def cli(ctx, workflow_id, **kwds):
"""
Get a list of invocations for a particular workflow ID or alias.
"""
workflow_id = translate_alias(ctx, workflow_id, kwds.get('profile'))
info("Looking for invocations for workflow {}...".format(workflow_id))
workflow_id = profiles.translate_alias(ctx, workflow_id,
kwds.get('profile'))
profile = profiles.ensure_profile(ctx, kwds.get('profile'))
invocations = get_invocations(url=profile['galaxy_url'],
key=profile['galaxy_admin_key']
or profile['galaxy_user_key'],
workflow_id=workflow_id)
if tabulate:
state_colors = {
'ok': '\033[92m', # green
'running': '\033[93m', # yellow
'error': '\033[91m', # red
'paused': '\033[96m', # cyan
'deleted': '\033[95m', # magenta
'deleted_new': '\033[95m', # magenta
'new': '\033[96m', # cyan
'queued': '\033[93m', # yellow
}
print(
tabulate(
{
"Invocation ID":
invocations.keys(),
"Jobs status": [
', '.join([
'{}{} jobs {}\033[0m'.format(
state_colors[k], v, k)
for k, v in inv['states'].items()
]) for inv in invocations.values()
],
"Invocation report URL": [
'{}/workflows/invocations/report?id={}'.format(
profile['galaxy_url'].strip('/'), inv_id)
for inv_id in invocations
],
"History URL": [
'{}/histories/view?id={}'.format(
profile['galaxy_url'].strip('/'),
invocations[inv_id]['history_id'])
for inv_id in invocations
]
},
headers="keys"))
else:
error(
"The tabulate package is not installed, invocations could not be listed correctly."
)
print(json.dumps(invocations, indent=4, sort_keys=True))
info("{} invocations found.".format(len(invocations)))
return
def handle_profile_options(*args, **kwds):
profile = kwds.get("profile", None)
if profile:
ctx = args[0]
profile_defaults = profiles.ensure_profile(ctx, profile, **kwds)
for key, value in profile_defaults.items():
if ctx.get_option_source(key) != OptionSource.cli:
kwds[key] = value
ctx.set_option_source(key, OptionSource.profile, force=True)
return f(*args, **kwds)
def handle_profile_options(*args, **kwds):
profile = kwds.get("profile", None)
if profile:
ctx = args[0]
profile_defaults = profiles.ensure_profile(ctx, profile, **kwds)
_setup_profile_options(ctx, profile_defaults, kwds)
try:
return f(*args, **kwds)
except ExitCodeException as e:
sys.exit(e.exit_code)
def handle_profile_options(*args, **kwds):
profile = kwds.get("profile", None)
if profile:
ctx = args[0]
profile_defaults = profiles.ensure_profile(ctx, profile, **kwds)
for key, value in profile_defaults.items():
if ctx.get_option_source(key) != OptionSource.cli:
kwds[key] = value
ctx.set_option_source(key,
OptionSource.profile,
force=True)
return f(*args, **kwds)
def handle_profile_options(*args, **kwds):
profile = kwds.get("profile", None)
if profile:
ctx = args[0]
profile_defaults = profiles.ensure_profile(
ctx, profile, **kwds
)
_setup_profile_options(ctx, profile_defaults, kwds)
try:
return f(*args, **kwds)
except ExitCodeException as e:
sys.exit(e.exit_code)