--- a/env/lib/python3.7/site-packages/cwltool/update.py	Thu May 14 16:47:39 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,203 +0,0 @@
-from __future__ import absolute_import
-
-import copy
-import re
-from typing import (Any, Callable, Dict, List, MutableMapping, MutableSequence,
-                    Optional, Tuple, Union)
-
-from functools import partial
-
-from ruamel.yaml.comments import CommentedMap, CommentedSeq
-from schema_salad import validate
-from schema_salad.ref_resolver import Loader  # pylint: disable=unused-import
-from six import string_types
-from six.moves import urllib
-from typing_extensions import Text
-from schema_salad.sourceline import SourceLine
-from .loghandler import _logger
-
-# move to a regular typing import when Python 3.3-3.6 is no longer supported
-
-from .utils import visit_class, visit_field, aslist
-
-
-def v1_0to1_1(doc, loader, baseuri):  # pylint: disable=unused-argument
-    # type: (Any, Loader, Text) -> Tuple[Any, Text]
-    """Public updater for v1.0 to v1.1."""
-    doc = copy.deepcopy(doc)
-
-    rewrite = {
-        "http://commonwl.org/cwltool#WorkReuse": "WorkReuse",
-        "http://arvados.org/cwl#ReuseRequirement": "WorkReuse",
-        "http://commonwl.org/cwltool#TimeLimit": "ToolTimeLimit",
-        "http://commonwl.org/cwltool#NetworkAccess": "NetworkAccess",
-        "http://commonwl.org/cwltool#InplaceUpdateRequirement": "InplaceUpdateRequirement",
-        "http://commonwl.org/cwltool#LoadListingRequirement": "LoadListingRequirement"
-    }
-    def rewrite_requirements(t):  # type: (MutableMapping[Text, Union[Text, Dict[Text, Any]]]) -> None
-        if "requirements" in t:
-            for r in t["requirements"]:
-                if isinstance(r, MutableMapping):
-                    if r["class"] in rewrite:
-                        r["class"] = rewrite[r["class"]]
-                else:
-                    raise validate.ValidationException(
-                            "requirements entries must be dictionaries: {} {}.".format(
-                                type(r), r))
-        if "hints" in t:
-            for r in t["hints"]:
-                if isinstance(r, MutableMapping):
-                    if r["class"] in rewrite:
-                        r["class"] = rewrite[r["class"]]
-                else:
-                    raise validate.ValidationException(
-                        "hints entries must be dictionaries: {} {}.".format(
-                            type(r), r))
-        if "steps" in t:
-            for s in t["steps"]:
-                if isinstance(s, MutableMapping):
-                    rewrite_requirements(s)
-                else:
-                    raise validate.ValidationException(
-                        "steps entries must be dictionaries: {} {}.".format(
-                            type(s), s))
-
-
-    def update_secondaryFiles(t, top=False):
-        # type: (Any, bool) -> Union[MutableSequence[MutableMapping[Text, Text]], MutableMapping[Text, Text]]
-        if isinstance(t, CommentedSeq):
-            new_seq = copy.deepcopy(t)
-            for index, entry in enumerate(t):
-                new_seq[index] = update_secondaryFiles(entry)
-            return new_seq
-        elif isinstance(t, MutableSequence):
-            return CommentedSeq([update_secondaryFiles(p) for p in t])
-        elif isinstance(t, MutableMapping):
-            return t
-        elif top:
-            return CommentedSeq([CommentedMap([("pattern", t)])])
-        else:
-            return CommentedMap([("pattern", t)])
-
-    def fix_inputBinding(t):  # type: (Dict[Text, Any]) -> None
-        for i in t["inputs"]:
-            if "inputBinding" in i:
-                ib = i["inputBinding"]
-                for k in list(ib.keys()):
-                    if k != "loadContents":
-                        _logger.warning(SourceLine(ib, k).makeError(
-                            "Will ignore field '{}' which is not valid in {} "
-                            "inputBinding".format(k, t["class"])))
-                        del ib[k]
-
-    visit_class(doc, ("CommandLineTool","Workflow"), rewrite_requirements)
-    visit_class(doc, ("ExpressionTool","Workflow"), fix_inputBinding)
-    visit_field(doc, "secondaryFiles", partial(update_secondaryFiles, top=True))
-
-    upd = doc
-    if isinstance(upd, MutableMapping) and "$graph" in upd:
-        upd = upd["$graph"]
-    for proc in aslist(upd):
-        proc.setdefault("hints", CommentedSeq())
-        proc["hints"].insert(0, CommentedMap([("class", "NetworkAccess"),( "networkAccess", True)]))
-        proc["hints"].insert(0, CommentedMap([("class", "LoadListingRequirement"),("loadListing", "deep_listing")]))
-        if "cwlVersion" in proc:
-            del proc["cwlVersion"]
-
-    return (doc, "v1.1")
-
-def v1_1_0dev1to1_1(doc, loader, baseuri):  # pylint: disable=unused-argument
-    # type: (Any, Loader, Text) -> Tuple[Any, Text]
-    return (doc, "v1.1")
-
-UPDATES = {
-    u"v1.0": v1_0to1_1,
-    u"v1.1": None
-}  # type: Dict[Text, Optional[Callable[[Any, Loader, Text], Tuple[Any, Text]]]]
-
-DEVUPDATES = {
-    u"v1.0": v1_0to1_1,
-    u"v1.1.0-dev1": v1_1_0dev1to1_1,
-    u"v1.1": None
-}  # type: Dict[Text, Optional[Callable[[Any, Loader, Text], Tuple[Any, Text]]]]
-
-ALLUPDATES = UPDATES.copy()
-ALLUPDATES.update(DEVUPDATES)
-
-INTERNAL_VERSION = u"v1.1"
-
-def identity(doc, loader, baseuri):  # pylint: disable=unused-argument
-    # type: (Any, Loader, Text) -> Tuple[Any, Union[Text, Text]]
-    """Default, do-nothing, CWL document upgrade function."""
-    return (doc, doc["cwlVersion"])
-
-
-def checkversion(doc,        # type: Union[CommentedSeq, CommentedMap]
-                 metadata,   # type: CommentedMap
-                 enable_dev  # type: bool
-):
-    # type: (...) -> Tuple[CommentedMap, Text]
-    """Check the validity of the version of the give CWL document.
-
-    Returns the document and the validated version string.
-    """
-    cdoc = None  # type: Optional[CommentedMap]
-    if isinstance(doc, CommentedSeq):
-        if not isinstance(metadata, CommentedMap):
-            raise Exception("Expected metadata to be CommentedMap")
-        lc = metadata.lc
-        metadata = copy.deepcopy(metadata)
-        metadata.lc.data = copy.copy(lc.data)
-        metadata.lc.filename = lc.filename
-        metadata[u"$graph"] = doc
-        cdoc = metadata
-    elif isinstance(doc, CommentedMap):
-        cdoc = doc
-    else:
-        raise Exception("Expected CommentedMap or CommentedSeq")
-
-    version = metadata[u"cwlVersion"]
-    cdoc["cwlVersion"] = version
-
-    if version not in UPDATES:
-        if version in DEVUPDATES:
-            if enable_dev:
-                pass
-            else:
-                keys = list(UPDATES.keys())
-                keys.sort()
-                raise validate.ValidationException(
-                    u"Version '%s' is a development or deprecated version.\n "
-                    "Update your document to a stable version (%s) or use "
-                    "--enable-dev to enable support for development and "
-                    "deprecated versions." % (version, ", ".join(keys)))
-        else:
-            raise validate.ValidationException(
-                u"Unrecognized version %s" % version)
-
-    return (cdoc, version)
-
-
-def update(doc, loader, baseuri, enable_dev, metadata):
-    # type: (Union[CommentedSeq, CommentedMap], Loader, Text, bool, Any) -> CommentedMap
-
-    if isinstance(doc, CommentedMap):
-            if metadata.get("http://commonwl.org/cwltool#original_cwlVersion") \
-                    or doc.get("http://commonwl.org/cwltool#original_cwlVersion"):
-                return doc
-
-    (cdoc, version) = checkversion(doc, metadata, enable_dev)
-    originalversion = copy.copy(version)
-
-    nextupdate = identity  # type: Optional[Callable[[Any, Loader, Text], Tuple[Any, Text]]]
-
-    while nextupdate:
-        (cdoc, version) = nextupdate(cdoc, loader, baseuri)
-        nextupdate = ALLUPDATES[version]
-
-    cdoc[u"cwlVersion"] = version
-    metadata[u"cwlVersion"] = version
-    metadata[u"http://commonwl.org/cwltool#original_cwlVersion"] = originalversion
-    cdoc[u"http://commonwl.org/cwltool#original_cwlVersion"] = originalversion
-
-    return cdoc