Source code for weaver.formats

import os
from typing import TYPE_CHECKING

from six.moves.urllib.error import HTTPError
from six.moves.urllib.request import urlopen

    from weaver.typedefs import JSON            # noqa: F401
    from typing import AnyStr, Tuple, Union     # noqa: F401

# Content-Types
[docs]CONTENT_TYPE_APP_FORM = "application/x-www-form-urlencoded"
[docs]CONTENT_TYPE_APP_NETCDF = "application/x-netcdf"
[docs]CONTENT_TYPE_APP_GZIP = "application/gzip"
[docs]CONTENT_TYPE_APP_HDF5 = "application/x-hdf5"
[docs]CONTENT_TYPE_APP_TAR = "application/x-tar"
[docs]CONTENT_TYPE_APP_ZIP = "application/zip"
[docs]CONTENT_TYPE_TEXT_HTML = "text/html"
[docs]CONTENT_TYPE_TEXT_PLAIN = "text/plain"
[docs]CONTENT_TYPE_APP_PDF = "application/pdf"
[docs]CONTENT_TYPE_APP_JSON = "application/json"
[docs]CONTENT_TYPE_APP_XML = "application/xml"
[docs]CONTENT_TYPE_TEXT_XML = "text/xml"
[docs]def get_extension(mime_type): # type: (AnyStr) -> AnyStr """Retrieves the extension corresponding to ``mime_type`` if explicitly defined, or by simple parsing otherwise.""" return _CONTENT_TYPE_EXTENSION_MAPPING.get(mime_type, mime_type.split("/")[-1].replace("x-", ""))
# Mappings for "CWL->File->Format" # IANA contains most standard MIME-types, but might not include special (application/x-hdf5, application/x-netcdf, etc.) # search: # - IANA: # - EDAM: (section 'Format')
[docs]IANA_NAMESPACE = "iana"
[docs]EDAM_NAMESPACE = "edam"
[docs]EDAM_SCHEMA = ""
[docs]EDAM_MAPPING = { CONTENT_TYPE_APP_HDF5: "format_3590", CONTENT_TYPE_APP_JSON: "format_3464", CONTENT_TYPE_APP_NETCDF: "format_3650", CONTENT_TYPE_TEXT_PLAIN: "format_1964",
[docs]def get_cwl_file_format(mime_type, make_reference=False, must_exist=False): # type: (AnyStr, bool, bool) -> Union[Tuple[Union[JSON, None], Union[AnyStr, None]], Union[AnyStr, None]] """ Obtains the corresponding `IANA`/`EDAM` ``format`` value to be applied under a `CWL` I/O ``File`` from the ``mime_type`` (`Content-Type` header) using the first matched one. If ``make_reference=False``: - If there is a match, returns ``tuple({<namespace-name: namespace-url>}, <format>)``: 1) corresponding namespace mapping to be applied under ``$namespaces`` in the `CWL`. 2) value of ``format`` adjusted according to the namespace to be applied to ``File`` in the `CWL`. - If there is no match but ``must_exist=False``: returns a literal and non-existing definition as ``tuple({"iana": <iana-url>}, <format>)`` - Otherwise, returns ``(None, None)`` If ``make_reference=True``: - If there is a match, returns the explicit format reference as ``<namespace-url>/<format>``. - If there is no match but ``must_exist=False``, returns the literal reference as ``<iana-url>/<format>``. - Otherwise, returns a single ``None``. Note: In situations where ``must_exist=False`` and the default non-existing namespace is returned, the `CWL` behaviour is to evaluate corresponding ``format`` for literal matching strings. """ def _make_if_ref(_map, _key, _fmt): return os.path.join(_map[_key], _fmt) if make_reference else (_map, "{}:{}".format(_key, _fmt)) # FIXME: ConnectionRefused with `requests.get`, using `urllib` instead try: mime_type_url = "{}{}".format(IANA_NAMESPACE_DEFINITION[IANA_NAMESPACE], mime_type) resp = urlopen(mime_type_url) # nosec: B310 # is hardcoded HTTP(S) if resp.code == 200: return _make_if_ref(IANA_NAMESPACE_DEFINITION, IANA_NAMESPACE, mime_type) except HTTPError: pass if mime_type in EDAM_MAPPING: return _make_if_ref(EDAM_NAMESPACE_DEFINITION, EDAM_NAMESPACE, EDAM_MAPPING[mime_type]) if not must_exist: return _make_if_ref(IANA_NAMESPACE_DEFINITION, IANA_NAMESPACE, mime_type) return None if make_reference else (None, None)
[docs]def clean_mime_type_format(mime_type): # type: (AnyStr) -> AnyStr """ Removes any additional namespace key or URL from ``mime_type`` so that it corresponds to the generic representation (ex: `application/json`) instead of the ``<namespace-name>:<format>`` variant used in `CWL->inputs/outputs->File->format`. """ for v in list(IANA_NAMESPACE_DEFINITION.values()) + list(EDAM_NAMESPACE_DEFINITION.values()): if v in mime_type: mime_type = mime_type.replace(v, "") for v in list(IANA_NAMESPACE_DEFINITION.keys()) + list(EDAM_NAMESPACE_DEFINITION.keys()): if mime_type.startswith(v + ":"): mime_type = mime_type.replace(v + ":", "") for v in EDAM_MAPPING.values(): if v.endswith(mime_type): mime_type = [k for k in EDAM_MAPPING if v.endswith(EDAM_MAPPING[k])][0] return mime_type