Merge aa11870 into c337ac7

WDL/StdLib.py

@@ -579,7 +579,7 @@ def infer_type(self, expr: "Expr.Apply") -> Type.Base:
         if t2 is None:
             # neither operand is a string; defer to _ArithmeticOperator
             return super().infer_type(expr)
-        if not t2.coerces(Type.String(optional=not expr._check_quant)):
+        if not t2.coerces(Type.String(), check_quant=expr._check_quant):
             raise Error.IncompatibleOperand(
                 expr,
                 "Cannot add/concatenate {} and {}".format(

WDL/Type.py

@@ -151,7 +151,7 @@ def __init__(self, optional: bool = False) -> None:
     def check(self, rhs: Base, check_quant: bool = True) -> None:
         """"""
         if isinstance(rhs, String):
-            return
+            return self._check_optional(rhs, check_quant)
         super().check(rhs, check_quant)
 
 
@@ -162,7 +162,7 @@ def __init__(self, optional: bool = False) -> None:
     def check(self, rhs: Base, check_quant: bool = True) -> None:
         """"""
         if isinstance(rhs, String):
-            return
+            return self._check_optional(rhs, check_quant)
         super().check(rhs, check_quant)
 
 
@@ -175,7 +175,7 @@ def check(self, rhs: Base, check_quant: bool = True) -> None:
         if isinstance(rhs, Float):
             return self._check_optional(rhs, check_quant)
         if isinstance(rhs, String):
-            return
+            return self._check_optional(rhs, check_quant)
         super().check(rhs, check_quant)
 
 
@@ -186,7 +186,7 @@ def __init__(self, optional: bool = False) -> None:
     def check(self, rhs: Base, check_quant: bool = True) -> None:
         """"""
         if isinstance(rhs, String):
-            return
+            return self._check_optional(rhs, check_quant)
         super().check(rhs, check_quant)
 
 
@@ -197,7 +197,7 @@ def __init__(self, optional: bool = False) -> None:
     def check(self, rhs: Base, check_quant: bool = True) -> None:
         """"""
         if isinstance(rhs, String):
-            return
+            return self._check_optional(rhs, check_quant)
         super().check(rhs, check_quant)
 
 
@@ -261,7 +261,9 @@ def check(self, rhs: Base, check_quant: bool = True) -> None:
             self.item_type.check(rhs.item_type, check_quant)
             return self._check_optional(rhs, check_quant)
         if isinstance(rhs, String):
-            return None if self.item_type is None else self.item_type.check(String())
+            if self.item_type is not None:
+                self.item_type.check(String())
+            return self._check_optional(rhs, check_quant)
         super().check(rhs, check_quant)
 
     def copy(self, optional: Optional[bool] = None, nonempty: Optional[bool] = None) -> Base:

tests/test_3corpi.py

@@ -425,7 +425,7 @@ class Contrived(unittest.TestCase):
         "NameCollision": 43,
         "StringCoercion": 11,
         "FileCoercion": 5,
-        "OptionalCoercion": 3,
+        "OptionalCoercion": 4,
         "NonemptyCoercion": 2,
         "UnnecessaryQuantifier": 9,
         "UnusedDeclaration": 9,
@@ -451,14 +451,16 @@ class Contrived2(unittest.TestCase):
         # these use the pattern 'input { Type? x = default }' and need check_quant=False
         "mergecounts",
         "somaticseq",
+        "bamstats",
+        "biopet",
+        "sampleconfig",
+        "seqstat",
     ],
     expected_lint={
-        "OptionalCoercion": 9,
-        "UnusedDeclaration": 18,
+        "OptionalCoercion": 2,
+        "UnusedDeclaration": 15,
         "NonemptyCoercion": 1,
-        "NameCollision": 1,
         "SelectArray": 1,
-        "UnverifiedStruct": 1,
         "UnnecessaryQuantifier": 8,
     },
 )

tests/test_7runner.py

@@ -926,6 +926,34 @@ def test_spec_select_all_wdl(self):
         self.assertEqual(outp["fivethree"], [5, 3])
         self.assertEqual(outp["is_true"], True)
 
+    def test_issue596(self):
+        self._run("""
+        task reference_prepare {
+            input {
+                # You need to define either this...
+                File? reference_fa_file
+
+                # Or both of these.
+                File?   reference_zipped_directory
+                String? reference_fa_filename_in_zipped_directory
+            }
+
+            # get the basename of the reference
+            String? basename_reference = basename(reference_zipped_directory)
+
+            command <<<
+                set -eux -o pipefail
+
+                if [[ ! "~{reference_zipped_directory}" = "" ]]
+                then
+                    cp ~{reference_zipped_directory} .
+                    unzip ~{basename_reference}
+                fi
+
+                # do other things here
+            >>>
+        }""", {}, expected_exception=WDL.Error.StaticTypeMismatch)
+
 class TestInlineDockerfile(RunnerTestCase):
     @log_capture()
     def test1(self, capture):