Docker mount directory "_:" (#355)

Author: michael-kotliar

cwltool/job.py

@@ -158,7 +158,11 @@ def run(self, dry_run=False, pull_image=True, rm_container=True,
                 if not vol.staged:
                     continue
                 if vol.type in ("File", "Directory"):
-                    runtime.append(u"--volume=%s:%s:ro" % (vol.resolved, vol.target))
+                    if vol.resolved.startswith("_:"):
+                        createtmp_dir = os.path.join(self.stagedir, os.path.basename(vol.target))
+                        runtime.append(u"--volume=%s:%s:rw" % (createtmp_dir, vol.target))
+                    else:
+                        runtime.append(u"--volume=%s:%s:ro" % (vol.resolved, vol.target))
                 if vol.type == "CreateFile":
                     createtmp = os.path.join(self.stagedir, os.path.basename(vol.target))
                     with open(createtmp, "w") as f:

cwltool/main.py

@@ -423,7 +423,7 @@ def load_job_order(args, t, stdin, print_input_deps=False, relative_deps=False,
     if len(args.job_order) == 1 and args.job_order[0][0] != "-":
         job_order_file = args.job_order[0]
     elif len(args.job_order) == 1 and args.job_order[0] == "-":
-        job_order_object = yaml.load(stdin, yaml.RoundTripLoader)
+        job_order_object = yaml.round_trip_load(stdin) # type: ignore
         job_order_object, _ = loader.resolve_all(job_order_object, file_uri(os.getcwd()) + "/")
     else:
         job_order_file = None