19109: test/fix for related bug, finding secondary files with expressions

[arvados.git] / sdk / cwl / arvados_cwl / runner.py

diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index e5a81cdc73fe77238b743705c1dd4c8847240d18..995b23c080c361f5ac387b9ea47e128946fb79e2 100644 (file)
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -128,6 +128,9 @@ 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:
@@ -174,9 +177,9 @@ 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):
@@ -213,7 +216,20 @@ 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)
 
@@ -358,6 +374,7 @@ def upload_dependencies(arvrunner, name, document_loader,
             if "location" not in f and "path" in f:
                 f["location"] = f["path"]
                 del f["path"]
+            normalizeFilesDirs(f)
             optional_deps.append(f)
         visit_class(obj["default"], ("File", "Directory"), defaults_are_optional)