Fix reverse mapping to set basename & ensure filenames are preserved. (#527)

* Fix reverse mapping to set basename & ensure filenames are preserved.

* Remove spurious Docker volume mount of runtime-created files.

Author: tetron

cwltool/draft2tool.py

@@ -119,38 +119,35 @@ def revmap_file(builder, outdir, f):
     # builder.outdir is the inner (container/compute node) output directory
     # outdir is the outer (host/storage system) output directory
 
-    if "location" in f:
+    if "location" in f and "path" not in f:
         if f["location"].startswith("file://"):
-            path = convert_pathsep_to_unix(uri_file_path(f["location"]))
-            revmap_f = builder.pathmapper.reversemap(path)
-
-            if revmap_f and not builder.pathmapper.mapper(revmap_f[0]).type.startswith("Writable"):
-                f["basename"] = os.path.basename(path)
-                f["location"] = revmap_f[1]
-            elif path == builder.outdir:
-                f["location"] = outdir
-            elif path.startswith(builder.outdir):
-                f["location"] = builder.fs_access.join(outdir, path[len(builder.outdir) + 1:])
-            elif f["location"].startswith(outdir):
-                revmap_f = builder.pathmapper.reversemap(builder.fs_access.join(builder.outdir, f["location"][len(outdir) + 1:]))
-                if revmap_f and not builder.pathmapper.mapper(revmap_f[0]).type.startswith("Writable"):
-                    f["basename"] = os.path.basename(path)
-                    f["location"] = revmap_f[1]
-        return f
+            f["path"] = convert_pathsep_to_unix(uri_file_path(f["location"]))
+        else:
+            return f
 
     if "path" in f:
         path = f["path"]
+        uripath = file_uri(path)
         del f["path"]
+
+        if "basename" not in f:
+            f["basename"] = os.path.basename(path)
+
         revmap_f = builder.pathmapper.reversemap(path)
-        if revmap_f:
+
+        if revmap_f and not builder.pathmapper.mapper(revmap_f[0]).type.startswith("Writable"):
             f["location"] = revmap_f[1]
-            return f
-        elif path.startswith(builder.outdir):
+        elif uripath == outdir or uripath.startswith(outdir+os.sep):
+            f["location"] = file_uri(path)
+        elif path == builder.outdir or path.startswith(builder.outdir+os.sep):
             f["location"] = builder.fs_access.join(outdir, path[len(builder.outdir) + 1:])
-            return f
+        elif not os.path.isabs(path):
+            f["location"] = builder.fs_access.join(outdir, path)
         else:
             raise WorkflowException(u"Output file path %s must be within designated output directory (%s) or an input "
                                     u"file pass through." % (path, builder.outdir))
+        return f
+
 
     raise WorkflowException(u"Output File object is missing both `location` and `path` fields: %s" % f)
 

cwltool/job.py

@@ -342,7 +342,8 @@ def add_volumes(self, pathmapper, runtime, stage_output):
                 createtmp = os.path.join(host_outdir, os.path.basename(vol.target))
                 with open(createtmp, "wb") as f:
                     f.write(vol.resolved.encode("utf-8"))
-                runtime.append(u"--volume=%s:%s:ro" % (docker_windows_path_adjust(createtmp), docker_windows_path_adjust(vol.target)))
+                if not vol.target.startswith(container_outdir):
+                    runtime.append(u"--volume=%s:%s:ro" % (docker_windows_path_adjust(createtmp), docker_windows_path_adjust(vol.target)))
 
 
     def run(self, pull_image=True, rm_container=True,