fix size() given a null input

chanzuckerberg · Feb 17, 2020 · 1aa1d3a · 1aa1d3a
1 parent 7a8ba9f
commit 1aa1d3a
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Showing 3 changed files with 14 additions and 2 deletions.
diff --git a/WDL/StdLib.py b/WDL/StdLib.py
@@ -657,12 +657,17 @@ def infer_type(self, expr: "Expr.Apply") -> Type.Base:
 
     def _call_eager(self, expr: "Expr.Apply", arguments: List[Value.Base]) -> Value.Base:
         # this default implementation attempts os.path.getsize() on the argument(s)
-        files = arguments[0].coerce(Type.Array(Type.File()))
+        files = arguments[0].coerce(Type.Array(Type.File(optional=True)))
         unit = arguments[1].coerce(Type.String()) if len(arguments) > 1 else None
 
         ans = []
         for file in files.value:
-            ans.append(os.path.getsize(self.stdlib._devirtualize_filename(file.value)))
+            if isinstance(file, Value.File):
+                ans.append(os.path.getsize(self.stdlib._devirtualize_filename(file.value)))
+            elif isinstance(file, Value.Null):
+                ans.append(0)
+            else:
+                assert False
         ans = float(sum(ans))
 
         if unit:

diff --git a/WDL/Value.py b/WDL/Value.py
@@ -301,6 +301,8 @@ def coerce(self, desired_type: Optional[Type.Base] = None) -> Base:
             # had check_quant=False
             if isinstance(desired_type, Type.String):
                 return String("", self.expr)
+            if isinstance(desired_type, Type.Array) and desired_type.item_type.optional:
+                return Array(desired_type, [self.coerce(desired_type.item_type)], self.expr)
             if self.expr:
                 raise Error.NullValue(self.expr)
             raise Error.InputError("'None' for non-optional input/declaration")

diff --git a/tests/test_5stdlib.py b/tests/test_5stdlib.py
@@ -289,6 +289,7 @@ def test_size(self):
         version 1.0
         task hello {
             Array[File] files
+            File? nullfile
             Array[Float] sizes_ = [
                 size(files[0]),
                 size(files),
@@ -301,6 +302,8 @@ def test_size(self):
             output {
                 Array[Float] sizes = flatten([sizes_, [size(files, "GB"), size(files, "Gi")]])
                 Float size2 = size("alyssa_ben.txt", "KiB")
+                Float nosize1 = size(nullfile)
+                Float nosize2 = size([files[0], nullfile])
             }
         }
         """, {"files": [ os.path.join(self._dir, "alyssa.txt"),
@@ -313,6 +316,8 @@ def test_size(self):
         self.assertAlmostEqual(outputs["sizes"][4], 11/1000000000)
         self.assertAlmostEqual(outputs["sizes"][5], 11/1073741824)
         self.assertAlmostEqual(outputs["size2"], 11/1024)
+        self.assertEqual(outputs["nosize1"], 0)
+        self.assertEqual(outputs["nosize2"], 7)
 
         self._test_task(R"""
         version 1.0