:57 PM Bug #4103: Add the capability of creating SECTIONS in the report.
i believe this was identified as a high priority for 2a1. we can retarget if i was mistaken ben leinfelder
03:06 PM Bug #4161 (Resolved): Develop kepler workflow execution engine
Here is the an email from matt:
I think the next stage would be to have you work on
putting together an execution...
Jing Tao
03:04 PM Bug #3672: Open/Save Workflow as KAR Archive
we absolutely need to Save and Open KARs that contain:
-1 workflow (MOML)
-1 report layout (ROML)
ben leinfelder
03:01 PM Bug #3649: determine if Provenance has everything needed by Reporting
we do have all the file artifacts being inserted.
I note the comment about provenance storing things from plotting ac...
ben leinfelder
03:01 PM Bug #4149: Workflow Run Manager - Export Runs feature
Exporting runs where reporting has been used is now broken. I don't know why yet. I get this error:
java.lang.NullPo...
Derik Barseghian
01:28 PM Bug #4149: Workflow Run Manager - Export Runs feature
perhaps split this bug into two - one for the very near 2a1 release and another for the full-REAP/2.0 version? ben leinfelder
03:00 PM Bug #4151: exported RIO and ROML doc run-pairs have same KeplerLSID
In the case where I don't do anything with reporting, I get ROML.xml and ROML.N.xml files. The files are identical an... Derik Barseghian
02:54 PM Bug #3936: Report Viewer - handle Image items
we are able to serialize to the XML file - even better! ben leinfelder
02:48 PM Bug #4160 (Resolved): EML - Dynamic data retrieval
The existing EML actor is able to get the latest revision of a datapackage.
We need to augment EML data access and a...
ben leinfelder
02:30 PM Bug #3992: Report Designer - finalize Report item properties
Some recommendations for 2a1:
Images:
-height/width
-scale-to-fit (either)
HR:
-width
-weight
Labels:
-N/S/E/W
-re...
ben leinfelder
02:28 PM Bug #3957: Report Designer - remove items of interest from the list
leave out of 2a1 - not needed if we use Outline view for the designer ben leinfelder
02:10 PM Bug #3942: Report Designer - add/edit item labels
we definitely need labels for the items ben leinfelder
02:01 PM Bug #4102: Add the ability to insert a static image into the report.
i believe this was also identified as important for the training ben leinfelder
01:56 PM Bug #3994: Report Designer - use "workflow outline" rather than Items of Interest
i'm going to push that this be the approach we take for the 2a1 release. ben leinfelder
01:51 PM Bug #3638: Report design features, Stage 2
The ability to add a section header has already been added. Still need to incorporate them into the report model and... debi staggs
01:40 PM Bug #3638: Report design features, Stage 2
I believe section headers are a must for this 2a1 release.
Headers and footers are more or less already there (the co...
ben leinfelder
01:42 PM Bug #4159 (Resolved): Cut 2.0-alpha/SanParks release
Tasks:
* Cut the release (tag)
* Create installers for mac, windows, linux
* test all 2.0-alpha targeted functi...
Chad Berkley
01:36 PM Bug #3635: Create ReportItem Type Hierarchy
not a 2a1-critical bug. leaving in sanparks release ben leinfelder
01:35 PM Bug #3632: TPC exceedence notification feature
for 2a1 release - we'll be using a "special" report item that will identify a TPC as being Normal or Exceeded. This n... ben leinfelder
01:33 PM Bug #3996: Report Model - [de]serialize Items of Interest
still advocating for shifting our efforts toward an Outline-view-based approach to items of interest.
Leaving this ou...
ben leinfelder
01:32 PM Bug #3995: Report Model - [de]serialize Report Item properties
item properties are being handled as expected ben leinfelder
01:31 PM Bug #4000: WRP - upload PRAs to repository
this overlaps with the KAR upload. almost entirely. maybe even entirely ben leinfelder
01:26 PM Bug #4148: Workflow Run Manager - Upload to Repository feature
crucial for the 2a1 release ben leinfelder
01:25 PM Bug #4036: WRM - connect to configurable provenance store
retarget for release. sounds as though it can be closed [soon]. ben leinfelder
11:37 AM Bug #4144: Workflow Run Manager - moving columns / new windows bug
Fixed in r19238. Refactored to rely on natural jtable mechanisms for tracking movement. Derik Barseghian
11:21 AM Bug #4101: Report Designer - Create a manager class for the Static Report Items
The manager class has been added, though it is likely to need to need additional enhancements. The SWING components ... debi staggs

06/14/2009

09:14 AM Bug #4002: RExpression2 - handle arbitrary R data structures
added handling (from the old RExpression1 implementation) for [un]serializing complex R data objects to disk.
This is...
ben leinfelder

06/13/2009

07:53 PM Bug #4147: Error message with selectable text
Fixed! Christopher Brooks
07:53 PM Bug #4147: Error message with selectable text
I'm lowering the priority of this and changing it to an enhancement because
the code works as expected.
I agree that ...
Christopher Brooks

06/12/2009

02:25 PM Bug #4020: WRP - create WorkflowRun object to encapsulate provenance/report instances
Thanks for the help Dan. I'm changing the _elementName of WorkflowRun to be property instead of entity (this probably... Derik Barseghian
10:54 AM Bug #4020: WRP - create WorkflowRun object to encapsulate provenance/report instances
I'm currently getting errors parsing the WorkflowRun moml back from disk using momlparser, and am looking into it.
A...
Derik Barseghian
02:14 PM Bug #4034: "Invalid memory access" when running workflow from the command line
This bug is no longer occurring on the Mac with either kepler.sh or with 'ant run-workflow.' However, kepler.sh does ... David Welker
01:50 PM Bug #4034: "Invalid memory access" when running workflow from the command line
Run the 'ant starupt-script' command to build the kepler.sh file. Not sure if this is still a bug with the new scrip... Chad Berkley
01:40 PM Bug #4034: "Invalid memory access" when running workflow from the command line
Does kepler.sh even exist anymore? I am not finding it in any of the modules I have downloaded. I cannot reproduce th... David Welker
02:04 PM Bug #4153 (In Progress): report-overrides
"ant report-overrides" build target does not include xml files (such as config.xml or configuration.xml). Aaron Aaron
01:59 PM Bug #4152: Modules should be able to add environment variables to the runtime
Added the ability to the build system to parse a $module/module-info/environment.txt file. This file lists the envir... Chad Berkley
01:53 PM Bug #4152: Modules should be able to add environment variables to the runtime
You can, in fact, add env vars to the runtime. We do it for the PATH variable (for JNI on windows). I'm implementin... Chad Berkley
01:50 PM Bug #4152: Modules should be able to add environment variables to the runtime
In Java 1.5 and later the java.lang.System.getEnv() method returns
environment variables.
The Javadoc for getEnv() ...
Christopher Brooks
01:48 PM Bug #4152: Modules should be able to add environment variables to the runtime
Right. It is distinct because it actually needs to load an environment variable. Chad Berkley
01:16 PM Bug #4152: Modules should be able to add environment variables to the runtime
Just so I understand this correctly, this is a distinct use case from setting System properties, correct? So, if you ... David Welker
01:09 PM Bug #4152 (Resolved): Modules should be able to add environment variables to the runtime
Modules such as R sometimes need to add environment variables to the runtime. R needs the R_HOME variable set in ord... Chad Berkley
01:40 PM Bug #4040: make a new module called globus to host globus actors and needed packages.
The old actors are being tested with globus environments, new globus actors are also being implemented and tested. jianwu jianwu
01:30 PM Bug #4091: Make it so the build system can use a "blessed" version of Ptolemy.
Forgot to close the bug with the last comment. David Welker
01:30 PM Bug #4091: Make it so the build system can use a "blessed" version of Ptolemy.
This functionality is now fully implemented. David Welker
01:29 PM Bug #4108: Do more extenstive testing before designating a revision of Ptolemy as stable
I am not sure that more extensive testing is really necessary. There have been very few developer problems associated... David Welker
01:28 PM Bug #4090: You should be able to specify a particular revision number or date with ant update.
You can now specify not only a particular revision, but also a particular date as well. This is documented in the bui... David Welker
01:27 PM Bug #4089: Ensure that module-manager, loader, and the build system all work with a new versioning system for modules.
All of these systems now work with the new versioning system. David Welker
01:25 PM Bug #4088: Create new configuration system
I am working on the configuration system now. It will be done post Sans Park release. David Welker
01:23 PM Bug #3947: Create a module manager
The module manager now works adequately for the purposes of the Sans Parks and 2.0 releases. I am closing this bug. David Welker
12:25 PM Bug #4151: exported RIO and ROML doc run-pairs have same KeplerLSID
now generating a new LSID when the reportInstance is assembled from provenance data ben leinfelder
12:05 PM Bug #4151 (Resolved): exported RIO and ROML doc run-pairs have same KeplerLSID
Exported RIO and ROML doc run-pairs have the same KeplerLSID. Try exporting a run from the WRM and then open up the k... Derik Barseghian
11:41 AM Bug #4087: No reset/x button to clear component searches
No objections on this proposal, so I plan to do it once many more important tasks are complete. Derik Barseghian
11:39 AM Bug #4150 (Resolved): Save in Library broken
Save in Library is giving me problems:
[run] Exception occurred during event dispatching:
[run] java....
Derik Barseghian
11:32 AM Bug #4047: Remove Component doesn't work
This is broken again.
[run] java.io.InvalidClassException: org.kepler.kar.KARFile; no valid constructor
[...
Derik Barseghian
11:22 AM Bug #4149 (Resolved): Workflow Run Manager - Export Runs feature
WRM needs to be able to Export Runs from a gui context menu, or without a gui by just accepting a list of run lsids. ... Derik Barseghian
11:16 AM Bug #4148: Workflow Run Manager - Upload to Repository feature
This also needs to be able to work without a gui, hopefully by just requiring a list of keplerlsids of runs to upload. Derik Barseghian
11:14 AM Bug #4148: Workflow Run Manager - Upload to Repository feature
That should read: "We also need to change to using setAccess". Derik Barseghian
11:10 AM Bug #4148 (Resolved): Workflow Run Manager - Upload to Repository feature
WRM needs to be able to upload runs to the repository. A user selects rows in the WRM and from a context menu clicks ... Derik Barseghian

06/11/2009

01:29 PM Bug #4147: Error message with selectable text
Ah, I never noticed you could get the text from the Stack Trace.
Chris Weed
01:14 PM Bug #4147: Error message with selectable text
This would likely be an issue with the Ptolemy Query widget in ptolemy.gui.
I tend not to see this because most erro...
Christopher Brooks
11:38 AM Bug #4147 (Resolved): Error message with selectable text
When Kepler displays an error message in the pop-up dialog, the text is not selectable so I can copy-paste it into an... Chris Weed
10:00 AM Bug #3238: Refactor NMI build
The NMI build has been refactored and is working. Any suite can now have a build via the NMI task in the build. Clo... Chad Berkley
09:50 AM Bug #4061: Documentation links are not active
Fixed. The documentation is now copied into the installer unless copyDocumentation is set to false. Chad Berkley
08:36 AM Bug #4143: "change failed" error while copy/paste-ing an ImageJ actor
Fixed checking to see if the parent directory exists before creating
the file. I fixed this in IJMacro, ImageJActor ...
Christopher Brooks
09:15 PM Bug #4143: "change failed" error while copy/paste-ing an ImageJ actor
I can replicate this under Mac OS X. (thanks for the sample demo, it is a bi
big help)
The stacktrace I get when I p...
Christopher Brooks

06/10/2009

12:53 PM Bug #4065: Copy documentation into installer
the installer now copies the documentation into the installer. closing this bug. Chad Berkley
07:32 AM Bug #3951: Report Viewer - improve TOC panel
now updating the TOC when the report instance in the viewer is updated/refreshed ben leinfelder
06:32 PM Bug #4144 (Resolved): Workflow Run Manager - moving columns / new windows bug
WRM - if you move a column, then open a new kepler window, there are problems with column and headers being out of or... Derik Barseghian

06/09/2009

04:22 PM Bug #4143: "change failed" error while copy/paste-ing an ImageJ actor
Copy/paste the ImageJ actor creates an error. Oliver Soong
04:21 PM Bug #4143 (Resolved): "change failed" error while copy/paste-ing an ImageJ actor
This seems to affect only Windows systems and has to do with saved values in the fileOrURL parameter in the ImageJ ac... Oliver Soong
03:14 PM Bug #2261: DIALOGS: Implement New "Advanced Search for Data" Dialog
I propose to take over this old bug -- REAP requires an Advanced Search dialog that allows a user to select a region ... Derik Barseghian
01:30 PM Bug #4141: EML 2 Dataset breaks when data table has 2 columns with the same name
Even with "As Field" and "As Column Vector" we only nd up with a single port for the Stem_pattern column (even though... ben leinfelder
12:26 PM Bug #4141: EML 2 Dataset breaks when data table has 2 columns with the same name
This has already been raised for the Kruger datasets. Isn't there already code to append actor names with a number? ... Oliver Soong
12:15 PM Bug #4141: EML 2 Dataset breaks when data table has 2 columns with the same name
This makes some sense: EML allows the names to be the same. A RecordToken cannot have two records with the same name.... ben leinfelder
11:56 AM Bug #4141 (Resolved): EML 2 Dataset breaks when data table has 2 columns with the same name
I am observing this problem with WoodyVCAtreesincirclea.txt in judithk.769.20, although this dataset requires authent... Oliver Soong
12:32 PM Bug #4132: Workflow Run Manager - Open in New Window is just opening the workflow, not the ROML or report
We can open the ROML - that'll make sense. Not sure how we would want to "open the report" - right now that UI is bas... ben leinfelder
12:10 PM Bug #4142: EML 2 Dataset caches restricted datasets, allows access across sessions
this is known behavior. as you say there is a certain "oh, really?" factor to it. I've marked to revisit at a "LATER"... ben leinfelder
12:05 PM Bug #4142 (Resolved): EML 2 Dataset caches restricted datasets, allows access across sessions
I authenticated to search and add an EML 2 Dataset actor for a restricted data table. If I save the workflow, close ... Oliver Soong
11:59 AM Bug #4119: Report Model - use LSID to link layout to workflow
will continue to use the WorkflowManager (for sanparks).
Using LSID for the linkage - that's a win!
ben leinfelder
11:09 AM Bug #3238: Refactor NMI build
I've created a new build task 'nmi' to build an NMI configuration for any given suite. It works like this:
You run ...
Chad Berkley
11:08 AM Bug #4140 (Resolved): Workflow Run Manager - delete runs functionality needs to be written
WRM - Delete run(s) functionality needs to be written. Argument: list of lsids Derik Barseghian
10:07 AM Bug #4022: undesired file:\ prefix added by FileParameter
A Ptolemy model that uses a FileParameter that works for me.
I can't reproduce this bug in Kepler, in part because I...
Christopher Brooks
06:30 PM Bug #4022: undesired file:\ prefix added by FileParameter
In Windows, it does prepend a "file:/" before the "C:/", which is slightly different from the OS X and linux behavior... Oliver Soong
06:05 PM Bug #4022: undesired file:\ prefix added by FileParameter
I can confirm this with 1.x dev under OS X and linux. It occurs when the file being selected by the chooser is both ... Oliver Soong
07:36 PM Bug #4139: port names are displayed twice
As a clarification, this only seems to occur in the top-level of the workflow in bug 4129 (http://bugzilla.ecoinforma... Oliver Soong
07:20 PM Bug #4139 (In Progress): port names are displayed twice
When I choose to show port names, they are displayed once next to the port as expected and once in the upper left cor... Oliver Soong

06/08/2009

01:50 PM Bug #4129: "unable to parse the metadata: null" with dataset judithk.306.21
i said i'd look at this... ben leinfelder
01:10 PM Bug #4138 (New): Workflow Run Manager - search cell edit focus isn't lost appropriately
WRM - For the most part, if you click on something else in Kepler while editing a WRM search cell, the cell inappropr... Derik Barseghian
01:06 PM Bug #4137 (New): Workflow Run Manager - resizing width of column while in edit mode of search cell does not resize edit field
WRM - resizing width of column while in edit mode of search cell does not resize edit field. It should, it looks stra... Derik Barseghian
01:02 PM Bug #4136 (Resolved): Workflow Run Manager - date and duration search should allow single operator-less arguments
WRM - the user should be able to enter a single date or duration without an operator (operators are currently: >, <).... Derik Barseghian
12:56 PM Bug #4135 (Resolved): Workflow Run Manager - default sorting (by date) should be applied
WRM - by default the runs have no sorting applied.
It would be more intuitive to sort by date by default (probably ...
Derik Barseghian
12:54 PM Bug #4134 (Resolved): Workflow Run Manager - double clicking on search cell shouldn't sort column
WRM - double clicking on a search cell column header also causes a sort. This is pretty annoying. Derik Barseghian
12:47 PM Bug #4133 (Resolved): Workflow Run Manager - column widths should be size appropriately
WRM column widths should be sized more appropriately by default, e.g. giving the date and duration columns enough roo... Derik Barseghian
12:44 PM Bug #4132 (New): Workflow Run Manager - Open in New Window is just opening the workflow, not the ROML or report
Open in New Window should open not just the workflow, but the roml and report (anything else?). Derik Barseghian
12:43 PM Bug #4131 (New): Workflow Run Manager - Open in New Window allows opening same wf multiple times
You can currently Open in New Window the same workflow from the WRM multiple times (i.e. into new Kepler windows). Th... Derik Barseghian
12:39 PM Bug #3655: create a Workflow Run Manager with ability to export Publication Ready Archives
Change referred to in #20 have been checked in.
This bug's become huge, going to create separate bugs that block this...
Derik Barseghian
11:39 AM Bug #3635: Create ReportItem Type Hierarchy
I think it will be very useful to make StaticReportItem subclasses - if only to make rendering them in the UI more st... ben leinfelder
11:34 AM Bug #3998: Report Viewer - render Report Instance on???Event
when the view changes, an event is fired and the viewer is now listening/responding that that event. ben leinfelder
11:33 AM Bug #3647: Create Report Assembler
the assembler is in place.
it's up to the various Item subclasses to get their values when needed.
ben leinfelder
11:29 AM Bug #4020: WRP - create WorkflowRun object to encapsulate provenance/report instances
We're now using a WorkflowRun object (subclass of NamedObj) to store the run provenance metadata. This moml snippet i... ben leinfelder
11:26 AM Bug #4001: WRP - Save/Open KARs containing MOMLs and ROMLs
created ReportLayoutKAREntryHandler for writing ROML to the KAR when it's associated workflow is saved as a KAR.
simi...
ben leinfelder

06/06/2009

05:00 PM Bug #4129: "unable to parse the metadata: null" with dataset judithk.306.21
Referenced workflow, zipped Oliver Soong

06/05/2009

04:59 PM Bug #4129 (Resolved): "unable to parse the metadata: null" with dataset judithk.306.21
This error occurs on XP but does not occur on linux. It only occurs if the dataset has not been previously cached. ... Oliver Soong
02:33 PM Bug #3655: create a Workflow Run Manager with ability to export Publication Ready Archives
Locally I've created a WorkflowRunManager class and associated Event and EventListener classes. With these I have the... Derik Barseghian

06/04/2009

04:50 PM Bug #4086: Port-Parameters half-work with composite actors
PortParameters work with opaque composite actors (composite actors
that have directors), but not transparent composit...
Christopher Brooks

06/03/2009

03:39 PM Bug #3637: Report Design Features, Stage 1
The following design features have been completed:
Ability to add:
Titles
Subtitles
Sections
Legends (will be accommo...
debi staggs
03:37 PM Bug #3734: Some demos no longer work after new build/repos
moved the smaller test garp workflows into a test-workflow subdir of ENM. This separates out the main ENM workflows ... Chad Berkley
02:49 PM Bug #3734: Some demos no longer work after new build/repos
Checked and fixed all workflows in outreach/resources/demos. Some in the demos/ENM directory do not work, but failur... Chad Berkley
02:24 PM Bug #3734: Some demos no longer work after new build/repos
checked and fixed all of the demos in outreach/resources/demos/getting-started Chad Berkley
03:31 PM Bug #3644: Create report layout controller
We did not end up creating a formal 'controller' for the layout, but we did create a method for rendering report layo... debi staggs
03:29 PM Bug #4128 (Resolved): Improve reporting static item icons
Make static item icons that are appealing and visually consistent, current icons were just initial 'placeholders' for... debi staggs
12:18 PM Bug #3668: Define contents of "Publication Ready Archive"
In a recent meeting with Matt and Ben, we discussed a proposal for a redefinition of KAR that would be able to contai... Derik Barseghian
08:29 AM Bug #4126 (Resolved): Allow user CLASSPATH to be loaded in Kepler
I have a jython actor that uses a java class I have in a jar file. Kepler fails when loading that actor via a kar fil... Enrique Garcia

06/02/2009

04:44 PM Bug #4125: ReportTest does not compile
I had added some additional classes to this test, but decided not to use them for now. This is what was causing the ... debi staggs
12:21 PM Bug #4125 (Resolved): ReportTest does not compile
I get the following when I try to run the reporting module:
[compile] Compiling 60 source files to /Users/sean/Dev...
Sean Riddle
03:47 PM Bug #4064: remove r installer after installation is complete
decided against doing this. There is no good place to do it in the install.xml file since the R installer is already... Chad Berkley
03:31 PM Bug #3949: Get the installer working with the new build system
Re-opening. forgot so many bugs blocked this one. Chad Berkley
03:29 PM Bug #3949: Get the installer working with the new build system
The installer creation task has been working well for while. Closing this bug. If any other issues pop up, new bugs... Chad Berkley
03:26 PM Bug #3238: Refactor NMI build
JUnit tests now work but they still run in the 'build' stage instead of the 'test' stage. I don't think this is a bi... Chad Berkley
03:22 PM Bug #3238: Refactor NMI build
In the process of getting the NMI build working for the kepler suite. I'm also getting it to build the installers an... Chad Berkley
03:21 PM Bug #4111: move test data to a more appropriate locations
removed all references to testdata in the demos and replaced it with the new path. closing this bug. Chad Berkley
03:08 PM Bug #4105: Make build system automatically build OS dependent modules
This now works. Adding an osextensions.txt file with the class names and java OS identifier of the OS they are suppo... Chad Berkley
12:31 PM Bug #4123: Image reader can't read URL
Fixed!
ImageReader is a very old actor, written in 2001.
The fileOrURL parameter was changed to a FileParameter in 20...
Christopher Brooks
10:10 AM Bug #4123: Image reader can't read URL
I meant "ImageReader" instead of "FileReader" in my comment Chris Weed
10:08 AM Bug #4123: Image reader can't read URL
I just noticed URLToImage is similar to what I want. I guess my confusion was that the parameter in FileReader is fil... Chris Weed
10:01 AM Bug #4123 (Resolved): Image reader can't read URL
In ptolemy.actor.lib.image.ImageReader
replace
_image = new ImageIcon(_fileRoot).getImage();
with:
try {
_im...
Chris Weed
11:56 AM Bug #4124: ant package fails
Confirmed fixed. David Welker
11:33 AM Bug #4124: ant package fails
This has probably been fixed. I am going to test and then close the bug. David Welker
11:23 AM Bug #4124 (Resolved): ant package fails
BUILD FAILED
.../build-area/build.xml:75: Warning: Could not find file .../build-area/ant-tasks/target/kepler-tasks....
Daniel Crawl
10:11 AM Bug #4121: Queryable - use LSID to look up workflows
I've added getLastExecutionForWorkflow(KeplerLSID) and getEntityId(String, LSID).
Feel free to re-open this bug if y...
Daniel Crawl
09:58 AM Bug #4122 (Resolved): File -> Save As does not assign new LSID
After saving a workflow to a different file name, both workflows have the same LSID. Daniel Crawl
07:11 PM Bug #3898: update .kepler instead of removing it between versions
Chad, David, and I had a discussion today about how to handle the .kepler directory for the 2.0 release. The conclus... Aaron Aaron
05:26 PM Bug #4107: Report Designer - Deserialize a ROML and display it back in the Report Layout Designer GUI
We can now read in a ROML and display it in the GUI. debi staggs

06/01/2009

11:24 AM Bug #4120: Bug in OpenDBConnector actor
I've updated OpenDBConnection to use the new string. Daniel Crawl
01:03 AM Bug #4120 (Resolved): Bug in OpenDBConnector actor
It also appears that the OpenDBConnector needs to be updated too. The previous version of the driver class required ... Jamie Vleeshouwer
10:54 AM Bug #4121 (Resolved): Queryable - use LSID to look up workflows
Now that we are using LSIDs to identify workflows, can the Queryable implementations also use that? Currently they pe... ben leinfelder
10:51 AM Bug #4119: Report Model - use LSID to link layout to workflow
making progress using ObjectManager to keep track of workflows and layouts. still using Workflow and WorkflowManager ... ben leinfelder

05/30/2009

03:28 PM Bug #4119 (Resolved): Report Model - use LSID to link layout to workflow
Now that he have a Kar Entry Handler for ROML, we need to use the cache+lsid for storing and retrieving that layout f... ben leinfelder

05/29/2009

09:42 AM Bug #4118: Web Service Actor stored in Library
Are you using Kepler from SVN? I think I've already fixed this bug in WebService.
(http://bugzilla.ecoinformatics.org...
Daniel Crawl
09:28 AM Bug #4118: Web Service Actor stored in Library
This line should be uncommented to make this work:
> //if(_urlStr.length()>0)
Chris Weed
09:26 AM Bug #4118 (Resolved): Web Service Actor stored in Library
After setting the wsdl and service name in org.sdm.spa.WebService and org.sdm.spa.WSWithComplexTypes, I store them ba... Chris Weed
06:10 PM Bug #4091: Make it so the build system can use a "blessed" version of Ptolemy.
How about:
ant update -Drev=head
Updates everything, including ptolemy, to the head?
David Welker
05:55 PM Bug #4091: Make it so the build system can use a "blessed" version of Ptolemy.
Thanks for adding the message, that will help.
I think if we had "ant update-head", then I'd be happy. The other co...
Christopher Brooks
05:47 PM Bug #4091: Make it so the build system can use a "blessed" version of Ptolemy.
Oh, I should add that per your suggestion, I have added an informative message when you are updating ptolemy:
Updati...
David Welker
05:44 PM Bug #4091: Make it so the build system can use a "blessed" version of Ptolemy.
Hi Christopher,
Good comments.
Actually, the command ant use-ptolemy-head and ant use-stable-ptolemy have been both...
David Welker
05:24 PM Bug #4091: Make it so the build system can use a "blessed" version of Ptolemy.
Actually, maybe "ant update-head" could replace "ant use-ptolemy-head"?
I'll never remember "ant use-ptolemy-head". ...
Christopher Brooks
05:04 PM Bug #4091: Make it so the build system can use a "blessed" version of Ptolemy.
So every time I run "ant update", I need to also run "ant use-ptolemy-head".
The README.txt and web pages should be u...
Christopher Brooks

05/28/2009

12:31 PM Bug #4111: move test data to a more appropriate locations
I changed kepler so that it will try to automatically open to the outreach/resources/demos directory. If it does not... Chad Berkley
12:28 PM Bug #4111: move test data to a more appropriate locations
To add the outreach module (or any module for that matter) to your suite temporarily, you can use the -Dunder switch ... Chad Berkley
12:23 PM Bug #4111: move test data to a more appropriate locations
I moved the testdata and the demos to the outreach module. I'm looking into ways to add the ability to the build sys... Chad Berkley
05:30 PM Bug #4113 (New): Kepler changes property position in XML but keeps values
This doesn't affect the operation of Kepler, but it makes it a major pain to diff workflows and causes large portions... Oliver Soong

05/27/2009

04:13 PM Bug #4112 (New): make kepler use OSX dialog boxes
Add configuration to the mac extensions to make kepler use the OSX file open/save dialog boxes instead of the default... Chad Berkley
02:47 PM Bug #4111 (Resolved): move test data to a more appropriate locations
Currently, there is ~54 MB of test data in common/lib/testdata. This could be moved to a new module that would be op... Chad Berkley
02:25 PM Bug #4105: Make build system automatically build OS dependent modules
The OS is just a special case of checking for a particular feature
such as a third party library. The build system s...
Christopher Brooks
02:23 PM Bug #4104: Need resource manager to handle objects in the resources directories
Please be sure to review how the Java I18N stuff works.
See
http://java.sun.com/developer/technicalArticles/Intl/Res...
Christopher Brooks
11:11 AM Bug #4091: Make it so the build system can use a "blessed" version of Ptolemy.
Ok, good news that I can build against the ptII head.
The word "update" in "ant update" means something specific, wh...
Christopher Brooks
11:10 PM Bug #4091: Make it so the build system can use a "blessed" version of Ptolemy.
Hi Christopher,
That was my bad. I forgot to include the names of the new commands in my comment closing the issue.
...
David Welker
06:42 PM Bug #4091: Make it so the build system can use a "blessed" version of Ptolemy.
I'm confused.
How do I build from the Ptolemy head?
It seem like "ant update" should actually update the tree to t...
Christopher Brooks

05/26/2009

03:49 PM Bug #4093: allow kepler to use OS specific UI elements
fixed. osx kepler now has a new icon set that fit the standard osx icon sizes. please open new bugs for any new Mac ... Chad Berkley
10:31 AM Bug #4093: allow kepler to use OS specific UI elements
fixed the about box. fixed apple-q. The icon shown is now the java icon. Will try to get the kepler icon to work. Chad Berkley
03:47 PM Bug #4067: Add "about" widget for kepler on the mac
Fixed. The mac version of kepler now has an about box, it correctly exits when using apple-q and it has a new icon s... Chad Berkley
03:44 PM Bug #4109: File Reader error message incorrect
fixed it. update ptolemy to see the change. Chad Berkley
02:51 PM Bug #4109 (Resolved): File Reader error message incorrect
The "File Reader" actor (ptolemy.actor.lib.io.FileReader) prints a message
"Failed to write '" + fileOrURL + "'"
...
Chris Weed
12:53 PM Bug #4104: Need resource manager to handle objects in the resources directories
Interesting ideas!
I want to point out a couple of things. First of all, we already have most of this functionality....
David Welker
10:53 AM Bug #4090: You should be able to specify a particular revision number or date with ant update.
As of now, you may specify a revision number with the ant update command. For more recent revisions, specifying a rev... David Welker
07:22 AM Bug #4090: You should be able to specify a particular revision number or date with ant update.
It would be very useful to be able to specify the revision as a date
or a revision number. Checking out by date migh...
Christopher Brooks
10:49 AM Bug #4108 (In Progress): Do more extenstive testing before designating a revision of Ptolemy as stable
Right now, before a revision of Ptolemy is considered "stable" all it must do is be able to compile and the trunk of ... David Welker
10:46 AM Bug #4091: Make it so the build system can use a "blessed" version of Ptolemy.
I agree with you that the word "stable" is better than "blessed" and that is the the word used in one of several new ... David Welker
07:40 AM Bug #4091: Make it so the build system can use a "blessed" version of Ptolemy.
We should use the term "stable" to refer to revisions of Ptolemy and Kepler
that are likely to build for users. A tr...
Christopher Brooks
10:26 AM Bug #4107 (Resolved): Report Designer - Deserialize a ROML and display it back in the Report Layout Designer GUI
We need to be able to deserialize a ROML and display it in the Layout Designer GUI. debi staggs
 

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