--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/env/lib/python3.7/site-packages/cwltool/load_tool.py	Sat May 02 07:14:21 2020 -0400
@@ -0,0 +1,392 @@
+"""Loads a CWL document."""
+from __future__ import absolute_import
+
+import hashlib
+import logging
+import os
+import re
+import uuid
+from typing import (Any, Callable, Dict, List, MutableMapping, MutableSequence,
+                    Optional, Tuple, Union, cast)
+
+import requests.sessions
+from ruamel.yaml.comments import CommentedMap, CommentedSeq
+from schema_salad import schema
+from schema_salad.ref_resolver import (ContextType,  # pylint: disable=unused-import
+                                       Fetcher, Loader, file_uri, SubLoader)
+from schema_salad.sourceline import SourceLine, cmap
+from schema_salad.validate import ValidationException
+from six import itervalues, string_types
+from six.moves import urllib
+from typing_extensions import Text  # pylint: disable=unused-import
+# move to a regular typing import when Python 3.3-3.6 is no longer supported
+
+from . import process, update
+from .context import LoadingContext  # pylint: disable=unused-import
+from .errors import WorkflowException
+from .loghandler import _logger
+from .process import (Process, get_schema,  # pylint: disable=unused-import
+                      shortname)
+from .software_requirements import (  # pylint: disable=unused-import
+    DependenciesConfiguration)
+from .update import ALLUPDATES
+from .utils import json_dumps
+
+
+
+
+jobloaderctx = {
+    u"cwl": "https://w3id.org/cwl/cwl#",
+    u"cwltool": "http://commonwl.org/cwltool#",
+    u"path": {u"@type": u"@id"},
+    u"location": {u"@type": u"@id"},
+    u"id": u"@id"
+}  # type: ContextType
+
+
+overrides_ctx = {
+    u"overrideTarget": {u"@type": u"@id"},
+    u"cwltool": "http://commonwl.org/cwltool#",
+    u"http://commonwl.org/cwltool#overrides": {
+        "@id": "cwltool:overrides",
+        "mapSubject": "overrideTarget",
+    },
+    "requirements": {
+        "@id": "https://w3id.org/cwl/cwl#requirements",
+        "mapSubject": "class"
+    }
+}  # type: ContextType
+
+
+FetcherConstructorType = Callable[
+    [Dict[Text, Union[Text, bool]], requests.sessions.Session], Fetcher]
+ResolverType = Callable[[Loader, Union[Text, Dict[Text, Any]]], Text]
+
+def default_loader(fetcher_constructor=None, enable_dev=False):
+    # type: (Optional[FetcherConstructorType], bool) -> Loader
+    return Loader(jobloaderctx, fetcher_constructor=fetcher_constructor,
+                  allow_attachments=lambda r: enable_dev)
+
+def resolve_tool_uri(argsworkflow,              # type: Text
+                     resolver=None,             # type: Optional[ResolverType]
+                     fetcher_constructor=None,  # type: Optional[FetcherConstructorType]
+                     document_loader=None       # type: Optional[Loader]
+                    ):  # type: (...) -> Tuple[Text, Text]
+
+    uri = None  # type: Optional[Text]
+    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 is not None:
+        if document_loader is None:
+            document_loader = default_loader(fetcher_constructor)
+        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]
+    return uri, fileuri
+
+
+def fetch_document(argsworkflow,        # type: Union[Text, Dict[Text, Any]]
+                   loadingContext=None  # type: Optional[LoadingContext]
+                  ):  # type: (...) -> Tuple[LoadingContext, CommentedMap, Text]
+    """Retrieve a CWL document."""
+    if loadingContext is None:
+        loadingContext = LoadingContext()
+        loadingContext.loader = default_loader()
+    else:
+        loadingContext = loadingContext.copy()
+        if loadingContext.loader is None:
+            loadingContext.loader = default_loader(loadingContext.fetcher_constructor)
+
+    if isinstance(argsworkflow, string_types):
+        uri, fileuri = resolve_tool_uri(argsworkflow,
+                                        resolver=loadingContext.resolver,
+                                        document_loader=loadingContext.loader)
+        workflowobj = loadingContext.loader.fetch(fileuri)
+        return loadingContext, workflowobj, uri
+    if isinstance(argsworkflow, dict):
+        uri = argsworkflow["id"] if argsworkflow.get("id") else "_:" + Text(uuid.uuid4())
+        workflowobj = cast(CommentedMap, cmap(argsworkflow, fn=uri))
+        loadingContext.loader.idx[uri] = workflowobj
+        return loadingContext, workflowobj, uri
+    raise ValidationException("Must be URI or object: '%s'" % argsworkflow)
+
+
+def _convert_stdstreams_to_files(workflowobj):
+    # type: (Union[Dict[Text, Any], List[Dict[Text, Any]]]) -> None
+
+    if isinstance(workflowobj, MutableMapping):
+        if workflowobj.get('class') == 'CommandLineTool':
+            with SourceLine(workflowobj, "outputs", ValidationException,
+                            _logger.isEnabledFor(logging.DEBUG)):
+                outputs = workflowobj.get('outputs', [])
+                if not isinstance(outputs, CommentedSeq):
+                    raise ValidationException('"outputs" section is not '
+                                              'valid.')
+                for out in workflowobj.get('outputs', []):
+                    if not isinstance(out, CommentedMap):
+                        raise ValidationException(
+                            "Output '{}' is not a valid "
+                            "OutputParameter.".format(out))
+                    for streamtype in ['stdout', 'stderr']:
+                        if out.get('type') == streamtype:
+                            if 'outputBinding' in out:
+                                raise ValidationException(
+                                    "Not allowed to specify outputBinding when"
+                                    " using %s shortcut." % streamtype)
+                            if streamtype in workflowobj:
+                                filename = workflowobj[streamtype]
+                            else:
+                                filename = Text(
+                                    hashlib.sha1(  # nosec
+                                        json_dumps(workflowobj, sort_keys=True
+                                                  ).encode('utf-8')).hexdigest())
+                                workflowobj[streamtype] = filename
+                            out['type'] = 'File'
+                            out['outputBinding'] = cmap({'glob': filename})
+            for inp in workflowobj.get('inputs', []):
+                if inp.get('type') == 'stdin':
+                    if 'inputBinding' in inp:
+                        raise ValidationException(
+                            "Not allowed to specify inputBinding when"
+                            " using stdin shortcut.")
+                    if 'stdin' in workflowobj:
+                        raise ValidationException(
+                            "Not allowed to specify stdin path when"
+                            " using stdin type shortcut.")
+                    else:
+                        workflowobj['stdin'] = \
+                            "$(inputs.%s.path)" % \
+                            inp['id'].rpartition('#')[2]
+                        inp['type'] = 'File'
+        else:
+            for entry in itervalues(workflowobj):
+                _convert_stdstreams_to_files(entry)
+    if isinstance(workflowobj, MutableSequence):
+        for entry in workflowobj:
+            _convert_stdstreams_to_files(entry)
+
+def _add_blank_ids(workflowobj):
+    # type: (Union[Dict[Text, Any], List[Dict[Text, Any]]]) -> None
+
+    if isinstance(workflowobj, MutableMapping):
+        if ("run" in workflowobj and
+                isinstance(workflowobj["run"], MutableMapping) and
+                "id" not in workflowobj["run"] and
+                "$import" not in workflowobj["run"]):
+            workflowobj["run"]["id"] = Text(uuid.uuid4())
+        for entry in itervalues(workflowobj):
+            _add_blank_ids(entry)
+    if isinstance(workflowobj, MutableSequence):
+        for entry in workflowobj:
+            _add_blank_ids(entry)
+
+def resolve_and_validate_document(
+        loadingContext,            # type: LoadingContext
+        workflowobj,               # type: Union[CommentedMap, CommentedSeq]
+        uri,                       # type: Text
+        preprocess_only=False,     # type: bool
+        skip_schemas=None,         # type: Optional[bool]
+                                 ):
+    # type: (...) -> Tuple[LoadingContext, Text]
+    """Validate a CWL document."""
+    if not loadingContext.loader:
+        raise ValueError("loadingContext must have a loader.")
+    else:
+        loader = loadingContext.loader
+    loadingContext = loadingContext.copy()
+
+    if not isinstance(workflowobj, MutableMapping):
+        raise ValueError("workflowjobj must be a dict, got '{}': {}".format(
+            type(workflowobj), workflowobj))
+
+    jobobj = None
+    if "cwl:tool" in workflowobj:
+        jobobj, _ = loader.resolve_all(workflowobj, uri)
+        uri = urllib.parse.urljoin(uri, workflowobj["https://w3id.org/cwl/cwl#tool"])
+        del cast(Dict[Text, Any], jobobj)["https://w3id.org/cwl/cwl#tool"]
+
+        workflowobj = fetch_document(uri, loadingContext)[1]
+
+    fileuri = urllib.parse.urldefrag(uri)[0]
+
+    cwlVersion = loadingContext.metadata.get("cwlVersion")
+    if not cwlVersion:
+        cwlVersion = workflowobj.get("cwlVersion")
+    if not cwlVersion and fileuri != uri:
+        # The tool we're loading is a fragment of a bigger file.  Get
+        # the document root element and look for cwlVersion there.
+        metadata = fetch_document(fileuri, loadingContext)[1]  # type: Dict[Text, Any]
+        cwlVersion = metadata.get("cwlVersion")
+    if not cwlVersion:
+        raise ValidationException(
+            "No cwlVersion found. "
+            "Use the following syntax in your CWL document to declare "
+            "the version: cwlVersion: <version>.\n"
+            "Note: if this is a CWL draft-2 (pre v1.0) document then it "
+            "will need to be upgraded first.")
+
+    if not isinstance(cwlVersion, string_types):
+        with SourceLine(workflowobj, "cwlVersion", ValidationException):
+            raise ValidationException("'cwlVersion' must be a string, "
+                                      "got {}".format(
+                                          type(cwlVersion)))
+    # strip out version
+    cwlVersion = re.sub(
+        r"^(?:cwl:|https://w3id.org/cwl/cwl#)", "",
+        cwlVersion)
+    if cwlVersion not in list(ALLUPDATES):
+        # print out all the Supported Versions of cwlVersion
+        versions = []
+        for version in list(ALLUPDATES):
+            if "dev" in version:
+                version += " (with --enable-dev flag only)"
+            versions.append(version)
+        versions.sort()
+        raise ValidationException(
+            "The CWL reference runner no longer supports pre CWL v1.0 "
+            "documents. Supported versions are: "
+            "\n{}".format("\n".join(versions)))
+
+    if isinstance(jobobj, CommentedMap) and "http://commonwl.org/cwltool#overrides" in jobobj:
+        loadingContext.overrides_list.extend(resolve_overrides(jobobj, uri, uri))
+        del jobobj["http://commonwl.org/cwltool#overrides"]
+
+    if isinstance(jobobj, CommentedMap) and "https://w3id.org/cwl/cwl#requirements" in jobobj:
+        if cwlVersion not in ("v1.1.0-dev1","v1.1"):
+            raise ValidationException(
+                    "`cwl:requirements` in the input object is not part of CWL "
+                    "v1.0. You can adjust to use `cwltool:overrides` instead; or you "
+                    "can set the cwlVersion to v1.1 or greater.")
+        loadingContext.overrides_list.append({"overrideTarget": uri,
+                                              "requirements": jobobj["https://w3id.org/cwl/cwl#requirements"]})
+        del jobobj["https://w3id.org/cwl/cwl#requirements"]
+
+    (sch_document_loader, avsc_names) = \
+        process.get_schema(cwlVersion)[:2]
+
+    if isinstance(avsc_names, Exception):
+        raise avsc_names
+
+    processobj = None  # type: Union[CommentedMap, CommentedSeq, Text, None]
+    document_loader = Loader(sch_document_loader.ctx,
+                             schemagraph=sch_document_loader.graph,
+                             idx=loader.idx,
+                             cache=sch_document_loader.cache,
+                             fetcher_constructor=loadingContext.fetcher_constructor,
+                             skip_schemas=skip_schemas)
+
+    if cwlVersion == "v1.0":
+        _add_blank_ids(workflowobj)
+
+    processobj, metadata = document_loader.resolve_all(workflowobj, fileuri)
+    if loadingContext.metadata:
+        metadata = loadingContext.metadata
+    if not isinstance(processobj, (CommentedMap, CommentedSeq)):
+        raise ValidationException("Workflow must be a CommentedMap or CommentedSeq.")
+    if not isinstance(metadata, CommentedMap):
+        raise ValidationException("metadata must be a CommentedMap, was %s" % type(metadata))
+
+    if isinstance(processobj, CommentedMap):
+        uri = processobj["id"]
+
+    _convert_stdstreams_to_files(workflowobj)
+
+    if preprocess_only:
+        return loadingContext, uri
+
+    if loadingContext.do_validate:
+        schema.validate_doc(avsc_names, processobj, document_loader, loadingContext.strict)
+
+    # None means default behavior (do update)
+    if loadingContext.do_update in (True, None):
+        if "cwlVersion" not in metadata:
+            metadata["cwlVersion"] = cwlVersion
+        processobj = update.update(
+            processobj, document_loader, fileuri, loadingContext.enable_dev, metadata)
+        document_loader.idx[processobj["id"]] = processobj
+
+    if jobobj is not None:
+        loadingContext.jobdefaults = jobobj
+
+    loadingContext.loader = document_loader
+    loadingContext.avsc_names = avsc_names
+    loadingContext.metadata = metadata
+
+    return loadingContext, uri
+
+
+def make_tool(uri,                # type: Union[Text, CommentedMap, CommentedSeq]
+              loadingContext      # type: LoadingContext
+             ):  # type: (...) -> Process
+    """Make a Python CWL object."""
+    if loadingContext.loader is None:
+        raise ValueError("loadingContext must have a loader")
+    resolveduri, metadata = loadingContext.loader.resolve_ref(uri)
+
+    processobj = None
+    if isinstance(resolveduri, MutableSequence):
+        for obj in resolveduri:
+            if obj['id'].endswith('#main'):
+                processobj = obj
+                break
+        if not processobj:
+            raise WorkflowException(
+                u"Tool file contains graph of multiple objects, must specify "
+                "one of #%s" % ", #".join(
+                    urllib.parse.urldefrag(i["id"])[1] for i in resolveduri
+                    if "id" in i))
+    elif isinstance(resolveduri, MutableMapping):
+        processobj = resolveduri
+    else:
+        raise Exception("Must resolve to list or dict")
+
+    tool = loadingContext.construct_tool_object(processobj, loadingContext)
+
+    if loadingContext.jobdefaults:
+        jobobj = loadingContext.jobdefaults
+        for inp in tool.tool["inputs"]:
+            if shortname(inp["id"]) in jobobj:
+                inp["default"] = jobobj[shortname(inp["id"])]
+
+    return tool
+
+
+def load_tool(argsworkflow,         # type: Union[Text, Dict[Text, Any]]
+              loadingContext=None   # type: Optional[LoadingContext]
+             ):  # type: (...) -> Process
+
+    loadingContext, workflowobj, uri = fetch_document(
+        argsworkflow, loadingContext)
+
+    loadingContext, uri = resolve_and_validate_document(
+        loadingContext, workflowobj, uri)
+
+    return make_tool(uri,
+                     loadingContext)
+
+def resolve_overrides(ov,      # type: CommentedMap
+                      ov_uri,  # type: Text
+                      baseurl  # type: Text
+                     ):  # type: (...) -> List[Dict[Text, Any]]
+    ovloader = Loader(overrides_ctx)
+    ret, _ = ovloader.resolve_all(ov, baseurl)
+    if not isinstance(ret, CommentedMap):
+        raise Exception("Expected CommentedMap, got %s" % type(ret))
+    cwl_docloader = get_schema("v1.0")[0]
+    cwl_docloader.resolve_all(ret, ov_uri)
+    return cast(List[Dict[Text, Any]],
+                ret["http://commonwl.org/cwltool#overrides"])
+
+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)