CLI: allow compound inputs as JSON (#688)

chanzuckerberg · May 1, 2024 · 2086bb9 · 2086bb9
1 parent c4db595
commit 2086bb9
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Showing 2 changed files with 11 additions and 5 deletions.
diff --git a/WDL/CLI.py b/WDL/CLI.py
@@ -1260,6 +1260,16 @@ def runner_input_value(s_value, ty, downloadable, root):
         return Value.Array(
             ty.item_type, [runner_input_value(s_value, ty.item_type, downloadable, root)]
         )
+    if isinstance(ty, (Type.Pair, Type.Map, Type.StructInstance)):
+        # parse JSON for compound types
+        try:
+            return Value.from_json(ty, json.loads(s_value))
+        except json.JSONDecodeError as exn:
+            raise Error.InputError(
+                "Invalid JSON for input of type {}, check syntax and shell quoting: {}".format(
+                    str(ty), exn
+                )
+            )
     if isinstance(ty, Type.Any):
         # infer dynamically-typed runtime overrides
         try:

diff --git a/tests/runner.t b/tests/runner.t
@@ -621,9 +621,5 @@ task test_task {
     >>>
 }
 EOF
-$miniwdl run issue686.wdl -i '{
-    "read_group": {
-        "ID": "test"
-    }
-}'
+$miniwdl run issue686.wdl read_group='{"ID":"test"}'
 is "$?" "0" "ensure optional fields in structs initialized from JSON (issue 686 regression)"