Hi Bill,
The Matlab actor in Kepler 2.4 has a bug that prevents more than
one instance from being added to the canvas. This has been fixed
in Kepler svn and you get can this version by running:
mkdir kepler.modules
cd kepler.modules
svn co
We are pleased to announce the release of bioKepler 1.1.
The bioKepler suite facilitates rapid development and scalable
distributed execution of bioinformatics workflows in Kepler while
simplifying access to a wide range of bioinformatics tools executed
locally or distributedly. bioKepler
Hi Vincenzo,
The default open directory can be specified by setting
_alternateDefaultOpenDirectory in:
common/configs/ptolemy/configs/kepler/configuration.xml
--dan
On 8/27/14 2:27 AM, Vincenzo Forchi wrote:
Hi,
Is there a way to change the default open directory by changing a
Hi Bruno,
The port names must match the Web Service operation's request and
response parameter names defined in the WSDL. If you change the
operation (set in the actor's method parameter), then the actor
will automatically change the ports to match the parameter names.
--dan
On 8/4/14
Hi Jon,
Are you running multiple instances of Kepler?
This error occurs when multiple instances are started, and the first
instance is not closed last. You can avoid this problem by running
the HSQL databases in a separate process. First run:
kepler.sh -hsql start
then start the Kepler
://www.isciences.com
http://www.terraviva.net
On Fri, Oct 25, 2013 at 3:18 PM, Daniel Crawl danielcr...@gmail.com wrote:
Hi Jon,
Are you running multiple instances of Kepler?
This error occurs when multiple instances are started, and the first
instance is not closed last. You can avoid this problem
Hi Tristan,
This looks like the problem described here:
https://chess.eecs.berkeley.edu/bugzilla/show_bug.cgi?id=321
You could try setting the SetVariable delayed parameter to true,
but this may result in the wrong behavior for your workflow.
Can you remove the SetVariable actors?
--dan
We are pleased to announce the release of bioKepler 1.0.
The bioKepler suite facilitates rapid development and scalable
distributed execution of bioinformatics workflows in Kepler while
simplifying access to a wide range of bioinformatics tools executed
locally or distributedly. bioKepler 1.0
Hi Vickie,
It sounds like you configured HSQL to directly access the database
files instead of starting servers.
If you are running Kepler compiled from the svn trunk, you no longer
have to do this: the default configuration (that starts HSQL servers)
will work for different users running
Hi Johan,
Based on the NoSuchMethodError, there appears to be a mismatch
between the versions of Kepler and Ptolemy. If you want to run
Kepler 2.3 from svn:
mkdir kepler-2.3
cd kepler-2.3
svn co
https://code.kepler-project.org/code/kepler/releases/release-branches/build-area-2.3
build-area
Hi Vickie,
You can use the -nogui option to run the workflow and exit without
typing control-c:
kepler.sh -runwf -nogui workflow.xml
--dan
On 6/14/13 6:42 AM, Lynch, Vickie E. wrote:
Hi,
Any way to run workflow from the command line and have it exit without typing
Ctrl-c?
Hi Tristan,
There are two job submission workflows included in Kepler 2.4.
You can open them in the actor tree, under Demos - Job.
Did you create a loop similar to Figure 7.35 in the User Manual?
If so, you need use DDF or PN, not SDF. It would be helpful if
you could send me the workflow.
Hi Jon,
You can use the force open option to open workflows created
using the trunk. If you then save the workflows using Kepler 2.4,
they will open without showing the missing modules dialog.
--dan
On 4/17/13 6:32 AM, Jonathan Boright wrote:
Hello all,
We would like to migrate Kepler
We are pleased to announce the release of the Reporting 2.4 suite for
Kepler 2.4. The Reporting suite includes the ability to create reports
displaying workflow results, capture provenance of workflow execution,
and manage workflow runs.
Reporting 2.4 fixes several bugs and has been updated to
Hi Marcin,
I saw a similar exception in Kepler 2.3 by putting a Display actor
inside a MultiInstanceComposite. However, this error does not occur
in Kepler 2.4.
Does the error occur for you with 2.4?
--dan
On 4/17/13 3:18 AM, Marcin Plociennik wrote:
Hi,
I have following case:
1. I'm
We are pleased to announce the release of Kepler 2.4. This release
contains numerous bug fixes and enhancements, and provides a platform
for the upcoming releases of bioKepler (biokepler.org) and the
Reporting Suite. Significant changes include:
- Better support for running KAR workflows on the
Hi Kianwee,
This problem occurs when running Kepler 2.3 with Java 1.7
and was fixed in the svn repository:
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5574
You can either run Kepler with Java 1.6, or download and
compile Kepler from svn.
--dan
On 3/4/13 12:20 AM, Kianwee Chen
Hi Joy,
Did you set the parameter inputMechanism in WSWithComplexTypes
to be composite? If the port type is xmltoken, that usually
means the corresponding SOAP parameter is composite. By setting
inputMechanism to composite, WSWithComplexTypes will construct
an actor that tries to build the
Hi Jonathan,
It might be helpful to see the threads' stack traces once the workflow
hangs. You can get this by using jstack, or control-break on Windows or
control-\ on Mac. If there is a deadlock, this could help determine
the cause.
--dan
On 2/14/13 8:05 AM, Christopher Brooks wrote:
Hi Tom,
I can't reproduce this with the trunk, but can with Kepler 2.3.
Are all of your sources at r31428?
--dan
On 2/12/13 7:19 AM, Tom Parris wrote:
Dear Kepler-Users:
I can save the attached workflow as an xml document. But when I try
to save as a kar, I get an error (see full stack
into. But please realize this
is not currently a show stopper for us, just an annoyance.
-- Tom
On Wed, Jan 9, 2013 at 4:23 PM, Daniel Crawl danielcr...@gmail.com wrote:
Hi Tom,
Are you using the MatrixViewer actor to display the matrix tokens?
I recently reported a similar problem
Hi Tom,
Are you using the MatrixViewer actor to display the matrix tokens?
I recently reported a similar problem with this actor:
The MatrixViewer actor pops up a window displaying a matrix. If the
window is closed, it does not reappear after running the model again
(unlike the Display or
The class action menu items used to work in Kepler.
I'll add them back.
However, can actor classes defined in one workflow be
instantiated in another?
Ian, you could try the ModelReference and VisualModelReference
actors, which execute a workflow defined in a file.
--dan
On 12/10/12 4:43
Hi Daren,
Do you have these files:
C:\Users\darthoma\KeplerData\modules\actors\kar\CoreActors.kar
C:\Users\darthoma\KeplerData\modules\directors\kar\CoreDirectors.kar
If they are missing, then the actor tree will be mostly empty.
These files are created when Kepler starts; you should see
I updated RunClasspath to include the files in the environment
variable CLASSPATH, and Brian says he can now run Kepler with
jfxrt.jar in the classpath.
--dan
On 11/7/12 8:42 AM, Brian Schlining wrote:
Hi Christopher,
Thanks for taking the time to respond, it's much appreciated.
I don't
:48 PM, Daniel Crawl wrote:
I can run the MatlabExpression workflow with Kepler 2.3 on
WinXP SP3 (32bit) using Matlab 2009A and Java 1.6.0_31-b05.
Your PATH looks ok (assuming you installed Matlab in C:\ and
not the default C:\Program Files). It's possible that ptmatlab.dll
is not compatible
Hi Albert,
You don't need to run ant force-ptolemy compile unless you change
any of the source files in the ptolemy module.
String parameters need to be quoted, either value or 'value'.
What problems do you have with the parameters? It's easier to
help if you email the workflow.
You can run
Hi Albert,
It looks like the error is from the HSQL database, which is
configured in:
/Applications/Kepler-2.3/Kepler.app/Contents/Resources/Java/common-2.3.0/configs/ptolemy/configs/kepler/configuration.xml.
If you send me this file, I can try to debug the problem.
--dan
On 3/26/12
.
_Christopher
On 2/15/12 1:34 PM, Daniel Crawl wrote:
Hi Edward and Daren,
Listen to Actor is invoked from the context menu on the canvas,
and the exception is also thrown when double-clicking on the Python
Actor to edit the script. These are probably run from the Swing
event thread.
Daren, thanks
just
from the menu, then I presume it is in the Swing event thread...
Edward
On 2/14/12 11:29 AM, Daniel Crawl wrote:
Hi Daren,
I get the same behavior with Windows 7. The error is the same for
both Listen to Actor and editing a Python script:
java.lang.NullPointerException
Hi Daren,
I get the same behavior with Windows 7. The error is the same for
both Listen to Actor and editing a Python script:
java.lang.NullPointerException
at ptolemy.actor.gui.TextEditor.getBackground(TextEditor.java:144)
at java.awt.Window.setBackground(Unknown Source)
at
Hi Muhannad,
It appears that the Oracle JDBC jar was removed from Kepler.
If you copy the jar into core/lib/jar/dbdrivers/, and restart Kepler,
the actor should work correctly.
--dan
On 11/24/11 6:34 AM, Ali, Muhannad wrote:
Hi,
I am trying to get data from Oracle Database using the
Hi Marc and Derik,
There are two bugs occurring here, and I just fixed one of them.
Kepler should no longer give errors about RunWithFeedbackChkBoxAction.
--dan
On 11/3/11 12:45 PM, Derik Barseghian wrote:
Hi Marc,
This is bug#4978 again. You're not doing anything wrong, it's related to
, and perhaps
you installed it some other way (e.g,. building from source)?
On Jun 29, 2011, at 2:15 PM, Daniel Crawl wrote:
Hi Joe,
In Kepler, you can see what $PATH contains by using the
Expression Evaluator in the Tools menu. Run this:
getenv('PATH')
On my mac, $PATH does not contain
28, 2011, at 3:20 PM, Daniel Crawl wrote:
The matlab binary must be in your $PATH.
--dan
On 6/28/11 12:12 PM, Joe Futrelle wrote:
This works.
And it gets me past the stack trace I was getting before! :)
Here's the transcript. I combined advice from two posts upthread.
bash-3.2
Hi Joan,
Here's the relevant error message:
[null] Caused by: ptolemy.kernel.util.IllegalActionException:
Unrecognized option: No parameter exists with name ExecutionId
Does your workflow have a parameter named ExecutionId at the top
level?
--dan
On 6/28/11 5:30 PM, Joan Iglesias
Hi Joe,
Did you edit launchd.conf directly? If so, you'll need to reboot.
Alternatively, you could use launchctl:
launchctl setenv DYLD_LIBRARY_PATH /Applications/MATLAB...
This worked for me. If this still doesn't work for you, try
starting Kepler from a terminal window:
# echo
I forgot to cc kepler-users.
Original Message
Hi Simon,
The WSWithComplexTypes actor should read your manually formatted
string if the inputMechanism is set to simple.
You can get the source by:
mkdir kepler.modules
cd kepler.modules
svn co
Hi Arwa,
The latest provenance documentation is in here:
http://code.kepler-project.org/code/kepler/trunk/modules/provenance/docs/
What do you mean by mapping some actor parameters to user
defined parameters? What are your user defined parameters?
You can record some information before
Hi Kris,
I updated the FTP Client actor so you can set the local directory.
Supporting MGET will take more work. The source code is in:
kepler.modules/actors/src/org/geon/FTPClient.java
Alternatively, you could use the External Execution actor to run
a command-line ftp client such as wget or
: Daniel Crawl [mailto:crawl at sdsc.edu]
Sent: Thursday, January 27, 2011 12:32 AM
To: Madhavi Tikhe
Cc: kepler-users at kepler-project.org
Subject: Re: [kepler-users] How to run kepler Command Line tool to generate
provenance data
Hi Madhavi,
After some investigation, I found
Hi David,
You can use the Expression actor to construct the output
file name as in the attached kar.
--dan
On 10/12/10 1:23 PM, David LeBauer wrote:
Hello,
Can anyone suggest a way to create a parameter, DATE, analagous to
using DATE=`date +%Y%m%d` in bash, and then use it to write my
Hi Roly,
You could try changing the parameter outputMechanism in WSWithComplexTypes
to composite.
If that doesn't work, I can try to fix the actor if you send me your
workflow.
Thanks,
--dan
On 7/12/10 11:38 AM, Roly Poly wrote:
Hi,
I am a new user of Kepler. We have a set of
Hi Christopher,
Are you still maintaining your KeplerFlexClient demo? It's
not running the demo workflows.
Thanks,
--dan
On 3/6/10 1:34 PM, Rick Giuly wrote:
Hello All,
I'm having problems running this demo. I'm not seeing any components
in the components list, and I'm receiving
Hi Eric,
You could try the WebService or WSWithComplexTypes actors.
I'm not familiar with the Soaplab actors. I'll take a look
at them and email you back.
--dan
On 3/5/10 3:10 PM, Eric Wooten wrote:
When trying to set up a soap URL like:
Hi Anne and Tomasz,
What is the default locale on your computer?
I get a similar behavior if I rename uiMenuMappings_en_US.xml,
in modules/gui/resources/configurations/, to, e.g.,
uiMenuMappings_fi_FI.xml, and restart Kepler (and clean out
KeplerData and .kepler).
Chad, what does the
Hi Moses,
You can view the contents of the database using HSQL's
DatabaseManager:
https://dev.kepler-project.org/developers/reference/accessing-hsql/
--dan
On 1/20/10 4:58 AM, Moses Gone wrote:
Dear list,
I am new to Kepler, but I am very interested in the Kepler Provenance
Framework.
Hi Tommy,
Could you send me the text file and the workflow?
Thanks,
--dan
On 12/11/09 2:33 PM, Tommy Stropp wrote:
I am using using the provenance module to generate a text file in one of my
workflows. I am using Windowd Vista. When I use notpad++ to open the text
file, the top line
Hi Tommy,
I've fixed the bug that causes this problem. If you update your
sources and recompile, it should not occur.
--dan
On 12/11/09 3:06 PM, Tommy Stropp wrote:
Sure here you go. In the workflow I am quantile normalizing three files which
I've also included.
Thanks.
- Tommy
Hi Josep,
Josep Morer Mu?oz wrote:
Hi,
I'm working with Provenance API (Queryable interface). Just a few questions:
- Is implemented a method which returns all parameter values given an
execution Id?
No, but should be easy to implement using the parameter_exec table.
- Is
Hi Josep,
Josep Maria Campanera Alsina wrote:
Hello,
I'm very interested with Provenance module and I'm trying to run it with
Kepler.
I have compiled Kepler including provenance sources that you described
in the provenance web page
Hi Arwa,
What compilation errors do you get?
Try 'ant change-to -Dsuite=provenance', which downloads all
the dependent modules and updates modules.txt.
--dan
Jamnagarwala, Arwa Mohmadi wrote:
I have checked out the provenance code using 'ant get -Dmodule=provenance'
I also added an
Hi Michael,
WebService and WSWithComplexTypes do not use port parameters.
I'll look into adding them and let you know when I'm done.
--dan
Michael Wang wrote:
Hello,
I'm trying to figure out how to use port parameters with Web Service Actors.
I've seen examples of other functions (like
Hi Pierre,
For methods with complex inputs or outputs, such as
getSNPByName, you'll have to use WSWithComplexTypes.
I tried it with your web service and found a bug in
the actor. I'll get back to you once it has been fixed.
Thanks,
--dan
Pierre LINDENBAUM wrote:
Hi All,
I'm Pierre
Hi Alberto,
It you don't have Kepler 1.x:
mkdir modules.dir
cd modules.dir
svn co https://code.kepler-project.org/code/kepler/trunk/modules/build-area
cd build-area
ant change-to -Dsuite=kepler-trunk
Then, get the provenance module:
ant get -Dmodule=provenance
ant run
Provenance Recorder
into your installed version of Kepler. Dan, do you
think this would be feasible?
Matt
On Wed, Oct 15, 2008 at 8:59 AM, Daniel Crawl crawl at sdsc.edu
mailto:crawl at sdsc.edu wrote:
Hi Jon,
The nightly build is temporarily not being generated, so you
Hi Jon,
I've updated the XPath actor with a new port that outputs
attribute or text() data. Attached is a modified version
of your workflow that uses this functionality.
Let me know if you have questions,
--dan
Jon Goodall wrote:
Hello,
I'm trying to extract XML attributes from a web
Hi Kyle,
I'm working on a new web service actor that can send and receive complex
data types.
The SignalP service would be a good test; can you give me some example
inputs and
expected outputs for using 'runService'?
Thanks,
--dan
Kyle Ellrott wrote:
I'm new to Kepler, so I'm still
58 matches
Mail list logo
