--- a/env/lib/python3.7/site-packages/cwltool/subgraph.py	Thu May 14 16:47:39 2020 -0400
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,148 +0,0 @@
-import copy
-from .utils import aslist, json_dumps
-from collections import namedtuple
-from typing import (Dict, MutableMapping, MutableSequence, Set, Any, Text, Optional, Tuple)
-from .process import shortname
-from six import itervalues
-from six.moves import urllib
-from .workflow import Workflow
-from ruamel.yaml.comments import CommentedMap
-
-Node = namedtuple('Node', ('up', 'down', 'type'))
-UP = "up"
-DOWN = "down"
-INPUT = "input"
-OUTPUT = "output"
-STEP = "step"
-
-def subgraph_visit(current,   # type: Text
-                   nodes,     # type: MutableMapping[Text, Node]
-                   visited,   # type: Set[Text]
-                   direction  # type: Text
-): # type: (...) -> None
-
-    if current in visited:
-        return
-    visited.add(current)
-
-    if direction == DOWN:
-        d = nodes[current].down
-    if direction == UP:
-        d = nodes[current].up
-    for c in d:
-        subgraph_visit(c, nodes, visited, direction)
-
-def declare_node(nodes, nodeid, tp):
-    # type: (Dict[Text, Node], Text, Optional[Text]) -> Node
-    if nodeid in nodes:
-        n = nodes[nodeid]
-        if n.type is None:
-            nodes[nodeid] = Node(n.up, n.down, tp)
-    else:
-        nodes[nodeid] = Node([], [], tp)
-    return nodes[nodeid]
-
-def get_subgraph(roots,  # type: MutableSequence[Text]
-                 tool    # type: Workflow
-                 ):  # type: (...) -> Optional[CommentedMap]
-    if tool.tool["class"] != "Workflow":
-        raise Exception("Can only extract subgraph from workflow")
-
-    nodes = {}  # type: Dict[Text, Node]
-
-    for inp in tool.tool["inputs"]:
-        declare_node(nodes, inp["id"], INPUT)
-
-    for out in tool.tool["outputs"]:
-        declare_node(nodes, out["id"], OUTPUT)
-        for i in aslist(out.get("outputSource", [])):
-            # source is upstream from output (dependency)
-            nodes[out["id"]].up.append(i)
-            # output is downstream from source
-            declare_node(nodes, i, None)
-            nodes[i].down.append(out["id"])
-
-    for st in tool.tool["steps"]:
-        step = declare_node(nodes, st["id"], STEP)
-        for i in st["in"]:
-            if "source" not in i:
-                continue
-            for src in aslist(i["source"]):
-                # source is upstream from step (dependency)
-                step.up.append(src)
-                # step is downstream from source
-                declare_node(nodes, src, None)
-                nodes[src].down.append(st["id"])
-        for out in st["out"]:
-            # output is downstream from step
-            step.down.append(out)
-            # step is upstream from output
-            declare_node(nodes, out, None)
-            nodes[out].up.append(st["id"])
-
-
-    # Find all the downstream nodes from the starting points
-    visited_down = set()  # type: Set[Text]
-    for r in roots:
-        if nodes[r].type == OUTPUT:
-            subgraph_visit(r, nodes, visited_down, UP)
-        else:
-            subgraph_visit(r, nodes, visited_down, DOWN)
-
-    def find_step(stepid):  # type: (Text) -> Optional[MutableMapping[Text, Any]]
-        for st in tool.steps:
-            if st.tool["id"] == stepid:
-                return st.tool
-        return None
-
-    # Now make sure all the nodes are connected to upstream inputs
-    visited = set()  # type: Set[Text]
-    rewire = {}  # type: Dict[Text, Tuple[Text, Text]]
-    for v in visited_down:
-        visited.add(v)
-        if nodes[v].type in (STEP, OUTPUT):
-            for u in nodes[v].up:
-                if u in visited_down:
-                    continue
-                if nodes[u].type == INPUT:
-                    visited.add(u)
-                else:
-                    # rewire
-                    df = urllib.parse.urldefrag(u)
-                    rn = df[0] + "#" + df[1].replace("/", "_")
-                    if nodes[v].type == STEP:
-                        wfstep = find_step(v)
-                        if wfstep is not None:
-                            for inp in wfstep["inputs"]:
-                                if u in inp["source"]:
-                                    rewire[u] = (rn, inp["type"])
-                                    break
-                        else:
-                            raise Exception("Could not find step %s" % v)
-
-
-    extracted = CommentedMap()
-    for f in tool.tool:
-        if f in ("steps", "inputs", "outputs"):
-            extracted[f] = []
-            for i in tool.tool[f]:
-                if i["id"] in visited:
-                    if f == "steps":
-                        for inport in i["in"]:
-                            if "source" not in inport:
-                                continue
-                            if isinstance(inport["source"], MutableSequence):
-                                inport["source"] = [rewire[s][0] for s in inport["source"] if s in rewire]
-                            elif inport["source"] in rewire:
-                                inport["source"] = rewire[inport["source"]][0]
-                    extracted[f].append(i)
-        else:
-            extracted[f] = tool.tool[f]
-
-    for rv in itervalues(rewire):
-        extracted["inputs"].append({
-            "id": rv[0],
-            "type": rv[1]
-        })
-
-    return extracted