Translating pegasus status

[soichih]

I am updating our freesurfer App to use the new pegasus workflow version.

For it to function properly on our system, I will need to query and translate pegasus status output to one of the following exit code.

#return code 0 = running
#return code 1 = finished successfully
#return code 2 = failed
#return code 3 = unknown status

I am currently working on the following script

https://github.com/brainlife/app-freesurfer-osg/blob/master/status.sh

My questions are..

1. What are the possible statuses that pegasus could generate?
2. Instead of grep/tail-ing the stdout output from pegasus-status (brittle) like I am doing, is there way to make pegasus-status outout in json/xml or any machine readable format?
3. When I run pegasus-remove, the state become "Failurer". Is this by design? Can the status become "removed" or "stopped" instead?

Thanks!

[rynge]

The next version of Pegasus will have a better API for this, but for now, yeah, parsing the output of pegasus-status is the best solution. I think --rows might be a little bit easier:

pegasus-status --noqueue --rows /home/rynge/workflows/freesurfer-1578961158 | tail -n 1 | perl -p -e 's/.*\(([\w]+):.*/\1/'

The states here should be Running, Failed, Success, and probably Unknown - but I would just leave that as catch all at the end if the 3 first one does not match.

I will have to check on the removed workflow - it might that we do not have enough states.

[soichih]

I've updated our script so that we record our stop event and use that to distinguish if the job was stopped by the user, or terminated.