def ctx_enter(cls, path, access):
"""
Function on context enter.
:param cls: ``class`` object
:param path: file path
:param access: access permission ('r' - read, 'w' - write, 'rw' - edit)
:return: an instance of ``cls``
"""
obj = None
if path and 'r' in access:
cwl = from_file(path)
if isinstance(cwl, dict):
if "class" in cwl:
if cwl['class'] == cls.__name__:
obj = cls(**cwl)
else:
raise ValueError("Expected class={}, got class={}".format(
cls.__name__, cwl['class']))
else:
raise ValueError("Missing class key.")
else:
raise ValueError('Type Error, got: {}'.format(type(cwl)))
if not obj:
obj = cls()
return obj
def load(cwl):
"""
Loads CWL document from file or JSON object and instantiate object of a
class specified by key ``class`` inside a document.
:param cwl: file (can be either in ``JSON`` or ``YAML`` format)
:return: depending on ``class`` can be either an instance of
``CommandLineTool`` or ``ExpressionTool`` or ``Workflow``
"""
if not isinstance(cwl, dict):
cwl = from_file(cwl)
if isinstance(cwl, dict):
if "class" in cwl:
if cwl['class'] == 'CommandLineTool':
return CommandLineTool(**cwl)
elif cwl['class'] == 'Workflow':
return Workflow(**cwl)
elif cwl['class'] == 'ExpressionTool':
return ExpressionTool(**cwl)
else:
raise ValueError("Unsupported class: {}".format(cwl['class']))
else:
raise ValueError("Missing class key.")
else:
raise ValueError('Type Error, got: {}'.format(type(cwl)))
def resolve_salad(self):
x = dict()
for k, v in self.items():
if k == "$mixin":
d = from_file(self["$mixin"])
for k2, v2 in d.items():
if k2 not in self:
x[k2] = v2
else:
x[k] = v
return x
def resolve_salad(self):
return resolve(from_file(self["$import"]))