Galaxy does indeed print a lot of log data to stdout (when not in daemon mode). But when something fails, it's just an exception; sometimes it's clear what it means, sometimes not. My problem is I can't get print debugging to work. Galaxy captures both stdout and stderr and stashes them in a db somewhere.

John Chilton suggested I try using the logging facility, but binary.py throws an exception when I try to do that:
An error occurred running this job:uploaded csra file No handlers could be found for logger "galaxy.datatypes.binary"

So it's back to square one. Debugging without even a working print statement is pretty difficult. Even trying log = logging.getLogger() or log = logging.getLogger('wsgi') produces exceptions. I would assume there'd be a way to set up logging in universe_wsgi.ini, but none of the logging parameters seem to set up a root logger that tools can use.

--mj

On 10/10/12 2:45 PM, John Chilton wrote:

Hey Mark,

A few things, instead of printing stuff out you could use the global
variable log in the binary.py file. Maybe something like
log.warn("SNIFFING csra"). I think your logging statements will be
more likely to show up then.