From 876c0fcabac3829cd48fb228502f3259488ce118 Mon Sep 17 00:00:00 2001
From: Peter Amstutz <tetron@interreality.org>
Date: Tue, 13 Sep 2016 13:10:24 -0400
Subject: [PATCH] Fix serializing Directory[] on command line.  (#190)

* Fix serializing Directory[] on command line.  Also handle Directory[] in
generate_parser.
---
 cwltool/builder.py |  2 +-
 cwltool/main.py    | 44 +++++++++++++++++++++-----------------------
 2 files changed, 22 insertions(+), 24 deletions(-)

diff --git a/cwltool/builder.py b/cwltool/builder.py
index e7abb9417..7ac35fecc 100644
--- a/cwltool/builder.py
+++ b/cwltool/builder.py
@@ -155,7 +155,7 @@ def generate_arg(self, binding):  # type: (Dict[Text,Any]) -> List[Text]
             if binding.get("itemSeparator"):
                 l = [binding["itemSeparator"].join([self.tostr(v) for v in value])]
             elif binding.get("valueFrom"):
-                value = [v["path"] if isinstance(v, dict) and v.get("class") == "File" else v for v in value]
+                value = [self.tostr(v) for v in value]
                 return ([prefix] if prefix else []) + value
             elif prefix:
                 return [prefix]
diff --git a/cwltool/main.py b/cwltool/main.py
index 5ca672f0a..e8c9f214a 100755
--- a/cwltool/main.py
+++ b/cwltool/main.py
@@ -237,45 +237,30 @@ def output_callback(out, processStatus):
     return final_output[0]
 
 
-class FileAction(argparse.Action):
+class FSAction(argparse.Action):
+    objclass = None  # type: Text
 
     def __init__(self, option_strings, dest, nargs=None, **kwargs):
         # type: (List[Text], Text, Any, **Any) -> None
         if nargs is not None:
             raise ValueError("nargs not allowed")
-        super(FileAction, self).__init__(option_strings, dest, **kwargs)
+        super(FSAction, self).__init__(option_strings, dest, **kwargs)
 
     def __call__(self, parser, namespace, values, option_string=None):
         # type: (argparse.ArgumentParser, argparse.Namespace, Union[AnyStr, Sequence[Any], None], AnyStr) -> None
         setattr(namespace,
             self.dest,  # type: ignore
-            {"class": "File",
+            {"class": self.objclass,
              "location": "file://%s" % os.path.abspath(cast(AnyStr, values))})
 
-
-class DirectoryAction(argparse.Action):
+class FSAppendAction(argparse.Action):
+    objclass = None  # type: Text
 
     def __init__(self, option_strings, dest, nargs=None, **kwargs):
         # type: (List[Text], Text, Any, **Any) -> None
         if nargs is not None:
             raise ValueError("nargs not allowed")
-        super(DirectoryAction, self).__init__(option_strings, dest, **kwargs)
-
-    def __call__(self, parser, namespace, values, option_string=None):
-        # type: (argparse.ArgumentParser, argparse.Namespace, Union[AnyStr, Sequence[Any], None], AnyStr) -> None
-        setattr(namespace,
-            self.dest,  # type: ignore
-            {"class": "Directory",
-             "location": "file://%s" % os.path.abspath(cast(AnyStr, values))})
-
-
-class FileAppendAction(argparse.Action):
-
-    def __init__(self, option_strings, dest, nargs=None, **kwargs):
-        # type: (List[Text], Text, Any, **Any) -> None
-        if nargs is not None:
-            raise ValueError("nargs not allowed")
-        super(FileAppendAction, self).__init__(option_strings, dest, **kwargs)
+        super(FSAppendAction, self).__init__(option_strings, dest, **kwargs)
 
     def __call__(self, parser, namespace, values, option_string=None):
         # type: (argparse.ArgumentParser, argparse.Namespace, Union[AnyStr, Sequence[Any], None], AnyStr) -> None
@@ -288,9 +273,20 @@ def __call__(self, parser, namespace, values, option_string=None):
                     self.dest,  # type: ignore
                     g)
         g.append(
-            {"class": "File",
+            {"class": self.objclass,
              "location": "file://%s" % os.path.abspath(cast(AnyStr, values))})
 
+class FileAction(FSAction):
+    objclass = "File"
+
+class DirectoryAction(FSAction):
+    objclass = "Directory"
+
+class FileAppendAction(FSAppendAction):
+    objclass = "File"
+
+class DirectoryAppendAction(FSAppendAction):
+    objclass = "Directory"
 
 def generate_parser(toolparser, tool, namemap):
     # type: (argparse.ArgumentParser, Process, Dict[Text, Text]) -> argparse.ArgumentParser
@@ -330,6 +326,8 @@ def generate_parser(toolparser, tool, namemap):
         elif isinstance(inptype, dict) and inptype["type"] == "array":
             if inptype["items"] == "File":
                 action = cast(argparse.Action, FileAppendAction)
+            elif inptype["items"] == "Directory":
+                action = cast(argparse.Action, DirectoryAppendAction)
             else:
                 action = "append"
         elif isinstance(inptype, dict) and inptype["type"] == "enum":