Understanding pipelines

[Rodrigo Perea]

(by the thanks for all your support, it makes my life much simpler
with all the posted),,,,,
I am trying to understand how pipelines work and when I follow the
steps on https://nrg.wikispaces.com/Integrating+Pipeline+Engine+and+XNAT?f=print
and after invoking the pipeline (Step 7), I got a Failed status in the
MRI Session with 50.0 as a note.

Again...looking into the application logs:
011-06-22 14:58:10,302 [Thread-64] ERROR
org.nrg.pipeline.ProcessLauncher - Couldnt launch /usr/local/xnat/
pipeline/bin/XnatPipelineLauncher -pipeline xnat_tools/AutoRun.xml -id
xnat15_E00008 -label SampleID2 -host http://localhost:8080/xnat -
supressNotification -u admin -dataType xnat:mrSessionData -project
"Pip_proAbr" -notify admini...@xnat.org -notify rpe...@ku.edu -
parameter xnat_project='Pip_proAbr' -parameter
userfullname='A.Admin' -parameter supressEmail='false' -parameter
useremail='admini...@xnat.org' -parameter
session='xnat15_E00008' -parameter xnatserver='xnat15' -parameter
mailhost='smtps.kumc.edu:989' -parameter
sessionType='xnat:mrSessionData' -parameter
adminemail='rpe...@ku.edu' -parameter sessionLabel='SampleID2' -pwd
'cfokl'


Then I tried to execute the command in the applicatio.log from the
command line and it works with no error....why can't it be doned
automatically? Also, I dont see any subfolders in the MRI session or
no process whatsoever in XNAT.
Thanks again!

[Mohana Ramaratnam]

Hi,

Could you check file execute permissions wrt to the user who launches
tomcat and pipeline/bin/XnatPipelineLauncher.

Regards,
Mohana

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[Rodrigo Perea]

User tomcat6 launched tomcat and XnatPipeLauncher has been created by
root but it also has other user permissions......any other
suggestions? Should I change root owner of XnatPipieLauncher to
tomcat6? How do I do that?

Thanks,
Rodrigo



XnatPipelineLauncher:
rperea@kus-imaging:~$ ls -l /usr/local/xnat/pipeline/bin/
total 28
-rwxrwxrwx 1 root root 14 2011-06-22 10:53 GenericCommand.sh
-rwxrwxrwx 1 root root 2083 2011-06-22 10:53 PipelineJobSubmitter
-rwxrwxrwx 1 root root 1843 2011-06-22 10:53 PipelineRunner
-rwxrwxrwx 1 root root 1489 2011-06-22 10:53 PlexiConverter
-rwxrwxrwx 1 root root 1391 2011-06-22 10:53 ResourceImporter
-rwxrwxrwx 1 root root 14 2011-06-22 10:53 schedule
-rwxrwxrwx 1 root root 2723 2011-06-22 10:53 XnatPipelineLauncher



Tomcat6:
rperea@kus-imaging:~$ ps aux | grep tomcat
rperea 13118 0.0 0.0 13124 1068 pts/0 S+ 12:09 0:00 grep
--color=auto tomcat
tomcat6 32098 0.1 13.2 838388 519376 ? Sl Jun22 2:21 /usr/
lib/jvm/java-6-sun/bin/java -Djava.util.logging.config.file=/var/lib/
tomcat6/conf/logging.properties -Djava.awt.headless=true -Xmx128m -XX:
+UseConcMarkSweepGC -
Djava.util.logging.manager=org.apache.juli.ClassLoaderLogManager -
Djava.endorsed.dirs=/usr/share/tomcat6/endorsed -classpath /usr/share/
tomcat6/bin/bootstrap.jar -Dcatalina.base=/var/lib/tomcat6 -
Dcatalina.home=/usr/share/tomcat6 -Djava.io.tmpdir=/tmp/tomcat6-tmp
org.apache.catalina.startup.Bootstrap start




On Jun 22, 10:10 pm, Mohana Ramaratnam <mohanakann...@gmail.com>
wrote:

> Hi,
>
> Could you check file execute permissions wrt to the user who launches
> tomcat and pipeline/bin/XnatPipelineLauncher.
>
> Regards,
> Mohana
>
>
>
>
>
>
>
> On Thu, Jun 23, 2011 at 1:36 AM, Rodrigo Perea <grandr...@gmail.com> wrote:
> > (by the thanks for all your support, it makes my life much simpler
> > with all the posted),,,,,
> > I am trying to understand how pipelines work and when I follow the

> > steps onhttps://nrg.wikispaces.com/Integrating+Pipeline+Engine+and+XNAT?f=print

> > and after invoking the pipeline (Step 7), I got a Failed status in the
> > MRI Session with 50.0 as a note.
>
> > Again...looking into the application logs:
> > 011-06-22 14:58:10,302 [Thread-64] ERROR
> > org.nrg.pipeline.ProcessLauncher -  Couldnt launch  /usr/local/xnat/
> > pipeline/bin/XnatPipelineLauncher -pipeline xnat_tools/AutoRun.xml -id
> > xnat15_E00008 -label SampleID2 -hosthttp://localhost:8080/xnat-
> > supressNotification  -u admin -dataType xnat:mrSessionData -project

> > "Pip_proAbr" -notify administra...@xnat.org -notify rpe...@ku.edu -

> > parameter xnat_project='Pip_proAbr'  -parameter
> > userfullname='A.Admin'  -parameter supressEmail='false'  -parameter

> > useremail='administra...@xnat.org'  -parameter

[Rodrigo Perea]

Well, thanks for your help!
I checked the PIPELINE_HOME/logs and it looks like there were no
permission in the /usr/share/tomcat6 folder. I edited this and the
pipeline successfully completed. Thanks for your help, I guess this
solves my problem. For future references, this problem occurred when I
was using Ubuntu 11.04 as my OS.

[Mohana Ramaratnam]

XnatPipelineLauncher writes some files into user.home unless, a system
variable, called pipeline.tmp, is set.

If you dont want to write to user.home (or cannt) then modify

PIPELINE_HOME/bin/XnatPipelineLauncher to contain

java -Dpipeline.tmp=<PATH TO A TEMP FOLDER> .....REST OF THE THINGS
HERE ........

Mohana