def add_single(id, alias):
"""
Add an alias to a single ID.
"""
gi, cnfg, aliases = utils._login()
if not alias:
alias = namesgenerator.get_random_name()
click.echo("Alias assigned to ID {}: ".format(id) +
click.style(alias, bold=True))
aliases[alias] = id
_update_aliases(aliases)
def list_():
"""
List all aliases currently assigned to IDs.
"""
gi, cnfg, aliases = utils._login()
alias, id = ['Alias'], ['ID']
for a in aliases:
alias.append(a)
id.append(aliases[a])
utils._tabulate([alias, id])
def upload(path, public, file_type):
gi, cnfg, aliases = utils._login()
# id = aliases.get(id, id) # if the user provided an alias, return the id; else assume they provided a raw id
if path[-3:] == '.ga': # decide based on ext whether to upload as wf or ds. is this sufficient?
with open(path) as f:
# quote from @bgruening: 'Only support the newer yaml based workflow files', don't know what this is though
# wf_dict = yaml.safe_load(f)
wf_dict = json.load(f)
wf_dict['tags'].append('gxwf')
gi.workflows.import_workflow_dict(wf_dict, publish=public) # could use import_workflow_from_local_path, but then would need a second call to add the gxwf tag as below
# gi.workflows.update_workflow(wf['id'], tags=wf['tags'] + ['gxwf'])
else:
ds_id = gi.tools.upload_file(path, cnfg['hid'], file_type=file_type)['outputs'][0]['id']
gi.histories.update_dataset(cnfg['hid'], ds_id, tags=['gxwf'])
def delete(alias, all_):
"""
Remove a single currently assigned alias with --alias, or all aliases with --all
"""
if bool(alias) == bool(all_):
click.echo(click.get_current_context().get_help(
)) # raise help, we need either option but not both or neither
return
gi, cnfg, aliases = utils._login()
if all_:
aliases = {}
elif alias:
aliases.pop(alias)
else:
return
_update_aliases(aliases)
def datasets(search, all):
gi, cnfg, aliases = utils._login()
aliases_inverted = {v: k for k, v in aliases.items()} # need this below
if all:
# replace all this rubbish with gi.datasets.get_datasets() when the PR is merged
dataset_list = gi.datasets._get('?limit=1000000000000')
# for h in gi.histories.get_histories():
# h_name = gi.histories.show_history(h['id'])['name']
# history_list = gi.histories.show_history(h['id'], contents=True)
# for dataset in history_list:
# dataset['history_name'] = h_name
# dataset_list += history_list
else:
dataset_list = gi.histories.show_history(cnfg['hid'], contents=True)
for dataset in dataset_list:
if 'gxwf' not in dataset['tags']:
gi.histories.update_dataset(cnfg['hid'],
dataset['id'],
tags=['gxwf'])
ds_name, ds_id, ds_alias, ds_ext = ['Dataset name'], ['ID'], ['Alias'], [
'Extension'
] #, ['History']
for ds in dataset_list:
if search:
if search not in ds.get('name', ''):
continue
if ds.get('deleted') == False and ds.get(
'state') == 'ok': # could show non-ok datasets too?
ds_name.append(ds.get('name', ''))
ds_id.append(ds.get('id', ''))
ds_alias.append(aliases_inverted.get(ds.get('id'), ''))
ds_ext.append(str(ds.get('extension', '')))
# ds_hist.append(ds.get('history_name', '')) # could hide this option when --all is not set
utils._tabulate([
ds_name,
ds_ext,
ds_id,
ds_alias,
]) # ds_hist])
def list_workflows(public, search):
gi, cnfg, aliases = utils._login()
aliases_inverted = {v: k for k, v in aliases.items()} # need this below
if search:
workflows = [wf for wf in gi.workflows.get_workflows(published=public) if search in wf['name'] or search in wf['owner']]
else:
workflows = gi.workflows.get_workflows(published=public)
wf_name, wf_id, wf_alias, steps, owner = ['Workflow name'], ['ID'], ['Alias'], ['Steps'], ['Owner']
# do we need separate id / alias columns? if we make sure everything can be done via alias
for wf in workflows:
wf_name.append(wf['name'])
wf_id.append(wf['id'])
wf_alias.append(aliases_inverted.get(wf['id'], ''))
steps.append(str(wf['number_of_steps']))
owner.append(wf['owner'])
utils._tabulate([wf_name, wf_id, wf_alias, steps, owner])
def add_all():
"""
Add randomly generated aliases to all workflows and datasets which do not currently have one.
"""
gi, cnfg, aliases = utils._login()
workflow_ids = [wf['id'] for wf in gi.workflows.get_workflows()]
dataset_ids = [
ds['id']
for ds in gi.histories.show_history(cnfg['hid'], contents=True)
]
for id in workflow_ids + dataset_ids:
if id not in aliases.values(
): # we do not overwrite if an alias already exists
while True:
alias = namesgenerator.get_random_name()
# we can allow one id to have multiple aliases but NOT the reverse
if alias not in aliases:
break
click.echo("Alias assigned to ID {}: ".format(id) +
click.style(alias, bold=True))
aliases[alias] = id
_update_aliases(aliases)
def invocations(id_):
gi, cnfg, aliases = utils._login()
if id_:
id_ = aliases.get(
id_, id_
) # if the user provided an alias, return the id; else assume they provided a raw id
invocations = gi.workflows.get_invocations(
id_) # will be deprecated, use line below in future
# invocations = gi.invocations.get_invocations(workflow_id=id_)
else: # get all invocations - whether this is actually useful or not I don't know, but you get to see a lot of pretty colours
invocations = gi.invocations.get_invocations()
for n in range(len(invocations)):
click.echo(click.style("\nInvocation {}".format(n + 1), bold=True))
invoc_id = invocations[n]['id']
step_no = 1
state_colors = {
'ok': 'green',
'running': 'yellow',
'error': 'red',
'paused': 'cyan',
'deleted': 'magenta',
'deleted_new': 'magenta',
'new': 'cyan',
'queued': 'yellow'
}
for state in state_colors:
for k in range(
gi.invocations.get_invocation_summary(invoc_id)
['states'].get(state, 0)):
click.echo(
click.style(u'\u2B24' +
' Job {} ({})'.format(k + step_no, state),
fg=state_colors[state]))
step_no += k + 1