Reverse map internal run files to original path

Handles mapping paths in Docker images and returned through JSON back
to original filesystem paths. Does reverse mapping of inputs as well
as anything in the output directory. Needs to remap at two locations:
before checking for secondaryFiles, and returning the final file
structure.
Fixes #36.

Author: chapmanb

cwltool/draft2tool.py

@@ -11,7 +11,7 @@
 import logging
 import hashlib
 import random
-from process import Process, shortname, uniquename
+from process import Process, shortname, uniquename, adjustFiles
 from errors import WorkflowException
 import schema_salad.validate as validate
 from aslist import aslist
@@ -200,6 +200,20 @@ def collect_output_ports(self, ports, builder, outdir):
             raise WorkflowException("Error validating output record, " + str(e) + "\n in " + json.dumps(ret, indent=4))
 
     def collect_output(self, schema, builder, outdir):
+        def revmap_file(f):
+            """Remap a file back to original path. For Docker, this is outside the container.
+
+            Uses either files in the pathmapper or remaps internal output directories
+            to the external directory.
+            """
+            revmap_f = builder.pathmapper.reversemap(f)
+            if revmap_f:
+                return revmap_f[-1]
+            elif f.startswith(builder.outdir):
+                return f.replace(builder.outdir, outdir)
+            else:
+                return f
+
         r = None
         if "outputBinding" in schema:
             binding = schema["outputBinding"]
@@ -263,6 +277,8 @@ def collect_output(self, schema, builder, outdir):
                         r = r[0]
 
             if "secondaryFiles" in schema:
+                # remap secondaryFiles since we check if they exist
+                adjustFiles(r, revmap_file)
                 for primary in aslist(r):
                     if isinstance(primary, dict):
                         primary["secondaryFiles"] = []
@@ -285,5 +301,6 @@ def collect_output(self, schema, builder, outdir):
             r = {}
             for f in schema["type"]["fields"]:
                 r[shortname(f["name"])] = self.collect_output(f, builder, outdir)
-
+        # Ensure files point to local references outside of the run environment
+        adjustFiles(r, revmap_file)
         return r