def create_sample_params(
params: Dict[str,
Any]) -> Tuple[Sample, Optional[UUID], Optional[int]]:
'''
Process the input from the create_sample API call and translate it into standard types.
:param params: The unmarshalled JSON recieved from the API as part of the create_sample
call.
:returns: A tuple of the sample to save, the UUID of the sample for which a new version should
be created or None if an entirely new sample should be created, and the previous version
of the sample expected when saving a new version.
:raises IllegalParameterError: if any of the arguments are illegal.
'''
_check_params(params)
if type(params.get('sample')) != dict:
raise _IllegalParameterError(
'params must contain sample key that maps to a structure')
s = params['sample']
if type(s.get('node_tree')) != list:
raise _IllegalParameterError(
'sample node tree must be present and a list')
if s.get('name') is not None and type(s.get('name')) != str:
raise _IllegalParameterError('sample name must be omitted or a string')
nodes = _check_nodes(s)
id_ = get_id_from_object(s, ID, name='sample.id')
pv = params.get('prior_version')
if pv is not None and type(pv) != int:
raise _IllegalParameterError(
'prior_version must be an integer if supplied')
s = Sample(nodes, s.get('name'))
return (s, id_, pv)
def validate_samples_params(params: Dict[str, Any]) -> List[Sample]:
'''
Process the input from the validate_samples API call and translate it into standard types.
:param params: The unmarshalled JSON recieved from the API as part of the create_sample
call.
:returns: A tuple of the sample to save, the UUID of the sample for which a new version should
be created or None if an entirely new sample should be created, and the previous version
of the sample expected when saving a new version.
:raises IllegalParameterError: if any of the arguments are illegal.
'''
_check_params(params)
if type(params.get('samples')) != list or len(params.get('samples',
[])) == 0:
raise _IllegalParameterError('params must contain list of `samples`')
samples = []
for s in params['samples']:
if type(s.get('node_tree')) != list:
raise _IllegalParameterError(
'sample node tree must be present and a list')
if type(s.get('name')) != str or len(s.get('name')) <= 0:
raise _IllegalParameterError(
'sample name must be included as non-empty string')
nodes = _check_nodes(s)
s = Sample(nodes, s.get('name'))
samples.append(s)
return samples
def create_sample_params(
params: Dict[str,
Any]) -> Tuple[Sample, Optional[UUID], Optional[int]]:
'''
Process the input from the create_sample API call and translate it into standard types.
:param params: The unmarshalled JSON recieved from the API as part of the create_sample
call.
:returns: A tuple of the sample to save, the UUID of the sample for which a new version should
be created or None if an entirely new sample should be created, and the previous version
of the sample expected when saving a new version.
:raises IllegalParameterError: if any of the arguments are illegal.
'''
_check_params(params)
if type(params.get('sample')) != dict:
raise _IllegalParameterError(
'params must contain sample key that maps to a structure')
s = params['sample']
if type(s.get('node_tree')) != list:
raise _IllegalParameterError(
'sample node tree must be present and a list')
if s.get('name') is not None and type(s.get('name')) != str:
raise _IllegalParameterError('sample name must be omitted or a string')
nodes = []
for i, n in enumerate(s['node_tree']):
if type(n) != dict:
raise _IllegalParameterError(
f'Node at index {i} is not a structure')
if type(n.get('id')) != str:
raise _IllegalParameterError(
f'Node at index {i} must have an id key that maps to a string')
try:
type_ = _SubSampleType(n.get('type'))
except ValueError:
raise _IllegalParameterError(
f'Node at index {i} has an invalid sample type: {n.get("type")}'
)
if n.get('parent') and type(n.get('parent')) != str:
raise _IllegalParameterError(
f'Node at index {i} has a parent entry that is not a string')
mc = _check_meta(n.get('meta_controlled'), i, 'controlled metadata')
mu = _check_meta(n.get('meta_user'), i, 'user metadata')
try:
nodes.append(
_SampleNode(n.get('id'), type_, n.get('parent'), mc, mu))
# already checked for the missing param error above, for id
except _IllegalParameterError as e:
raise _IllegalParameterError(f'Error for node at index {i}: ' +
_cast(str, e.message)) from e
id_ = get_id_from_object(s)
pv = params.get('prior_version')
if pv is not None and type(pv) != int:
raise _IllegalParameterError(
'prior_version must be an integer if supplied')
s = Sample(nodes, s.get('name'))
return (s, id_, pv)