def _pacbio_choice_option_from_dict(d):
"""
Factory/dispatch method for returning a PacBio Choice Option Type
:rtype: PacBioOption
"""
choices = d['choices']
default_value = d['default']
# this will immediately raise
option_type_id = TaskOptionTypes.from_choice_str(d['optionTypeId'])
opt_id = d['id']
name = d['name']
desc = to_utf8(d['description'])
klass_map = {TaskOptionTypes.CHOICE_STR: PacBioStringChoiceOption,
TaskOptionTypes.CHOICE_FLOAT: PacBioFloatChoiceOption,
TaskOptionTypes.CHOICE_INT: PacBioIntChoiceOption}
k = klass_map[option_type_id]
# Sanitize Unicode hack
if k is PacBioStringChoiceOption:
default_value = to_ascii(default_value)
choices = [to_ascii(i) for i in choices]
opt = k(opt_id, name, default_value, desc, choices)
return opt
def load_analysis_job_json(d):
"""Translate a dict to args for scenario runner inputs"""
job_name = to_ascii(d['name'])
pipeline_template_id = to_ascii(d["pipelineId"])
service_epoints = [ServiceEntryPoint.from_d(x) for x in d['entryPoints']]
tags = d.get('tags', [])
return job_name, pipeline_template_id, service_epoints, tags
def __simple_option_by_type(
option_id, name, default, description, option_type_id):
option_type = TaskOptionTypes.from_simple_str(option_type_id)
klass_map = {TaskOptionTypes.INT: PacBioIntOption,
TaskOptionTypes.FLOAT: PacBioFloatOption,
TaskOptionTypes.STR: PacBioStringOption,
TaskOptionTypes.BOOL: PacBioBooleanOption}
k = klass_map[option_type]
# This requires a hack for the unicode to ascii for string option type.
if k is PacBioStringOption:
# sanitize unicode
default = to_ascii(default)
opt = k(option_id, name, default, description)
return opt
def _pacbio_legacy_option_from_dict(d):
"""
Load the legacy (jsonschema-ish format)
Note, choice types are not supported here.
:rtype: PacBioOption
"""
warnings.warn(
"This is obsolete and will disappear soon",
DeprecationWarning)
opt_id = d['pb_option']['option_id']
name = d['pb_option']['name']
default = d['pb_option']['default']
desc = d['pb_option']['description']
option_type_id = to_ascii(d['pb_option']['type'])
# Hack to support "number"
if option_type_id == "number":
option_type_id = "float"
return __simple_option_by_type(opt_id, name, default, desc, option_type_id)