test optional inputs

WDL/runtime/task.py

@@ -13,9 +13,6 @@
 import WDL
 
 
-# InputError
-
-
 class CommandError(WDL.Error.RuntimeError):
     pass
 
@@ -446,29 +443,37 @@ def map_files(v: WDL.Value.Base) -> WDL.Value.Base:
         posix_inputs, lambda namespace, binding: map_files(copy.deepcopy(binding.rhs))
     )
 
-    # Collect task declarations requiring evaluation.
-    decls_to_eval = {}
+    # initialize value environment with the inputs
+    container_env = []
+    for b in container_inputs:
+        assert isinstance(b, WDL.Env.Binding)
+        v = b.rhs
+        assert isinstance(v, WDL.Value.Base)
+        container_env = WDL.Env.bind(container_env, [], b.name, v)
+        vj = json.dumps(v.json)
+        logger.info("input {} -> {}".format(b.name, vj if len(vj) < 4096 else "(large)"))
+
+    # collect remaining declarations requiring evaluation.
+    decls_to_eval = []
     for decl in (task.inputs or []) + (task.postinputs or []):
         try:
-            WDL.Env.resolve(container_inputs, [], decl.name)
+            WDL.Env.resolve(container_env, [], decl.name)
         except KeyError:
-            decls_to_eval[decl.name] = decl
+            decls_to_eval.append(decl)
 
     # TODO: topsort decls_to_eval according to internal dependencies
 
-    container_env = container_inputs
-    for b in container_env:
-        assert isinstance(b, WDL.Env.Binding)
-        logger.info("input {} -> {}".format(b.name, json.dumps(b.rhs.json)))
-
     # evaluate each declaration in order
     # note: the write_* functions call container.add_files as a side-effect
     stdlib = container.stdlib_input()
-    for decl in decls_to_eval.values():
+    for decl in decls_to_eval:
         v = WDL.Value.Null()
         if decl.expr:
             v = decl.expr.eval(container_env, stdlib=stdlib)
-        logger.info("eval {} -> {}".format(decl.name, json.dumps(v.json)))
+        else:
+            assert decl.type.optional
+        vj = json.dumps(v.json)
+        logger.info("eval {} -> {}".format(decl.name, vj if len(vj) < 4096 else "(large)"))
         container_env = WDL.Env.bind(container_env, [], decl.name, v)
 
     return container_env

tests/test_5taskrun.py

@@ -300,3 +300,49 @@ def test_compound_files(self):
             self.assertEqual(infile.read(), "Alyssa,")
         with open(friends.value[1].value) as infile:
             self.assertEqual(infile.read(), "Ben,")
+
+    def test_optional_inputs(self):
+        code = R"""
+        version 1.0
+        task defaults {
+            input {
+                String s0
+                String s1 = "ben"
+                String? s2
+            }
+            command {
+                echo "~{s0}"
+                echo "~{s1}"
+                echo "~{if (defined(s2)) then s2 else 'None'}"
+            }
+            output {
+                String out = read_string(stdout())
+            }
+        }
+        """
+        outputs = self._test_task(code, WDL.Env.bind([], [], "s0", WDL.Value.String("alyssa")))
+        self.assertEqual(WDL.Env.resolve(outputs, [], "out").value, "alyssa\nben\nNone\n")
+
+        outputs = self._test_task(code,
+            WDL.Env.bind(WDL.Env.bind([], [], "s1", WDL.Value.String("cy")),
+                            [], "s0", WDL.Value.String("alyssa")))
+        self.assertEqual(WDL.Env.resolve(outputs, [], "out").value, "alyssa\ncy\nNone\n")
+
+        outputs = self._test_task(code,
+            WDL.Env.bind(WDL.Env.bind([], [], "s2", WDL.Value.String("mallory")),
+                            [], "s0", WDL.Value.String("alyssa")))
+        self.assertEqual(WDL.Env.resolve(outputs, [], "out").value, "alyssa\nben\nmallory\n")
+
+        # FIXME: need some restrictions on what File inputs can default to
+        self._test_task(R"""
+        version 1.0
+        task hacker {
+            File host_passwords = "/etc/passwd"
+            command {
+                >&2 cat "~{host_passwords}"
+            }
+            output {
+                String owned = read_string(stderr())
+            }
+        }
+        """)