def parameters(cls):
cls.uuids_param = ParameterFactory.uuid(required=False)
parameters = [
cls.uuids_param,
ParameterFactory.format(),
]
return parameters
def parameters(cls):
sid_enum = cls._DB_CONNECTOR.distinct(PROBE_EXPERIMENTS_COLLECTION,
SAMPLE_ID)
rid_enum = cls._DB_CONNECTOR.distinct(PROBE_EXPERIMENTS_COLLECTION,
RUN_ID)
pid_enum = cls._DB_CONNECTOR.distinct(PROBE_EXPERIMENTS_COLLECTION,
PROBE_ID)
date_enum = cls._DB_CONNECTOR.distinct(PROBE_EXPERIMENTS_COLLECTION,
DATE)
date_enum = map(lambda x: x.strftime("%Y_%m_%d"), date_enum)
parameters = [
ParameterFactory.format(),
ParameterFactory.lc_string(SAMPLE_ID,
"Genomic DNA Sample ID(s).",
required=False,
allow_multiple=True,
enum=sid_enum),
ParameterFactory.lc_string(RUN_ID, "Run ID(s).",
required=False,
allow_multiple=True,
enum=rid_enum),
ParameterFactory.lc_string(PROBE_ID, "Probe ID(s).",
required=False,
allow_multiple=True,
enum=pid_enum),
ParameterFactory.date(required=False, enum=date_enum)
]
return parameters
def parameters(cls):
parameters = [
ParameterFactory.format(),
ParameterFactory.sequence_names(required=True),
ParameterFactory.sequences(required=True),
]
return parameters
def _parse_query_params(cls, query_params):
'''
Valid query_params are defined by parameters(). However, a user can
supply parameters not contained in this list. Therefore, invalid
parameters are discarded and a params_dict is populated only with those
parameters that are valid. Since format is a special required input
parameter for every API function, it is parsed and returned separately.
Note that each parameter parses its own arguments. This allows it to
set a default when the parameter isn't included in the API call, as well
as format the input appropriately (string, float, int, date, etc.).
'''
params_dict = dict()
_format = FORMATS.json # @UndefinedVariable
parameters = cls.parameters()
for parameter in parameters:
# Path parameters are parsed in _handle_path_fields()
if not parameter.is_path():
# query_params is a default_dict(list), so it returns an empty
# list if this parameter was not provided - parse_args must
# be called on every parameter to set its default value if one
# exists.
args = parameter.parse_args(
query_params[parameter.alias.lower()])
if args:
if parameter == ParameterFactory.format():
_format = args[0]
else:
params_dict[parameter] = args
return (params_dict, _format)
def parameters(cls):
cls.refresh_parameter = ParameterFactory.boolean("refresh",
"Refresh available " \
"run reports.",
default_value=False)
cls.cart_sn_parameter = ParameterFactory.cartridge_sn()
cls.start_date = DateParameter("start",
"Start date of the form YYYY_MM_DD.",
allow_multiple=False,
required=False)
cls.end_date = DateParameter("end",
"End date of the form YYYY_MM_DD.",
allow_multiple=False,
required=False)
cls.uuid_parameter = ParameterFactory.uuid(required=False,
allow_multiple=False)
parameters = [
cls.cart_sn_parameter,
cls.refresh_parameter,
cls.start_date,
cls.end_date,
cls.uuid_parameter,
ParameterFactory.format(),
]
return parameters
def parameters(cls):
cls.ac_method = ParameterFactory.ac_method(AC_METHOD,
AC_METHOD_DESCRIPTION)
parameters = [
cls.ac_method,
ParameterFactory.format(),
]
return parameters
def parameters(cls):
cls.refresh_parameter = ParameterFactory.boolean("refresh",
"Refresh available dyes.",
default_value=False)
parameters = [
cls.refresh_parameter,
ParameterFactory.format(),
]
return parameters
def parameters(cls):
parameters = [
ParameterFactory.format(),
ParameterFactory.snpsearch_name(required=True),
ParameterFactory.chromosome_num(required=True),
ParameterFactory.chromosome_start(required=True),
ParameterFactory.chromosome_stop(required=True),
]
return parameters
def parameters(cls):
cls.tags_parameter = ParameterFactory.tags("Run report tags.")
cls.report_uuid_parameter = ParameterFactory.uuid(allow_multiple=False)
parameters = [
cls.tags_parameter,
cls.report_uuid_parameter,
ParameterFactory.format(),
]
return parameters
def parameters(cls):
cls.dataset_parameter = ParameterFactory.pa_data_source()
cls.report_uuid_parameter = ParameterFactory.uuid(allow_multiple=False)
parameters = [
cls.dataset_parameter,
cls.report_uuid_parameter,
ParameterFactory.format(),
]
return parameters
def parameters(cls):
cls.filenames_parameter = ParameterFactory.filenames()
cls.report_uuid_parameter = ParameterFactory.uuid(allow_multiple=False)
parameters = [
cls.filenames_parameter,
cls.report_uuid_parameter,
ParameterFactory.format(),
]
return parameters
def parameters(cls):
pid_enum = cls._DB_CONNECTOR.distinct(PROBE_METADATA_COLLECTION,
PROBE_ID)
parameters = [
ParameterFactory.format(),
ParameterFactory.lc_string(PROBE_ID,
"Probe ID(s).",
required=False,
allow_multiple=True,
enum=pid_enum),
]
return parameters
def parameters(cls):
parameters = [
ParameterFactory.format(),
]
return parameters