Bugfix --preserve-environment and add --preserve-entire-environment. (#199)

Author: tetron

cwltool/job.py

@@ -137,6 +137,8 @@ def run(self, dry_run=False, pull_image=True, rm_container=True,
             if not os.path.exists(self.tmpdir):
                 os.makedirs(self.tmpdir)
             vars_to_preserve = kwargs.get("preserve_environment")
+            if kwargs.get("preserve_entire_environment"):
+                vars_to_preserve = os.environ
             if vars_to_preserve is not None:
                 for key, value in os.environ.items():
                     if key in vars_to_preserve and key not in env:

cwltool/main.py

@@ -50,12 +50,17 @@ def arg_parser():  # type: () -> argparse.ArgumentParser
                         help="Do not execute jobs in a Docker container, even when specified by the CommandLineTool",
                         dest="use_container")
 
-    parser.add_argument("--preserve-environment", type=Text, nargs='+',
-                        help="Preserve specified environment variables when running CommandLineTools",
-                        metavar=("VAR1,VAR2"),
-                        default=("PATH",),
+    parser.add_argument("--preserve-environment", type=Text, action="append",
+                        help="Preserve specific environment variable when running CommandLineTools.  May be provided multiple times.",
+                        metavar="ENVVAR",
+                        default=["PATH"],
                         dest="preserve_environment")
 
+    parser.add_argument("--preserve-entire-environment", action="store_true",
+                        help="Preserve entire parent environment when running CommandLineTools.",
+                        default=False,
+                        dest="preserve_entire_environment")
+
     exgroup = parser.add_mutually_exclusive_group()
     exgroup.add_argument("--rm-container", action="store_true", default=True,
                         help="Delete Docker container used by jobs after they exit (default)",