def run_workflow(job, config, log_level):
"""
Run a GeneFlow workflow.
Args:
job: job dict describing run.
config: GeneFlow configuration dict.
log_level: logging level for this run.
Returns:
On success: Workflow job dict.
On failure: False.
"""
if job['log']:
# reconfig log location for this run
Log.config(log_level, job['log'])
Log.some().info('job loaded: %s -> %s', job['name'], job['id'])
# run job
workflow = Workflow(job['id'], config)
if not workflow.initialize():
Log.an().error('workflow initialization failed: job_id=%s', job['id'])
return False
Log.some().info('running workflow:\n%s', str(workflow))
if not workflow.run():
Log.an().error('workflow run failed: job_id=%s', job['id'])
return False
Log.some().info('workflow complete:\n%s', str(workflow))
return workflow.get_job()
def main():
"""
Geneflow CLI main entrypoint.
Args:
None.
Returns:
Nothing.
"""
args, subparser = parse_args()
if not args:
sys.exit(1)
# configure logging
Log.config(args[0].log_level, args[0].log_file)
# display GeneFlow version
Log.some().info('GeneFlow %s', __version__)
# call the appropriate command
if not args[0].func(args=args[0], other_args=args[1], subparser=subparser):
sys.exit(1)
sys.exit(0)
def main():
"""
Geneflow CLI main entrypoint.
Args:
None.
Returns:
Nothing.
"""
args = parse_args()
if not args:
sys.exit(1)
# configure logging
Log.config(args.log_level, args.log_file)
# call the appropriate command
if not args.func(args):
sys.exit(1)
sys.exit(0)
