[kepler-users] Fwd: How to pass String and File Parameters using Command Line
Derik Barseghian
barseghian at nceas.ucsb.edu
Thu Jul 15 17:40:52 PDT 2010
Hi Joesp,
This is a problem with our kepler.sh script being hardcoded to accept
only a certain number of arguments. If you change the relevant line in
kepler.sh to accept two more, your workflow should run:
java -classpath build-area/lib/ant.jar:kepler.jar
org.kepler.build.runner.Kepler "$1" "$2" "$3" "$4" "$5" "$6" "$7" "$8"
"$9" "${10}" "${11}"
Let me know if it doesn't. I'll file a bug for us to fix that script.
Derik
On Jul 14, 2010, at 7:37 AM, Josep Morer Muñoz wrote:
> 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
> <KeplerMDAnalyser-Module1-RMSD-
> CBI[0].kar><PerlScript.java><PerlScript.class><PerlScript
> $_StreamReaderThread.class>
----------
Derik Barseghian
http://nceas.ucsb.edu/ecoinfo | office: 805-893-5127
Rm 3411, Marine Science Research Building, UCSB
Santa Barbara, CA, 93106-6150
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