--- a/env/lib/python3.7/site-packages/cwltool/expression.py	Thu May 14 16:47:39 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,309 +0,0 @@
-"""Parse CWL expressions."""
-from __future__ import absolute_import
-
-import copy
-import re
-from typing import (Any, Dict, List, Mapping, MutableMapping, MutableSequence, Optional,
-                    Union)
-
-import six
-from six import string_types, u
-from future.utils import raise_from
-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 .sandboxjs import default_timeout, execjs, JavascriptException
-from .errors import WorkflowException
-from .utils import bytes2str_in_dicts, docker_windows_path_adjust, json_dumps
-
-
-def jshead(engine_config, rootvars):
-    # type: (List[Text], Dict[Text, Any]) -> Text
-
-    # make sure all the byte strings are converted
-    # to str in `rootvars` dict.
-
-    return u"\n".join(
-        engine_config + [u"var {} = {};".format(k, json_dumps(v, indent=4))
-                         for k, v in rootvars.items()])
-
-
-# decode all raw strings to unicode
-seg_symbol = r"""\w+"""
-seg_single = r"""\['([^']|\\')+'\]"""
-seg_double = r"""\["([^"]|\\")+"\]"""
-seg_index = r"""\[[0-9]+\]"""
-segments = r"(\.%s|%s|%s|%s)" % (seg_symbol, seg_single, seg_double, seg_index)
-segment_re = re.compile(u(segments), flags=re.UNICODE)
-param_str = r"\((%s)%s*\)$" % (seg_symbol, segments)
-param_re = re.compile(u(param_str), flags=re.UNICODE)
-
-JSON = Union[Dict[Any, Any], List[Any], Text, int, float, bool, None]
-
-
-class SubstitutionError(Exception):
-    pass
-
-
-def scanner(scan):  # type: (Text) -> List[int]
-    DEFAULT = 0
-    DOLLAR = 1
-    PAREN = 2
-    BRACE = 3
-    SINGLE_QUOTE = 4
-    DOUBLE_QUOTE = 5
-    BACKSLASH = 6
-
-    i = 0
-    stack = [DEFAULT]
-    start = 0
-    while i < len(scan):
-        state = stack[-1]
-        c = scan[i]
-
-        if state == DEFAULT:
-            if c == '$':
-                stack.append(DOLLAR)
-            elif c == '\\':
-                stack.append(BACKSLASH)
-        elif state == BACKSLASH:
-            stack.pop()
-            if stack[-1] == DEFAULT:
-                return [i - 1, i + 1]
-        elif state == DOLLAR:
-            if c == '(':
-                start = i - 1
-                stack.append(PAREN)
-            elif c == '{':
-                start = i - 1
-                stack.append(BRACE)
-            else:
-                stack.pop()
-        elif state == PAREN:
-            if c == '(':
-                stack.append(PAREN)
-            elif c == ')':
-                stack.pop()
-                if stack[-1] == DOLLAR:
-                    return [start, i + 1]
-            elif c == "'":
-                stack.append(SINGLE_QUOTE)
-            elif c == '"':
-                stack.append(DOUBLE_QUOTE)
-        elif state == BRACE:
-            if c == '{':
-                stack.append(BRACE)
-            elif c == '}':
-                stack.pop()
-                if stack[-1] == DOLLAR:
-                    return [start, i + 1]
-            elif c == "'":
-                stack.append(SINGLE_QUOTE)
-            elif c == '"':
-                stack.append(DOUBLE_QUOTE)
-        elif state == SINGLE_QUOTE:
-            if c == "'":
-                stack.pop()
-            elif c == '\\':
-                stack.append(BACKSLASH)
-        elif state == DOUBLE_QUOTE:
-            if c == '"':
-                stack.pop()
-            elif c == '\\':
-                stack.append(BACKSLASH)
-        i += 1
-
-    if len(stack) > 1:
-        raise SubstitutionError(
-            "Substitution error, unfinished block starting at position {}: {}".format(start, scan[start:]))
-    else:
-        return []
-
-
-def next_seg(parsed_string, remaining_string, current_value):  # type: (Text, Text, JSON) -> JSON
-    if remaining_string:
-        m = segment_re.match(remaining_string)
-        if not m:
-            return current_value
-        next_segment_str = m.group(0)
-
-        key = None  # type: Optional[Union[Text, int]]
-        if next_segment_str[0] == '.':
-            key = next_segment_str[1:]
-        elif next_segment_str[1] in ("'", '"'):
-            key = next_segment_str[2:-2].replace("\\'", "'").replace('\\"', '"')
-
-        if key is not None:
-            if isinstance(current_value, MutableSequence) and key == "length" and not remaining_string[m.end(0):]:
-                return len(current_value)
-            if not isinstance(current_value, MutableMapping):
-                raise WorkflowException("%s is a %s, cannot index on string '%s'" % (parsed_string, type(current_value).__name__, key))
-            if key not in current_value:
-                raise WorkflowException("%s does not contain key '%s'" % (parsed_string, key))
-        else:
-            try:
-                key = int(next_segment_str[1:-1])
-            except ValueError as v:
-                raise_from(WorkflowException(u(str(v))), v)
-            if not isinstance(current_value, MutableSequence):
-                raise WorkflowException("%s is a %s, cannot index on int '%s'" % (parsed_string, type(current_value).__name__, key))
-            if key >= len(current_value):
-                raise WorkflowException("%s list index %i out of range" % (parsed_string, key))
-
-        if isinstance(current_value, Mapping):
-            try:
-                return next_seg(parsed_string + remaining_string, remaining_string[m.end(0):], current_value[key])
-            except KeyError:
-                raise WorkflowException("%s doesn't have property %s" % (parsed_string, key))
-        elif isinstance(current_value, list) and isinstance(key, int):
-            try:
-                return next_seg(parsed_string + remaining_string, remaining_string[m.end(0):], current_value[key])
-            except KeyError:
-                raise WorkflowException("%s doesn't have property %s" % (parsed_string, key))
-        else:
-            raise WorkflowException("%s doesn't have property %s" % (parsed_string, key))
-    else:
-        return current_value
-
-
-def evaluator(ex,                       # type: Text
-              jslib,                    # type: Text
-              obj,                      # type: Dict[Text, Any]
-              timeout,                  # type: float
-              fullJS=False,             # type: bool
-              force_docker_pull=False,  # type: bool
-              debug=False,              # type: bool
-              js_console=False          # type: bool
-             ):
-    # type: (...) -> JSON
-    match = param_re.match(ex)
-
-    expression_parse_exception = None
-    expression_parse_succeeded = False
-
-    if match is not None:
-        first_symbol = match.group(1)
-        first_symbol_end = match.end(1)
-
-        if first_symbol_end + 1 == len(ex) and first_symbol == "null":
-            return None
-        try:
-            if obj.get(first_symbol) is None:
-                raise WorkflowException("%s is not defined" % first_symbol)
-
-            return next_seg(first_symbol, ex[first_symbol_end:-1], obj[first_symbol])
-        except WorkflowException as werr:
-            expression_parse_exception = werr
-        else:
-            expression_parse_succeeded = True
-
-    if fullJS and not expression_parse_succeeded:
-        return execjs(
-            ex, jslib, timeout, force_docker_pull=force_docker_pull,
-            debug=debug, js_console=js_console)
-    else:
-        if expression_parse_exception is not None:
-            raise JavascriptException(
-                "Syntax error in parameter reference '%s': %s. This could be "
-                "due to using Javascript code without specifying "
-                "InlineJavascriptRequirement." % \
-                    (ex[1:-1], expression_parse_exception))
-        else:
-            raise JavascriptException(
-                "Syntax error in parameter reference '%s'. This could be due "
-                "to using Javascript code without specifying "
-                "InlineJavascriptRequirement." % ex)
-
-
-def interpolate(scan,                     # type: Text
-                rootvars,                 # type: Dict[Text, Any]
-                timeout=default_timeout,  # type: float
-                fullJS=False,             # type: bool
-                jslib="",                 # type: Text
-                force_docker_pull=False,  # type: bool
-                debug=False,              # type: bool
-                js_console=False,         # type: bool
-                strip_whitespace=True     # type: bool
-               ):  # type: (...) -> JSON
-    if strip_whitespace:
-        scan = scan.strip()
-    parts = []
-    w = scanner(scan)
-    while w:
-        parts.append(scan[0:w[0]])
-
-        if scan[w[0]] == '$':
-            e = evaluator(scan[w[0] + 1:w[1]], jslib, rootvars, timeout,
-                          fullJS=fullJS, force_docker_pull=force_docker_pull,
-                          debug=debug, js_console=js_console)
-            if w[0] == 0 and w[1] == len(scan) and len(parts) <= 1:
-                return e
-            leaf = json_dumps(e, sort_keys=True)
-            if leaf[0] == '"':
-                leaf = leaf[1:-1]
-            parts.append(leaf)
-        elif scan[w[0]] == '\\':
-            e = scan[w[1] - 1]
-            parts.append(e)
-
-        scan = scan[w[1]:]
-        w = scanner(scan)
-    parts.append(scan)
-    return ''.join(parts)
-
-def needs_parsing(snippet):  # type: (Any) -> bool
-    return isinstance(snippet, string_types) \
-        and ("$(" in snippet or "${" in snippet)
-
-def do_eval(ex,                       # type: Union[Text, Dict[Text, Text]]
-            jobinput,                 # type: Dict[Text, JSON]
-            requirements,             # type: List[Dict[Text, Any]]
-            outdir,                   # type: Optional[Text]
-            tmpdir,                   # type: Optional[Text]
-            resources,                # type: Dict[str, int]
-            context=None,             # type: Any
-            timeout=default_timeout,  # type: float
-            force_docker_pull=False,  # type: bool
-            debug=False,              # type: bool
-            js_console=False,         # type: bool
-            strip_whitespace=True     # type: bool
-           ):  # type: (...) -> Any
-
-    runtime = copy.deepcopy(resources)  # type: Dict[str, Any]
-    runtime["tmpdir"] = docker_windows_path_adjust(tmpdir) if tmpdir else None
-    runtime["outdir"] = docker_windows_path_adjust(outdir) if outdir else None
-
-    rootvars = {
-        u"inputs": jobinput,
-        u"self": context,
-        u"runtime": runtime}
-
-    # TODO: need to make sure the `rootvars dict`
-    # contains no bytes type in the first place.
-    if six.PY3:
-        rootvars = bytes2str_in_dicts(rootvars)  # type: ignore
-
-    if isinstance(ex, string_types) and needs_parsing(ex):
-        fullJS = False
-        jslib = u""
-        for r in reversed(requirements):
-            if r["class"] == "InlineJavascriptRequirement":
-                fullJS = True
-                jslib = jshead(r.get("expressionLib", []), rootvars)
-                break
-
-        try:
-            return interpolate(ex,
-                               rootvars,
-                               timeout=timeout,
-                               fullJS=fullJS,
-                               jslib=jslib,
-                               force_docker_pull=force_docker_pull,
-                               debug=debug,
-                               js_console=js_console,
-                               strip_whitespace=strip_whitespace)
-
-        except Exception as e:
-            raise_from(WorkflowException("Expression evaluation error:\n%s" % Text(e)), e)
-    else:
-        return ex