--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/planemo/lib/python3.7/site-packages/cwltool/update.py	Fri Jul 31 00:18:57 2020 -0400
@@ -0,0 +1,203 @@
+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