Run workflow permission denied

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Run workflow permission denied

Jason Kwan
Hi Everyone,

So thanks to Joshua and Chris I have almost got ergatis to run on the
lab mac pro.  The front page and creating projects/pipelines seems to
work.  When I try to run a simple one-component pipeline (e.g.
ncbi-blastp or formatdb) it seems to just stay in incomplete mode
forever.  The pipeline.xml.out reads something like:

/usr/local/scratch/workflow/scripts/pipeline.15.run.sh: line 37:
/usr/workflow_manager/RunWorkflow: Permission denied

I made sure RunWorkflow has chmod a+x.  I feel like I am missing
something simple here.  Does cgi need permissions set to allow running
things outside the webserver directory tree?

Jason

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Re: Run workflow permission denied

Chris Hemmerich

Jason,

I'm not sure of the solution to your problem, but I have some general
advice. When debugging workflows, if you can identify the script that is
failing, it is often easiest to sudo to the user the pipeline runs as and
run the command by hand. In this case working with pipeline.15.run.sh or
even the RunWorkflow command it contains might make the error more clear.

  Chris

On Fri, 22 Apr 2011, Jason Kwan wrote:

> Hi Everyone,
>
> So thanks to Joshua and Chris I have almost got ergatis to run on the
> lab mac pro.  The front page and creating projects/pipelines seems to
> work.  When I try to run a simple one-component pipeline (e.g.
> ncbi-blastp or formatdb) it seems to just stay in incomplete mode
> forever.  The pipeline.xml.out reads something like:
>
> /usr/local/scratch/workflow/scripts/pipeline.15.run.sh: line 37:
> /usr/workflow_manager/RunWorkflow: Permission denied
>
> I made sure RunWorkflow has chmod a+x.  I feel like I am missing
> something simple here.  Does cgi need permissions set to allow running
> things outside the webserver directory tree?
>
> Jason
>
> ------------------------------------------------------------------------------
> Fulfilling the Lean Software Promise
> Lean software platforms are now widely adopted and the benefits have been
> demonstrated beyond question. Learn why your peers are replacing JEE
> containers with lightweight application servers - and what you can gain
> from the move. http://p.sf.net/sfu/vmware-sfemails
> _______________________________________________
> Ergatis-users mailing list
> [hidden email]
> https://lists.sourceforge.net/lists/listinfo/ergatis-users
>

------------------------------------------------------------------------------
Fulfilling the Lean Software Promise
Lean software platforms are now widely adopted and the benefits have been
demonstrated beyond question. Learn why your peers are replacing JEE
containers with lightweight application servers - and what you can gain
from the move. http://p.sf.net/sfu/vmware-sfemails
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Re: Run workflow permission denied

Jason Kwan
Thanks Chris, I followed your advice and I found that the problem was
that I set permissions for the files within /usr/workflow_manager but
not for the actual directory.  Unfortunately another problem came up.  
The pipelines now start to run, but pretty much stop straight away and
end in "error".  The problem seems to occur when running
replace_config_keys.  Here is the contents of replace_config_keys.stderr:

Died with 'Couldn't add key $; PIPELINEID $;=29 to section [component]'
at /opt/ergatis/bin/replace_config_keys.pl line 241

The first part of pipeline.xml.out:
The Workflow is invoked. View Workflow Monitor to check the progress.
log4j:WARN No appenders could be found for logger
(org.tigr.antware.shared.util.AppConfig).
log4j:WARN Please initialize the log4j system properly.
FATAL 15:49:38:601 [Thread: ID:44 - replace_config_keys]
ExceptionHandler handleExceptionQuietMode:137 Runtime error executing
command /opt/ergatis/bin/replace_config_keys
--keys=PIPELINEID=29,PIPELINE_XML=/usr/local/projects/test/workflow/runtime/pipeline/29/pipeline.xml,COMPONENT_XML=/usr/local/projects/test/workflow/runtime/ncbi-blastp/29_default/component.xml
--output_conf=/usr/local/projects/test/workflow/runtime/ncbi-blastp/29_default/ncbi-blastp.default.final.config
--template_conf=/usr/local/projects/test/workflow/runtime/ncbi-blastp/29_default/ncbi-blastp.default.user.config
1>
/usr/local/projects/test/workflow/runtime/ncbi-blastp/29_default/replace_config_keys.stdout
2>
/usr/local/projects/test/workflow/runtime/ncbi-blastp/29_default/replace_config_keys.stderr
Error executing script exit value: 255

java.lang.RuntimeException: Error executing script exit value: 255
     at
org.tigr.antware.shared.util.RunSystemCommand.runCommand(RunSystemCommand.java:336)
     at
org.tigr.antware.shared.util.RunSystemCommand.runCommand(RunSystemCommand.java:160)
     at
org.tigr.workflow.common.JavaSystemCommandProcessor.process(JavaSystemCommandProcessor.java:192)
     at
org.tigr.workflow.common.CommandProcessor.executeCommand(CommandProcessor.java:167)
     at
org.tigr.workflow.common.CommandProcessor.run(CommandProcessor.java:271)
     at
org.tigr.antware.shared.concurrent.ThreadPoolWorker.runTarget(ThreadPoolWorker.java:243)
     at
org.tigr.antware.shared.concurrent.ThreadPoolWorker.runTarget(ThreadPoolWorker.java:222)
     at
org.tigr.antware.shared.concurrent.ThreadPoolWorker.access$000(ThreadPoolWorker.java:26)
     at
org.tigr.antware.shared.concurrent.ThreadPoolWorker$1.run(ThreadPoolWorker.java:102)
     at java.lang.Thread.run(Thread.java:680)

I tried a few things like adding /usr/workflow_manager (where
log4j.properties is) to the CLASSPATH environmental variable after
googling about log4j, but this did not help.  Does anyone have any idea
how to start troubleshooting this?

Thanks again

Jason



On 4/23/11 10:56 AM, Chris Hemmerich wrote:

> Jason,
>
> I'm not sure of the solution to your problem, but I have some general
> advice. When debugging workflows, if you can identify the script that is
> failing, it is often easiest to sudo to the user the pipeline runs as and
> run the command by hand. In this case working with pipeline.15.run.sh or
> even the RunWorkflow command it contains might make the error more clear.
>
>    Chris
>
> On Fri, 22 Apr 2011, Jason Kwan wrote:
>
>> Hi Everyone,
>>
>> So thanks to Joshua and Chris I have almost got ergatis to run on the
>> lab mac pro.  The front page and creating projects/pipelines seems to
>> work.  When I try to run a simple one-component pipeline (e.g.
>> ncbi-blastp or formatdb) it seems to just stay in incomplete mode
>> forever.  The pipeline.xml.out reads something like:
>>
>> /usr/local/scratch/workflow/scripts/pipeline.15.run.sh: line 37:
>> /usr/workflow_manager/RunWorkflow: Permission denied
>>
>> I made sure RunWorkflow has chmod a+x.  I feel like I am missing
>> something simple here.  Does cgi need permissions set to allow running
>> things outside the webserver directory tree?
>>
>> Jason
>>
>> ------------------------------------------------------------------------------
>> Fulfilling the Lean Software Promise
>> Lean software platforms are now widely adopted and the benefits have been
>> demonstrated beyond question. Learn why your peers are replacing JEE
>> containers with lightweight application servers - and what you can gain
>> from the move. http://p.sf.net/sfu/vmware-sfemails
>> _______________________________________________
>> Ergatis-users mailing list
>> [hidden email]
>> https://lists.sourceforge.net/lists/listinfo/ergatis-users
>>


------------------------------------------------------------------------------
Fulfilling the Lean Software Promise
Lean software platforms are now widely adopted and the benefits have been
demonstrated beyond question. Learn why your peers are replacing JEE
containers with lightweight application servers - and what you can gain
from the move. http://p.sf.net/sfu/vmware-sfemails
_______________________________________________
Ergatis-users mailing list
[hidden email]
https://lists.sourceforge.net/lists/listinfo/ergatis-users