Beispiel #1
0
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
Beispiel #2
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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
Beispiel #3
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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
Beispiel #4
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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
Beispiel #5
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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
Beispiel #7
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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)
Beispiel #8
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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)
Beispiel #9
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def load_overrides(ov: str, base_url: str) -> List[CWLObjectType]:
    ovloader = Loader(overrides_ctx)
    return resolve_overrides(ovloader.fetch(ov), ov, base_url)