def validate_workflow_options(d):
"""
1. warn if an option provided in not a valid workflow option.
2. try to coerce raw string values if possible
Return a list of tuples [(id, value)] to be consistent with the existing API
"""
for option_id in d:
if option_id not in REGISTERED_WORKFLOW_OPTIONS:
msg = "Unknown option. Ignoring workflow option '{i}'.".format(i=option_id)
sys.stderr.write(msg + "\n")
log.warn(msg)
wopts = []
for option_id, schema in REGISTERED_WORKFLOW_OPTIONS.iteritems():
if option_id in d:
raw_value = d[option_id]
types_ = schema["properties"][option_id]["type"]
coerced_value = crude_coerce_type_from_str(raw_value, types_)
_ = jsonschema.validate(schema, {option_id: coerced_value})
wopts.append((option_id, coerced_value))
else:
# grab default
value = OP.get_default_from_schema(schema)
wopts.append((option_id, value))
return wopts
def validate_workflow_options(d):
"""
1. warn if an option provided in not a valid workflow option.
2. try to coerce raw string values if possible
Return a list of tuples [(id, value)] to be consistent with the existing API
"""
for option_id in d:
if option_id not in REGISTERED_WORKFLOW_OPTIONS:
msg = "Unknown option. Ignoring workflow option '{i}'.".format(
i=option_id)
sys.stderr.write(msg + "\n")
log.warn(msg)
wopts = []
for option_id, schema in REGISTERED_WORKFLOW_OPTIONS.iteritems():
if option_id in d:
raw_value = d[option_id]
types_ = schema['properties'][option_id]['type']
coerced_value = crude_coerce_type_from_str(raw_value, types_)
_ = jsonschema.validate(schema, {option_id: coerced_value})
wopts.append((option_id, coerced_value))
else:
# grab default
value = OP.get_default_from_schema(schema)
wopts.append((option_id, value))
return wopts
def _raw_option_with_schema(option_id, raw_value, pacbio_option):
"""
This will attempt to coerce and validate the raw option type provided.
The option id provided must be the same or as the provided PacBioOption
instance, otherwise a KeyError will be raised.
:type pacbio_option: PacBioOption
:type option_id: str
:param option_id:
:param raw_value:
:param pacbio_option:
:return:
"""
error_msg = "Incompatible option id '{i}' and " \
"defined option type id '{o}'".format(i=option_id, o=pacbio_option.OPTION_TYPE_ID)
if option_id == pacbio_option.option_id:
# from raw string, try to coerce to the expected type
coerced_value = crude_coerce_type_from_str(
raw_value, pacbio_option.OPTION_TYPE_ID)
if pacbio_option.OPTION_TYPE_ID == "string" and raw_value is None:
coerced_value = ""
_ = pacbio_option.validate_option(coerced_value)
return coerced_value
else:
raise KeyError(error_msg)
def _raw_option_with_schema(option_id, raw_value, schema):
option_id = option_id.strip()
schema_option_id = schema['properties'].keys()[0]
if option_id == schema_option_id:
types_ = schema['properties'][option_id]['type']
coerced_value = crude_coerce_type_from_str(raw_value, types_)
_ = jsonschema.validate(schema, {option_id: coerced_value})
value = coerced_value
else:
raise KeyError("Incompatible option id '{o}' and schema id '{i}'".format(o=option_id, i=schema_option_id))
return value
def _raw_option_with_schema(option_id, raw_value, schema):
option_id = option_id.strip()
schema_option_id = schema["properties"].keys()[0]
if option_id == schema_option_id:
types_ = schema["properties"][option_id]["type"]
coerced_value = crude_coerce_type_from_str(raw_value, types_)
_ = jsonschema.validate(schema, {option_id: coerced_value})
value = coerced_value
else:
raise KeyError("Incompatible option id '{o}' and schema id '{i}'".format(o=option_id, i=schema_option_id))
return value
def _raw_option_with_schema(option_id, raw_value, schema):
option_id = option_id.strip()
schema_option_id = schema['pb_option']['option_id']
if option_id == schema_option_id:
pb_type = schema['pb_option']['type']
coerced_value = crude_coerce_type_from_str(raw_value, pb_type)
if pb_type == "string" and raw_value is None:
coerced_value = ""
_ = jsonschema.validate(schema, {option_id: coerced_value})
value = coerced_value
else:
raise KeyError("Incompatible option id '{o}' and schema id '{i}'".format(o=option_id, i=schema_option_id))
return value
def _raw_option_with_schema(option_id, raw_value, schema):
option_id = option_id.strip()
schema_option_id = schema['pb_option']['option_id']
if option_id == schema_option_id:
pb_type = schema['pb_option']['type']
coerced_value = crude_coerce_type_from_str(raw_value, pb_type)
if pb_type == "string" and raw_value is None:
coerced_value = ""
_ = jsonschema.validate(schema, {option_id: coerced_value})
value = coerced_value
else:
raise KeyError(
"Incompatible option id '{o}' and schema id '{i}'".format(
o=option_id, i=schema_option_id))
return value
