def print_group(doc):
"""Print group handle information to console.
Parameters
----------
doc: dict
Serialization of a workflow group handle.
"""
members = list()
for u in doc[labels.GROUP_MEMBERS]:
members.append(u[labels.USER_NAME])
click.echo('ID : {}'.format(doc[labels.GROUP_ID]))
click.echo('Name : {}'.format(doc[labels.GROUP_NAME]))
click.echo('Members : {}'.format(','.join(members)))
# -- Uploaded files -----------------------------------------------
click.echo('\nUploaded Files\n--------------\n')
table = ResultTable(
headline=['ID', 'Name', 'Created At', 'Size'],
types=[PARA_STRING, PARA_STRING, PARA_STRING, PARA_INT])
for f in doc[labels.GROUP_UPLOADS]:
table.add([
f[filelabels.FILE_ID], f[filelabels.FILE_NAME],
f[filelabels.FILE_DATE][:19], f[filelabels.FILE_SIZE]
])
for line in table.format():
click.echo(line)
def show_ranking(ctx, workflow, all):
"""Show ranking for workflow results."""
workflow_id = ctx.obj.get_workflow(ctx.params)
with service() as api:
doc = api.workflows().get_ranking(workflow_id=workflow_id,
include_all=all)
# Print ranking.
headline = ['Rank', 'Name']
types = [PARA_INT, PARA_STRING]
mapping = dict()
for col in doc[labels.WORKFLOW_SCHEMA]:
headline.append(col[labels.COLUMN_TITLE])
types.append(col[labels.COLUMN_TYPE])
mapping[col[labels.COLUMN_NAME]] = len(mapping)
table = ResultTable(headline=headline, types=types)
rank = 1
for run in doc[labels.RANKING]:
group = run[labels.WORKFLOW_GROUP][labels.GROUP_NAME]
row = [rank, group] + ([None] * (len(headline) - 2))
for r in run[labels.RUN_RESULTS]:
row[mapping[r[labels.COLUMN_NAME]] + 2] = r[labels.COLUMN_VALUE]
table.add(row)
rank += 1
for line in table.format():
click.echo(line)
def list_users():
"""List all registered users."""
with service() as api:
doc = api.users().list_users()
table = ResultTable(['Name', 'ID'], [PARA_STRING, PARA_STRING])
for user in doc[labels.USER_LIST]:
table.add([user[labels.USER_NAME], user[labels.USER_ID]])
for line in table.format():
click.echo(line)
def list_groups():
"""List user groups (for current user)."""
with service() as api:
doc = api.groups().list_groups()
# Print listing of groups as output table.
table = ResultTable(['ID', 'Name'], [PARA_STRING] * 2)
for g in doc[labels.GROUP_LIST]:
table.add([g[labels.GROUP_ID], g[labels.GROUP_NAME]])
for line in table.format():
click.echo(line)
def list_obsolete_runs(before, state):
"""List old runs."""
table = ResultTable(headline=['ID', 'Submitted at', 'State'],
types=[PARA_STRING] * 3)
with service() as api:
runs = api.runs().run_manager.list_obsolete_runs(date=before,
state=state)
for run in runs:
table.add([run.run_id, run.created_at[:19], run.state_type])
for line in table.format():
click.echo(line)
def list_runs(ctx, group, state):
"""List workflow runs."""
group_id = ctx.obj.get_group(ctx.params)
with service() as api:
doc = api.runs().list_runs(group_id=group_id, state=state)
table = ResultTable(
headline=['ID', 'Submitted at', 'State'],
types=[PARA_STRING] * 3
)
for r in doc[labels.RUN_LIST]:
run = list([r[labels.RUN_ID], r[labels.RUN_CREATED][:19], r[labels.RUN_STATE]])
table.add(run)
for line in table.format():
click.echo(line)
def list_files(ctx, group):
"""List uploaded files for a submission."""
group_id = ctx.obj.get_group(ctx.params)
with service() as api:
doc = api.uploads().list_uploaded_files(group_id)
table = ResultTable(
headline=['ID', 'Name', 'Created At', 'Size'],
types=[PARA_STRING, PARA_STRING, PARA_STRING, PARA_INT])
for f in doc['files']:
table.add([
f[labels.FILE_ID], f[labels.FILE_NAME], f[labels.FILE_DATE][:19],
f[labels.FILE_SIZE]
])
for line in table.format():
click.echo(line)
def read_file(
para: Parameter, scanner: Scanner, files: Optional[Tuple[str, str, str]] = None
):
"""Read value for a file parameter.
Parameters
----------
para: flowserv.model.parameter.base.Parameter
Workflow template parameter declaration
scanner: flowserv.scanner.Scanner
Input scanner.
files: list, default=None
List of tuples representing uploaded files. Each tuple has three
elements: file_id, name, timestamp.
"""
# Distinguish between the case where a list of uploaded files
# is given or not.
if files is not None:
print('\nSelect file identifier from uploaded files:\n')
table = ResultTable(
headline=['ID', 'Name', 'Created at'],
types=[PARA_STRING] * 3
)
for file_id, name, created_at in files:
table.add([file_id, name, created_at])
for line in table.format():
print(line)
print('\n{}'.format(para.prompt()), end='')
filename = scanner.next_string()
else:
filename = scanner.next_file()
target_path = None
if para.target is None:
print('Target Path:', end='')
target_path = scanner.next_string()
if target_path == '':
target_path = para.default
else:
target_path = para.target
# The type of the returned value depends on whether the list of
# uploaded files is given or not.
if files is not None:
return serialize_fh(file_id=filename, target=target_path)
else:
return InputFile(FSFile(filename), target_path)