def fetch_document(
argsworkflow, # type: Union[Text, Dict[Text, Any]]
resolver=None, # type: Callable[[Loader, Union[Text, Dict[Text, Any]]], Text]
fetcher_constructor=None
# type: Callable[[Dict[Text, Text], requests.sessions.Session], Fetcher]
):
# type: (...) -> Tuple[Loader, CommentedMap, Text]
"""Retrieve a CWL document."""
document_loader = Loader(
jobloaderctx, fetcher_constructor=fetcher_constructor) # type: ignore
uri = None # type: Text
workflowobj = None # type: CommentedMap
if isinstance(argsworkflow, string_types):
uri, fileuri = resolve_tool_uri(argsworkflow,
resolver=resolver,
document_loader=document_loader)
workflowobj = document_loader.fetch(fileuri)
elif isinstance(argsworkflow, dict):
uri = "#" + Text(id(argsworkflow))
workflowobj = cast(CommentedMap, cmap(argsworkflow, fn=uri))
else:
raise ValidationException("Must be URI or object: '%s'" % argsworkflow)
return document_loader, workflowobj, uri
def fetch_document(
argsworkflow, # type: Union[Text, dict[Text, Any]]
resolver=None, # type: Callable[[Loader, Union[Text, dict[Text, Any]]], Text]
fetcher_constructor=None
# type: Callable[[Dict[unicode, unicode], requests.sessions.Session], Fetcher]
):
# type: (...) -> Tuple[Loader, CommentedMap, Text]
"""Retrieve a CWL document."""
document_loader = Loader({
"cwl": "https://w3id.org/cwl/cwl#",
"id": "@id"
},
fetcher_constructor=fetcher_constructor)
uri = None # type: Text
workflowobj = None # type: CommentedMap
if isinstance(argsworkflow, string_types):
split = urllib.parse.urlsplit(argsworkflow)
if split.scheme:
uri = argsworkflow
elif os.path.exists(os.path.abspath(argsworkflow)):
uri = file_uri(str(os.path.abspath(argsworkflow)))
elif resolver:
uri = resolver(document_loader, argsworkflow)
if uri is None:
raise ValidationException("Not found: '%s'" % argsworkflow)
if argsworkflow != uri:
_logger.info("Resolved '%s' to '%s'", argsworkflow, uri)
fileuri = urllib.parse.urldefrag(uri)[0]
workflowobj = document_loader.fetch(fileuri)
elif isinstance(argsworkflow, dict):
uri = "#" + Text(id(argsworkflow))
workflowobj = cast(CommentedMap, cmap(argsworkflow, fn=uri))
else:
raise ValidationException("Must be URI or object: '%s'" % argsworkflow)
return document_loader, workflowobj, uri
def fetch_document(argsworkflow):
# type: (Union[Text, Text, dict[Text, Any]]) -> Tuple[Loader, Dict[Text, Any], Text]
"""Retrieve a CWL document."""
document_loader = Loader({"cwl": "https://w3id.org/cwl/cwl#", "id": "@id"})
uri = None # type: Text
workflowobj = None # type: Dict[Text, Any]
if isinstance(argsworkflow, basestring):
split = urlparse.urlsplit(argsworkflow)
if split.scheme:
uri = argsworkflow
else:
uri = "file://" + os.path.abspath(argsworkflow)
fileuri = urlparse.urldefrag(uri)[0]
workflowobj = document_loader.fetch(fileuri)
elif isinstance(argsworkflow, dict):
workflowobj = argsworkflow
uri = "#" + Text(id(argsworkflow))
else:
raise ValidationException("Must be URI or object: '%s'" % argsworkflow)
return document_loader, workflowobj, uri
def fetch_document(
argsworkflow, # type: Union[Text, Dict[Text, Any]]
resolver=None, # type: Callable[[Loader, Union[Text, Dict[Text, Any]]], Text]
fetcher_constructor=None
# type: Callable[[Dict[Text, Text], requests.sessions.Session], Fetcher]
):
# type: (...) -> Tuple[Loader, CommentedMap, Text]
"""Retrieve a CWL document."""
document_loader = Loader(
jobloaderctx, fetcher_constructor=fetcher_constructor) # type: ignore
uri = None # type: Text
workflowobj = None # type: CommentedMap
if isinstance(argsworkflow, string_types):
split = urllib.parse.urlsplit(argsworkflow)
# In case of Windows path, urlsplit misjudge Drive letters as scheme, here we are skipping that
if split.scheme and split.scheme in [u'http', u'https', u'file']:
uri = argsworkflow
elif os.path.exists(os.path.abspath(argsworkflow)):
uri = file_uri(str(os.path.abspath(argsworkflow)))
elif resolver:
uri = resolver(document_loader, argsworkflow)
if uri is None:
raise ValidationException("Not found: '%s'" % argsworkflow)
if argsworkflow != uri:
_logger.info("Resolved '%s' to '%s'", argsworkflow, uri)
fileuri = urllib.parse.urldefrag(uri)[0]
workflowobj = document_loader.fetch(fileuri)
elif isinstance(argsworkflow, dict):
uri = "#" + Text(id(argsworkflow))
workflowobj = cast(CommentedMap, cmap(argsworkflow, fn=uri))
else:
raise ValidationException("Must be URI or object: '%s'" % argsworkflow)
return document_loader, workflowobj, uri
def fetch_document(argsworkflow):
# type: (Union[Text, Text, dict[Text, Any]]) -> Tuple[Loader, Dict[Text, Any], Text]
"""Retrieve a CWL document."""
document_loader = Loader({"cwl": "https://w3id.org/cwl/cwl#", "id": "@id"})
uri = None # type: Text
workflowobj = None # type: Dict[Text, Any]
if isinstance(argsworkflow, basestring):
split = urlparse.urlsplit(argsworkflow)
if split.scheme:
uri = argsworkflow
else:
uri = "file://" + os.path.abspath(argsworkflow)
fileuri = urlparse.urldefrag(uri)[0]
workflowobj = document_loader.fetch(fileuri)
elif isinstance(argsworkflow, dict):
workflowobj = argsworkflow
uri = "#" + Text(id(argsworkflow))
else:
raise ValidationException("Must be URI or object: '%s'" % argsworkflow)
return document_loader, workflowobj, uri
def fetch_document(argsworkflow, # type: Union[Text, dict[Text, Any]]
resolver=None, # type: Callable[[Loader, Union[Text, dict[Text, Any]]], Text]
fetcher_constructor=None # type: Callable[[Dict[unicode, unicode], requests.sessions.Session], Fetcher]
):
# type: (...) -> Tuple[Loader, CommentedMap, Text]
"""Retrieve a CWL document."""
document_loader = Loader({"cwl": "https://w3id.org/cwl/cwl#", "id": "@id"},
fetcher_constructor=fetcher_constructor)
uri = None # type: Text
workflowobj = None # type: CommentedMap
if isinstance(argsworkflow, basestring):
split = urlparse.urlsplit(argsworkflow)
if split.scheme:
uri = argsworkflow
elif os.path.exists(os.path.abspath(argsworkflow)):
uri = "file://" + os.path.abspath(argsworkflow)
elif resolver:
uri = resolver(document_loader, argsworkflow)
if uri is None:
raise ValidationException("Not found: '%s'" % argsworkflow)
if argsworkflow != uri:
_logger.info("Resolved '%s' to '%s'", argsworkflow, uri)
fileuri = urlparse.urldefrag(uri)[0]
workflowobj = document_loader.fetch(fileuri)
elif isinstance(argsworkflow, dict):
uri = "#" + Text(id(argsworkflow))
workflowobj = cast(CommentedMap, cmap(argsworkflow, fn=uri))
else:
raise ValidationException("Must be URI or object: '%s'" % argsworkflow)
return document_loader, workflowobj, uri
def load_overrides(ov,
base_url): # type: (Text, Text) -> List[Dict[Text, Any]]
ovloader = Loader(overrides_ctx)
return resolve_overrides(ovloader.fetch(ov), ov, base_url)
def load_overrides(ov, base_url): # type: (Text, Text) -> List[Dict[Text, Any]]
ovloader = Loader(overrides_ctx)
return resolve_overrides(ovloader.fetch(ov), ov, base_url)
def load_overrides(ov: str, base_url: str) -> List[CWLObjectType]:
ovloader = Loader(overrides_ctx)
return resolve_overrides(ovloader.fetch(ov), ov, base_url)