UnusedImport linter: detect use of imported struct typedefs

rename 'called' markers to 'used

WDL/CLI.py

@@ -175,7 +175,7 @@ def descend(dobj=None, first_descent=first_descent):
         if obj.workflow:
             descend(obj.workflow)
         # tasks
-        for task in sorted(obj.tasks, key=lambda task: (not task.called, task.name)):
+        for task in sorted(obj.tasks, key=lambda task: (not task.used, task.name)):
             descend(task)
         # imports
         for imp in sorted(obj.imports, key=lambda t: t.namespace):
@@ -185,7 +185,7 @@ def descend(dobj=None, first_descent=first_descent):
     elif isinstance(obj, Workflow):
         print(
             "{}workflow {}{}".format(
-                s, obj.name, " (not called)" if show_called and not obj.called else ""
+                s, obj.name, " (not called)" if show_called and not obj.used else ""
             ),
             file=file,
         )
@@ -195,7 +195,7 @@ def descend(dobj=None, first_descent=first_descent):
     elif isinstance(obj, Task):
         print(
             "{}task {}{}".format(
-                s, obj.name, " (not called)" if show_called and not obj.called else ""
+                s, obj.name, " (not called)" if show_called and not obj.used else ""
             ),
             file=file,
         )

WDL/Lint.py

@@ -78,7 +78,7 @@ def lint(doc, descend_imports: bool = True):
 
     # Add additional markups to the AST for use by the linters
     Walker.SetParents()(doc)
-    Walker.MarkCalled()(doc)
+    Walker.MarkUsed()(doc)
     Walker.SetReferrers()(doc)
 
     # instantiate linters
@@ -605,15 +605,21 @@ class UnusedImport(Linter):
     def document(self, obj: Tree.Document) -> Any:
         for imp in obj.imports:
             assert imp.doc is not None
-            any_called = False
+            any_used = False
+            for stb in obj.struct_typedefs:
+                st: Tree.StructTypeDef = stb.value
+                if st.imported and st.imported[0] is imp and getattr(st, "used", False):
+                    any_used = True
             for task in imp.doc.tasks:
-                if getattr(task, "called", False):
-                    any_called = True
-            if imp.doc.workflow and getattr(imp.doc.workflow, "called", False):
-                any_called = True
-            if not any_called and (imp.doc.tasks or imp.doc.workflow):
+                if getattr(task, "used", False):
+                    any_used = True
+            if imp.doc.workflow and getattr(imp.doc.workflow, "used", False):
+                any_used = True
+            if not any_used and (imp.doc.tasks or imp.doc.workflow):
                 self.add(
-                    obj, "no calls to tasks/workflow in the imported document " + imp.namespace
+                    obj,
+                    "no calls to tasks/workflow, nor use of structs defined, in the imported document "
+                    + imp.namespace,
                 )
 
 

WDL/Walker.py

@@ -1,6 +1,6 @@
 # pylint: disable=assignment-from-no-return
 from typing import Any, List, Optional
-from . import Error, Expr, Tree
+from . import Error, Expr, Tree, Type
 
 
 class Base:
@@ -236,22 +236,36 @@ def expr(self, obj: Expr.Base) -> None:
         obj.parent = self._parent_stack[-1]
 
 
-class MarkCalled(Base):
+class MarkUsed(Base):
     """
-    Mark each Task and Workflow with ``called : bool`` according to whether
-    there exists a Call to it in the top-level workflow (or a subworkflow it
-    calls). Requires SetParents to have been applied previously.
+    Mark each Task and Workflow with ``used : bool`` according to whether there exists a Call to it
+    in the top-level workflow (or a called sub-workflow). The top-level workflow is considered
+    called.
 
-    The top-level workflow is considered called.
+    Also mark each StructTypeDef used if there exists a Decl instance of it in any workflow,
+    sub-workflow, or task (regardless of whether those are called). If the StructTypeDef is imported
+    from another document, propagate the flag there as well.
+
+    Requires SetParents to have been applied previously.
     """
 
     marking: bool = False  # True while recursing from the top-level workflow
 
+    def document(self, obj: Tree.Document) -> None:
+        for stb in obj.struct_typedefs:
+            st: Tree.StructTypeDef = stb.value
+            st.used = False
+            # if struct has members that are imported structs, mark those used
+            for ty in st.members.values():
+                self._mark_structs(obj, ty, imported_only=True)
+
+        super().document(obj)
+
     def workflow(self, obj: Tree.Workflow) -> None:
-        obj.called = False
+        obj.used = False
         if obj.parent.parent is None:  # pyre-ignore
             assert not self.marking
-            obj.called = True
+            obj.used = True
             self.marking = True
             super().workflow(obj)
             self.marking = False
@@ -262,10 +276,29 @@ def call(self, obj: Tree.Call) -> None:
         assert self.marking
         if isinstance(obj.callee, Tree.Workflow):
             self(obj.callee)
-        obj.callee.called = True
+        obj.callee.used = True
 
     def task(self, obj: Tree.Task) -> None:
-        obj.called = False
+        obj.used = False
+        super().task(obj)
+
+    def decl(self, obj: Tree.Decl) -> None:
+        doc = obj
+        while not isinstance(doc, Tree.Document):
+            doc = getattr(doc, "parent")
+        self._mark_structs(doc, obj.type)
+
+    def _mark_structs(self, doc: Tree.Document, ty: Type.Base, imported_only: bool = False) -> None:
+        if isinstance(ty, Type.StructInstance):
+            st: Tree.StructTypeDef = doc.struct_typedefs[ty.type_name]
+            if not imported_only:
+                st.used = True
+            while st.imported:
+                st.used = True
+                st = st.imported[1]
+                st.used = True
+        for ch in ty.parameters:
+            self._mark_structs(doc, ch, imported_only=imported_only)
 
 
 class SetReferrers(Base):

tests/test_3corpi.py

@@ -268,30 +268,30 @@ class Contrived2(unittest.TestCase):
         # these use the pattern 'input { Type? x = default }' and need check_quant=False
         "mergecounts","somaticseq"
     ],
-    expected_lint={'UnusedImport': 8, 'OptionalCoercion': 9, 'StringCoercion': 14, 'UnusedDeclaration': 18, 'UnnecessaryQuantifier': 41, 'NonemptyCoercion': 1, 'NameCollision': 1, 'SelectArray': 1},
+    expected_lint={'OptionalCoercion': 9, 'StringCoercion': 14, 'UnusedDeclaration': 18, 'UnnecessaryQuantifier': 41, 'NonemptyCoercion': 1, 'NameCollision': 1, 'SelectArray': 1},
 )
 class BioWDLTasks(unittest.TestCase):
     pass
 
 @wdl_corpus(
     ["test_corpi/biowdl/aligning/**"],
-    expected_lint={'UnusedImport': 12, 'OptionalCoercion': 12, 'StringCoercion': 14, 'UnusedDeclaration': 12, 'UnnecessaryQuantifier': 41, 'NonemptyCoercion': 1, 'NameCollision': 1},
+    expected_lint={'OptionalCoercion': 12, 'StringCoercion': 14, 'UnusedDeclaration': 12, 'UnnecessaryQuantifier': 41, 'NonemptyCoercion': 1, 'NameCollision': 1},
     check_quant=False,
 )
 class BioWDLAligning(unittest.TestCase):
     pass
 
 @wdl_corpus(
     ["test_corpi/biowdl/expression-quantification/**"],
-    expected_lint={'UnusedImport': 12, 'OptionalCoercion': 11, 'StringCoercion': 14, 'UnusedDeclaration': 12, 'UnnecessaryQuantifier': 41, 'NonemptyCoercion': 3, 'NameCollision': 1},
+    expected_lint={'OptionalCoercion': 11, 'StringCoercion': 14, 'UnusedDeclaration': 12, 'UnnecessaryQuantifier': 41, 'NonemptyCoercion': 3, 'NameCollision': 1},
     check_quant=False,
 )
 class BioWDLExpressionQuantification(unittest.TestCase):
     pass
 
 @wdl_corpus(
     ["test_corpi/biowdl/somatic-variantcalling"],
-    expected_lint={'UnusedImport': 12, 'OptionalCoercion': 11, 'StringCoercion': 16, 'UnusedDeclaration': 11, 'UnnecessaryQuantifier': 166, 'NonemptyCoercion': 37, 'SelectArray': 5},
+    expected_lint={'UnusedImport': 2, 'OptionalCoercion': 11, 'StringCoercion': 16, 'UnusedDeclaration': 11, 'UnnecessaryQuantifier': 166, 'NonemptyCoercion': 37, 'SelectArray': 5},
     check_quant=False,
 )
 class BioWDLSomaticVariantCalling(unittest.TestCase):