subworkflow input namespacing

WDL/Lint.py

@@ -478,7 +478,6 @@ def call(self, obj: Tree.Call) -> Any:
 class NameCollision(Linter):
     # Name collisions between
     # - call and import
-    # - call and its containing workflow
     # - call and struct type/alias
     # - decl and import
     # - decl and workflow
@@ -503,13 +502,10 @@ def call(self, obj: Tree.Call) -> Any:
             if imp.namespace == obj.name:
                 msg = "call name '{}' collides with imported document namespace".format(obj.name)
                 self.add(obj, msg)
-        if doc.workflow and doc.workflow.name == obj.name:
-            msg = "call name '{}' collides with workflow name".format(obj.name)
-            self.add(obj, msg)
         for stb in doc.struct_typedefs:
             assert isinstance(stb, Env.Binding) and isinstance(stb.value, Tree.StructTypeDef)
             if stb.name == obj.name:
-                msg = "call name '{}' colides with {}struct type".format(
+                msg = "call name '{}' collides with {}struct type".format(
                     obj.name, "imported " if stb.value.imported else ""
                 )
                 self.add(obj, msg)

WDL/Tree.py

@@ -483,6 +483,11 @@ def resolve(self, doc: "Document") -> None:
                         self.callee = task
         if self.callee is None:
             raise Error.NoSuchTask(self, ".".join(self.callee_id))
+        assert doc.workflow
+        if self.name == doc.workflow.name:
+            raise Error.MultipleDefinitions(
+                self, "Call's name may not equal the containing workflow's"
+            )
         assert isinstance(self.callee, (Task, Workflow))
 
     def add_to_type_env(

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:

test_corpi/contrived/contrived.wdl

@@ -17,7 +17,7 @@ workflow contrived {
         Float required
     }
     Int? fallaciously_optional = 123
-    call popular as contrived { input:
+    call popular as c1 { input:
         popular = popular,
         i = fortytwo,
         y = [select_first([fortytwo,23])]
@@ -28,8 +28,8 @@ workflow contrived {
     Pair[Pair[String,String],Pair[Int,Int]] p2 = ((c2.left_contents, c2.right_contents), (4,2))
 
     output {
-        Int read_int = read_json(contrived.json) + p2.right.left + p2.right.right
-        Array[Boolean] read_array = read_json(contrived.json)
+        Int read_int = read_json(c1.json) + p2.right.left + p2.right.right
+        Array[Boolean] read_array = read_json(c1.json)
         String left_contents = p2.left.left
         String right_contents = p2.left.right
     }

tests/test_2calls.py

@@ -319,6 +319,15 @@ def test_collision(self):
         with self.assertRaises(WDL.Error.MultipleDefinitions):
             doc.typecheck()
 
+        txt = task_no_outputs + r"""
+        workflow contrived {
+            call p as contrived
+        }
+        """
+        doc = WDL.parse_document(txt)
+        with self.assertRaises(WDL.Error.MultipleDefinitions):
+            doc.typecheck()
+
     def test_if_defined(self):
         # test how we typecheck a construct like
         #   if defined(x) then EXPR_WITH_x else SOME_DEFAULT
@@ -497,8 +506,8 @@ def test_io_propagation(self):
         doc.workflow.available_inputs.resolve("popular")
         doc.workflow.available_inputs.resolve("fortytwo")
         doc.workflow.available_inputs.resolve("required")
-        self.assertTrue(doc.workflow.available_inputs.has_namespace("contrived"))
-        doc.workflow.available_inputs.resolve("contrived.opt")
+        self.assertTrue(doc.workflow.available_inputs.has_namespace("c1"))
+        doc.workflow.available_inputs.resolve("c1.opt")
         self.assertTrue(doc.workflow.available_inputs.has_namespace("c2"))
         doc.workflow.available_inputs.enter_namespace("c2").resolve("opt")
         doc.workflow.available_inputs.enter_namespace("c2").resolve("i")

tests/test_3corpi.py

@@ -247,15 +247,15 @@ class dxWDL(unittest.TestCase):
 
 @wdl_corpus(
     ["test_corpi/contrived/**"],
-    expected_lint={'UnusedImport': 4, 'NameCollision': 30, 'StringCoercion': 4, 'FileCoercion': 2, 'NonemptyCoercion': 1, 'UnnecessaryQuantifier': 2, 'UnusedDeclaration': 2, "IncompleteCall": 2, 'SelectArray': 1},
+    expected_lint={'UnusedImport': 4, 'NameCollision': 27, 'StringCoercion': 4, 'FileCoercion': 2, 'NonemptyCoercion': 1, 'UnnecessaryQuantifier': 2, 'UnusedDeclaration': 2, "IncompleteCall": 2, 'SelectArray': 1},
     blacklist=["check_quant", "incomplete_call"],
 )
 class Contrived(unittest.TestCase):
     pass
 
 @wdl_corpus(
     ["test_corpi/contrived/**"],
-    expected_lint={'UnusedImport': 6, 'NameCollision': 49, 'StringCoercion': 9, 'FileCoercion': 4, 'OptionalCoercion': 3, 'NonemptyCoercion': 2, 'UnnecessaryQuantifier': 4, 'UnusedDeclaration': 9, 'IncompleteCall': 3, 'ArrayCoercion': 2, 'SelectArray': 4},
+    expected_lint={'UnusedImport': 6, 'NameCollision': 43, 'StringCoercion': 9, 'FileCoercion': 4, 'OptionalCoercion': 3, 'NonemptyCoercion': 2, 'UnnecessaryQuantifier': 4, 'UnusedDeclaration': 9, 'IncompleteCall': 3, 'ArrayCoercion': 2, 'SelectArray': 4},
     check_quant=False,
     blacklist=["incomplete_call"],
 )

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