def to_listing(value):
@salad
def map_obj(obj):
if isinstance(obj, str):
return obj
elif isinstance(obj, dict):
if 'class' in obj:
if obj['class'] == 'File':
return File(**obj)
elif obj['class'] == 'Directory':
return Directory(**obj)
else:
raise TypeError('Unsupported {}'.format(obj))
elif 'entry' in obj:
return Dirent(**obj)
else:
return obj
else:
raise TypeError('Unsupported {}'.format(obj))
if value is not None:
if isinstance(value, str) or is_instance_all(File, Directory, Dirent,
str):
return value
elif isinstance(value, list):
return list(map(map_obj, value))
else:
raise TypeError('TypeError, got {}'.format(type(value)))
def to_out(value):
@salad
def map_obj(obj):
if isinstance(obj, str):
return obj
return StepOutput(**obj)
if value is not None:
if is_instance_all(value, str, StepOutput):
return value
elif is_instance_all(value, dict, str):
return list(map(map_obj, value))
else:
raise TypeError('TypeError, got: {}'.format(type(value)))
else:
return []
def to_file_dir_list(value):
@salad
def map_dict(d):
if d['class'] == 'Directory':
return Directory(**d)
elif d['class'] == 'File':
return File(**d)
else:
raise ValueError('Unsupported class')
if value is not None:
if is_instance_all(value, File, Directory):
return value
elif is_instance_all(value, dict):
return list(map(map_dict, value))
else:
raise TypeError('Expected list[File|Directory], got: {}'.format(
type(value)))
def to_steps(value):
"""Converts `value` into workflow steps."""
@salad
def map_to_cls(obj):
return Step(**obj)
if value is not None:
if is_instance_all(value, Step):
return value
elif isinstance(value, list):
return list(map(map_to_cls, value))
else:
raise TypeError('Expected steps, got: {}'.format(type(value)))
def to_str_ibinding(value):
"""Converts list of values to list of str|input_binding|$directive"""
@salad
def map_obj(obj):
if isinstance(obj, str):
return obj
return InputBinding(**obj)
if value is not None:
if is_instance_all(value, str, InputBinding):
return value
elif isinstance(value, list):
return list(map(map_obj, value))
else:
raise TypeError('Expected list, got {}'.format(type(value)))
def get_requirements(value):
"""Converts value to CommandLineTool requirements."""
if value is not None:
if is_instance_all(value, InlineJavascript, SchemaDef, Docker,
Software, InitialWorkDir, EnvVar, ShellCommand,
Resource):
return value
elif is_instance_all_dict(value, InlineJavascript, SchemaDef, Docker,
Software, InitialWorkDir, EnvVar,
ShellCommand, Resource):
return value
elif isinstance(value, list):
return list(map(to_cmd_req, value))
elif isinstance(value, dict):
return {k: to_salad_obj(v) for k, v in value.items()}
else:
raise ValueError("Expected list, got {}.".format(type(value)))
def to_step_req(value):
@salad
def map_obj(obj):
return obj
@salad
def map_to_cls(d):
m = dict(InlineJavascriptRequirement=InlineJavascript,
SchemaDefRequirement=SchemaDef,
DockerRequirement=Docker,
SoftwareRequirement=Software,
InitialWorkDirRequirement=InitialWorkDir,
EnvVarRequirement=EnvVar,
ShellCommandRequirement=ShellCommand,
ResourceRequirement=Resource,
SubworkflowFeatureRequirement=SubworkflowFeature,
ScatterFeatureRequirement=ScatterFeature,
MultipleInputFeatureRequirement=MultipleInputFeature,
StepInputExpressionRequirement=StepInputExpression)
if 'class' in d:
return m[d['class']](**d)
else:
raise Exception("Unsupported class: {}".format(d['class']))
if value is not None:
if is_instance_all(value, InlineJavascript, SchemaDef, Docker,
Software, InitialWorkDir, EnvVar, ShellCommand,
Resource, SubworkflowFeature, ScatterFeature,
MultipleInputFeature, StepInputExpression):
return value
elif is_instance_all_dict(value, InlineJavascript, SchemaDef, Docker,
Software, InitialWorkDir, EnvVar,
ShellCommand, Resource, SubworkflowFeature,
ScatterFeature, MultipleInputFeature,
StepInputExpression):
return value
elif isinstance(value, list):
return list(map(map_to_cls, value))
elif isinstance(value, dict):
return {k: map_obj(v) for k, v in value.items()}
else:
raise TypeError('TypeError got: {}'.format(type(value)))
def to_schemadef_type(value):
@salad
def map_obj(obj):
if isinstance(obj, dict):
if obj['type'] == 'enum':
return InputEnum(**obj)
elif obj['type'] == 'record':
return InputRecord(**obj)
elif obj['type'] == 'array':
return InputArray(**obj)
else:
raise ValueError("Unsupported type for shemadef: {}".format(
obj['type']))
return obj
if value is not None:
if is_instance_all(value, InputRecord, InputEnum, InputArray):
return value
elif isinstance(value, list):
return list(map(map_obj, value))
else:
raise TypeError(
'Expected list[SchemaDef requirements], got {}'.format(
type(value)))