Source code for weaver.formats

import os
from typing import TYPE_CHECKING

from pyramid.httpexceptions import HTTPNotFound, HTTPOk
from pywps.inout.formats import FORMATS, Format
from requests.exceptions import ConnectionError
from six.moves.urllib.error import HTTPError
from six.moves.urllib.request import urlopen

from weaver.utils import request_extra

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

# Content-Types
#   MIME-type nomenclature:
#       <type> "/" [x- | <tree> "."] <subtype> ["+" suffix] *[";" parameter=value]
[docs]CONTENT_TYPE_APP_CWL = "application/x-cwl"
[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" # map to existing gzip for CWL
[docs]CONTENT_TYPE_APP_TAR_GZ = "application/tar+gzip" # map to existing gzip for CWL
[docs]CONTENT_TYPE_APP_YAML = "application/x-yaml"
[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_GEOJSON = "application/vnd.geo+json"
[docs]CONTENT_TYPE_APP_XML = "application/xml"
[docs]CONTENT_TYPE_IMAGE_GEOTIFF = "image/tiff; subtype=geotiff"
[docs]CONTENT_TYPE_TEXT_XML = "text/xml"
[docs]CONTENT_TYPE_ANY = "*/*"
# explicit mime-type to extension when not literally written in item after '/' (excluding 'x-' prefix)
} # type: Dict[AnyStr, AnyStr] # extend with all known pywps formats
[docs]_CONTENT_TYPE_FORMAT_MAPPING = { # content-types here are fully defined with extra parameters (e.g.: geotiff as subtype of tiff) fmt.mime_type: fmt for _, fmt in FORMATS._asdict().items() # noqa: W0212
} # type: Dict[AnyStr, Format] _CONTENT_TYPE_EXTENSION_MAPPING.update({ ctype: fmt.extension for ctype, fmt in _CONTENT_TYPE_FORMAT_MAPPING.items() # noqa: W0212 }) # redirect type resolution semantically equivalent CWL validators # should only be used to map CWL 'format' field if they are not already resolved through existing IANA/EDAM reference
} # Mappings for "CWL->File->Format" # IANA contains most standard MIME-types, but might not include special (application/x-hdf5, application/x-netcdf, etc.) # EDAM contains many field-specific schemas, but don't have an implicit URL definition (uses 'format_<id>' instead) # search: # - IANA: # - EDAM-classes: (section 'Format') # - EDAM-browser:
[docs]IANA_NAMESPACE = "iana"
[docs]EDAM_NAMESPACE = "edam"
[docs]EDAM_SCHEMA = ""
[docs]EDAM_MAPPING = { CONTENT_TYPE_APP_CWL: "format_3857", CONTENT_TYPE_APP_HDF5: "format_3590", CONTENT_TYPE_APP_JSON: "format_3464", CONTENT_TYPE_APP_NETCDF: "format_3650", CONTENT_TYPE_APP_YAML: "format_3750", CONTENT_TYPE_TEXT_PLAIN: "format_1964",
[docs]def get_format(mime_type): # type: (AnyStr) -> Format """Obtains a :class:`Format` with predefined extension and encoding details from known MIME-types.""" ctype = clean_mime_type_format(mime_type, strip_parameters=True) return _CONTENT_TYPE_FORMAT_MAPPING.get(mime_type, Format(ctype, extension=get_extension(ctype)))
[docs]def get_extension(mime_type): # type: (AnyStr) -> AnyStr """ Retrieves the extension corresponding to :paramref:`mime_type` if explicitly defined, or by parsing it. """ fmt = _CONTENT_TYPE_FORMAT_MAPPING.get(mime_type) if fmt: return fmt.extension ext = _CONTENT_TYPE_EXTENSION_MAPPING.get(mime_type) if ext: return ext ctype = clean_mime_type_format(mime_type, strip_parameters=True) return _CONTENT_TYPE_EXTENSION_MAPPING.get(ctype, ".{}".format(ctype.split("/")[-1].replace("x-", "")))
[docs]def get_cwl_file_format(mime_type, make_reference=False, must_exist=True, allow_synonym=True): # type: (AnyStr, bool, bool, bool) -> Union[Tuple[Optional[JSON], Optional[AnyStr]], Optional[AnyStr]] """ Obtains the corresponding `IANA`/`EDAM` ``format`` value to be applied under a `CWL` I/O ``File`` from the :paramref:`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>)`` with: 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>`` (N.B.: literal non-official MIME-type reference will be returned even if an official synonym exists). - If there is no match but ``must_exist=True`` **AND** ``allow_reference=True``, retry the call with the synonym if available, or move to next step. Skip this step if ``allow_reference=False``. - Returns a single ``None`` as there is not match (directly or synonym). Note: In situations where ``must_exist=False`` is used and that the namespace and/or full format URL cannot be resolved to an existing reference, `CWL` will raise a validation error as it cannot confirm the ``format``. You must therefore make sure that the returned reference (or a synonym format) really exists when using ``must_exist=False`` before providing it to the `CWL` I/O definition. Setting ``must_exist=False`` should be used only for literal string comparison or pre-processing steps to evaluate formats. :param mime_type: Some reference, namespace'd or literal (possibly extended) MIME-type string. :param make_reference: Construct the full URL reference to the resolved MIME-type. Otherwise return tuple details. :param must_exist: Return result only if it can be resolved to an official MIME-type (or synonym if enabled), otherwise ``None``. Non-official MIME-type can be enforced if disabled, in which case `IANA` namespace/URL is used as it preserves the original ``<type>/<subtype>`` format. :param allow_synonym: Allow resolution of non-official MIME-type to an official MIME-type synonym if available. Types defined as *synonym* have semantically the same format validation/resolution for `CWL`. Requires ``must_exist=True``, otherwise the non-official MIME-type is employed directly as result. :returns: Resolved MIME-type format for `CWL` usage, accordingly to specified arguments (see description details). """ def _make_if_ref(_map, _key, _fmt): return os.path.join(_map[_key], _fmt) if make_reference else (_map, "{}:{}".format(_key, _fmt)) def _request_extra_various(_mime_type): """ Attempts multiple request-retry variants to be as permissive as possible to sporadic/temporary failures. """ _mime_type_url = "{}{}".format(IANA_NAMESPACE_DEFINITION[IANA_NAMESPACE], _mime_type) try: resp = request_extra("get", _mime_type_url, retries=3, allowed_codes=[HTTPOk.code, HTTPNotFound.code]) if resp.status_code == HTTPOk.code: return _make_if_ref(IANA_NAMESPACE_DEFINITION, IANA_NAMESPACE, _mime_type) except ConnectionError: pass try: resp = urlopen(_mime_type_url) # nosec: B310 # is hardcoded HTTP(S) if resp.code == HTTPOk.code: return _make_if_ref(IANA_NAMESPACE_DEFINITION, IANA_NAMESPACE, _mime_type) except HTTPError: pass return None mime_type = clean_mime_type_format(mime_type, strip_parameters=True) result = _request_extra_various(mime_type) if result is not None: return result 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) if result is None and allow_synonym and mime_type in _CONTENT_TYPE_SYNONYM_MAPPING: mime_type = _CONTENT_TYPE_SYNONYM_MAPPING.get(mime_type) return get_cwl_file_format(mime_type, make_reference=make_reference, must_exist=True, allow_synonym=False) return None if make_reference else (None, None)
[docs]def clean_mime_type_format(mime_type, suffix_subtype=False, strip_parameters=False): # type: (AnyStr, bool, bool) -> AnyStr """ Removes any additional namespace key or URL from :paramref:`mime_type` so that it corresponds to the generic representation (e.g.: ``application/json``) instead of the ``<namespace-name>:<format>`` mapping variant used in `CWL->inputs/outputs->File->format` or the complete URL reference. According to provided arguments, it also cleans up additional parameters or extracts sub-type suffixes. :param mime_type: MIME-type, full URL to MIME-type or namespace-formatted string that must be cleaned up. :param suffix_subtype: Remove additional sub-type specializations details separated by ``+`` symbol such that an explicit format like ``application/vnd.api+json`` returns only its most basic suffix format defined as``application/json``. :param strip_parameters: Removes additional MIME-type parameters such that only the leading part defining the ``type/subtype`` are returned. For example, this will get rid of ``; charset=UTF-8`` or ``; version=4.0`` parameters. .. note:: Parameters :paramref:`suffix_subtype` and :paramref:`strip_parameters` are not necessarily exclusive. """ if strip_parameters: mime_type = mime_type.split(";")[0] if suffix_subtype and "+" in mime_type: # parameters are not necessarily stripped, need to re-append them after if any parts = mime_type.split(";", 1) if len(parts) < 2: parts.append("") else: parts[1] = ";{}".format(parts[1]) typ, sub = parts[0].split("/") sub = sub.split("+")[-1] mime_type = "{}/{}{}".format(typ, sub, parts[1]) 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