def test_read_file_parameter_with_uploads(tmpdir):
"""Test reading a file parameter with a given list of upload files."""
parameters = [File(name='A', index=0, target='target1')]
sc = Scanner(reader=ListReader(['f1']))
arguments = cli.read(parameters, sc, files=[('f1', 'F', '123')])
assert len(arguments) == 1
assert arguments['A'] == serialize_fh('f1', target='target1')
def start_run(ctx, group, configfile):
"""Start new workflow run."""
group_id = ctx.obj.get_group(ctx.params)
config = factory.read_config(configfile) if configfile else None
with service() as api:
doc = api.groups().get_group(group_id=group_id)
config = config if config else doc[glbls.ENGINE_CONFIG]
# Create list of file descriptors for uploaded files that are included
# in the submission handle
files = []
for fh in doc[glbls.GROUP_UPLOADS]:
files.append((
fh[flbls.FILE_ID],
fh[flbls.FILE_NAME],
fh[flbls.FILE_DATE][:19])
)
# Create list of additional user-provided template parameters
parameters = ParameterIndex.from_dict(doc[glbls.GROUP_PARAMETERS])
# Read values for all parameters.
user_input = read(parameters.sorted(), files=files)
args = [serialize_arg(key, val) for key, val in user_input.items()]
# Start the run and print returned run state information.
doc = api.runs().start_run(group_id=group_id, arguments=args, config=config)
run_id = doc[labels.RUN_ID]
run_state = doc[labels.RUN_STATE]
click.echo('started run {} is {}'.format(run_id, run_state))
def test_read_file_parameters(tmpdir):
"""Test reading lists of file parameters."""
parameters = [
File(name='A', index=0, target='target1'),
File(name='B', index=1, default='target2'),
File(name='C', index=2),
]
sc = Scanner(reader=ListReader([tmpdir, tmpdir, '', tmpdir, 'target3']))
arguments = cli.read(parameters, sc)
assert len(arguments) == 3
def test_read_string_parameters():
"""Test reading lists of string parameters."""
parameters = [
String(name='A', index=0),
String(name='B', index=1, default='ABC')
]
sc = Scanner(reader=ListReader(['true', '']))
arguments = cli.read(parameters, sc)
assert len(arguments) == 2
assert arguments['A'] == 'true'
assert arguments['B'] == 'ABC'
def test_read_boolean_parameters():
"""Test reading lists of boolean parameters."""
parameters = [
Bool(name='A', index=0),
Bool(name='B', index=1, default=False),
Bool(name='C', index=2, default=False),
]
sc = Scanner(reader=ListReader(['true', 'xyz', '', 'True']))
arguments = cli.read(parameters, sc)
assert len(arguments) == 3
assert arguments['A']
assert not arguments['B']
assert arguments['C']
def test_read_numeric_parameters():
"""Test reading lists of numeric parameters."""
parameters = [
Int(name='A', index=0),
Int(name='B', index=1, default=10),
Float(name='C', index=2),
Float(name='D', index=3, default=1.23)
]
sc = Scanner(reader=ListReader(['1', 'xyz', '', 'True', '3.4', '']))
arguments = cli.read(parameters, sc)
assert len(arguments) == 4
assert arguments['A'] == 1
assert arguments['B'] == 10
assert arguments['C'] == 3.4
assert arguments['D'] == 1.23
def test_read_empty_list():
"""Test reading empty lists of parameter declarations."""
assert cli.read([]) == dict()