Kepler

08/07/2012

05:23 PM Bug #5663: KeplerGraphFrame has much duplicated code

r30371:
Moved org.kepler.gui.KeplerGraphFrameExtension to ptolemy.vergil.basic.BasicGraphFrameExtension.
Removed du... Christopher Brooks

04:19 PM Bug #5668 (Resolved): module manager should support batch mode execution.

a blocker for batch execution support for Kepler module manager. Users should be able to use command line to check wo... jianwu jianwu

04:17 PM Bug #5266: Two empty boxes inside Sinewave actor and other icon problems for attributes

Hi Sean,
If I were you, I'd focus on the other bug because the Sinewave icon bug may be tricky because Sinewave is an... Christopher Brooks

02:48 PM Bug #5266: Two empty boxes inside Sinewave actor and other icon problems for attributes

I get this behavior under kepler trunk, reporting suite is not needed. Sean Riddle

04:05 PM Bug #5348: Opening KAR or opening workflow under KAR behaves differently.

correct new bug id: A further reevaluation bug is created at bug 5667. jianwu jianwu

04:04 PM Bug #5348: Opening KAR or opening workflow under KAR behaves differently.

close this bug. A further reevaluation bug is created at bug 5348. jianwu jianwu

04:03 PM Bug #5667 (New): reevaluate how opening kars vs. XML should work from actor library.

currently, opening kar is different from opening xml from actor library (see bug 5348). One more difference is that o... jianwu jianwu

03:55 PM Bug #5489: Module Manager GUI should fail gracefully if a remote module cannot be downloaded

two ways to reproduce the bug: 1) close internet connection just before downloading start; 2) have a unpublished modu... jianwu jianwu

02:12 PM Bug #5655: sdm spa Repeat is a duplicate of a Ptolemy actor

Kepler actors/src/org/sdm/spa/Repeat.java has:
public TypedIOPort portOutput;
public TypedIOPort portInput;
... Christopher Brooks

01:56 PM Bug #5655: sdm spa Repeat is a duplicate of a Ptolemy actor

These two actors have different ports and parameters. Ptolemy one has one input port and two parameters; Sdm one has ... jianwu jianwu

11:07 AM Feature #5666 (New): Build system needs a target to build all common or blessed non-core modules

There should be a way to easily build all the common or "blessed"
non-core modules.
For example, "ant change-to -Ds... Christopher Brooks

08/06/2012

10:14 PM Bug #5660: ExtensionFileFilter is a duplicate of a Ptolemy class

Dan did most of the work, all I had to do was remove ExtensionFileFilter.java
and update the imports in two locations... Christopher Brooks

04:49 PM Bug #5660 (Resolved): ExtensionFileFilter is a duplicate of a Ptolemy class

./gui/src/org/kepler/gui/util/ExtensionFileFilter.java
FIXME: This matched ptolemy/src/diva/gui/ExtensionFileFilter.... Christopher Brooks

09:55 PM Bug #5661: Remove SwingWorker and use javax.swing.SwingWorker

I removed util.SwingWorker and updated
authentication-gui/src/org/kepler/authentication/GAMAAuthenticationService.jav... Christopher Brooks

08:17 PM Bug #5661: Remove SwingWorker and use javax.swing.SwingWorker

I've removed ptolemy/src/ptolemy/gui/SwingWorker.java
Unfortunately, org.kepler.gui.ProgressMonitorSwingWorker uses ... Christopher Brooks

04:51 PM Bug #5661 (Resolved): Remove SwingWorker and use javax.swing.SwingWorker

./util/src/util/SwingWorker.java
FIXME: Remove and use javax.swing.SwingWorker.
See http://docs.oracle.com/javas... Christopher Brooks

08:19 PM Bug #5665 (Resolved): modulemanager et al.: swing-worker-1.2.jar should be removed

bug #5661 is about removing util.SwingWorker.
Unfortunately, there is code that uses a different SwingWorker from ... Christopher Brooks

07:44 PM Bug #5648: FileCopier code duplication

./core/src/org/kepler/util/FileCopier.java was used by tagging. I've temporarily resurrected it, but into the tagging... Derik Barseghian

04:23 PM Bug #5648 (Resolved): FileCopier code duplication

FileCopier:
./core/src/org/kepler/util/FileCopier.java - Fixed. Unused code which was removed.
./actors/src/... Christopher Brooks

05:01 PM Bug #5664 (New): Check for duplicate code

See bug #4926 for how to check for duplicate code.
This bug is targeted to 2.5.0 so that we don't forget to do it. Christopher Brooks

05:00 PM Bug #4926: Examine Kepler for duplicated Ptolemy code

To find files that have the same name in both Ptolemy II and Kepler:
Look for duplicate file names:
# Get all the .ja... Christopher Brooks

12:02 PM Bug #4926: Examine Kepler for duplicated Ptolemy code

This should be done for each release in the end. It shouldn't be released if it doesn't meet some metrics or criteria... Ilkay Altintas

04:55 PM Bug #5663 (Resolved): KeplerGraphFrame has much duplicated code

I looked in to why KeplerGraphFrame has so much duplicated code
and it looks like Comad uses KeplerGraphFrameExtensi... Christopher Brooks

04:52 PM Bug #5662 (Resolved): resurgence ArrayAccumulator is a duplicate of Ptolemy ArrayAccumulate

./actors/src/org/resurgence/actor/ArrayAccumulator.java
Duplicate of ptolemy/src/ptolemy/actor/lib/ArrayAccumulate.j... Christopher Brooks

04:45 PM Bug #5659 (Closed): Kepler CaseGraphFrame and CaseGraphTableau have duplicated Ptolemy code.

./gui/src/org/kepler/gui/frame/CaseGraphFrame.java
FIXME: Refactor!
Duplicate of ptolemy/src/ptolemy/vergil/... Christopher Brooks

04:43 PM Bug #5658 (Resolved): Rename kepler/moml/filter classes so that they don't have the same name as the Ptolemy filter classes

./core/src/org/kepler/moml/filter/BackwardCompatibility.java
./core/src/org/kepler/moml/filter/ClassChanges.java
./... Christopher Brooks

04:42 PM Bug #5657 (Resolved): kepler moml FileAttribute should probably be a FileParameter

./core/src/org/kepler/moml/FileAttribute.java
The Kepler version extends StringAttribute
This matches ptolemy/src... Christopher Brooks

04:40 PM Bug #5656 (Resolved): sdm spa StringConst is a duplicate of a Ptolemy actor

./actors/src/org/sdm/spa/StringConst.java
FIXME: Deprecate and extend ptolemy/src/ptolemy/actor/lib/StringConst.java Christopher Brooks

04:39 PM Bug #5655 (Resolved): sdm spa Repeat is a duplicate of a Ptolemy actor

./actors/src/org/sdm/spa/Repeat.java
FIXME: No documentation? If possible, Deprecate and extend
ptolemy/src/ptolem... Christopher Brooks

04:38 PM Bug #5654 (Resolved): Geon ArrayRemoveElement is a duplicate of a Ptolemy actor

./actors/src/org/geon/ArrayRemoveElement.java
FIXME: Duplicate of ptolemy/src/ptolemy/actor/lib/ArrayRemoveElemen... Christopher Brooks

04:36 PM Bug #5653 (Resolved): Geon ArrayContains is a duplicate of a Ptolemy actor

./actors/src/org/geon/ArrayContains.java
FIXME: Duplicate of ptolemy/src/ptolemy/actor/lib/ArrayContains.java
... Christopher Brooks

04:35 PM Bug #5652 (New): Geon Scp and spa Ssh2Exec have duplicate code.

Duplicate code detected with CPD. See
actors/src/org/geon/Scp.java line 295
actors/src/org/sdm/spa/Ssh2Exec.j... Christopher Brooks

04:33 PM Bug #5651 (Resolved): WebService, WebServiceStub and MessageBasedWebService have duplicate code

##########
actors/src/org/sdm/spa/WebService.java line 1094
actors/src/org/sdm/spa/WebServiceStub.java line 52... Christopher Brooks

04:31 PM Bug #5650: actors LidarWorkflowExecute and load WorkflowExecute have duplicated code

Also:
actors/src/org/geon/LidarWorkflowExecute.java line 373
actors/src/org/geon/ModelService.java line 2... Christopher Brooks

04:27 PM Bug #5650 (Resolved): actors LidarWorkflowExecute and load WorkflowExecute have duplicated code

Duplicates detected with CPD. See
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=4926#c1
actors/src/org/ge... Christopher Brooks

04:30 PM Bug #5649: opendap/{DapObjectsToToken,TokenManager,TypeManager} are almost identical

Also:
pendap/src/org/kepler/dataproxy/datasource/opendap/DapObjectsToType.java line 73
o
pendap/src/org/keple... Christopher Brooks

04:24 PM Bug #5649 (Resolved): opendap/{DapObjectsToToken,TokenManager,TypeManager} are almost identical

opendap/src/org/kepler/dataproxy/datasource/opendap/DapObjectsToToken.java line 65
opendap/src/org/kepler/datap... Christopher Brooks

03:29 PM Bug #5247: Allow user to set memory allocated to Kepler from within Kepler

I increased max memory to 1gb at r30353. You will have to delete your existing build-area/settings/memory.xml Derik Barseghian

12:59 PM Bug #5247: Allow user to set memory allocated to Kepler from within Kepler

Derik will increase the default memory heap size to 1 Gig. Ilkay Altintas

01:33 PM Bug #5646 (New): Switching some of the add-on modules to core

Before 2.5, we need a discussion on switching some of the key modules, e.g., modules in the reporting suite, to the c... Ilkay Altintas

01:15 PM Bug #5645 (New): kar uploading should need user account.

Currently, anonymous users can upload their kars to Kepler kar repository. They could bring malicious actors and be h... jianwu jianwu

12:54 PM Bug #5633: Actor/Attribute Search/Find Facility needs menu choices

Decided that a search bar will be added to the outline. Ilkay Altintas

12:46 PM Bug #5458: Moving between 2.2 and 2.3 and back requires deleting ~/KeplerData

It is fixed as of 2.3 and this will not happen between 2.3 & 2.4. What could still happen is if you start 2.3 and re... Ilkay Altintas

12:37 PM Bug #4281: ant update produces message about running svn cleanup

This is a bug for developers. A potential fix is a two stage update that copies the file and writes on the copy. Late... Ilkay Altintas

12:30 PM Bug #5348: Opening KAR or opening workflow under KAR behaves differently.

Add a new bug to reevaluate how opening kars vs. XML should work. Ilkay Altintas

12:26 PM Bug #5495: released kepler should allow getting patches and changing suites from command line

Report the small fix and add/link to the 2.5 bug. Ilkay Altintas

12:24 PM Bug #5398: Re-install of Kepler-x.y doesn't overwrite modules.txt

This was a 2.2 bug. It has been solved for 2.3. The behavior right now seems to be ok for 2.4, but the user needs to ... Ilkay Altintas

12:15 PM Bug #5487: blank modules.txt files created for non-suite modules

Needs to be tested and evaluated at the end of release cycle. Ilkay Altintas

12:07 PM Bug #5440: special checkout behavior for hardcoded ptolemy module names

We agree that we will have a special Ptolemy II branch for each Kepler release. The branch should stay in the ptII re... Ilkay Altintas

11:40 AM Bug #4068: File Menu should display 5 most recently used workflows

Decided to change it to be 10 instead of 5. Ilkay Altintas

11:38 AM Bug #4908: actor/director/attribute .xml file documentation needs to be updated

PN needs to be updated for 2.4. Ilkay Altintas

11:36 AM Bug #4908: actor/director/attribute .xml file documentation needs to be updated

A future RFE needs to be issued for a future release to combine the forked pieces. Dan investigated the technical par... Ilkay Altintas

11:26 AM Bug #5485: standalone Module Manager can break Kepler app ability to startup

Not able to reproduce this. Will try more and close it if not reproducible. Ilkay Altintas

11:22 AM Bug #5426: workflow lsid changes when running from command line

Added a command line option to stop it. Closed for 2.4 release. For 2.5, add a new bug with investigation of alternat... Ilkay Altintas

11:18 AM Bug #5280: missing command line execution for KAR files

See http://stackoverflow.com/questions/620993/determining-binary-text-file-type
for ideas about how to detect binary ... Christopher Brooks

11:16 AM Bug #5280: missing command line execution for KAR files

Still need to update the docs and the user manual. Also the text effigy will be updated to not open binaries. Ilkay Altintas

11:00 AM Bug #4978: Create additional 'module' property for any menu entries that are inserted by non-core modules

I briefly tried to reproduce this and was unable (changing to sensor-view suite, changing various add-on module setti... Derik Barseghian

10:56 AM Bug #5416: downloaded modules by Kepler module manager should know the path of main Kepler installation.

One problem with your change at r30323 is that it only writes this install-path.txt on a new install. A user could su... Derik Barseghian

08/03/2012

02:15 PM Bug #5602: Timezone confusion using the scheduler

Hey Jing, let's discuss this bug when you get back. Derik Barseghian

02:05 PM Bug #5580: create sensor-view module documentation

Closing. Derik Barseghian

07/31/2012

03:14 PM Bug #4068: File Menu should display 5 most recently used workflows

The history menu uses Configuration.openModel() to open files. If the file is a KAR, but cannot be opened, then the K... Daniel Crawl

01:44 PM Bug #5416: downloaded modules by Kepler module manager should know the path of main Kepler installation.

I updated class in build-area to write install-path.txt to ~/KeplerDatat/kepler.modules/build-area dir at version 303... jianwu jianwu

12:57 PM Bug #5495: released kepler should allow getting patches and changing suites from command line

It seems like a bug to display a window when running -nogui. If patches are available, kepler.sh could print a messag... Daniel Crawl

10:57 AM Bug #5495: released kepler should allow getting patches and changing suites from command line

We needs a full command line support for Module Manager to support workflow module dependency checking and Kepler upd... jianwu jianwu

10:45 AM Bug #5495: released kepler should allow getting patches and changing suites from command line

It is related to bug 4516 since both need module manager interaction through command line. jianwu jianwu

12:48 PM Bug #5625: create kepler documentation for 2.4

We should verify all the exercises in the getting started guide. While updating it for 5452, I noticed that the Run W... Daniel Crawl

12:45 PM Bug #5509: How do I run the demos

The Help -> Kepler Documentation links to the demos are working again.
The demos are now accessible in the actor tre... Daniel Crawl

12:43 PM Bug #5452: uneasy access to the demo workflows

The demos are now accessible in the actor tree. I've updated the getting started guide to describe opening them from ... Daniel Crawl

10:55 AM Bug #3997: Supporting display actor conversion for command line execution.

I updated ptolemy version 64086 and kepler version 30298 to support redisplay for MonitorValue and ImageDisplay actor... jianwu jianwu

10:46 AM Bug #4516: Module Manager needs ability to install modules needed by KARs

It is related to bug 5495 since both need module manager interaction through command line. jianwu jianwu

07/30/2012

02:17 PM Bug #5398: Re-install of Kepler-x.y doesn't overwrite modules.txt

After discussion with Dan, we think it is correct to keep its suite configuration even a Kepler version is uninstalle... jianwu jianwu

07/27/2012

05:37 PM Bug #5589: Add missing ptolemy actors to library

Thanks again, Christopher. After your fix, I was able to add entries for ComputeHistogram, RecursiveLattice, Variable... Daniel Crawl

04:06 PM Bug #5582: DataTurbine server crashing the JRE

I ran 500 iterations of the GDD workflow configured to request 300days of data as a stress test. No crash using the o... Derik Barseghian

02:05 PM Bug #5582: DataTurbine server crashing the JRE

Crashing on nibbler resolves when using older version of java (jdk-6u20-linux-x64.bin).
Probably there's an issue w/ ... Derik Barseghian

01:30 PM Bug #5415: module releasing and downloading by module manager should keep file mode.

it is fixed at version 30300. Now the file mode is set before zipping. jianwu jianwu

10:10 AM Bug #5398: Re-install of Kepler-x.y doesn't overwrite modules.txt

After discussing with Derik, the information about the bug is clearer.
I can reproduce the first scenario for kepler... jianwu jianwu

07/26/2012

02:53 PM Feature #5626: interacting with kepler.sh to know the status and other information in batch-mode.

It turns out a future requirement for CAMERA to get the detailed status for batch execution. It will be like Kepler m... jianwu jianwu

01:51 PM Bug #5440: special checkout behavior for hardcoded ptolemy module names

I updated Get class at version 30290 using solution like !PTOLEMY_KEPLER_2_2 &&
startsWith(PTOLEMY_KEPLER). If we dec... jianwu jianwu

07:57 AM Bug #5589: Add missing ptolemy actors to library

I added a test that, for each configuration, instantiates an actor and then
calls clone on the actor.
I fixed clon... Christopher Brooks

07/25/2012

04:11 PM Bug #5589: Add missing ptolemy actors to library

Thanks, Christopher! I added most of the actors and attributes on the list. I also updated ptolemy-excludes.
I could... Daniel Crawl

04:03 PM Bug #5642: Kepler should have access to the ShowTypes attribute

ShowTypes has been added to the actor library.
As with instantiating manually, dropping it on the canvas results in... Daniel Crawl

02:41 PM Bug #5643: [Fatal Error] :79:7: The element type "nextDiagram" must be terminated by the matching end-tag "</nextDiagram>".

The module demo workflows are now in the actor library, and all XML files in these directories are parsed. The file o... Daniel Crawl

02:03 PM Bug #5643 (Resolved): [Fatal Error] :79:7: The element type "nextDiagram" must be terminated by the matching end-tag "</nextDiagram>".

Since a few weeks ago, I begin to see this info when start kepler from trunk. Although Kepler still works well. This ... jianwu jianwu

02:26 PM Bug #4516: Module Manager needs ability to install modules needed by KARs

My current tests are still the same. With GUI, Kepler in trunk can identify missing modules and download needed modul... jianwu jianwu

11:27 AM Bug #5440: special checkout behavior for hardcoded ptolemy module names

Thanks Derik. I didn't know Kepler 2.2 has ptolemy branch (namely ptolemy-kepler-2.2) at kepler svn yet other Kepler ... jianwu jianwu

07/24/2012

06:10 PM Bug #5440: special checkout behavior for hardcoded ptolemy module names

That looks similar to the regex I mentioned I didn't use so as not to change the checkout behavior of ptolemy-kepler-... Derik Barseghian

05:08 PM Bug #5440: special checkout behavior for hardcoded ptolemy module names

Hi Derik,
I changed the code locally from
"if (module.getName().equals(Module.PTOLEMY) || module.getName().equals... jianwu jianwu

07/20/2012

10:50 AM Bug #5589: Add missing ptolemy actors to library

The list did not include attributes in vergil/actor/lib?
There are some actors that are listed that are base classes... Christopher Brooks

10:20 AM Bug #5642: Kepler should have access to the ShowTypes attribute

There are many Ptolemy components not in the Kepler library; see bug #5589. It would be good to know which ones are a... Daniel Crawl

10:09 AM Bug #5642 (Resolved): Kepler should have access to the ShowTypes attribute

Edward added a ShowTypes attribute, that when dragged in to a model, annotates
the ports with the types.
In vergi... Christopher Brooks

07/18/2012

01:14 PM Bug #5641 (New): once timezones are added to provenance, Workflow Run Manager must utilize them

Once timezones are added to provenance (bug#5640), Workflow Run Manager needs to utilize them. WRM should continue to... Derik Barseghian

01:12 PM Bug #5640 (New): associate timezones with all timestamps recorded in provenance tables

Right now provenance records timestamps in local time without recording timezone. This is lossy. E.g. one problem sce... Derik Barseghian

07/17/2012

04:04 PM Bug #3997: Supporting display actor conversion for command line execution.

I saw that the hydrant code was checked in awhile ago.
I have no plans to modify MonitorValue and ImageDisplay so th... Christopher Brooks

02:56 PM Bug #3997: Supporting display actor conversion for command line execution.

Now it works with Display, Plot and ImageJ actors at version 30211. A new module called "display-redirect" is adde... jianwu jianwu

07/16/2012

12:59 PM Bug #5639 (New): ant update ptolemy -Drev=stable doesn't update you to latest "stable"

If you run ant update ptolemy -Drev=stable, ptolemy/module-info/revision.txt isn't updated first, so ptolemy is simpl... Derik Barseghian

07/13/2012

03:43 PM Bug #5194: demos are difficult to find

Classpath updated, and demo hyperlinks put back in the help docs. Daniel Crawl

10:58 AM Bug #5638: "Ok" behavior of Use Module Manager prompt doesn't do what it should when opening from Recent Files

This is already described in bug#5280#c1 Derik Barseghian

10:38 AM Bug #5638 (Resolved): "Ok" behavior of Use Module Manager prompt doesn't do what it should when opening from Recent Files

If you attempt to open a kar from File=>Recent Files=>yourKar.kar and you're in a suite that doesn't include needed m... Derik Barseghian

07/12/2012

04:11 PM Bug #4846: error opening kar from local repository

This has been fixed for awhile. Daniel Crawl

04:07 PM Bug #5188: closing workflow does not save the location change of popup display windows.

I was able to reproduce this for both KAR and MoML files, and also in Ptolemy. The problem is that if you change a po... Daniel Crawl

07/11/2012

06:12 PM Bug #5194: demos are difficult to find

Thanks for updating HTMLViewer, Christopher. The demos were moved from module/resources/ to module/workflows/ since t... Daniel Crawl

05:07 PM Bug #5194: demos are difficult to find

I updated ptolemy.actor.gui.HTMLViewer so that if the URL cannot
be found, then it is passed to ptolemy.util.FileUtil... Christopher Brooks

03:46 PM Bug #5194: demos are difficult to find

I agree that getting the hyperlinks working again for the demos would be good. The difficulty is that the demos liste... Daniel Crawl

03:10 PM Bug #5444: Kepler can't run workflow if two instances exist at same time

I've fixed the problem due to running different suites by storing the cached objects and database tables on a per-sui... Daniel Crawl

02:53 PM Bug #5444: Kepler can't run workflow if two instances exist at same time

There are 3 different problems in this bug.
The problem in the original description is that 2 Kepler are started, th... Daniel Crawl

01:57 PM Bug #5637 (Resolved): composite window size & position not always saved

It would be nice if the position and size of a window for a composite actor were saved. I thought this was done in th... Daniel Crawl

07/10/2012

02:07 PM Bug #5142: comma improperly inserted in kar filename rather than a period (.)

This was fixed recently. NamedObj.setDisplayName() can be used for names with periods. Daniel Crawl