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

Module Contents

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)

Attributes

logger

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]