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 from_id_dict(d):
"""
Create an instance from a id dict of options (pbsmrtpipe.options.x:value}
"""
from pbsmrtpipe.pb_io import REGISTERED_WORKFLOW_OPTIONS
import pbsmrtpipe.schema_opt_utils as OP
adict = {}
for opt_id, schema in REGISTERED_WORKFLOW_OPTIONS.iteritems():
if opt_id in d:
v = d[opt_id]
OP.validate_value(schema, {opt_id: v})
adict[opt_id] = v
else:
value = OP.get_default_from_schema(schema)
d[opt_id] = value
# build map to instance var names
adict = {
k: d[v]
for k, v in WorkflowLevelOptions.ATTR_TO_ID.iteritems()
}
return WorkflowLevelOptions(**adict)
def from_id_dict(d):
"""
Create an instance from a id dict of options (pbsmrtpipe.options.x:value}
"""
adict = {}
for opt_id, schema in REGISTERED_WORKFLOW_OPTIONS.iteritems():
if opt_id in d:
v = d[opt_id]
OP.validate_value(schema, {opt_id: v})
adict[opt_id] = v
else:
value = OP.get_default_from_schema(schema)
d[opt_id] = value
# build map to instance var names
adict = {k: d[v] for k, v in WorkflowLevelOptions.ATTR_TO_ID.iteritems()}
return WorkflowLevelOptions(**adict)
