Merge b0c1c8b into b242d59

chanzuckerberg · Nov 17, 2019 · 2760237 · 2760237
2 parents b242d59 + b0c1c8b
commit 2760237
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Showing 3 changed files with 16 additions and 6 deletions.
diff --git a/WDL/Lint.py b/WDL/Lint.py
@@ -717,15 +717,24 @@ class UnnecessaryQuantifier(Linter):
     # A declaration like T? x = :T: where the right-hand side can't be null.
     # The optional quantifier is unnecessary except within a task/workflow
     # input section (where it denotes that the default value can be overridden
-    # by expressly passing null)
+    # by expressly passing null). Another exception is File? outputs of tasks,
+    # e.g. File? optional_file_output = "filename.txt"
 
     def decl(self, obj: Tree.Decl) -> Any:
         if obj.type.optional and obj.expr and not obj.expr.type.optional:
             tw = obj
             while not isinstance(tw, (Tree.Task, Tree.Workflow)):
                 tw = getattr(tw, "parent")
             assert isinstance(tw, (Tree.Task, Tree.Workflow))
-            if isinstance(tw.inputs, list) and obj not in tw.inputs:
+            if (
+                isinstance(tw.inputs, list)
+                and obj not in tw.inputs
+                and not (
+                    isinstance(tw, Tree.Task)
+                    and isinstance(obj.type, Type.File)
+                    and obj in tw.outputs
+                )
+            ):
                 self.add(
                     obj,
                     "unnecessary optional quantifier (?) for non-input {} {}".format(

diff --git a/test_corpi/contrived/contrived.wdl b/test_corpi/contrived/contrived.wdl
@@ -57,5 +57,6 @@ task popular {
         Array[String] nums = [1]
         String left_contents = contents.left
         String right_contents = contents.right
+        File? optional_file = "nonexistent.txt"
     }
 }
diff --git a/tests/test_3corpi.py b/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={'OptionalCoercion': 9, 'StringCoercion': 14, 'UnusedDeclaration': 18, 'UnnecessaryQuantifier': 41, 'NonemptyCoercion': 1, 'NameCollision': 1, 'SelectArray': 1},
+    expected_lint={'OptionalCoercion': 9, 'StringCoercion': 14, 'UnusedDeclaration': 18, 'NonemptyCoercion': 1, 'NameCollision': 1, 'SelectArray': 1},
 )
 class BioWDLTasks(unittest.TestCase):
     pass
 
 @wdl_corpus(
     ["test_corpi/biowdl/aligning/**"],
-    expected_lint={'OptionalCoercion': 12, 'StringCoercion': 14, 'UnusedDeclaration': 12, 'UnnecessaryQuantifier': 41, 'NonemptyCoercion': 1, 'NameCollision': 1},
+    expected_lint={'OptionalCoercion': 12, 'StringCoercion': 14, 'UnusedDeclaration': 12, 'NonemptyCoercion': 1, 'NameCollision': 1},
     check_quant=False,
 )
 class BioWDLAligning(unittest.TestCase):
     pass
 
 @wdl_corpus(
     ["test_corpi/biowdl/expression-quantification/**"],
-    expected_lint={'OptionalCoercion': 11, 'StringCoercion': 14, 'UnusedDeclaration': 12, 'UnnecessaryQuantifier': 41, 'NonemptyCoercion': 3, 'NameCollision': 1},
+    expected_lint={'OptionalCoercion': 11, 'StringCoercion': 14, 'UnusedDeclaration': 12, 'NonemptyCoercion': 3, 'NameCollision': 1},
     check_quant=False,
 )
 class BioWDLExpressionQuantification(unittest.TestCase):
     pass
 
 @wdl_corpus(
     ["test_corpi/biowdl/somatic-variantcalling"],
-    expected_lint={'UnusedImport': 2, 'OptionalCoercion': 11, 'StringCoercion': 16, 'UnusedDeclaration': 11, 'UnnecessaryQuantifier': 166, 'NonemptyCoercion': 37, 'SelectArray': 5},
+    expected_lint={'UnusedImport': 2, 'OptionalCoercion': 11, 'StringCoercion': 16, 'UnusedDeclaration': 11, 'NonemptyCoercion': 37, 'SelectArray': 5},
     check_quant=False,
 )
 class BioWDLSomaticVariantCalling(unittest.TestCase):