WDL.values_from_json: remove extra subworkflow name component from in…

…put keys
chanzuckerberg · Dec 6, 2019 · 4369f07 · 4369f07
1 parent 49456fc
commit 4369f07
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Showing 2 changed files with 19 additions and 0 deletions.
diff --git a/WDL/__init__.py b/WDL/__init__.py
@@ -178,6 +178,11 @@ def values_from_json(
             key2 = key
             if namespace and key.startswith(namespace):
                 key2 = key[len(namespace) :]
+            if key2 not in available:
+                # attempt to simplify <call>.<subworkflow>.<input>
+                key2parts = key2.split(".")
+                if len(key2parts) == 3 and key2parts[0] and key2parts[1] and key2parts[2]:
+                    key2 = ".".join([key2parts[0], key2parts[2]])
             try:
                 ty = available[key2].type
             except KeyError:

diff --git a/tests/test_6workflowrun.py b/tests/test_6workflowrun.py
@@ -580,6 +580,20 @@ def test_subworkflow(self):
         self.assertEqual(outputs["sums"], [1, 5, 14])
         self.assertEqual(outputs["sum"], 20)
 
+        subwf_input = R"""
+        version 1.0
+        import "sum_sq.wdl" as lib
+
+        workflow subwf_input {
+            call lib.sum_sq as summer
+            output {
+                Int ans = summer.ans
+            }
+        }
+        """
+        self._test_workflow(subwf_input, {"summer.n": 3})
+        self._test_workflow(subwf_input, {"summer.sum_sq.n": 3})
+
     def test_host_file_access(self):
         exn = self._test_workflow("""
         version 1.0