Handled the pickValue in the check_types function to avoid unnecessary warnings.

Author: LanderOtto

cwl_utils/parser/cwl_v1_2_utils.py

@@ -210,6 +210,7 @@ def check_all_types(
         extra_message = (
             "pickValue is %s" % sink.pickValue if sink.pickValue is not None else None
         )
+        sink_type = type_dict[sink.id]
         match sink:
             case cwl.WorkflowOutputParameter():
                 sourceName = "outputSource"
@@ -231,6 +232,8 @@ def check_all_types(
                     srcs_of_sink += [src_dict[parm_id]]
                     if (
                         _is_conditional_step(param_to_step, parm_id)
+                        and "null" != sink_type
+                        and "null" not in sink_type
                         and sink.pickValue is not None
                     ):
                         validation["warning"].append(
@@ -289,8 +292,9 @@ def check_all_types(
             for src in srcs_of_sink:
                 check_result = check_types(
                     type_dict[cast(str, src.id)],
-                    type_dict[sink.id],
+                    sink_type,
                     linkMerge,
+                    sink.pickValue,
                     getattr(sink, "valueFrom", None),
                 )
                 if check_result in ("warning", "exception"):
@@ -304,6 +308,7 @@ def check_types(
     srctype: Any,
     sinktype: Any,
     linkMerge: str | None,
+    pickValue: str | None = None,
     valueFrom: str | None = None,
 ) -> str:
     """
@@ -313,6 +318,26 @@ def check_types(
     """
     if valueFrom is not None:
         return "pass"
+    if pickValue is not None:
+        if isinstance(srctype, cwl.ArraySchema):
+            match pickValue:
+                case "all_non_null":
+                    srctype = cwl.ArraySchema(items=srctype.items, type_="array")
+                    if (
+                        isinstance(srctype.items, MutableSequence)
+                        and "null" in srctype.items
+                    ):
+                        srctype.items.remove("null")
+                case "first_non_null" | "the_only_non_null":
+                    if (
+                        isinstance(srctype.items, MutableSequence)
+                        and "null" in srctype.items
+                    ):
+                        srctype = [elem for elem in srctype.items if elem != "null"]
+                case _:
+                    raise WorkflowException(
+                        f"Unrecognized pickValue enum {pickValue!r}"
+                    )
     if linkMerge is None:
         if can_assign_src_to_sink(srctype, sinktype, strict=True):
             return "pass"
@@ -321,10 +346,10 @@ def check_types(
         return "exception"
     if linkMerge == "merge_nested":
         return check_types(
-            cwl.ArraySchema(items=srctype, type_="array"), sinktype, None, None
+            cwl.ArraySchema(items=srctype, type_="array"), sinktype, None, None, None
         )
     if linkMerge == "merge_flattened":
-        return check_types(merge_flatten_type(srctype), sinktype, None, None)
+        return check_types(merge_flatten_type(srctype), sinktype, None, None, None)
     raise ValidationException(f"Invalid value {linkMerge} for linkMerge field.")