Kill Docker container if --cidfile is specified (#996)

Author: michael-kotliar

cwltool/main.py

@@ -8,6 +8,7 @@
 import logging
 import os
 import signal
+import subprocess  # nosec
 import sys
 import time
 import urllib
@@ -112,7 +113,18 @@ def _terminate_processes() -> None:
     # It's possible that another thread will spawn a new task while
     # we're executing, so it's not safe to use a for loop here.
     while processes_to_kill:
-        processes_to_kill.popleft().kill()
+        process = processes_to_kill.popleft()
+        cidfile = [str(arg).split("=")[1] for arg in process.args if "--cidfile" in str(arg)]
+        if cidfile:
+            try:
+                with open(cidfile[0], "r") as inp_stream:
+                    p = subprocess.Popen(["docker", "kill", inp_stream.read()], shell=False)  # nosec
+                    try:
+                        p.wait(timeout=10)
+                    except subprocess.TimeoutExpired:
+                        p.kill()
+            except FileNotFoundError:
+                pass
 
 
 def _signal_handler(signum: int, _: Any) -> None: