[kepler-users] Fwd: How to pass String and File Parameters using Command Line
Josep Morer Muñoz
josep.morer at gmail.com
Wed Jul 14 07:37:22 PDT 2010
Hi Derik,
Attached the KAR. This workflow also needs a custom actor that executes a
Perl script. I have also attached it.
Thanks for your help
2010/7/14 Derik Barseghian <barseghian at nceas.ucsb.edu>
> Hi Josep,
> I'm unable to replicate this problem. I've created a simple workflow and
> tried:
>
> ./kepler.sh -runwf -nogui -ExecutionId 77 -namejob 'SEPT09' -anotherVar 66
> /Users/derik/KeplerData/workflows/MyWorkflows/testwf\[0\].kar
>
> and this works for me. I've set keepResultantRunKars true in reporting's
> configuration.xml, and I'm seeing the result kar in workflow-runs, and it
> looks good. I'm at kepler revision 25100. Are you able to send me your kar
> to test?
>
> Derik
>
>
> On Jul 13, 2010, at 1:31 PM, Josep Morer Muñoz wrote:
>
> Hi all,
>>
>> Can anyone reply to my question?
>>
>> Thanks
>>
>> ---------- Forwarded message ----------
>> From: Josep Morer Muñoz <josep.morer at gmail.com>
>> Date: 2010/6/28
>> Subject: How to pass String and File Parameters using Command Line
>> To: Kepler Users <kepler-users at kepler-project.org>
>>
>>
>> Hi all,
>>
>> I am having problems when I try to execute a KAR using the command line
>> with String and File Parameters. As I understand, when a parameter is a
>> number, you put -parameter 2 f.e and if it is a string or a file path, you
>> put -parameter "string". However, for string and file parameters does not
>> work because I am having errors like this:
>>
>> urops at ubuntu:~/KeplerLastVersion$ ./kepler.sh -runwf -nogui -stepsrmsd
>> 42 -ExecutionId 35 -namejob 'SEPT09' -numclustersrmsd 5
>> /home/urops/CBI/Projectes/2/Execucions/35/KeplerMDAnalyser-Module1-RMSD-CBI[0].kar
>> [null] /home/urops/KeplerLastVersion
>> [null] Found OS Extension file:
>> /home/urops/KeplerLastVersion/apple-extensions/module-info/osextension.txt
>> [null] Ran additional initialization for module gui from class
>> org.kepler.module.gui.Initialize
>> [null] Ran additional initialization for module tagging from class
>> org.kepler.module.tagging.Initialize
>> [null] Ran additional initialization for module provenance from class
>> org.kepler.module.provenance.Initialize
>> [null] common tabpane configuration overridden by workflow-run-manager
>> [null] Ran additional initialization for module workflowrunmanager
>> from class org.kepler.module.workflowrunmanager.Initialize
>> [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 -stepsrmsd 42
>> -ExecutionId 35 -namejob SEPT09 -numclustersrmsd
>> [null] invoking: org.kepler.KeplerConfigurationApplication.main
>> [null] Kepler Initializing...
>> [null] Command failed
>> [null] java.lang.Exception: Failed to parse
>> "ptolemy/configs/kepler/ConfigNoGUIWithCache.xml -runThenExit -stepsrmsd 42
>> -ExecutionId 35 -namejob SEPT09 -numclustersrmsd"
>> [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:57)
>> [null] at
>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>> [null] at java.lang.reflect.Method.invoke(Method.java:616)
>> [null] at org.kepler.Kepler.load(Kepler.java:362)
>> [null] at org.kepler.Kepler.load(Kepler.java:380)
>> [null] at org.kepler.Kepler.parseArgsAndRun(Kepler.java:308)
>> [null] at org.kepler.Kepler.main(Kepler.java:210)
>> [null] Caused by: ptolemy.kernel.util.IllegalActionException: Cannot
>> set parameter -numclustersrmsd when no value is given.
>> [null] at
>> org.kepler.KeplerConfigurationApplication.parseArgs(KeplerConfigurationApplication.java:308)
>> [null] at
>> org.kepler.KeplerConfigurationApplication.<init>(KeplerConfigurationApplication.java:193)
>> [null] ... 9 more
>> [null] java.lang.Exception: Failed to parse
>> "ptolemy/configs/kepler/ConfigNoGUIWithCache.xml -runThenExit -stepsrmsd 42
>> -ExecutionId 35 -namejob SEPT09 -numclustersrmsd"
>> [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:57)
>> [null] at
>> sun.reflect.DelegatingMethodAccessorImpl.invoke(DelegatingMethodAccessorImpl.java:43)
>> [null] at java.lang.reflect.Method.invoke(Method.java:616)
>> [null] at org.kepler.Kepler.load(Kepler.java:362)
>> [null] at org.kepler.Kepler.load(Kepler.java:380)
>> [null] at org.kepler.Kepler.parseArgsAndRun(Kepler.java:308)
>> [null] at org.kepler.Kepler.main(Kepler.java:210)
>> [null] Caused by: ptolemy.kernel.util.IllegalActionException: Cannot
>> set parameter -numclustersrmsd when no value is given.
>> [null] at
>> org.kepler.KeplerConfigurationApplication.parseArgs(KeplerConfigurationApplication.java:308)
>> [null] at
>> org.kepler.KeplerConfigurationApplication.<init>(KeplerConfigurationApplication.java:193)
>> [null] ... 9 more
>> Exception in thread "main" Java returned: 1
>> at org.kepler.build.modules.ModulesTask.execute(ModulesTask.java:105)
>> at org.kepler.build.runner.Kepler.main(Kepler.java:78)
>> Caused by: Java returned: 1
>> at org.apache.tools.ant.taskdefs.Java.execute(Java.java:108)
>> at org.kepler.build.Run.runSuite(Run.java:298)
>> at org.kepler.build.Run.run(Run.java:202)
>> at org.kepler.build.modules.ModulesTask.execute(ModulesTask.java:101)
>> ... 1 more
>> --- Nested Exception ---
>> Java returned: 1
>> at org.apache.tools.ant.taskdefs.Java.execute(Java.java:108)
>> at org.kepler.build.Run.runSuite(Run.java:298)
>> at org.kepler.build.Run.run(Run.java:202)
>> at org.kepler.build.modules.ModulesTask.execute(ModulesTask.java:101)
>> at org.kepler.build.runner.Kepler.main(Kepler.java:78)
>>
>> I get this error when I try to pass a String or File parameter with "".
>> Any idea?
>>
>> Thanks
>> --
>> Josep
>>
>>
>>
>> --
>> Josep
>> _______________________________________________
>> Kepler-users mailing list
>> Kepler-users at kepler-project.org
>> http://mercury.nceas.ucsb.edu/kepler/mailman/listinfo/kepler-users
>>
>
> ----------
> Derik Barseghian
> http://nceas.ucsb.edu/ecoinfo | office: 805-893-5127
> Rm 3411, Marine Science Research Building, UCSB
> Santa Barbara, CA, 93106-6150
>
>
--
Josep
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