19280: Handle expressions that return secondary files

Arvados-DCO-1.1-Signed-off-by: Peter Amstutz <peter.amstutz@curii.com>

diff --git a/sdk/cwl/arvados_cwl/runner.py b/sdk/cwl/arvados_cwl/runner.py
index d2dfcf26bc0e9c8b2b1c98e12f339597ecd5f256..225f4ae60ed9b5cdfe83f9ffa240e8dcf08da5f5 100644 (file)
--- a/sdk/cwl/arvados_cwl/runner.py
+++ b/sdk/cwl/arvados_cwl/runner.py
@@ -253,23 +253,33 @@ def set_secondary(fsaccess, builder, inputschema, secondaryspec, primary, discov
                 if sfname is None:
                     continue
 
-                p_location = primary["location"]
-                if "/" in p_location:
-                    sfpath = (
-                        p_location[0 : p_location.rindex("/") + 1]
-                        + sfname
-                    )
+                if isinstance(sfname, str):
+                    p_location = primary["location"]
+                    if "/" in p_location:
+                        sfpath = (
+                            p_location[0 : p_location.rindex("/") + 1]
+                            + sfname
+                        )
 
             required = builder.do_eval(required, context=primary)
 
-            if fsaccess.exists(sfpath):
-                if pattern is not None:
-                    found.append({"location": sfpath, "class": "File"})
-                else:
-                    found.append(sf)
-            elif required:
-                raise SourceLine(primary["secondaryFiles"], i, validate.ValidationException).makeError(
-                    "Required secondary file '%s' does not exist" % sfpath)
+            if isinstance(sfname, list) or isinstance(sfname, dict):
+                each = aslist(sfname)
+                for e in each:
+                    if required and not fsaccess.exists(e.get("location")):
+                        raise SourceLine(primary["secondaryFiles"], i, validate.ValidationException).makeError(
+                            "Required secondary file '%s' does not exist" % e.get("location"))
+                found.extend(each)
+
+            if isinstance(sfname, str):
+                if fsaccess.exists(sfpath):
+                    if pattern is not None:
+                        found.append({"location": sfpath, "class": "File"})
+                    else:
+                        found.append(sf)
+                elif required:
+                    raise SourceLine(primary["secondaryFiles"], i, validate.ValidationException).makeError(
+                        "Required secondary file '%s' does not exist" % sfpath)
 
         primary["secondaryFiles"] = cmap(found)
         if discovered is not None: