cwl_utils.pack

CWL document packing functions.

The link resolution is as follows:

We always have two components: the base and the link If the link is a url or absolute path it is what is used to fetch the data. If the link is a relative path it is combined with the base and that is what is used to fetch data

From https://github.com/rabix/sbpack/blob/b8404a0859ffcbe1edae6d8f934e51847b003320/sbpack/lib.py

Attributes

logger

Functions

`get_inner_dict`(cwl, path)
`pack_process`(cwl, base_url, cwl_version[, ...])
`listify_everything`(cwl)
`dictify_requirements`(cwl)
`normalize_sources`(cwl)
`load_schemadefs`(cwl, base_url[, parent_user_defined_types])
`resolve_schemadefs`(cwl, base_url, user_defined_types)
`resolve_imports`(cwl, base_url)
`resolve_steps`(cwl, base_url, cwl_version[, ...])
`add_missing_requirements`(cwl)
`pack`(cwl_path)

Module Contents

cwl_utils.pack.logger

cwl_utils.pack.get_inner_dict(cwl, path)

Parameters:

cwl (Dict[str, Any])
path (List[Dict[str, Any]])

Return type:

Optional[Dict[str, Any]]

cwl_utils.pack.pack_process(cwl, base_url, cwl_version, parent_user_defined_types=None)

Parameters:

cwl (Dict[str, Any])
base_url (urllib.parse.ParseResult)
cwl_version (str)
parent_user_defined_types (Optional[Dict[str, Any]])

Return type:

Dict[str, Any]

cwl_utils.pack.listify_everything(cwl)

Parameters:: cwl (Dict[str, Any])
Return type:: Dict[str, Any]

cwl_utils.pack.dictify_requirements(cwl)

Parameters:: cwl (Dict[str, Any])
Return type:: Dict[str, Any]

cwl_utils.pack.normalize_sources(cwl)

Parameters:: cwl (Dict[str, Any])
Return type:: Dict[str, Any]

cwl_utils.pack.load_schemadefs(cwl, base_url, parent_user_defined_types=None)

Parameters:

cwl (Dict[str, Any])
base_url (urllib.parse.ParseResult)
parent_user_defined_types (Optional[Dict[str, Any]])

Return type:

Tuple[Dict[str, Any], Dict[str, Any]]

cwl_utils.pack.resolve_schemadefs(cwl, base_url, user_defined_types)

Parameters:

cwl (Dict[str, Any])
base_url (urllib.parse.ParseResult)
user_defined_types (Dict[str, Any])

Return type:

Dict[str, Any]

cwl_utils.pack.resolve_imports(cwl, base_url)

Parameters:

cwl (Any)
base_url (urllib.parse.ParseResult)

Return type:

Any

cwl_utils.pack.resolve_steps(cwl, base_url, cwl_version, parent_user_defined_types=None)

Parameters:

cwl (Dict[str, Any])
base_url (urllib.parse.ParseResult)
cwl_version (str)
parent_user_defined_types (Optional[Dict[str, Any]])

Return type:

Dict[str, Any]

cwl_utils.pack.add_missing_requirements(cwl)

Parameters:: cwl (Dict[str, Any])
Return type:: Dict[str, Any]

cwl_utils.pack.pack(cwl_path)

Parameters:: cwl_path (str)
Return type:: Dict[str, Any]