X-Git-Url: https://git.arvados.org/arvados.git/blobdiff_plain/93380e6aec7e11607019cdce88419b6f708327d7..a89fbc8b4f2d8db8654175428bd1f041eed6f109:/sdk/cwl/arvados_cwl/runner.py

diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index 50b3bb94d8..f232178c5d 100644
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -129,6 +129,9 @@ def set_secondary(fsaccess, builder, inputschema, secondaryspec, primary, discov
             set_secondary(fsaccess, builder, i, secondaryspec, primary, discovered)
         return
 
+    if inputschema == "File":
+        inputschema = {"type": "File"}
+
     if isinstance(inputschema, basestring):
         sd = search_schemadef(inputschema, reversed(builder.hints+builder.requirements))
         if sd:
@@ -164,10 +167,13 @@ def set_secondary(fsaccess, builder, inputschema, secondaryspec, primary, discov
             set_secondary(fsaccess, builder, {"type": inputschema["items"]}, secondaryspec, p, discovered)
 
     elif (inputschema["type"] == "File" and
-          secondaryspec and
           isinstance(primary, Mapping) and
-          primary.get("class") == "File" and
-          "secondaryFiles" not in primary):
+          primary.get("class") == "File"):
+
+        if "secondaryFiles" in primary or not secondaryspec:
+            # Nothing to do.
+            return
+
         #
         # Found a file, check for secondaryFiles
         #
@@ -175,9 +181,9 @@ def set_secondary(fsaccess, builder, inputschema, secondaryspec, primary, discov
         primary["secondaryFiles"] = secondaryspec
         for i, sf in enumerate(aslist(secondaryspec)):
             if builder.cwlVersion == "v1.0":
-                pattern = builder.do_eval(sf, context=primary)
+                pattern = sf
             else:
-                pattern = builder.do_eval(sf["pattern"], context=primary)
+                pattern = sf["pattern"]
             if pattern is None:
                 continue
             if isinstance(pattern, list):
@@ -214,7 +220,20 @@ def set_secondary(fsaccess, builder, inputschema, secondaryspec, primary, discov
                     "Expression must return list, object, string or null")
 
             if pattern is not None:
-                sfpath = substitute(primary["location"], pattern)
+                if "${" in pattern or "$(" in pattern:
+                    sfname = builder.do_eval(pattern, context=primary)
+                else:
+                    sfname = substitute(primary["basename"], pattern)
+
+                if sfname is None:
+                    continue
+
+                p_location = primary["location"]
+                if "/" in p_location:
+                    sfpath = (
+                        p_location[0 : p_location.rindex("/") + 1]
+                        + sfname
+                    )
 
             required = builder.do_eval(required, context=primary)