Re: [kepler-users] Problem with MatlabExpression
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 https://code.kepler-project.org/code/kepler/trunk/modules/build-area cd build-area ant change-to -Dsuite=kepler ant run Documentation about getting Kepler from svn can be found here: https://kepler-project.org/developers/teams/build/systems/build-system/extension-build-system --dan On 3/24/15 8:00 AM, William Hunt wrote: I'm having some problems getting the MatlabExpression actor to work in Kepler. I am running the latest version of Kepler, downloaded yesterday, and I did the module upgrades recommended when I first ran the program.I am running on a Mac with OS X version 10.10.2., with Matlab R2015a installed. I believe I have followed the instructions for setting the environment variable required by the MatlabExpression actor, and I am able to run the MatlabExpression Demo supplied, which would think indicates the configuration is ok. However, if I create a new workflow, and add a MatlabExpression actor to it, I get an error dialog box. I've copied the text of the dialog, as well as the associated stack trace and console output at the end of the email. I get the same behaviour if I restart Kepler, and attempt to add two MatlabExpression actors to a new workspace - the first one seems to add ok, but the second gives the same error. If I delete the first actor, any subsequent attempts to add a MatlabExpresion actor fail in the same way, even if a new workflow has been created. Is this a bug, or am I doing something wrong ? Should I be able to add two MatlabExpression actors ? Thanks, Bill Text of error dialog : *Change Failed Cannot create entity without class name. In [external stream] at line 2 and column 26* If I click the Display Stack Trace button on the dialog, I get this : com.microstar.xml.XmlException: Cannot create entity without a class name. in [external stream] at line 2 and column 26 at ptolemy.moml.MoMLParser._checkForNull(MoMLParser.java:4013) at ptolemy.moml.MoMLParser._createEntity(MoMLParser.java:4194) at ptolemy.moml.MoMLParser.startElement(MoMLParser.java:2697) at com.microstar.xml.XmlParser.parseElement(XmlParser.java:921) at com.microstar.xml.XmlParser.parseContent(XmlParser.java:1104) at com.microstar.xml.XmlParser.parseElement(XmlParser.java:924) at com.microstar.xml.XmlParser.parseDocument(XmlParser.java:481) at com.microstar.xml.XmlParser.doParse(XmlParser.java:159) at com.microstar.xml.XmlParser.parse(XmlParser.java:132) at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1540) at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1512) at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1668) at ptolemy.moml.MoMLChangeRequest._execute(MoMLChangeRequest.java:289) at ptolemy.kernel.util.ChangeRequest.execute(ChangeRequest.java:171) at ptolemy.kernel.util.NamedObj._executeChangeRequests(NamedObj.java:2559) at ptolemy.kernel.util.NamedObj.executeChangeRequests(NamedObj.java:725) at ptolemy.kernel.util.NamedObj.requestChange(NamedObj.java:1776) at ptolemy.actor.CompositeActor.requestChange(CompositeActor.java:1957) at ptolemy.vergil.basic.EditorDropTargetListener.drop(EditorDropTargetListener.java:394) at java.awt.dnd.DropTarget.drop(DropTarget.java:434) at sun.awt.dnd.SunDropTargetContextPeer.processDropMessage(SunDropTargetContextPeer.java:519) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchDropEvent(SunDropTargetContextPeer.java:832) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchEvent(SunDropTargetContextPeer.java:756) at sun.awt.dnd.SunDropTargetEvent.dispatch(SunDropTargetEvent.java:30) at java.awt.Component.dispatchEventImpl(Component.java:4633) at java.awt.Container.dispatchEventImpl(Container.java:2142) at java.awt.Component.dispatchEvent(Component.java:4604) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4618) at java.awt.LightweightDispatcher.processDropTargetEvent(Container.java:4353) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4204) at java.awt.Container.dispatchEventImpl(Container.java:2128) at java.awt.Window.dispatchEventImpl(Window.java:2492) at java.awt.Component.dispatchEvent(Component.java:4604) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:717) at java.awt.EventQueue.access$400(EventQueue.java:82) at java.awt.EventQueue$2.run(EventQueue.java:676) at java.awt.EventQueue$2.run(EventQueue.java:674) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:86) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:97) at java.awt.EventQueue$3.run(EventQueue.java:690) at java.awt.EventQueue$3.run(EventQueue.java:688) at java.security.AccessController.doPrivileged(Native Method) at
[kepler-users] bioKepler 1.1 released
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 contains a set of Kepler actors, called bioActors, which are specialized for running bioinformatics tools along with Kepler directors for distributed data-parallel (DDP) execution on Big Data platforms such as Hadoop and Spark. bioKepler 1.1 includes the following new features since 1.0: - Support for Apache Spark (http://spark.apache.org) and Hadoop 2 - DDP Director supporting multiple execution platforms - Execution of DDP workflows in the same JVM as Kepler - Token input/output formats to directly transfer data between Kepler workflows and Big Data platforms - and many bug fixes bioKepler 1.1 can be installed using the Module Manager in Kepler 2.4. If you have an older version of Kepler, we recommend that you first download and install Kepler 2.4, and then use the Module Manager to install bioKepler 1.1. Kepler 2.4 can be downloaded from the Kepler website (https://kepler-project.org/users/downloads). bioKepler is built on top of the DDP, provenance, reporting, and workflow run manager modules, and does not require a separate installation of these modules. The bioKepler website (http://www.biokepler.org) provides more information about the project including the bioKepler User Guide and descriptions of the bioActors and demo workflows. We are building virtual machine images with bioKepler 1.1 for Amazon EC2 and OpenStack. These images are based on CloudBioLinux and include many bioinformatics tools. A separate announcement will be sent when the virtual machine images are completed. ___ Kepler-users mailing list Kepler-users@kepler-project.org http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
Re: [kepler-users] default open directory
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 configuration file? It looks to me it¹s hardcoded. Cheers, Vincenzo ___ Kepler-users mailing list Kepler-users@kepler-project.org http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users ___ Kepler-users mailing list Kepler-users@kepler-project.org http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
Re: [kepler-users] Web Service Tasks with Different Port Names
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 12:24 PM, Bruno Bastos wrote: Hello everybody, I'm having a problem while creating a WSWithComplexTypes Task on Kepler and maybe you can help me. The problem is due to the name of the ports that are automatically generated on Kepler. Kepler automatically generates the name result for the output port, but I tried to change it for r, since its more legible. After changing the port name I and exported the workflow as an XML file and it seems to be OK. But when I open this workflow on another machine Kepler automatically renames the port to result again, and the connections bound to this port are lost. Is there any way to tell Kepler to stop generating the ports automatically for a WSWithComplexTypes Task? Thanks. ___ Kepler-users mailing list Kepler-users@kepler-project.org http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users ___ Kepler-users mailing list Kepler-users@kepler-project.org http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
Re: [kepler-users] Trouble closing down Kepler Release
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 instances. When you are done, exit all the instances, and run: kepler.sh -hsql stop --dan On 10/25/13 11:55 AM, Jonathan Boright wrote: Hi all, I seem to be having trouble closing down Kepler. When I attempt to close Kepler (either file/quit, or closing the last open workflow window) The system hangs for a while and then gives the following message: [image: Inline image 1] I'm working on the stable 2.4 branch built on OSx Mountain Lion. I recently updated (ant update). Build info below: .../build-area$ svn info URL: https://code.kepler-project.org/code/kepler/releases/release-branches/build-area-2.4 Repository Root: https://code.kepler-project.org/code/kepler Repository UUID: edc41a2b-3e5c-0410-9d3f-8540a70682f1 Revision: 32509 Node Kind: directory Schedule: normal Last Changed Author: jianwu Last Changed Rev: 32503 Last Changed Date: 2013-10-21 18:53:14 -0400 (Mon, 21 Oct 2013) Any ideas? Thanks Jon - Jonathan Boright Research Scientist ISciences, LLC ___ Kepler-users mailing list Kepler-users@kepler-project.org http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users ___ Kepler-users mailing list Kepler-users@kepler-project.org http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
Re: [kepler-users] Trouble closing down Kepler Release
What does Kepler print to the terminal when it starts? Can you send me the full output? Does it print something like: INFO (org.kepler.util.sql.HSQL:_getConnection:654) started HSQL server at jdbc:hsqldb:hsql://localhost:. If you don't see this, then Kepler is connecting to an HSQL server running in another process. Does the error message always occur when you quit Kepler or only sometimes? You could try deleting $HOME/.kepler and renaming $HOME/KeplerData/modules to something else. --dan On 10/25/13 12:32 PM, Jonathan Boright wrote: Thanks for the responses. I'm sorry I didn't post the stack trace up front. I've added it to the end of this e-mail. I'm not running more than one instance of Kepler, and I'm not (intentionally) using HSQL at all. I find that this happens only when running on OSX, I have cygwin installs (same revision number) that close just fine... Thanks for your time. J stack trace below... java.sql.SQLException: socket creation error at org.hsqldb.jdbc.Util.sqlException(Unknown Source) at org.hsqldb.jdbc.jdbcConnection.init(Unknown Source) at org.hsqldb.jdbcDriver.getConnection(Unknown Source) at org.hsqldb.jdbcDriver.connect(Unknown Source) at java.sql.DriverManager.getConnection(DriverManager.java:579) at java.sql.DriverManager.getConnection(DriverManager.java:221) at org.kepler.util.sql.HSQL._getConnectionForServer(HSQL.java:837) at org.kepler.util.sql.HSQL.shutdownServers(HSQL.java:338) at org.kepler.module.core.Shutdown.shutdownModule(Shutdown.java:56) at org.kepler.Kepler._initializeModules(Kepler.java:704) at org.kepler.Kepler.access$100(Kepler.java:88) at org.kepler.Kepler$Shutdown.shutdown(Kepler.java:880) at org.kepler.util.ShutdownNotifier.shutdown(ShutdownNotifier.java:46) at org.kepler.gui.KeplerGraphFrame.dispose(KeplerGraphFrame.java:201) at ptolemy.actor.gui.TableauFrame._close(TableauFrame.java:722) at ptolemy.actor.gui.PtolemyFrame._close(PtolemyFrame.java:286) at ptolemy.vergil.basic.BasicGraphFrame._close(BasicGraphFrame.java:2078) at ptolemy.vergil.basic.ExtendedGraphFrame._close(ExtendedGraphFrame.java:248) at ptolemy.vergil.actor.ActorGraphFrame._close(ActorGraphFrame.java:380) at ptolemy.gui.Top$CloseWindowAdapter.windowClosing(Top.java:1955) at java.awt.AWTEventMulticaster.windowClosing(AWTEventMulticaster.java:349) at java.awt.AWTEventMulticaster.windowClosing(AWTEventMulticaster.java:349) at java.awt.Window.processWindowEvent(Window.java:2051) at javax.swing.JFrame.processWindowEvent(JFrame.java:296) at java.awt.Window.processEvent(Window.java:2009) at java.awt.Component.dispatchEventImpl(Component.java:4861) at java.awt.Container.dispatchEventImpl(Container.java:2287) at java.awt.Window.dispatchEventImpl(Window.java:2719) at java.awt.Component.dispatchEvent(Component.java:4687) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:729) at java.awt.EventQueue.access$200(EventQueue.java:103) at java.awt.EventQueue$3.run(EventQueue.java:688) at java.awt.EventQueue$3.run(EventQueue.java:686) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:87) at java.awt.EventQueue$4.run(EventQueue.java:702) at java.awt.EventQueue$4.run(EventQueue.java:700) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:699) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:242) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:161) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:150) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:146) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:138) at java.awt.EventDispatchThread.run(EventDispatchThread.java:91) - Jonathan Boright Research Scientist ISciences, LLC 61 Main Street, Suite 200 Burlington, VT 05401 802 864-2999 bori...@isciences.com http://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 by running the HSQL databases in a separate process. First run: kepler.sh -hsql start then start the Kepler instances. When you are done, exit all the instances, and run: kepler.sh -hsql stop --dan On 10/25/13 11:55 AM, Jonathan Boright wrote: Hi all, I seem to be having trouble closing down Kepler. When I attempt to close Kepler (either file/quit, or closing the last open workflow window) The system hangs for a while and then gives the following message: [image: Inline image 1
Re: [kepler-users] Kepler Workflow dependency error
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 On 9/25/13 5:53 PM, Mullis, Tristan Lloyd wrote: To whom it may concern I'm having an error in Kepler 2.4 that doesn't always happen, sometimes it works just fine. Otherwise its the same type of error, but is different places. I suspect its related to how I'm concatenating parameter strings, because that's always what it complains about. I'm hoping someone will be able to clue me as to what the problem is. Any feed back at all will be helpful. I have attached the workflow in question, although you will not be able to run it. I have also attach error messages which are all from different runs. Thanks in advance, Tristan ___ Kepler-users mailing list Kepler-users@kepler-project.org http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users ___ Kepler-users mailing list Kepler-users@kepler-project.org http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
[kepler-users] bioKepler 1.0 released
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 contains a set of Kepler actors, called “bioActors”, which are specialized for running bioinformatics tools along with Kepler directors for distributed data-parallel (DDP) execution on Hadoop and Stratosphere engines. Additionally, over 40 example workflows demonstrating how to use these actors and directors have been packaged in this first release of bioKepler. bioKepler can be installed using the Module Manager in Kepler 2.4. If you have an older version of Kepler, we recommend that you first download and install Kepler 2.4, and then use the Module Manager to install bioKepler 1.0. Kepler 2.4 can be downloaded from the Kepler website (https://kepler-project.org/users/downloads). bioKepler is built on top of DDP, provenance, reporting, and workflow run manager modules, and does not require a separate installation of these modules. The bioKepler website (http://www.biokepler.org) provides more information about the project including the bioKepler User Guide and descriptions of the bioActors and demo workflows. We are building virtual machine images with bioKepler 1.0 for Amazon EC2 and OpenStack. These images are based on CloudBioLinux and include many bioinformatics tools. A separate announcement will be sent when the virtual machine images are completed. ___ Kepler-users mailing list Kepler-users@kepler-project.org http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
Re: [kepler-users] Multiple users run multiple workflows on shared computer
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 multiple workflows on the same
computer.
I will be releasing a patch for Kepler 2.4 with this fix for the
upcoming bioKepler release, which should be in the next week or two.
Once it's released, I'll update the instructions on the wiki.
--dan
On 8/7/13 6:01 AM, Marcin Plociennik wrote:
Hi,
We have similar case, as you have and but we are running Kepler 2.3.
Please find below what is our procedure, that works for our
applications/users.
I'm convinced others might give you better way to do it.
1. We are using central installation of the Kepler on the machine
2. We generate unique value for location of each instance of Kepler
running for each user
export HOME=$USER_HOME/kepler_tmp/${UNIQUE_VALUE}
export KEPLER_NEW_HOME=${HOME}/${KEPLER_SHADOW_DIR_NAME}
3. We do symbolic links to the central installation in that temporary
directory
4. We change configuration files to prevent mulitple kepler instances
from using the same hsql DB
(every single instance of kepler will be using separated hsql database
file)
(/common-2.3.0/resources/configurations/configuration.xml)
(/core-2.3.0/resources/configurations/configuration.xml )
5. We replace all necessary jars with provided kepler.jar with a patch
(there was one line needed to be patched in 2.3, I think it is not the
case for 2.4, but I'm not sure)
6. We run each instance of Kepler like that:
java -Duser.home=${HOME} -classpath
${KEPLER_NEW_HOME}/build-area/lib/ant.jar:${KEPLER_NEW_HOME}/kepler.jar
org.kepler.build.runner.Kepler -runwf -nogui ${PARAMETERS} -dir_path
${CURRENT_DIR}/ -nocache ${CURRENT_DIR}/${WORKFLOW_LOCATION}
${CURRENT_DIR}/kepler.log
I hope this will help you.
regards
Marcin Plociennik
--
Marcin Plociennik
Poznan Supercomputing and Networking Center
61-704 Poznan, ul. Noskowskiego 10 POLAND
phone (+48 61) 8582181
e-mail: marc...@man.poznan.pl
W dniu 2013-08-07 00:59, Lynch, Vickie E. pisze:
Hi,
We are developing a Kepler workflow for users that will run on a
shared computer for many hours/days optimizing models of experimental
data. Our requirement is for multiple users to run kepler workflows
on a shared machine and those users run multiple workflows. We have
made the changes on this webpage,
https://kepler-project.org/developers/reference/accessing-hsql, so
that kepler will run for multiple users, but now each user can only
run one workflow at a time. Much time has been invested in developing
a complicated workflow and we did not find this problem until two
developers started running on the shared machine. It is not mentioned
in the user's manual.
Is there some way to turn off the HSQL database? Will this problem be
fixed in a future release? Is there some workaround?
Vickie E. Lynch
Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN 37831-6454
(865)250-4795, Bldg. 8600, Room C-509-F, MS6454, lync...@ornl.gov
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Re: [kepler-users] Kepler-2.3 Ljava/lang/String problems
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 cd build-area ant change-to -Dsuite=kepler-2.3 ant run To run the sensor view suite: ant change-to -Dsuite=sensor-view-0.9 ant run For the second issue, are you running a SPAN server or simulator? If not, you'll need to start one. For more information, see the sensor view documentation: https://code.kepler-project.org/code/kepler/trunk/modules/sensor-view/docs/sensor-view.pdf --dan On 6/27/13 7:34 AM, JohanScholtz wrote: I am running Kepler 2.3 using Linux Mint terminal commands Issue 1: Following the guidelines: starting Kepler2.3 and SensorView works fine, when separately initiated in 2 terminals. Start: SensorView in terminal 1 . Kepler 2.3 (Trunk) in terminal 2. The last command in terminal 2 is/ant run - and Kepler2.3 starts with SensorView functioning -- with Localhost connections. But, when I start 2.3 and try to run any of my MyWorkflows it starts with: /[Exception// // //Because:// // // Ptolemy.util.StringUtilities.isB=ValidIdentifier(Ljava/lang/String;)Z errors.// // //...// // //Caused by: java.lang.NoSuchMethodError:Ptolemy.util.StringUtilties.isValidIdenfier(Ljava/lang/String;)Z ]/ Issue2: (I should not bundle this in the same email...) Using Kepler-2.4 in MAC works fine. But when I go to ModuleManager and download SensorView, add a few sensor actors and director- the ssh Localhost connection has problems? With the same Localhost problems in Data Logger. [/Unable to connect to control port in .Unnamed1.Sensor Because Unknown SPAN host:http://localhost/] Any advice please? ___ Kepler-users mailing list Kepler-users@kepler-project.org http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users ___ Kepler-users mailing list Kepler-users@kepler-project.org http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
Re: [kepler-users] Ctrl-c to exit
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? /usr/local/kepler/kepler.sh -runwf /tmp/code/kepler/Strategist.xml The base dir is /usr/local/kepler-2.4 Kepler.run going to run.setMain(org.kepler.Kepler) JVM Memory = 256m 1000m [null] Not checking for patches. [null] Kepler Initializing... [null] INFO (org.kepler.actor.job.JobStatus:initialize:315) Initializing lastStatusCode to null [null] INFO (org.kepler.actor.job.JobStatus:initialize:315) Initializing lastStatusCode to null [null] INFO (org.kepler.actor.job.JobStatus:initialize:315) Initializing lastStatusCode to null [null] 15437 ms. Memory: 492352K Free: 295891K (60%) [null] Done. [null] Ctrl-c to exit. Vickie E. Lynch Oak Ridge National Laboratory, PO Box 2008, Oak Ridge, TN 37831-6454 (865)250-4795, Bldg. 8600, Room C-509-F, MS6454, lync...@ornl.gov ___ Kepler-users mailing list Kepler-users@kepler-project.org http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users ___ Kepler-users mailing list Kepler-users@kepler-project.org http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
Re: [kepler-users] Job Submission Example
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. --dan On 5/16/13 10:36 AM, Mullis, Tristan Lloyd wrote: To whom it may concern I'm a graduate student working on a research project, and I was wondering if I could get a example workflow for a Job Submission workflow that works on Kepler 2.4. I don't know what the problem is, but the example I have out of the Kepler User manual in Chapter 7.3.1 that was implemented by another student complains about being deadlocked when attempting to run it, and what I'm currently working on that uses pieces of it is complaining about graph is not consistent under the sdf domain in the wait for finish section at the Boolean input. Thanks, Tristan ___ Kepler-users mailing list Kepler-users@kepler-project.org http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users ___ Kepler-users mailing list Kepler-users@kepler-project.org http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
Re: [kepler-users] Migrating from trunk to 2.4 branch
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 built from the trunk to the recently released stable 2.4 branch. When I try to open any of my workflows built on the trunk, however, Kepler can't see any of the required modules becasue the module names now all end in -2.4 or -2.3. How do I get around this? As usual, many thanks for your continued help. Jon Boright ___ Kepler-users mailing list Kepler-users@kepler-project.org http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
[kepler-users] Reporting 2.4 suite released
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 work with Kepler 2.4. Reporting 2.4 can be installed using the Module Manager in Kepler 2.4 and Kepler 2.3. If you have an older version of Kepler, we recommend that you first download and install Kepler 2.4, and then use the Module Manager to install Reporting 2.4. Kepler 2.4 can be downloaded from: https://kepler-project.org/users/downloads The Reporting 2.4 suite is comprised of the following modules: - Reporting: creates PDF reports of workflow results. - Workflow Run Manager: searches, tags, exports, imports past workflow runs. - Provenance: captures and queries workflow execution history. - Tagging: manages and organizes workflows and workflow executions. - Workflow Scheduler: schedules workflows for periodic execution on a remote server. Documentation for these modules is available from the Help = Modules Documentation menu in Kepler, or online: https://kepler-project.org/users/documentation Details on bugs fixed in this release may be found here: https://projects.ecoinformatics.org/ecoinfo/projects/kepler-12/issues?utf8=%E2%9C%93set_filter=1f%5B%5D=fixed_version_idop%5Bfixed_version_id%5D=%3Dv%5Bfixed_version_id%5D%5B%5D=143f%5B%5D=status_idop%5Bstatus_id%5D=cf%5B%5D=c%5B%5D=trackerc%5B%5D=statusc%5B%5D=priorityc%5B%5D=subjectc%5B%5D=assigned_toc%5B%5D=updated_ongroup_by= ___ Kepler-users mailing list Kepler-users@kepler-project.org http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
Re: [kepler-users] Question about the Display actor and the composite class
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 generating the Composite, putting just in and out port 2. Inside composite I'm connecting in and out, 3. I'm saving that composite to xml (so only the internal part of composite) to place on the Kepler path 4. I'm editing the xml file and changing the entity to class for the composite. That way as you know I can use that composite in many place, and the changes would be applied to all the instances. 5. I can use that actor in the workflows , I can edit and add there inside most of the actors including other composite, and it works 6. The only problem I have so far is with the Display Actor: When I try to add it to such created composite I'm getting error that is pasted below I know maybe it is not standard way but, maybe you will know how to solve that problem, or what is the reason for that thanks in advance regards Marcin ptolemy.kernel.util.InternalErrorException: Failed to initialize implementation in .Unnamed1.test.Display Because: Attempt to insert object named _windowProperties into a container that already contains an object with that name. at ptolemy.actor.lib.gui.Display._getImplementation(Display.java:396) at ptolemy.actor.lib.gui.Display.attributeChanged(Display.java:205) at ptolemy.data.expr.Variable._setTokenAndNotify(Variable.java:1992) at ptolemy.data.expr.Variable._evaluate(Variable.java:1646) at ptolemy.data.expr.Variable._propagate(Variable.java:1732) at ptolemy.data.expr.Variable.validate(Variable.java:1430) at ptolemy.moml.MoMLParser.endDocument(MoMLParser.java:808) at com.microstar.xml.XmlParser.doParse(XmlParser.java:162) at com.microstar.xml.XmlParser.parse(XmlParser.java:132) at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1538) at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1510) at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1666) at ptolemy.moml.MoMLChangeRequest._execute(MoMLChangeRequest.java:289) at ptolemy.kernel.util.ChangeRequest.execute(ChangeRequest.java:171) at ptolemy.kernel.util.NamedObj.executeChangeRequests(NamedObj.java:738) at ptolemy.kernel.util.NamedObj.requestChange(NamedObj.java:1778) at ptolemy.actor.CompositeActor.requestChange(CompositeActor.java:1922) at ptolemy.vergil.basic.EditorDropTargetListener.drop(EditorDropTargetListener.java:369) at java.awt.dnd.DropTarget.drop(DropTarget.java:434) at sun.awt.dnd.SunDropTargetContextPeer.processDropMessage(SunDropTargetContextPeer.java:519) at sun.awt.X11.XDropTargetContextPeer.processDropMessage(XDropTargetContextPeer.java:165) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchDropEvent(SunDropTargetContextPeer.java:832) at sun.awt.dnd.SunDropTargetContextPeer$EventDispatcher.dispatchEvent(SunDropTargetContextPeer.java:756) at sun.awt.dnd.SunDropTargetEvent.dispatch(SunDropTargetEvent.java:30) at java.awt.Component.dispatchEventImpl(Component.java:4517) at java.awt.Container.dispatchEventImpl(Container.java:2097) at java.awt.Component.dispatchEvent(Component.java:4488) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4575) at java.awt.LightweightDispatcher.processDropTargetEvent(Container.java:4310) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4161) at java.awt.Container.dispatchEventImpl(Container.java:2083) at java.awt.Window.dispatchEventImpl(Window.java:2489) at java.awt.Component.dispatchEvent(Component.java:4488) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:668) at java.awt.EventQueue.access$400(EventQueue.java:81) at java.awt.EventQueue$2.run(EventQueue.java:627) at java.awt.EventQueue$2.run(EventQueue.java:625) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:98) at java.awt.EventQueue$3.run(EventQueue.java:641) at java.awt.EventQueue$3.run(EventQueue.java:639) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87) at java.awt.EventQueue.dispatchEvent(EventQueue.java:638) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:269) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:184) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:174) at
[kepler-users] Kepler 2.4 released
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 command line. - Display and plotting actors write their text or images to files when run headless with the -redirectgui option. - Workflow demos now appear in the actor library. - New workflow demos for branching and looping. - Documentation added for many actors and parameters. - Recent history added to the file menu. - Entities in a workflow can now be searched in the outline tab. - Over 100 additional Ptolemy actors are included in the actor library. - The Job actors now support the LSF scheduler. - The SDF Director now defaults to one iteration. Kepler 2.4 can be downloaded from: https://kepler-project.org/users/downloads If you already have Kepler 2.3, you can use the Module Manager to upgrade to 2.4. If you have Kepler 2.2 or older, we do not recommend using the Module Manager; instead download the installer (there's no need to uninstall the old version). For a detailed list of all bug fixes and enhancements included in this release, see: https://projects.ecoinformatics.org/ecoinfo/projects/kepler-12/issues?c%5B%5D=trackerc%5B%5D=statusc%5B%5D=priorityc%5B%5D=subjectc%5B%5D=assigned_toc%5B%5D=updated_onf%5B%5D=status_idf%5B%5D=fixed_version_idf%5B%5D=group_by=op%5Bfixed_version_id%5D=%3Dop%5Bstatus_id%5D=cper_page=100set_filter=1utf8=%E2%9C%93v%5Bfixed_version_id%5D%5B%5D=134 ___ Kepler-users mailing list Kepler-users@kepler-project.org http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
Re: [kepler-users] cannot open python actor editor
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 wrote: Hi, I am having trouble with the python actor. I cannot seem to edit my python code in the python actor. When I try to open the editor it shows error (pythonactor_error.png, pythonactor_error1.png) and when I try to open the actor it shows these error pythonactor_error2.png, pythonactor_error3.png. I am really confuse I use to be able to use edit it until I format my computer recently and reinstall kepler. What seems to be the problem ? kian wee ___ Kepler-users mailing list Kepler-users@kepler-project.org http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users ___ Kepler-users mailing list Kepler-users@kepler-project.org http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
Re: [kepler-users] (no subject)
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 composite SOAP type.
Can you send me your workflow?
--dan
On 2/26/13 8:12 PM, 袁钢 wrote:
Hello,everybody,
I have some troubles in using the WSWithComplexTypes Actors.
HelloWorld2.wsdl is a BPEL service which is provided by the Apache
ODE's example, and if I set the wsdl properties of the actor with it , the
actor can identify the port part's type successfully and the process can
run well.
The process BpelHello.bpel is modeled by the Eclipse BPEL Designer
Tools, and it produces the file BpelHelloArtifacts.wsdl which is in the
attachment.The process can run successfully in ODE Engine. And it also can
run successfully through Command Line of SENDSOAP instruction . If I set
the wsdl properties of the actor with this wsdl file , the actor identify
the port part's type is XMLTOKEN, and i draw the process as the
wrong.png‘s show which located in the attachment ,it runs in error, the
exceptions as follow:
ptolemy.kernel.util.IllegalActionException: Error invoking service.
in .callBpel.WSWithComplexTypes
Because:
Unexpected element in SOAP body: message {
http://ode/bpel/unit-test.wsdl}process element {
http://ode/bpel/unit-test.wsdl}BpelHelloRequest.
at org.sdm.spa.WSWithComplexTypes.fire(WSWithComplexTypes.java:403)
at ptolemy.actor.AtomicActor.iterate(AtomicActor.java:466)
at
ptolemy.actor.sched.StaticSchedulingDirector.fire(StaticSchedulingDirector.java:208)
at ptolemy.actor.CompositeActor.fire(CompositeActor.java:450)
at ptolemy.actor.Manager.iterate(Manager.java:767)
at ptolemy.actor.Manager.execute(Manager.java:352)
at ptolemy.actor.Manager.run(Manager.java:1182)
at ptolemy.actor.Manager$PtolemyRunThread.run(Manager.java:1725)
Caused by: Unexpected element in SOAP body: message {
http://ode/bpel/unit-test.wsdl}process element {
http://ode/bpel/unit-test.wsdl}BpelHelloRequest.
at
org.apache.axis.message.SOAPFaultBuilder.createFault(SOAPFaultBuilder.java:222)
at
org.apache.axis.message.SOAPFaultBuilder.endElement(SOAPFaultBuilder.java:129)
at
org.apache.axis.encoding.DeserializationContext.endElement(DeserializationContext.java:1087)
at org.apache.xerces.parsers.AbstractSAXParser.endElement(Unknown Source)
at org.apache.xerces.impl.XMLNSDocumentScannerImpl.scanEndElement(Unknown
Source)
at
org.apache.xerces.impl.XMLDocumentFragmentScannerImpl$FragmentContentDispatcher.dispatch(Unknown
Source)
at
org.apache.xerces.impl.XMLDocumentFragmentScannerImpl.scanDocument(Unknown
Source)
at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
at org.apache.xerces.parsers.XML11Configuration.parse(Unknown Source)
at org.apache.xerces.parsers.XMLParser.parse(Unknown Source)
at org.apache.xerces.parsers.AbstractSAXParser.parse(Unknown Source)
at org.apache.xerces.jaxp.SAXParserImpl$JAXPSAXParser.parse(Unknown Source)
at javax.xml.parsers.SAXParser.parse(Unknown Source)
at
org.apache.axis.encoding.DeserializationContext.parse(DeserializationContext.java:227)
at org.apache.axis.SOAPPart.getAsSOAPEnvelope(SOAPPart.java:696)
at org.apache.axis.Message.getSOAPEnvelope(Message.java:435)
at
org.apache.axis.handlers.soap.MustUnderstandChecker.invoke(MustUnderstandChecker.java:62)
at org.apache.axis.client.AxisClient.invoke(AxisClient.java:206)
at org.apache.axis.client.Call.invokeEngine(Call.java:2784)
at org.apache.axis.client.Call.invoke(Call.java:2767)
at org.apache.axis.client.Call.invoke(Call.java:1792)
at
org.sdm.spa.WSWithComplexTypes._invokeMethod(WSWithComplexTypes.java:1644)
at org.sdm.spa.WSWithComplexTypes.fire(WSWithComplexTypes.java:398)
... 7 more
Caused by: AxisFault
faultCode: {java:package org.apache.ode.axis2}org.apache.ode.axis2.OdeFault
faultSubcode:
faultString: Unexpected element in SOAP body: message {
http://ode/bpel/unit-test.wsdl}process element {
http://ode/bpel/unit-test.wsdl}BpelHelloRequest.
faultActor:
faultNode:
faultDetail:
{}Exception:org.apache.ode.axis2.OdeFault: Unexpected element in SOAP body:
message {http://ode/bpel/unit-test.wsdl}process element {
http://ode/bpel/unit-test.wsdl}BpelHelloRequest.
at
org.apache.ode.axis2.ODEService.onAxisMessageExchange(ODEService.java:146)
at
org.apache.ode.axis2.hooks.ODEMessageReceiver.invokeBusinessLogic(ODEMessageReceiver.java:69)
at
org.apache.ode.axis2.hooks.ODEMessageReceiver.invokeBusinessLogic(ODEMessageReceiver.java:52)
at
org.apache.axis2.receivers.AbstractMessageReceiver.receive(AbstractMessageReceiver.java:96)
at org.apache.axis2.engine.AxisEngine.receive(AxisEngine.java:145)
at
org.apache.axis2.transport.http.HTTPTransportUtils.processHTTPPostRequest(HTTPTransportUtils.java:275)
at org.apache.axis2.transport.http.AxisServlet.doPost(AxisServlet.java:120)
at
Re: [kepler-users] Problems running workflows with newer revisions
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: Jonathan, As Edward wrote, a small example would help. One thing to would be to try the brute force method of determining what change or changes caused the problem. The way to do this is to do a binary search of the tree by checking out different versions and testing them. It can take awhile, but the amount of actual effort is low. If you are using only actors that are in Ptolemy II and you are not using Kepler-only actors, then you could export your model as MoML, verify that the model works in r64636 of Ptolemy II and fails in r65658 and then check out an intermediate version of Ptolemy II. (65658-64636)/2+64636 = 65147 I would do this with svn co -r 65147 https://source.eecs.berkeley.edu/svn/chess/ptII/trunk ptII.65147 cd ptII.65147 export PTII=`pwd` ./configure ant Then rerun the model and try either an earlier or later version and repeat the above. You could also look at the ChangeLog for the ptII tree at http://chess.eecs.berkeley.edu/ptexternal/nightly/ChangeLog.txt You could also try diffing ptolemy/directors/pn between the version that worked and the version that failed. If your tree uses Kepler actors, then you will need to use the Kepler build system to check out different versions of Kepler. Offhand, I'm not sure how to do that. _Christopher On 2/13/13 8:20 PM, Edward A. Lee wrote: This sounds like a threading bug. If you would like to know how I feel about threads, read this: http://ptolemy.eecs.berkeley.edu/publications/papers/06/problemwithThreads/ If you are using only built-in actors, then it really would be great to have reproducible example. And I would really like to fix it. If you have custom actors, then we probably can't help... Without a reproducible example, threading bugs are impossible to fix. (sometimes even with a reproducible example they are impossible to fix). Threads are a _really bad_ concurrency model. Sadly, they dominate concurrency today... Edward On 2/13/13 2:33 PM, Jonathan Boright wrote: Dear Kepler users, We have been using kepler for a while now and have developed a number of fairly large and complex workflows. We recently updated kepler and have found that our old workflows 'hang' after only a short time (less than a minute). As far as I can tell they don't always hang in the same spot. We have been trying to create a model to post on this forum that demonstrates this behavior, but as soon as we pare the model down to a size small enough to post and strip out our customized code... they tend to work fine. So in lieu of an example model I'll attempt to describe the strucure of our models, the symptoms, and some avenues that we have used to try and narrow down the issues. Our old models run in the following svn revision(s): svn info details: Working Copy Root Path: /cygdrive/c/Kepler/svn/[build-area etc.] Revision: 30654 Working Copy Root Path: /cygdrive/c/Kepler/svn/ptolemy/src Revision: 64636 They 'hang' when run in the following revision(s) svn info details: Working Copy Root Path: /cygdrive/c/Kepler/svn/build-area Revision: 31428 - 31431 (current) Working Copy Root Path: /cygdrive/c/Kepler/svn/ptolemy/src Revision: *65654 - *65658 (current) I'll describe one particular model as an example: The workflow is a hydrlogic model which has the following attributes: - a PN director. - the most comon token is a double matrix token ([double]) of size 360x270. - many composite actors, some with sdf directors (opaque) and some without directors (transparant). - an opaque composite actor made into a class object with many (~30?) instances of this class. - multiple Nondeterministic Merge actors (to re-use tokens) When this model is run in newer revisions, it runs for a bit (usually less than 1 minute) and then just stops going forwards... no error messages... just hung. When we then attempt to stop the model it gives the message wrapping up but hangs there. Sometimes I'm able to close the window, sometimes I need to kill kepler throught the task-manager... We have noticed some changes in kepler/ptolemy... for example, it is now possible to make transparant composite actors into classes (which is useful... thank you). We hypothesized that perhaps something changed in the way that the PN director handles the opaque composite actors, and that this change is causing the log-jam (or an un-satisfied 'race condition'?) ... so we removed all of the sdf directors making all of the composite actors transparant. This made some difference in some of our smaller workflows but still the larger noes hang... I'll end this note here and see if I can come up with a concrete example. In the mean time, any new perspectives or thoughts would be helpful. Thanks in
Re: [kepler-users] Can save workflow as xml, but not as kar.
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 trace below). Kepler Version: Trunk (rev 31428) OS: Windows 7 Pro (x64) Java: 1.7.0_11 The problem appears to be with the class. I can save a simpler workflow that is identical, but does not use a class. Note that C:\Kepler\svn\ is my Kepler root directory. Any help would be much appreciated. -- Tom ptolemy.kernel.util.IllegalActionException: Cannot find class: TestClass Because: -- C:\Kepler\svn\TestClass.xml (The system cannot find the file specified) -- XML file not found relative to classpath. -- C:\Kepler\svn\TestClass.xml C:\Kepler\svn\TestClass.xml (The system cannot find the file specified) in file:/C:/Kepler/svn/ at line 176 and column 43 at ptolemy.moml.MoMLParser._createEntity(MoMLParser.java:4098) at ptolemy.moml.MoMLParser.startElement(MoMLParser.java:2697) at com.microstar.xml.XmlParser.parseElement(XmlParser.java:921) at com.microstar.xml.XmlParser.parseContent(XmlParser.java:1104) at com.microstar.xml.XmlParser.parseElement(XmlParser.java:924) at com.microstar.xml.XmlParser.parseDocument(XmlParser.java:481) at com.microstar.xml.XmlParser.doParse(XmlParser.java:159) at com.microstar.xml.XmlParser.parse(XmlParser.java:132) at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1556) at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1512) at ptolemy.moml.MoMLParser.parse(MoMLParser.java:1655) at org.kepler.objectmanager.ActorMetadata.lookForMoml(ActorMetadata.java:1596) at org.kepler.objectmanager.ActorMetadata.getActorClass(ActorMetadata.java:1668) at org.kepler.objectmanager.ActorMetadata.init(ActorMetadata.java:296) at org.kepler.objectmanager.cache.ActorCacheObject.getMetadata(ActorCacheObject.java:292) at org.kepler.objectmanager.cache.ActorCacheObject.getObject(ActorCacheObject.java:180) at org.kepler.kar.handlers.ActorMetadataKAREntryHandler.open(ActorMetadataKAREntryHandler.java:273) at org.kepler.kar.KARFile.open(KARFile.java:972) at org.kepler.kar.KARFile.openKARContents(KARFile.java:740) at org.kepler.gui.kar.ExportArchiveAction.actionPerformed(ExportArchiveAction.java:503) at javax.swing.AbstractButton.fireActionPerformed(AbstractButton.java:2018) at javax.swing.AbstractButton$Handler.actionPerformed(AbstractButton.java:2341) at javax.swing.DefaultButtonModel.fireActionPerformed(DefaultButtonModel.java:402) at javax.swing.DefaultButtonModel.setPressed(DefaultButtonModel.java:259) at javax.swing.AbstractButton.doClick(AbstractButton.java:376) at javax.swing.plaf.basic.BasicMenuItemUI.doClick(BasicMenuItemUI.java:833) at javax.swing.plaf.basic.BasicMenuItemUI$Handler.mouseReleased(BasicMenuItemUI.java:877) at java.awt.Component.processMouseEvent(Component.java:6505) at javax.swing.JComponent.processMouseEvent(JComponent.java:3321) at java.awt.Component.processEvent(Component.java:6270) at java.awt.Container.processEvent(Container.java:2229) at java.awt.Component.dispatchEventImpl(Component.java:4861) at java.awt.Container.dispatchEventImpl(Container.java:2287) at java.awt.Component.dispatchEvent(Component.java:4687) at java.awt.LightweightDispatcher.retargetMouseEvent(Container.java:4832) at java.awt.LightweightDispatcher.processMouseEvent(Container.java:4492) at java.awt.LightweightDispatcher.dispatchEvent(Container.java:4422) at java.awt.Container.dispatchEventImpl(Container.java:2273) at java.awt.Window.dispatchEventImpl(Window.java:2719) at java.awt.Component.dispatchEvent(Component.java:4687) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:723) at java.awt.EventQueue.access$200(EventQueue.java:103) at java.awt.EventQueue$3.run(EventQueue.java:682) at java.awt.EventQueue$3.run(EventQueue.java:680) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76) at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:87) at java.awt.EventQueue$4.run(EventQueue.java:696) at java.awt.EventQueue$4.run(EventQueue.java:694) at java.security.AccessController.doPrivileged(Native Method) at java.security.ProtectionDomain$1.doIntersectionPrivilege(ProtectionDomain.java:76) at java.awt.EventQueue.dispatchEvent(EventQueue.java:693) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:242) at
Re: [kepler-users] Problem with multiple plays of same KAR.
Hi Tom, I fixed the problem. --dan On 1/9/13 1:33 PM, Tom Parris wrote: Dan, Yes. That's what we are using and that is the observed behavior. I just assumed the problem originated with our own code (which is generally a safe assumption). We would be most grateful if you could look 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 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 plotting actors). http://bugzilla.**ecoinformatics.org/show_bug.**cgi?id=5759http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5759 I can look into fixing MatrixViewer. --dan On 1/9/13 9:27 AM, Tom Parris wrote: Dear Kepler-Users: I am hoping you can help point me in the right direction to track down an odd problem we are having (with Kepler trunk on Windows 7 x64 pro, but has been happening for a couple of years through multiple versions of the trunk and on x86 XP systems as well) 1. It involves a simple test KAR for a self-developed actor that uses GDAL to read a matrix and produce two tokens (the matrix and the metadata for the matrix). I know it is customary to provide an example for replication purposes and I am willing to do so, but it is non trivial to get it installed correctly. I'm also willing to share the code of the actor for review (with the usual caveats that we know it is not pretty). 2. The KAR opens and runs once without difficulty. Three display windows are generated. One with the name of the input file, one with the metadata, and one with the matrix. If one closes these three windows and presses the play button a second time, only the first two windows are produced. The display window with the matrix is not produced. 3. Closing Kepler and relaunching solves the problem. 4. After pressing play a second time, closing the KAR and re-opening fails (due to an issue resolving a simple jython class and instance for an actor that subsets the matrix). 5. If instead of pressing play a second time, I close the KAR and re-open it, then it opens successfully and runs once, but not a second time. 6. We have not tracked this problem down previously because in real workflows we don't seem to encounter this problem (though we typically only run once per open). These workflows typically make extensive use of this actor, with multiple instances and multiple firings per workflow. I suspect this is a problem in our code (either the GDAL actor or the jython actor) understanding differences in the roles of initalize(), prefire(), and postfire(). One oddity is that self developed GDAL actor outputs the metadata token after it outputs the matrix token. So, it is odd that the metadata token is displayed on multiple runs, but not the matrix token. -- Tom __**_ Kepler-users mailing list Kepler-users@kepler-project.**org Kepler-users@kepler-project.org http://lists.nceas.ucsb.edu/**kepler/mailman/listinfo/**kepler-usershttp://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users ___ Kepler-users mailing list Kepler-users@kepler-project.org http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
Re: [kepler-users] Problem with multiple plays of same KAR.
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 plotting actors). http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5759 I can look into fixing MatrixViewer. --dan On 1/9/13 9:27 AM, Tom Parris wrote: Dear Kepler-Users: I am hoping you can help point me in the right direction to track down an odd problem we are having (with Kepler trunk on Windows 7 x64 pro, but has been happening for a couple of years through multiple versions of the trunk and on x86 XP systems as well) 1. It involves a simple test KAR for a self-developed actor that uses GDAL to read a matrix and produce two tokens (the matrix and the metadata for the matrix). I know it is customary to provide an example for replication purposes and I am willing to do so, but it is non trivial to get it installed correctly. I'm also willing to share the code of the actor for review (with the usual caveats that we know it is not pretty). 2. The KAR opens and runs once without difficulty. Three display windows are generated. One with the name of the input file, one with the metadata, and one with the matrix. If one closes these three windows and presses the play button a second time, only the first two windows are produced. The display window with the matrix is not produced. 3. Closing Kepler and relaunching solves the problem. 4. After pressing play a second time, closing the KAR and re-opening fails (due to an issue resolving a simple jython class and instance for an actor that subsets the matrix). 5. If instead of pressing play a second time, I close the KAR and re-open it, then it opens successfully and runs once, but not a second time. 6. We have not tracked this problem down previously because in real workflows we don't seem to encounter this problem (though we typically only run once per open). These workflows typically make extensive use of this actor, with multiple instances and multiple firings per workflow. I suspect this is a problem in our code (either the GDAL actor or the jython actor) understanding differences in the roles of initalize(), prefire(), and postfire(). One oddity is that self developed GDAL actor outputs the metadata token after it outputs the matrix token. So, it is odd that the metadata token is displayed on multiple runs, but not the matrix token. -- Tom ___ Kepler-users mailing list Kepler-users@kepler-project.org http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users ___ Kepler-users mailing list Kepler-users@kepler-project.org http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
Re: [kepler-users] Kepler-users Digest, Vol 91, Issue 3
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 PM, Edward A. Lee wrote: No, I wasn't referring to actors written in Java. I was referring to composite actors that are themselves class definitions. It appears that Kepler does not expose this capability in the GUI (the commands aren't there to convert a composite actor to a class nor to instantiate classes). So what you have in your example is a _copy_ of the composite actor. Hence, updates to the original have no effect on the copy. The mechanism I'm referring to is that a composite actor may define a _class_, and you can then have multiple instances of the class. You can also have subclasses that override certain aspects. If someone is interested in making this capability available in Kepler, it would be great. I think it's mostly a matter of adding it to the menu commands. There is a paper on this mechanism here: http://ptolemy.eecs.berkeley.edu/publications/papers/07/classesandInheritance/index.htm There are demos in the Ptolemy tree here: $PTII/ptolemy/configs/doc/ClassesIllustrated.xml $PTII/ptolemy/domains/sdf/demo/NoisySinewave/NoisySinewave.xml $PTII/ptolemy/domains/sdf/demo/RijndaelEncryption/RijndaelEncryption.xml Edward On 12/10/12 3:56 PM, Alvin Sebastian wrote: I am also interested to know the details behind this problem. What Edward referred as base classes and sub classes apply only to Java codes, where you have to write and compile an actor in Java. I believe the type of “base” actor that you described is called a composite actor/workflow. Is it possible to share the same instance of a composite actor among multiple workflows? I know that besides dragging an existing kar from the panel as described by Ian, you can also use an actor called CompositeActor. Are there any other methods to use a composite actor? Alvin *From:*kepler-users-boun...@kepler-project.org [mailto:kepler-users-boun...@kepler-project.org] *On Behalf Of *Ian Szarka *Sent:* Tuesday, 11 December 2012 9:25 AM *To:* 'kepler-users@kepler-project.org' *Subject:* Re: [kepler-users] Kepler-users Digest, Vol 91, Issue 3 Hi Edward , thank you for the reply. Where can I find the Open Instance option? Only Open Actor appears in context or any other menu, see picture, if it is not scrubbed. Example attached, details also written below. I have tried a new scenario from scratch which results in the same problem, Ie changes not propagating. It appears that actors are just getting plain copied into workflows that use them. Thank you for your attention, Ian. Steps to create problem: -I made a simple work flow “A”, return a string -Saved the .kar for A in the MyWorkflows directory, and closed Kepler -Relaunched Kepler, -Made a second work flow “B” dragging actor A from the components panel -Ran B, verified expected result -Saved B to desktop and closed Kepler. -Relaunched Kepler -Opened actor A and modified string -Saved A, and closed Kepler -Relaunched Kepler, opened B -Ran B, received previous result – the first string and not the updated string -Opened the A actor located on the canvas of B – it had the previous string -Opened the file A in the MyWorkflows directory – it had the update string. -Original Message- From: kepler-users-boun...@kepler-project.org mailto:kepler-users-boun...@kepler-project.org [mailto:kepler-users-boun...@kepler-project.org] On Behalf Of kepler-users-requ...@kepler-project.org mailto:kepler-users-requ...@kepler-project.org Sent: Friday, 7 December 2012 7:00 AM To: kepler-users@kepler-project.org mailto:kepler-users@kepler-project.org Subject: Kepler-users Digest, Vol 91, Issue 3 Send Kepler-users mailing list submissions to kepler-users@kepler-project.org mailto:kepler-users@kepler-project.org To subscribe or unsubscribe via the World Wide Web, visit http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users or, via email, send a message with subject or body 'help' to kepler-users-requ...@kepler-project.org mailto:kepler-users-requ...@kepler-project.org You can reach the person managing the list at kepler-users-ow...@kepler-project.org mailto:kepler-users-ow...@kepler-project.org When replying, please edit your Subject line so it is more specific than Re: Contents of Kepler-users digest... Today's Topics: 1. Re: I need help making modular actors please. (Edward A. Lee) -- Message: 1 Date: Wed, 05 Dec 2012 18:13:15 -0800 From: Edward A. Lee e...@eecs.berkeley.edu mailto:e...@eecs.berkeley.edu To: Ian Szarka ian.sza...@anu.edu.au mailto:ian.sza...@anu.edu.au Cc: 'kepler-users@kepler-project.org' kepler-users@kepler-project.org
Re: [kepler-users] Fwd: Can't find Kepler Actors / Directors anymore
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 this: [run] Building Kars... What happens if you select Build in the menu - Tools - Preferences dialog? You could also try removing .kepler. --dan On 11/14/12 8:01 AM, Daren Thomas wrote: Starting this morning, I can't find the standard Kepler actors / directors anymore. Including: SDF Director, String Parameter etc. Really basic stuff just *missing*. After uninstalling / deleting / upgrading, I was able to get it to work briefly, JOY - and then: Suddenly after adding the first String Parameter, the toolbox is set back to nearly empty. See Screenshot :[image: Inline image 1] One thing I do recall doing is: * menu - Tools - Preferences * in tab Components: [Add] * (added a folder) * checked the Save box for the new folder Now, when I open up that dialog, all it shows is this: [image: Inline image 2] Clicking on Use Defaults adds back some default folders, but the problem stays. I am running off the trunk with `ant run`. I have attached the output, in case that helps (see ant_run.log) Regards, Daren ___ Kepler-users mailing list Kepler-users@kepler-project.org http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users ___ Kepler-users mailing list Kepler-users@kepler-project.org http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
Re: [kepler-users] classpath issues
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 have a good answer. To fix this might require changing the code in build-area/src/org/kepler/build. I'm not sure, but using ant's -lib argument might do the trick. However, it seems unusual to need to specify the jre directory and I'm not sure if -lib would help. See https://ant.apache.org/manual/running.html That was a good thought and I gave it a whirl, but Kepler is still unable to see the JavaFX classes when I use the -lib arg. It seems like it is a bit of a bug in the jvm if jre/lib/jfxrt.jar is not being found. Maybe try some of the JavaFX and ant resources on the net? Does a simple ant file outside of Kepler find the contents of jfxrt.jar? No, it's not a JVM bug. Oracle is being very conservative about how they deploy JavaFX. For now, the JavaFX SDK is included with Java 7 but until Java 8 next summer, you have to manually include the jfxrt.jar when building and running your apps. (They do have a very detailed deployment instructions for stand alone apps at http://docs.oracle.com/javafx/2/deployment/jfxpub-deployment.htm ) Perhaps $JDK_HOME is not the JDK that is being used by ant? I checked that. I modified Kepler's org.kepler.build.Run task to dump out info on which Java is actually being run and it's using the correct version. So for now, it sounds like I need to hack up org.kepler.build.project.RunClasspath to make this work. If you have any tips or better suggestions please let me know. Thanks again. -- B ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ ~ Brian Schlining MBARI Software Engineer, Research and Development br...@mbari.org (mailto:br...@mbari.org) (831) 775-1855 http://www.mbari.org/staff/brian ___ Kepler-users mailing list Kepler-users@kepler-project.org http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users ___ Kepler-users mailing list Kepler-users@kepler-project.org http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
Re: [kepler-users] Kepler 2.3 and MATLAB
I've already started on a JNA version and it looks promising. An alternative is to use matlabcontrol, which does not rely on JNI or JNA, but uses the Java Matlab interface. Unfortunately, this interface is undocumented and there's no guarantee it will work in future Matlab versions. --dan On 4/24/12 5:07 PM, Christopher Brooks wrote: Reimplementing the Matlab interface to use JNA instead of JNI directly would mean that we would not have to have a separate Ptolemy/Kepler Matlab-specific dll. This *might* remove some of the platform dependency issues. JNA is released under the GNU Lesser GPL. I've been using JNA as an interface to C-based Functional Mock-up Unit (FMU) code and it works well. In theo Another issue is 32 vs. 64 bit width. Many tools (Dymola) are only 32-bit. At least Mac OS X has a way of bundling both 32 and 64 bit shared objects in one file. I don't believe Windows has such a facility. JNA would help us get out of the business of building shared libraries for linux32, linux64, darwin32, darwin64, win32 and win64. _Christopher On 4/23/12 10:18 AM, Wade Sheldon wrote: I agree with you Edward, but I figured it was worth a try. I think tool chaining is more sustainable than integration in the long run, so data interchange formats and standards are more important than program hooks. To follow up on my subsequent note, and reinforce your point, the JNI for Matlab in Kepler 2.3 breaks in 2010a and 2011b, but works in 2009a. I don't use COM-based or command line calls to Matlab for anything else, so I'll keep 2009a configured in the path for Kepler and continue to use 2011b for my normal work. Thanks. Wade On 4/23/2012 12:59 PM, Edward A. Lee wrote: If it's any consolation, my experience is that tool integration is almost impossible to achieve, in practice... Even if you get it working once, it will break when something changes... There is clearly a technical challenge here. Edward On 4/23/12 9:08 AM, Wade Sheldon wrote: Hi folks, Thanks for all the advice last week, but I'm throwing in to towel unless someone has a radically new idea. I installed Matlab 2009a and that also failed to run the demo, but with a different error message: Caused by: java.lang.UnsatisfiedLinkError: C:\Program Files\Kepler-2.3\common-2.3.0\lib\ptolemy\matlab\ptmatlab.dll: The specified procedure could not be found I also tried R2007b (mentioned in help files) and had the same result as 2009a. So R2010a and R2011b error with ...The operating system cannot run %1 and R2007b and R2009a error with the above procedure call error, in case that's of any diagnostic value. I also installed Kepler on a different workstation run WinXP and had the same issues. To eliminate potential Java version issues, I wiped Kepler 2.3 and all the settings files, uninstalled an old version of the JDK I had on the box (1.6_18), installed a matching JDK to the Java libraries previously installed (1.6.0_31-b05) and reinstalled Kepler. Same result. I also added C:\Program Files\Kepler-2.3\common-2.3.0\lib\ptolemy\matlab to the path (based on Ptolemy Matlab troubleshooting guidelines) but that didn't help either. I then tried to follow the build instructions from the url Dan sent, spending most of the weekend setting up the software and source code and ironing out cygwin and mingw configurations and dependencies (the instructions on the reference page are out of date, and the mingw shell scripts described are not online and no mention is made of what libraries are needed for cygwin, so I had to guess and reinstall several times to get what was needed). After climbing down ever darker rabbit holes I managed to get a working build system set up, but then hit syntax errors with the .config files (apparently due to line terminator issues) and never could successfully build a dll. I concluded that this process is really untenable for someone not already set up to do Java development and use the entire Kepler build system, so at this point I rolled back my system and dumped the gig of software I spent all weekend messing with. So it was an informative, but ultimately futile, exercise. Thanks anyway. For my work it will be more productive to generate delimited files from Kepler and pick them up in Matlab, but I wanted to kick the tires and see if I could roll our Matlab code into native workflows. I'm about to rebuild that system using Win7/64 dual booting with Ubuntu, so I may try again if I feel adventurous. -Wade On 4/21/2012 4:48 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 with newer versions of Matlab. You can find instructions on building ptmatlab.dll here: https://kepler-project.org/developers/teams/build/matlab-lib-build-instructions-in-kepler-for-matlab-actor/ --dan
Re: [kepler-users] KAR Command line Fail running with parameters
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 kepler -h to see the command line usage. --dan On 4/18/12 9:50 AM, Albert Vilà Picas wrote: Hi, well, with ptolemy there are no specific problems. With Ubuntu and Mac I have downloaded the source from https://code.kepler-project.org/code/kepler/trunk/modules/build-area and compiled with ant change-to -Dsuite=reporting ant compile and there many warnings that say: you may compile ptolemy with: ant force-ptolemy compile and it reappears but don't fail. Sorry, I don't know how it works, but thanks for the appointment. Dan, again! I have some troubles with the command line execution with parameters. It doesn't work with some type of parameters or maybe multiple. With non-integer params what should I do? with simple comas like 'value' ? -Integer 1 -String value words -Decimals 0.85 Sorry, where I can find this information clearly? Thanks a lot once again! --Albert 2012/4/18 Christopher Brooksc...@eecs.berkeley.edu I'm just curious, what are the problems with ant force-ptolemy compile? Also, Ptolemy has and Export PDF feature that works if the configuration has !-- Add support for exporting PDFs. -- !-- Used in BasicGraphFrame.java -- property name=_exportPDFActionClassName class=ptolemy.data.expr.StringParameter value=ptolemy.vergil.basic.export.itextpdf.ExportPDFAction/ and com.itextpdf.text.Document is in the path. $PTII/configure looks for $PTII/vendors/misc/itext/iText.jar iText.jar is AGPL'd, which is why it is not part of the default. To experiment with this, I suggest downloading the Ptolemy II development tree, see http://chess.eecs.berkeley.edu/ptexternal _Christopher On 4/17/12 11:48 AM, Albert Vilà Picas wrote: Great job Dan! It works! Thank you a lot again! The revision 29738 is ok. I have some R warnings and with Ptolemy at revision 63376 I still have some troubles with ant force-ptolemy compile but the generation of the PDF is doing it as well. If I have new suggestions or problems I'll notice them. Thanks! Albert 2012/4/17 Daniel Crawldanielcr...@gmail.com I fixed the problem and you can now specify parameters when executing KAR workflows: kepler -runkar -nogui [-param1 value1 ...] workflow.kar --dan On 4/17/12 5:57 AM, Josep Maria Campanera Alsina wrote: Dear All, This is Josep M. Campanera who has been using kepler for bioinformatics. Now I'm developing with Albert Vilà (and others) a web front-end for kepler that we will make available once the first tests are satisfactory. Additionally we are also developing a perl actor for kepler. As mentioned by Albert, It is crucial the command line execution with parameters of kar files for continuing our project. Dan says that there is a bug which impedes the execution of kar files by means of command line execution with parameters. In line with Dan's comments, we would like to know aproximately when this bug is going to be fixed. 1) Are you thinking of days, weeks or months? 2) In case we need to wait for a long period, which is the best strategy to surpass that drawback meanwhile? Thank you very much, Josep M. Campanera, Hi Albert, I'll look into fixing this. It would be nice to have a consistent set of command-line options for executing momls and kars. --dan On 4/16/12 3:00 AM, Albert Vilà Picas wrote: Hi all, I have read in other e-mails that now is not possible to execute .kar workflows with parameters? We run a command line KAR with reporting layout added running -runwf -nogui [-param value]*. I have tried also with -runkar and I have the same error. Is that a Ptolemy error that is not suitable? We're doing a great project with Kepler and is necessary to run command line kar wf changing the value of the input parameters. Here is the stack trace: [null] common tabpane configuration overridden by reporting [null] Ran additional initialization for module reporting from class org.kepler.module.reporting.Initialize [null] loading: org.kepler.KeplerConfigurationApplication args: ptolemy/configs/kepler/ConfigNoGUIWithCache.xml -runThenExit -epochs 100 /home/sbi/sbi-services/sbi-home/Temporal/MLRAlbert.kar [null] invoking: org.kepler.KeplerConfigurationApplication.main [null] Kepler Initializing... [null] Unsupported file type or connection not available: file:/home/sbi/sbi-services/sbi-home/Temporal/MLRAlbert.kar [null] Command failed [null] java.lang.Exception: Failed to parse ptolemy/configs/kepler/ConfigNoGUIWithCache.xml -runThenExit -epochs 100
Re: [kepler-users] Mac Lion Failed to parse -kepler
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 12:01 PM, Albert Vilà Picas wrote: Hey thanks but, My database is ok, also the parameters from resource configuration file at provenance. After some good command line executions from Apache with DB connect, then me I can't execute Kepler, just when the thumb panel appears I have the Exception: Command failed Arguments: -kepler Failed to parse -kepler It occurs with OS Application, ./kepler.sh and with ant run I think it should be some Apache or Mac restrictions, absolutely no idea. Thanks a lot, but with Linux I never had this problems like that with Kepler. Best regards, Albert 2012/3/26 Derik Barseghianbarsegh...@nceas.ucsb.edu Hi Albert, This sounds and looks like a database or provenance configuration issue: Caused by: java.sql.SQLException: S1000 General error java.lang.RuntimeException: database alias does not exist You say you've configured provenance to use MySQL. I would verify you can connect to the MySQL server using another program with the same settings. Derik On Mar 26, 2012, at 7:01 AM, Albert Vilà Picas wrote: Hi all, sorry but I'm new in Mac OS X and now I don't know how to enable Kepler start. After the firsts runs with reporting suite with configured provenance to MySQL, the third execution failed to start. By OS Application or command line everyways fail. I don't know if it's my sys-admin fault or the database, maybe ptolemy or folder permissions... Any idea would be great to solve that BIG problem to execute Kepler 2.3 or trunk. I have deleted all cache, KeplerData and uninstalled all the versions and the problem persists :( This is my java stack error display: java.lang.Exception: Failed to parse -kepler at ptolemy.actor.gui.ConfigurationApplication.throwArgsException(ConfigurationApplication.java:791) at ptolemy.actor.gui.ConfigurationApplication.init(ConfigurationApplication.java:320) at ptolemy.actor.gui.MoMLApplication.init(MoMLApplication.java:80) at ptolemy.vergil.VergilApplication.init(VergilApplication.java:110) at ptolemy.vergil.VergilApplication$1.run(VergilApplication.java:226) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209) at java.awt.EventQueue.dispatchEventImpl(EventQueue.java:677) at java.awt.EventQueue.access$000(EventQueue.java:85) at java.awt.EventQueue$1.run(EventQueue.java:638) at java.awt.EventQueue$1.run(EventQueue.java:636) at java.security.AccessController.doPrivileged(Native Method) at java.security.AccessControlContext$1.doIntersectionPrivilege(AccessControlContext.java:87) at java.awt.EventQueue.dispatchEvent(EventQueue.java:647) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread.java:296) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.java:211) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread.java:201) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:196) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:188) at java.awt.EventDispatchThread.run(EventDispatchThread.java:122) Caused by: java.lang.Exception: Failed to read configuration 'file:/Applications/Kepler-2.3/Kepler.app/Contents/Resources/Java/common-2.3.0/configs/ptolemy/configs/kepler/configuration.xml' at ptolemy.vergil.VergilApplication._createDefaultConfiguration(VergilApplication.java:318) at ptolemy.vergil.VergilApplication._createEmptyConfiguration(VergilApplication.java:354) at ptolemy.actor.gui.ConfigurationApplication._parseArgs(ConfigurationApplication.java:1273) at ptolemy.vergil.VergilApplication._parseArgs(VergilApplication.java:484) at ptolemy.actor.gui.ConfigurationApplication.init(ConfigurationApplication.java:244) ... 17 more Caused by: java.lang.Exception: Failed to call application initializer class org.kepler.gui.KeplerInitializer. Perhaps the configuration file file:/Applications/Kepler-2.3/Kepler.app/Contents/Resources/Java/common-2.3.0/configs/ptolemy/configs/kepler/configuration.xml has a problem? at ptolemy.actor.gui.ConfigurationApplication.readConfiguration(ConfigurationApplication.java:632) at ptolemy.vergil.VergilApplication._createDefaultConfiguration(VergilApplication.java:316) ... 21 more Caused by: java.sql.SQLException: S1000 General error java.lang.RuntimeException: database alias does not exist at org.hsqldb.jdbc.Util.sqlException(Unknown Source) at org.hsqldb.jdbc.jdbcConnection.init(Unknown Source) at org.hsqldb.jdbcDriver.getConnection(Unknown
Re: [kepler-users] Why doesn't Listen to Actor work on Kepler 2.2/2.3 for Windows?
Hi Christopher,
Thanks for the fix. I agree with you that it'd be good to fix the ptII
branch in svn for Kepler 2.3. Before creating a new patch release, I
would wait until we've had more time to test since there could be
additional Java 7 problems.
--dan
On 2/16/12 9:53 AM, Christopher Brooks wrote:
All:
It looks like the problem has to do with Java 1.7. I was able to
reproduce this on the Mac
with two different early release versions of 1.7. The bug occurs in
Ptolemy II, outside of
Kepler.
The bug report is at
http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5574
The fix is to modify ptolemy/actor/gui/TextEditor.java to check if
_scrollbar is null:
public Color getBackground() {
// Under Java 1.7 on the Mac, the _scrollbar is sometimes null.
// See http://bugzilla.ecoinformatics.org/show_bug.cgi?id=5574
if (_scrollPane != null) {
return _scrollPane.getBackground();
} else {
return null;
}
}
I'm not sure why this is happening, but I suspect the problem is that in
Java 1.7
setBackground is calling getBackground on subcomponents and the TextEditor
subcomponent is not completely instantiated.
There could be other places where this problem occurs. I'll switch over
to Java 1.7 and see
what turned up. It would be worth running the debugger and verifying
that we are in the
Swing Event Thread when the problem occurs.
I'll leave it to the Kepler Team to decide how to handle this. My
proposal is that I patch the
ptII branch used in the release with the above change. I'd like to wait
until a few people have exercised
Kepler under 1.7 before doing so though. If we patch the ptII tree used
in Kepler-2.3, then at
least people who are working from the 2.3 tree can get the update. I'm
not sure about releasing
a patch release to Kepler, that is up to others.
_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 for verifying this problem occurs with Java 7 but not 6.
I updated Kepler a few months ago so that it would compile with Java 7.
However, when I ran it, I didn't exhaustively test all the
functionality. I'll create bug report so this error is not forgotten.
--dan
On 2/14/12 11:59 PM, Daren Thomas wrote:
i resolved this issue temporarily by uninstalling java 7, thus
ensuring java 6 is being used. it all works fine now. hope that helps!
daren
On 15.02.2012, at 00:51, Edward A. Leee...@eecs.berkeley.edu wrote:
This sort of thing can happen for GUI code that invoked outside
the Swing event thread. How is this being invoked? If it's 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
at ptolemy.actor.gui.TextEditor.getBackground(TextEditor.java:144)
at java.awt.Window.setBackground(Unknown Source)
at java.awt.Frame.setBackground(Unknown Source)
at ptolemy.gui.Top.access$1001(Top.java:141)
at ptolemy.gui.Top$SetBackgroundRunnable.run(Top.java:1889)
at ptolemy.gui.Top.deferIfNecessary(Top.java:247)
at ptolemy.gui.Top.setBackground(Top.java:501)
at ptolemy.actor.gui.TextEditor.setBackground(TextEditor.java:238)
...
Christopher, do you know what causes this?
Thanks,
--dan
On 2/8/12 4:28 AM, Daren Thomas wrote:
I can use Listen to Actor for Kepler 2.3 on Mac OS X, but not under
Windows. When I select the option from the context menu, nothing
happens.
Also, when I try to edit a script for the Python actor, I get an
error
message Failed to open a dialog to edit the target (null) - this
doesn't bother me ATM, but I guess I should mention it, as it
could be
an additional symptom of a wrongly configured system.
I installed Kepler 2.3 on Windows with the installer provided on the
website. It seems all questions in the users list refer to
compiling
your own version/environment. Is that the way to go?
Regards,
Daren Thomas
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Re: [kepler-users] Why doesn't Listen to Actor work on Kepler 2.2/2.3 for Windows?
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 for verifying this problem occurs with Java 7 but not 6. I updated Kepler a few months ago so that it would compile with Java 7. However, when I ran it, I didn't exhaustively test all the functionality. I'll create bug report so this error is not forgotten. --dan On 2/14/12 11:59 PM, Daren Thomas wrote: i resolved this issue temporarily by uninstalling java 7, thus ensuring java 6 is being used. it all works fine now. hope that helps! daren On 15.02.2012, at 00:51, Edward A. Leee...@eecs.berkeley.edu wrote: This sort of thing can happen for GUI code that invoked outside the Swing event thread. How is this being invoked? If it's 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 at ptolemy.actor.gui.TextEditor.getBackground(TextEditor.java:144) at java.awt.Window.setBackground(Unknown Source) at java.awt.Frame.setBackground(Unknown Source) at ptolemy.gui.Top.access$1001(Top.java:141) at ptolemy.gui.Top$SetBackgroundRunnable.run(Top.java:1889) at ptolemy.gui.Top.deferIfNecessary(Top.java:247) at ptolemy.gui.Top.setBackground(Top.java:501) at ptolemy.actor.gui.TextEditor.setBackground(TextEditor.java:238) ... Christopher, do you know what causes this? Thanks, --dan On 2/8/12 4:28 AM, Daren Thomas wrote: I can use Listen to Actor for Kepler 2.3 on Mac OS X, but not under Windows. When I select the option from the context menu, nothing happens. Also, when I try to edit a script for the Python actor, I get an error message Failed to open a dialog to edit the target (null) - this doesn't bother me ATM, but I guess I should mention it, as it could be an additional symptom of a wrongly configured system. I installed Kepler 2.3 on Windows with the installer provided on the website. It seems all questions in the users list refer to compiling your own version/environment. Is that the way to go? Regards, Daren Thomas ___ Kepler-users mailing list Kepler-users@kepler-project.org http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users ___ Kepler-users mailing list Kepler-users@kepler-project.org http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users eal.vcf ___ Kepler-users mailing list Kepler-users@kepler-project.org http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
Re: [kepler-users] Why doesn't Listen to Actor work on Kepler 2.2/2.3 for Windows?
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 java.awt.Frame.setBackground(Unknown Source) at ptolemy.gui.Top.access$1001(Top.java:141) at ptolemy.gui.Top$SetBackgroundRunnable.run(Top.java:1889) at ptolemy.gui.Top.deferIfNecessary(Top.java:247) at ptolemy.gui.Top.setBackground(Top.java:501) at ptolemy.actor.gui.TextEditor.setBackground(TextEditor.java:238) ... Christopher, do you know what causes this? Thanks, --dan On 2/8/12 4:28 AM, Daren Thomas wrote: I can use Listen to Actor for Kepler 2.3 on Mac OS X, but not under Windows. When I select the option from the context menu, nothing happens. Also, when I try to edit a script for the Python actor, I get an error message Failed to open a dialog to edit the target (null) - this doesn't bother me ATM, but I guess I should mention it, as it could be an additional symptom of a wrongly configured system. I installed Kepler 2.3 on Windows with the installer provided on the website. It seems all questions in the users list refer to compiling your own version/environment. Is that the way to go? Regards, Daren Thomas ___ Kepler-users mailing list Kepler-users@kepler-project.org http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users ___ Kepler-users mailing list Kepler-users@kepler-project.org http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
Re: [kepler-users] Connect to Oracle Database
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 Database Query Actor. I am using the Open Database Connection Actor to establish a database connection. I am always getting this error message: ptolemy.kernel.util.IllegalActionException: fire exception DB connection in .DatabaseAccess.Open Database Connection Because: ptolemy.kernel.util.IllegalActionException: java.lang.ClassNotFoundException: oracle.jdbc.driver.OracleDriver in .DatabaseAccess.Open Database Connection Because: java.lang.ClassNotFoundException: oracle.jdbc.driver.OracleDriver at org.geon.OpenDBConnection.fire(OpenDBConnection.java:276) at ptolemy.actor.AtomicActor.iterate(AtomicActor.java:461) at ptolemy.actor.sched.StaticSchedulingDirector.fire(StaticSchedulingDirector.java:188) at ptolemy.actor.CompositeActor.fire(CompositeActor.java:459) at ptolemy.actor.Manager.iterate(Manager.java:749) at ptolemy.actor.Manager.execute(Manager.java:351) at ptolemy.actor.Manager.run(Manager.java:1164) at ptolemy.actor.Manager$3.run(Manager.java:1217) ... Doesn't Kepler come with Oracle Driver? If not, how could I tell Kepler where the driver is? Thanks in advance! Regards, Muhannad P.S. I am working on a Mac OS X. ___ Kepler-users mailing list Kepler-users@kepler-project.org http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users ___ Kepler-users mailing list Kepler-users@kepler-project.org http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
Re: [kepler-users] Error messages from simple ExternalExecution actor...
Hi Marc and Derik, There are two bugs occurring here, and I just fixed one of them. Kepler should no longer give errors about RunWithFeedbackChkBoxAction. --dan On 11/3/11 12:45 PM, Derik Barseghian wrote: Hi Marc, This is bug#4978 again. You're not doing anything wrong, it's related to the menu and configuration system, and not actors or workflows. These messages can safely be ignored until we fix the bug. Apologies for the inconvenience. http://bugzilla.ecoinformatics.org/show_bug.cgi?id=4978 Derik On Nov 3, 2011, at 11:32 AM, J. Marc Edwards wrote: I have attached a simple workflow on which I first noticed this, but the 07-CommandLine_1.xml exhibits the same behavior in outputting the messages below to the xterm from which Kepler was invoked. Can someone help me understand these messages? Do I have a bad Kepler installation? Am I going something wrong? Kind regards, Marc jmarcedwards@jmarcedwards-Z68X-UD5-B3:~$ [null] ERROR (org.kepler.gui.MenuMapper:getActionFor:269) Exception trying to create an Action for classname:org.kepler.gui.RunWithFeedbackChkBoxAction: [null] java.lang.IllegalArgumentException: RunWithFeedbackChkBoxAction constructor could not get actions for DEBUG-ANIMATE EXECUTION or DEBUG-STOP ANIMATING (java.lang.reflect.InvocationTargetException) [null] ERROR (org.kepler.gui.MenuMapper:getActionFor:269) Exception trying to create an Action for classname:org.kepler.tagging.TagManagerAction: [null] null (java.lang.ClassNotFoundException: org.kepler.tagging.TagManagerAction) [null] ERROR (org.kepler.gui.MenuMapper:getActionFor:269) Exception trying to create an Action for classname:org.kepler.gui.RunWithFeedbackChkBoxAction: [null] java.lang.IllegalArgumentException: RunWithFeedbackChkBoxAction constructor could not get actions for DEBUG-ANIMATE EXECUTION or DEBUG-STOP ANIMATING (java.lang.reflect.InvocationTargetException) [null] ERROR (org.kepler.gui.MenuMapper:getActionFor:269) Exception trying to create an Action for classname:org.kepler.tagging.TagManagerAction: [null] null (java.lang.ClassNotFoundException: org.kepler.tagging.TagManagerAction) [null] ERROR (org.kepler.gui.MenuMapper:getActionFor:269) Exception trying to create an Action for classname:org.kepler.gui.RunWithFeedbackChkBoxAction: [null] java.lang.IllegalArgumentException: RunWithFeedbackChkBoxAction constructor could not get actions for DEBUG-ANIMATE EXECUTION or DEBUG-STOP ANIMATING (java.lang.reflect.InvocationTargetException) [null] ERROR (org.kepler.gui.MenuMapper:getActionFor:269) Exception trying to create an Action for classname:org.kepler.tagging.TagManagerAction: [null] null (java.lang.ClassNotFoundException: org.kepler.tagging.TagManagerAction) [null] 465 ms. Memory: 349312K Free: 200464K (57%) -- J. Marc Edwards Lead Architect - Semiconductor Design Portals Nimbis Services, Inc. Skype: (919) 747-3775 Cell: (919) 345-1021 Fax: (919) 882-8602 marc.edwa...@nimbisservices.com www.nimbisservices.com chrome.xmlmarc_edwards.vcf___ Kepler-users mailing list Kepler-users@kepler-project.org http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users ___ Kepler-users mailing list Kepler-users@kepler-project.org http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users ___ Kepler-users mailing list Kepler-users@kepler-project.org http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
Re: [kepler-users] Mac OS, Matlab, and library paths
Hi Joe,
The Matlab installer most likely created the symlink; the Kepler
installer does not.
--dan
On 6/30/11 6:25 AM, Joe Futrelle wrote:
Interesting ... I have no such symlink in /usr/bin, but that must be because I
installed Kepler by dragging the app into my Applications folder, 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 /Applications/Matlab...,
but does have /usr/bin, which has a symlink to the Matlab
binary. Matlab probably created the link when it installed.
If you can't edit $PATH, you could make a symlink in a
directory in $PATH.
--dan
On 6/29/11 9:28 AM, Joe Futrelle wrote:
Further results. My advice upthread use launchctl to set [PATH] is not
correct.
Putting Matlab on your path so that Kepler can invoke it turns out to be a
different process depending on whether you are running Kepler from a shell
prompt, or whether you're double-clicking the application icon.
As of Snow Leopard, it appears that the only way to set the PATH variable seen
by GUI applications when they are launched from the Finder/Dock is using
~/.MacOSX/environment.plist.
However this approach is somewhat problematic in that in environment.plist
variable references (i.e., $PATH) are not expanded, so there is no non-kludgy
way I've found to *append* the Matlab executable's path to the PATH seen by GUI
applications, using environment.plist.
The PATH approach that does work is using ordinary shell methods to append the
Matlab bin directory to the path, and then invoking Kepler from that shell,
like so:
$ launchctl getenv DYLD_LIBRARY_PATH
/Applications/MATLAB_R2011a.app/bin/maci64
$ export PATH=$PATH:/Applications/MATLAB_R2011a.app/bin
$ echo $PATH
/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin:/Applications/MATLAB_R2011a.app/bin
$ open /Applications/Kepler-2.2/Kepler.app/
Can anyone advise how I might be able to get this working for launching Kepler
from Finder/Dock? Obviously I can just stick with the shell approach, but I'd
really like to be able to launch Kepler from the Dock.
On Jun 28, 2011, at 3:48 PM, Joe Futrelle wrote:
OK, this thread resolved all of my issues. Thanks a lot guys! :)
To summarize:
DYLD_LIBRARY_PATH must include the Matlab libraries. Setting them with
launchctl works, but don't expect to see them as shell environment variables
unless you export them to the shell.
The Matlab executable (from its app package's bin directory) must be in your
path. (Again, use launchctl to set).
I get different results when I use open from the command line to launch
Kepler (works!) and when I double-click Kepler's app icon (doesn't), but I hypothesize
that if I put both the DYLD_LIBRARY_PATH and PATH settings in /etc/launchd.conf and
reboot, that it'll work. Unconfirmed as of yet.
Hopefully the above account is accurate and not confused ...
On Jun 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# DYLD_LIBRARY_PATH=/Applications/MATLAB_R2011a.app/bin/maci64/ env |
grep DYLD
DYLD_LIBRARY_PATH=/Applications/MATLAB_R2011a.app/bin/maci64/
bash-3.2# open /Applications/Kepler-2.2/Kepler.app
Now I'm getting a different stacktrace. I have a properly-licensed Matlab
instance running and csh is @ /bin/csh.
ptolemy.kernel.util.IllegalActionException: matlabEngine.open(null) : can't find Matlab
engine. Try starting Matlab by hand as an application to verify that Matlab is set up
properly and the license is correct. Under Windows, try running matlab
/regserver, the Matlab C API communicates with Matlab via COM, and apparently the
COM interface is not automatically registered when Matlab is installed. Under Linux and
other types of UNIX, csh must be installed in /bin/csh.
at ptolemy.matlab.Engine.open(Engine.java:280)
at ptolemy.matlab.Engine.open(Engine.java:232)
at ptolemy.matlab.Expression.preinitialize(Expression.java:303)
at ptolemy.actor.Director.preinitialize(Director.java:1010)
at ptolemy.actor.Director.preinitialize(Director.java:991)
at
ptolemy.domains.ct.kernel.CTDirector.preinitialize(CTDirector.java:748)
at
ptolemy.domains.ct.kernel.CTMultiSolverDirector.preinitialize(CTMultiSolverDirector.java:637)
at ptolemy.actor.CompositeActor.preinitialize(CompositeActor.java:1735)
at ptolemy.actor.Manager.preinitializeAndResolveTypes(Manager.java:983)
at ptolemy.actor.Manager.initialize(Manager.java:643)
at ptolemy.actor.Manager.execute(Manager.java:340
Re: [kepler-users] Mac OS, Matlab, and library paths
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 /Applications/Matlab...,
but does have /usr/bin, which has a symlink to the Matlab
binary. Matlab probably created the link when it installed.
If you can't edit $PATH, you could make a symlink in a
directory in $PATH.
--dan
On 6/29/11 9:28 AM, Joe Futrelle wrote:
Further results. My advice upthread use launchctl to set [PATH] is not
correct.
Putting Matlab on your path so that Kepler can invoke it turns out to be a
different process depending on whether you are running Kepler from a shell
prompt, or whether you're double-clicking the application icon.
As of Snow Leopard, it appears that the only way to set the PATH variable seen
by GUI applications when they are launched from the Finder/Dock is using
~/.MacOSX/environment.plist.
However this approach is somewhat problematic in that in environment.plist
variable references (i.e., $PATH) are not expanded, so there is no non-kludgy
way I've found to *append* the Matlab executable's path to the PATH seen by GUI
applications, using environment.plist.
The PATH approach that does work is using ordinary shell methods to append the
Matlab bin directory to the path, and then invoking Kepler from that shell,
like so:
$ launchctl getenv DYLD_LIBRARY_PATH
/Applications/MATLAB_R2011a.app/bin/maci64
$ export PATH=$PATH:/Applications/MATLAB_R2011a.app/bin
$ echo $PATH
/opt/local/bin:/opt/local/sbin:/usr/bin:/bin:/usr/sbin:/sbin:/usr/local/bin:/usr/X11/bin:/Applications/MATLAB_R2011a.app/bin
$ open /Applications/Kepler-2.2/Kepler.app/
Can anyone advise how I might be able to get this working for launching Kepler
from Finder/Dock? Obviously I can just stick with the shell approach, but I'd
really like to be able to launch Kepler from the Dock.
On Jun 28, 2011, at 3:48 PM, Joe Futrelle wrote:
OK, this thread resolved all of my issues. Thanks a lot guys! :)
To summarize:
DYLD_LIBRARY_PATH must include the Matlab libraries. Setting them with
launchctl works, but don't expect to see them as shell environment variables
unless you export them to the shell.
The Matlab executable (from its app package's bin directory) must be in your
path. (Again, use launchctl to set).
I get different results when I use open from the command line to launch
Kepler (works!) and when I double-click Kepler's app icon (doesn't), but I hypothesize
that if I put both the DYLD_LIBRARY_PATH and PATH settings in /etc/launchd.conf and
reboot, that it'll work. Unconfirmed as of yet.
Hopefully the above account is accurate and not confused ...
On Jun 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# DYLD_LIBRARY_PATH=/Applications/MATLAB_R2011a.app/bin/maci64/ env |
grep DYLD
DYLD_LIBRARY_PATH=/Applications/MATLAB_R2011a.app/bin/maci64/
bash-3.2# open /Applications/Kepler-2.2/Kepler.app
Now I'm getting a different stacktrace. I have a properly-licensed Matlab
instance running and csh is @ /bin/csh.
ptolemy.kernel.util.IllegalActionException: matlabEngine.open(null) : can't find Matlab
engine. Try starting Matlab by hand as an application to verify that Matlab is set up
properly and the license is correct. Under Windows, try running matlab
/regserver, the Matlab C API communicates with Matlab via COM, and apparently the
COM interface is not automatically registered when Matlab is installed. Under Linux and
other types of UNIX, csh must be installed in /bin/csh.
at ptolemy.matlab.Engine.open(Engine.java:280)
at ptolemy.matlab.Engine.open(Engine.java:232)
at ptolemy.matlab.Expression.preinitialize(Expression.java:303)
at ptolemy.actor.Director.preinitialize(Director.java:1010)
at ptolemy.actor.Director.preinitialize(Director.java:991)
at
ptolemy.domains.ct.kernel.CTDirector.preinitialize(CTDirector.java:748)
at
ptolemy.domains.ct.kernel.CTMultiSolverDirector.preinitialize(CTMultiSolverDirector.java:637)
at ptolemy.actor.CompositeActor.preinitialize(CompositeActor.java:1735)
at ptolemy.actor.Manager.preinitializeAndResolveTypes(Manager.java:983)
at ptolemy.actor.Manager.initialize(Manager.java:643)
at ptolemy.actor.Manager.execute(Manager.java:340)
at ptolemy.actor.Manager.run(Manager.java:1164)
at ptolemy.actor.Manager$3.run(Manager.java:1217)
On Jun 28, 2011, at 3:02 PM, Sean Riddle wrote:
I can't get launchd.conf to set DYLD_LIBRARY_PATH, but for some reason
it doesn't set anything else either. But DYLD_LIBRARY_PATH is
settable, at least in some ways:
dhcp33-gc5:~ sean$ DYLD_LIBRARY_PATH=hello env | grep DYLD_LIBRARY_PATH
DYLD_LIBRARY_PATH=hello
I would
Re: [kepler-users] kepler.sh execution failed [ Kepler 2.2 ]
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 wrote: Hello I'm executing a Kar file using kepler in a command line form: ./kepler.sh -runwf -nogui -ExecutionId 6 -function1 5 /home/xxx/KeplerData/workflows/MyWorkflows/R_3D_Plot.kar This kar file also has a report to generate a pdf. But when it's close to finish, it seems it's looking for a configuration file that doesn't exists. I found this configuration at: /home/xxx/KeplerData/kepler.modules/common-2.1.0/configs/ptolemy/configs/kepler/ConfigNoGUIWithCache.xml The stack trace: [null] Processing entry, LSID=urn:lsid:kepler-project.org/ns/:6129:54:14, type=org.kepler.reporting.roml.ReportLayout [null] Opening entry, LSID=urn:lsid:kepler-project.org/ns/:6129:54:14, type=org.kepler.reporting.roml.ReportLayout [null] Command failed [null] java.lang.Exception: Failed to parse ptolemy/configs/kepler/ConfigNoGUIWithCache.xml -runThenExit -ExecutionId 6 -function1 5 /tmp/moml7351140526961285021.xml [null] at ptolemy.actor.gui.ConfigurationApplication.throwArgsException(ConfigurationApplication.java:651) [null] at org.kepler.KeplerConfigurationApplication.init(KeplerConfigurationApplication.java:288) [null] at org.kepler.KeplerConfigurationApplication.main(KeplerConfigurationApplication.java:582) [null] at sun.reflect.NativeMethodAccessorImpl.invoke0(Native Method) [null] at sun.reflect.NativeMethodAccessorImpl.invoke(NativeMethodAccessorImpl.java:39) [null] at sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:25) [null] at java.lang.reflect.Method.invoke(Method.java:597) [null] at org.kepler.Kepler.load(Kepler.java:374) [null] at org.kepler.Kepler.load(Kepler.java:392) [null] at org.kepler.Kepler.parseArgsAndRun(Kepler.java:320) [null] at org.kepler.Kepler.main(Kepler.java:222) [null] Caused by: ptolemy.kernel.util.IllegalActionException: Unrecognized option: No parameter exists with name ExecutionId [null] at org.kepler.KeplerConfigurationApplication.parseArgs(KeplerConfigurationApplication.java:394) [null] at org.kepler.KeplerConfigurationApplication.init(KeplerConfigurationApplication.java:193) [null] ... 9 more My system is Linux one. Thank you very much Joan ___ Kepler-users mailing list Kepler-users@kepler-project.org http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users ___ Kepler-users mailing list Kepler-users@kepler-project.org http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
Re: [kepler-users] Mac OS, Matlab, and library paths
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 $DYLD_LIBRARY_PATH /Applications/MATLAB_R2010a.app/bin/maci64/ # open /Applications/Kepler-2.2/Kepler.app --dan On 6/28/11 11:27 AM, Joe Futrelle wrote: I tried that, didn't work. Again, I have no problem setting system-wide environment variables in launchd.conf. If I set foo to bar then foo is set to bar in my environment. But if I set DYLD_LIBRARY_PATH to anything, it's like I didn't set it at all. Exactly the same behavior with environment.plist. It seems to me like DYLD_LIBRARY_PATH is on some kind of blacklist. On Jun 28, 2011, at 2:15 PM, Sean Riddle wrote: I always heard that if you wanted to set environment variables for GUI applications in OS X, you needed to edit the environment.plist file. A stackoverflow thread (http://stackoverflow.com/questions/135688/setting-environment-variables-in-os-x) says it can be set on a per-user basis at ~/.MacOSX/environment.plist. However, that thread also says that launchd.conf also works for GUI applications. Maybe try setting it in environment.plist to see if that makes a difference. - Sean PS - Property List Editor in Utilities is what creates and edits .plist files. On Tue, Jun 28, 2011 at 11:09 AM, Joe Futrellejfutre...@whoi.edu wrote: Hi, I'm trying to run Matlab codes from Kepler in Mac OS (Snow Leopard). As an inexperienced user I'm simply firing up the prepackaged Mac OS distribution of Kepler and double-clicking on the app icon. It's no problem constructing a workflow with a Matlab expression in it, but when I run I get a stacktrace about the Matlab libraries not being on the DYLD_LIBRARY_PATH. I'm having no trouble finding those libraries manually; they're right where they should be in my Matlab install, and they're 64 bit, and everything seems in order. Setting DYLD_LIBRARY_PATH doesn't seem possible in Mac OS; I can set environment variables in launchd.conf, but launchd appears to silently ignore DYLD_LIBRARY_PATH; maybe it's special-casing it for some reason. I'm having trouble finding a previous post on this list, or a bug in Kepler's bugzilla database, or a documentation section or FAQ entry that explains how to solve this. It's clear that some people have had problems with this in the past, but I don't see a clear description of what I should be doing. Any and all advice welcome. Mac OS version: 10.6.7 Java version: 1.6.0_24 (Java HotSpot(TM) 64-Bit Server VM (build 19.1-b02-334, mixed mode)) Kepler version: 2.2 Matlab version: R2011a -- Joe Futrelle Woods Hole Oceanographic Institution jfutre...@whoi.edu ___ Kepler-users mailing list Kepler-users@kepler-project.org http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users -- Joe Futrelle Woods Hole Oceanographic Institution jfutre...@whoi.edu ___ Kepler-users mailing list Kepler-users@kepler-project.org http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users ___ Kepler-users mailing list Kepler-users@kepler-project.org http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
[kepler-users] Fwd: Re: WebServices/WSWithComplexTypes Actor behaviour issue
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 http://code.kepler-project.org/code/kepler/trunk/modules/build-area cd build-area ant change-to -Dsuite=kepler The web service actors are in kepler.modules/actors/src/org/sdm/spa/. --dan On 6/20/11 9:16 PM, Simon Collins wrote: Hi, Im currently attempting to access a web service via wsdl i have setup (attached is the wsdl served to clients that query ?wsdl). I can format a string manually for testing that adheres to the required response format, however when it is passed into the WebServices actor, all the XML gets escaped by the actor, ive tried escaping the XML symbols myself (hoping it might escape the escapes) but i still end up getting a mangled message on the server side. I also tried using the complex type option for the WSWithComplexTypes actor, and unfortunately despite playing around with different settings and arrangements, i always end up with the server receiving parameters/parameters as the response payload, ie. its like the complex types are ignored/discarded. So i have 2 questions for how i might move forward on this: 1. is there a way to deliver an XML payload as-is via any actor that then delivers the payload as a http post to a specified endpoint? (this might be a web service actor that wraps the payload as appropriate to the parsed wsdl, or perhaps a more raw http comms actor that might require more explicit post content construction). 2. is it reasonably straight forward to grab the source for the project and edit the webservices actor to allow a user option for delivering a non-escaped XML payload, or perhaps looking at WSWithComplexTypes actor and exploring (fixing?) its behaviour. Cheers, Simon ___ Kepler-users mailing list Kepler-users@kepler-project.org http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users ___ Kepler-users mailing list Kepler-users@kepler-project.org http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
Re: [kepler-users] provenance related question
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 workflow execution by setting the provenance recorder's Delay Recording Specification parameter to false. --dan On 5/16/11 8:51 PM, Jamnagarwala, Arwa Mohmadi wrote: Hi All, I was looking into provenance recorder and had some questions related to its usage: Before firing the workflow, we are currently mapping some actor parameters to user defined parameters. Is it possible to record such kind of mapping data in the database? If yes, what API can we use? Is it possible to have it record this information even before firing the workflow? Where can I find the latest Provenance related documentation? Thanks a lot, Arwa ___ Kepler-users mailing list Kepler-users@kepler-project.org http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users ___ Kepler-users mailing list Kepler-users@kepler-project.org http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
Re: [kepler-users] FTP Client
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 curl. --dan On 3/25/11 3:47 PM, Kris McN wrote: Hello Users, I'm trying to use the FTP Client to download a bunch of big binaries off of a remote server, but there's no option to designate the local directory, so when I run it the files end up in the ...home/Program Files/Kepler-2.0 directory. I don't know enough to edit the actor's underlying script. Has anyone done this? Or is there another ftp actor I can use that is more flexible? I'd also like to be able to change the operation from GET to MGET so I can use a wildcard designation rather than having every file name specifically designated. I suppose I could just use the Python Actor to work around both of these issues, but a dedicated FTP actor seems preferable. Best, Kris ___ Kepler-users mailing list Kepler-users@kepler-project.org http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
[kepler-users] How to run kepler Command Line tool to generate provenance data
Hi Madhavi, You can run a KAR from the command line: kepler.sh -runwf -nogui workflow.kar. None of the other options currently work for KARs. You can set parameters: kepler -runwf workflow.xml -x 4 -y hello but only for xml workflows, not KARs. --dan On 1/27/11 3:57 AM, Madhavi Tikhe wrote: Thanks Daneil. So this is possible to run the workflows from commandline. But I can use .kar file to run the workflows from command line? How can I pass on the parameters required by the workflow to run from command line? Thanks again, Madhavi -Original Message- From: 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 that it is possible to run multiple workflows from the command line: kepler.sh -runwf workflow1.xml workflow2.xml ... This appears to work for all command-line options except -nogui -nocache. --dan On 1/25/11 11:27 AM, Derik Barseghian wrote: Hi Madhavi, I'm not aware of a way to have 1 kepler process launch and run 2 or more workflows in a row before quitting. You could simply run a series from command line like: ant run-w...; ant run-w...; etc. or write a script to loop through workflow files in a directory, and/or a cron job. On a somewhat related note, Jing has added a scheduler module to kepler, which allows you to schedule a workflow to run periodically on a remote kepler server. Any resulting run-kars from these executions are written into a kepler repository (currently MetaCat). This module is not yet released, but will probably be available in the near future. Derik On Jan 24, 2011, at 9:39 PM, Madhavi Tikhe wrote: Thanks a lot for your reply Derik. It helped. When we talk about workflow execution from command line, it is possible to execute the two or more workflows in a batch (batch processing of the workflows)? Thanks again, Madhavi -Original Message- From: Derik Barseghian [mailto:barseghian at nceas.ucsb.edu] Sent: Tuesday, January 25, 2011 1:02 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, Yes. The workflow must contain a ProvenanceRecorder, i.e. it must be saved from the GUI while using the provenance suite. Executions of this workflow will then write provenance data. Additionally, if you would like your execution to generate a run-kar containing some metadata about the execution and a report pdf upon completion, from within the reporting suite you should create a report design from the Reporting view and save to a kar, set keepResultantRunKars true in reporting/resources/configurations/configuration.xml, and then execute from the command line. There are a few ways to execute from command line. One is: ant run-workflow-no-gui-server -Dworkflow=/Users/derik/KeplerData/workflows/MyWorkflows/yourWorkflow.kar The resultant run-kar will be created in KeplerData/workflow-runs Derik On Jan 23, 2011, at 10:37 PM, Madhavi Tikhe wrote: Hello, I would like to run the Kepler from command line to execute a workflow. In this case is it possible to generate provenance data? Regards, Madhavi DISCLAIMER == This e-mail may contain privileged and confidential information which is the property of Persistent Systems Ltd. It is intended only for the use of the individual or entity to which it is addressed. If you are not the intended recipient, you are not authorized to read, retain, copy, print, distribute or use this message. If you have received this communication in error, please notify the sender and delete all copies of this message. Persistent Systems Ltd. does not accept any liability for virus infected mails. ___ Kepler-users mailing list Kepler-users at kepler-project.org http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users DISCLAIMER == This e-mail may contain privileged and confidential information which is the property of Persistent Systems Ltd. It is intended only for the use of the individual or entity to which it is addressed. If you are not the intended recipient, you are not authorized to read, retain, copy, print, distribute or use this message. If you have received this communication in error, please notify the sender and delete all copies of this message. Persistent Systems Ltd. does not accept any liability for virus infected mails. ___ Kepler-users mailing list Kepler-users at kepler-project.org http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users DISCLAIMER == This e-mail may contain privileged and confidential
[kepler-users] How can I create log file name based on the current date?
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 output to the file out$DATE.log Please see my attempt in the attached kar file. Thank you, David ___ Kepler-users mailing list Kepler-users at kepler-project.org http://lists.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users -- next part -- A non-text attachment was scrubbed... Name: date-v2.kar Type: audio/midi Size: 7334 bytes Desc: not available URL: http://mercury.nceas.ucsb.edu/kepler/pipermail/kepler-users/attachments/20101013/c701191f/attachment-0001.kar
[kepler-users] Kepler/WSDL multi-dimensional array
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 2-dimensional data that served
by a PHP SOAP server. The format of the data is like:
Time outTemperate inTemperate
123 91.171.8
124 92.272.5
The WSDL's data format is defined as:
xsd:complexType name=RecordType
xsd:sequence
xsd:element name=values type=xsd:float minOccurs=0
maxOccurs=unbounded
/xsd:element
/xsd:sequence
/xsd:complexType
xsd:complexType name=ArrayOfRecords
xsd:sequence
xsd:element name=item minOccurs=0 maxOccurs=unbounded
type=tns:RecordType
/xsd:element
/xsd:sequence
/xsd:complexType
A web service function outputs data of the type ArrayOfRecords defined in
this WSDL.
I tried to WsWithComplexType in Kepler. When I directly hook up the output
the the display, the output is like:
{?xml version=1.0?item xmlns:xsi=
http://www.w3.org/2001/XMLSchema-instance;
xsi:type=ns2:RecordType1values
xsi:type=xsd:float1277823600/valuesvalues
xsi:type=xsd:float86.42/valuesvalues
xsi:type=xsd:float73.83/values/item,?xml version=1.0?item
xmlns:xsi=http://www.w3.org/2001/XMLSchema-instance;
xsi:type=ns2:RecordType1values
xsi:type=xsd:float1277823900/valuesvalues
xsi:type=xsd:float86.5/valuesvalues
xsi:type=xsd:float74/values/item, .}
I can use arrayToSequence actor to split those xml tokens to sequnce. But I
do not know how to convert them to arrays. I tried xml disassembler but no
success.
Could anyone give me a suggestion on how to let WSDL and Kepler handler the
multi-dimensional arrays?
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[kepler-users] KeplerFlexClient not running test
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 this error (attached) when I attempt to run a test. (Test1 under Debug) http://serv-4101.dfki.uni-kl.de/demos/extern/KFlexClient/KeplerFlexClient.html# (Firefox 2.0.0.20) Any help is appreciated. -Rick ___ Kepler-users mailing list Kepler-users at kepler-project.org http://mercury.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
[kepler-users] WSDL Issues
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: http://www.ebi.ac.uk/soaplab/typed/services/edit.seqret?wsdl to a soaplab actor I get errors about the wsdl service not being reachable. No problem with reaching these URLs in a browser. Does Kepler pass these web-service queries through port 80? I tried using a web proxy (and setting that in kepler.sh) but it didn't help matters. Get a bunch of these errors on startup in the log: 05 Mar 2010 17:41:11,561 [thread: pool-1-thread-1] ERROR - org.ecoinformatics.seek.ecogrid.EcoGridServicesController - could not add service:The service type is invalid or null: KeplerSlaveNode. Couldn't be added to list Nothing seems to be logged as a result of the four dialogues that come up in succession when I try to add the wsdl. It just asks me to confirm the URL and fails. OS os Macintosh 10.6.2. Native java is 1.6.0_17 (not 1.5)...not so sure if that could be the problem, everything else I've tinkered with in Kepler seemingly works fine. Thanks for any thoughts, Eric ___ Kepler-users mailing list Kepler-users at kepler-project.org http://mercury.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
[kepler-users] No menu bar in Kepler 1.x
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 configuration manager do when it cannot find the config file for the current locale? --dan On 2/5/10 7:52 AM, Ngu, Anne Hee Hiong wrote: Tomasz, I just did a fresh checkout of kepler under mac os and compiled it with JDK 1.6, the menu bar did not appear as well. I am interested in the answer to that problem as well. Anne From: kepler-users-bounces at kepler-project.org [kepler-users-bounces at kepler-project.org] On Behalf Of Chad Berkley [berkley at nceas.ucsb.edu] Sent: Thursday, February 04, 2010 2:06 PM To: Tomasz ?ok Cc: kepler-users at kepler-project.org Subject: Re: [kepler-users] No menu bar in Kepler 1.x Hmm, that's really weird. I just did a fresh checkout any everything worked. I'm using JDK 1.5.0_19, but I think others are using 1.6 with no problems. Let us know if you figure it out. chad Tomasz ?ok wrote: Hi Chad, Today I tried many different combinations: - Kepler from head revision and Ptolemy from stable revision (does not compile due to some broken dependency) - Kepler from head revision and Ptolemy from head revision (compiles, but doesn't have menu bar) I also tried revision from yesterday and the day before yesterday, both with no success. At one moment I thought it is a JDK problem, as I have the newest one 1.6u18 released just recently. But switching to my backup 1.6u16 did not help. All these trials suggest that there is something wrong on my side. I will try again tomorrow to install everything from scratch as you said. Thanks, Tomek On czwartek 04 luty 2010 at 20:43:07 Chad Berkley wrote: Hi Tomek, If you've deleted your .kepler directory and run an 'ant clean-all', I'm actually not sure what the problem could be. You might make sure that all of the code updated correctly. You can run the 'ant change-to -Dsuite=kepler' command again to make sure you got all of the source. You can also run 'ant update' to pull any new changes from SVN. If you still can't get it to work, I'd recommend trying everything from scratch again. Delete your ~/.kepler directory and your ~/KeplerData directory, then checkout the build-area again, and do a new change-to. Let me know if you figure it out. thanks, chad Tomasz ?ok wrote: Small update. After `ant clean-all` I do not get this error with SQL. However the main problem with missing menu bar is still there. Regards, Tomek On czwartek 04 lutego 2010 at 12:39:41 Tomasz ?ok wrote: Dear Kepler users and maintainers, Today I tried to install Kepler from trunk using this instruction: https://kepler-project.org/developers/teams/build/documentation/build-sy ste m-instructions I prepared everything and compiled Kepler, but when I try to run it, in the beginning I get the following exception and the menu bar in Kepler is missing: java.lang.NullPointerException at org.kepler.gui.MenuMapper.createKeplerMenuBar(MenuMapper.java:392) at org.kepler.gui.MenuMapper.run(MenuMapper.java:173) at ptolemy.gui.Top.deferIfNecessary(Top.java:235) at org.kepler.gui.KeplerMenuHandler.pack(KeplerMenuHandler.java:60) at ptolemy.actor.gui.TableauFrame.pack(TableauFrame.java:331) at ptolemy.actor.gui.Tableau.show(Tableau.java:355) at ptolemy.actor.gui.Configuration.createPrimaryTableau(Configuration.java: 58 2) at ptolemy.vergil.VergilApplication._createEmptyConfiguration(VergilApplica ti on.java:401) at ptolemy.actor.gui.ConfigurationApplication._parseArgs(ConfigurationAppli ca tion.java:1121) at ptolemy.vergil.VergilApplication._parseArgs(VergilApplication.java:477) at ptolemy.actor.gui.ConfigurationApplication.init(ConfigurationApplicati on .java:226) at ptolemy.actor.gui.MoMLApplication.init(MoMLApplication.java:81) at ptolemy.vergil.VergilApplication.init(VergilApplication.java:110) at ptolemy.vergil.VergilApplication$1.run(VergilApplication.java:219) at java.awt.event.InvocationEvent.dispatch(InvocationEvent.java:209) at java.awt.EventQueue.dispatchEvent(EventQueue.java:597) at java.awt.EventDispatchThread.pumpOneEventForFilters(EventDispatchThread. ja va:269) at java.awt.EventDispatchThread.pumpEventsForFilter(EventDispatchThread.jav a: 184) at java.awt.EventDispatchThread.pumpEventsForHierarchy(EventDispatchThread. ja va:174) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:169) at java.awt.EventDispatchThread.pumpEvents(EventDispatchThread.java:161) at java.awt.EventDispatchThread.run(EventDispatchThread.java:122) Before this exception I received another one from SQL. I am not sure if these two are related
[kepler-users] Viewing the provenance file.
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. I have checked out the source and built Kepler from the current version in the SVN repo including the provenance module. I can run it and everything is fine. I loaded one of the examples that comes with the version1, and recorded the provenance of the run. All works fine(after configuring the HSQL DB). Now I want to have a look at my recorded provenance filebut I don't know how to go about it. Any help here? Moses ___ Kepler-users mailing list Kepler-users at kepler-project.org http://mercury.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
[kepler-users] Provenance Text File
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 looks similar to what it looks like when I use notepad++ to open an executable file. The rest of the file looks fine however. I tried doing it under Linux with gedit and sure enough it tells me that I am trying to open a binary file. Any ideas? - Tommy _ Windows Live: Friends get your Flickr, Yelp, and Digg updates when they e-mail you. http://go.microsoft.com/?linkid=9691817 ___ Kepler-users mailing list Kepler-users at kepler-project.org http://mercury.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
[kepler-users] Provenance Text File
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 Date: Fri, 11 Dec 2009 14:59:20 -0800 From: crawl at sdsc.edu To: tommystropp at hotmail.com CC: kepler-users at kepler-project.org Subject: Re: [kepler-users] Provenance Text File 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 looks similar to what it looks like when I use notepad++ to open an executable file. The rest of the file looks fine however. I tried doing it under Linux with gedit and sure enough it tells me that I am trying to open a binary file. Any ideas? - Tommy _ Windows Live: Friends get your Flickr, Yelp, and Digg updates when they e-mail you. http://go.microsoft.com/?linkid=9691817 ___ Kepler-users mailing list Kepler-users at kepler-project.org http://mercury.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users _ Eligible CDN College University students can upgrade to Windows 7 before Jan 3 for only $39.99. Upgrade now! http://go.microsoft.com/?linkid=9691819
[kepler-users] PROVENACE API
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 implemented a method which return all port values given an execution id? I'm not sure what you mean by port values, but if you want to get the tokens, you can use the following: /** Get an sequence of tokens for an execution. * @param execId the execution id * @param last if true, the sequence starts at the last token created * and goes backwards to the first; otherwise the sequence starts at * the first token. */ public ListInteger getTokensForExecution(int execId, boolean last) throws QueryException; /** Get the Token. */ public Token getToken(int tokenId) throws QueryException; --dan
[kepler-users] Troubles in installing provenance module
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 (https://kepler-project.org/developers/interest-groups/provenance-interest-group/provenance-recorder-instructions). I noticed if I follow these steps I can not compile and run Kepler because Provenance module requires another modules to compile it. In modules.txt, I write '*provenance' instead 'provenance', to compile another ones in provenance modules.txt. Thanks for finding this; I've updated the instructions to use *provenance. I run Kepler typing 'ant run' and all modules compile well and Kepler starts. I see a button on the toolbar with a P and a green background, which means that provenance is being recorded. Then, I connect to the HSQL database and ONLY see Kepler's chache tables (six in total) such as CACHE_SEARCH, CACHECONTENTTABLE, KARS_CACHED, KAR_CONTENTS, KAR_LOCAL_REPOS and KEPLERTEXTTABLES. Obviusly, Provenance schema it is not created in the database. Did you run a workflow? The provenance schema is not created until the first workflow execution. --dan My questions are: Have I installed Provenance well (P appears in the toolbar)? When provenance module creates the schema? Do I follow the right steps? Thanks for your cooperation you are doing a very good job. Josep Maria, - Josep Maria Campanera Alsina Professor Lector Departament de Fisicoqu?mica Facultat de Farm?cia Universitat de Barcelona Avgda Joan XXIII, s/n 08028 Barcelona ? Catalonia ? Spain Tel: +34 93 4035985 Fax: +34 93 4035987 campanera at ub.edu ___ Kepler-users mailing list Kepler-users at kepler-project.org http://mercury.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
[kepler-users] Problem compiling the Provenance recorder module
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 entry in the modules.txt. However when I do an ant run, I get several compilation errors and build fails. Any pointers will be very helpful. Thanks, Arwa
[kepler-users] Port Parameters for the Web Service Actors?
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 the file retrieval examples) using parameter references in the individual fields within those actors, but are port parameters usable in the Web Service Actors (both simple and complex)? I did read on another article dated in 2008 that port parameters were suppose to be implemented in the WSComplex Actor, but I can't figure out whether it actually has been implemented yet or not. Thanks for your time, Michael Wang ___ Kepler-users mailing list Kepler-users at kepler-project.org http://mercury.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
[kepler-users] Newbie: Running a webService with Kepler
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 Lindenbaum, and I'm new on this list. I'm currently evaluating Kepler for sending and retrieving data to/from a web service I've deployed here: http://cabernet.cng.fr:8080/snp2rdf/SNPToolWebService?wsdl I've tried to use the simple method getAssemblyName: this method takes no parameter and return a string. OK : I was able to run and display it with Kepler using either a 'WebServiceActor' or a 'WSWithComplexType' Then, with a more complicated method, I'm a little lost. The method 'getSNPByName' takes as input a string (e.g.rs25) and return an array of objects 'SNP' (with properties acn/chromosome/position...). How should I process this method and loop over the results/SNP ? Thanks for your help Pierre -- http://plindenbaum.blogspot.com ___ Kepler-users mailing list Kepler-users at kepler-project.org http://mercury.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
[kepler-users] Provenance Recorder Actor
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 will then appear in the actor tree. --dan Dear Kepler Staff, I'm researcher intrested in using the Provenance Recorder Actor you described in detail in several paper (e.g: Provenance collection support in the Kepler Scientific Workflow System,Altintas, I., Barney, O., amp; Jaeger-Frank, E. (2006).). Could you explain me where this actor is downloadable becouse inside the Component Toolbox it seems to be absent. Or if it is not, in which way I could create it. Thanks for this important help. Best Regards, Alberto Redolfi. ___ Kepler-users mailing list Kepler-users at kepler-project.org http://mercury.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
[kepler-users] Extracting XML Attributes
Hi Jon,
Attached is a KAR containing the updated actor. You can import
it via File - Import Archive. The new version should show up
in the actor tree named something like XPath Processor_2_.
--dan
Jon Goodall wrote:
That would be helpful if its not too much trouble. Otherwise, I don't
mind compiling from source.
Jon
On Wed, Oct 15, 2008 at 1:20 PM, Matt Jones jones at nceas.ucsb.edu
mailto:jones at nceas.ucsb.edu wrote:
As an alternative, if compiling the source isn't something you
want to undertake, maybe Dan could package up a KAR file for you
to import 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
will have to download and compile the source. The instructions
for this can be found here:
https://dev.kepler-project.org/developers/reference/downloading-and-building-the-kepler-source-code/
Please let us know if you have any problems,
--dan
Jon Goodall wrote:
Hi Dan,
Do I need to use the nightly build of Kepler to get the
updated XPath actor? I'm having trouble running the
attached workflow with the 1.0 Kepler version.
Thanks,
Jon
On Tue, Oct 14, 2008 at 6:41 PM, Daniel Crawl
crawl at sdsc.edu mailto:crawl at sdsc.edu
mailto:crawl at sdsc.edu mailto:crawl at sdsc.edu wrote:
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
service in
Kepler and
could use some help. I've tried doing this a
couple different
ways.
First, I tried the following xpath query:
/timeSeriesResponse/timeSeries/values/value/@dateTime and the
exception is ...
ptolemy.kernel.util.IllegalActionException: XPath: node
selected with
XPath isn't an element.
at org.sdm.spa.XPath.fire(XPath.java:167)
at
ptolemy.actor.AtomicActor.iterate(AtomicActor.java:398)
at
ptolemy.actor.sched.StaticSchedulingDirector.fire(StaticSchedulingDirector.java:170)
at
ptolemy.actor.CompositeActor.fire(CompositeActor.java:400)
at
ptolemy.actor.Manager.iterate(Manager.java:688)
at
ptolemy.actor.Manager.execute(Manager.java:332)
at ptolemy.actor.Manager.run(Manager.java:1071)
at ptolemy.actor.Manager$3.run(Manager.java:1112)
The xpath query
/timeSeriesResponse/timeSeries/values/value
works fine
and gives this response ..
send to channel 0: {value
dateTime=2000-01-01T00:00:00
qualifiers=A483/value, value
dateTime=2000-01-02T00:00:00
qualifiers=A464/value ...
I've also tried using an XMLDisassembler actor to
access the
dateTime
attributes, but no luck. I was able to get the
values, but
unable to
get the dateTimes (I tried setting the port name to
@dateTime
and to
dateTime). See attached workflow for details.
One other thing to note is that this service I'm
using can return
either simple or complex types. Right now, I'm
working with the
simple type, which is a XML string. I tried using
the complex web
service actor, but still was unable to get at the
dateTime
attributes.
If you want to try this yourself, the service is
http://river.sdsc.edu/wateroneflow/NWIS/DailyValues.asmx?WSDL.
The
method GetValues returns the XML string, the method
GetValuesObject
returns a complex type
[kepler-users] Extracting XML Attributes
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 service in Kepler and
could use some help. I've tried doing this a couple different ways.
First, I tried the following xpath query:
/timeSeriesResponse/timeSeries/values/value/@dateTime and the
exception is ...
ptolemy.kernel.util.IllegalActionException: XPath: node selected with
XPath isn't an element.
at org.sdm.spa.XPath.fire(XPath.java:167)
at ptolemy.actor.AtomicActor.iterate(AtomicActor.java:398)
at
ptolemy.actor.sched.StaticSchedulingDirector.fire(StaticSchedulingDirector.java:170)
at ptolemy.actor.CompositeActor.fire(CompositeActor.java:400)
at ptolemy.actor.Manager.iterate(Manager.java:688)
at ptolemy.actor.Manager.execute(Manager.java:332)
at ptolemy.actor.Manager.run(Manager.java:1071)
at ptolemy.actor.Manager$3.run(Manager.java:1112)
The xpath query /timeSeriesResponse/timeSeries/values/value works fine
and gives this response ..
send to channel 0: {value dateTime=2000-01-01T00:00:00
qualifiers=A483/value, value dateTime=2000-01-02T00:00:00
qualifiers=A464/value ...
I've also tried using an XMLDisassembler actor to access the dateTime
attributes, but no luck. I was able to get the values, but unable to
get the dateTimes (I tried setting the port name to @dateTime and to
dateTime). See attached workflow for details.
One other thing to note is that this service I'm using can return
either simple or complex types. Right now, I'm working with the
simple type, which is a XML string. I tried using the complex web
service actor, but still was unable to get at the dateTime attributes.
If you want to try this yourself, the service is
http://river.sdsc.edu/wateroneflow/NWIS/DailyValues.asmx?WSDL. The
method GetValues returns the XML string, the method GetValuesObject
returns a complex type.
The workflow is attached if you want to take a look. The goal is
simply to create a chart of the streamflow time series. I would
appreciate any help on this. Thanks in advance!
Jon
Jonathan Goodall
Civil and Environmental Engineering
University of South Carolina
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[kepler-users] SOAP Complex type packing
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 getting used to how things work. I'm making a small test workflow that takes an amino acid sequence and runs it on a SignalP soap server, described at http:// www.cbs.dtu.dk/ws/SignalP/SignalP_3_1.wsdl The example included with Kepler, 06- WebServicesAndDataTransformation.xml, the service uses a standard string as input. SignalP uses a complex type 'runService' described in http://www.cbs.dtu.dk/ws/SignalP/ws_signalp_3_1.xsd and http:// www.cbs.dtu.dk/ws//common/ws_common_1_0.xsd Basically I need to take an input string and an id, pack it into the complex 'sequences', pack that into a 'runService', with some parameters, and then use that as input to the web server actor. Are there some default actors that can take several individual types and pack them into a complex type? Does anybody have any examples of how to do this sort of thing? Thanks, Kyle Ellrott ___ Kepler-users mailing list Kepler-users at ecoinformatics.org http://mercury.nceas.ucsb.edu/ecoinformatics/mailman/listinfo/kepler-users
