[WDL 1.2] override task requirements in inputs

Author: mlin

WDL/CLI.py

@@ -1035,11 +1035,21 @@ def runner_input(
         decl = available_inputs.get(name)
 
         if not decl:
-            # allow arbitrary runtime overrides
+            # allow arbitrary runtime overrides (or "requirements" in WDL 1.2)
             nmparts = name.split(".")
-            runtime_idx = next((i for i, term in enumerate(nmparts) if term in ("runtime",)), -1)
-            if runtime_idx >= 0 and len(nmparts) > (runtime_idx + 1):
-                decl = available_inputs.get(".".join(nmparts[:runtime_idx] + ["_runtime"]))
+            for override in (
+                "requirements",
+                "runtime",
+            ):
+                runtime_idx = next(
+                    (i for i, term in enumerate(nmparts) if term == override),
+                    -1,
+                )
+                if runtime_idx >= 0 and len(nmparts) > (runtime_idx + 1):
+                    if decl := available_inputs.get(
+                        ".".join(nmparts[:runtime_idx] + ["_" + override])
+                    ):
+                        break
 
         if not decl:
             runner_input_help(target)

WDL/Tree.py

@@ -338,6 +338,8 @@ def available_inputs(self) -> Env.Bindings[Decl]:
         if self.effective_wdl_version not in ("draft-2", "1.0"):
             # synthetic placeholder to expose runtime overrides
             ans = ans.bind("_runtime", Decl(self.pos, Type.Any(), "_runtime"))
+            if self.effective_wdl_version not in ("1.1",):
+                ans = ans.bind("_requirements", Decl(self.pos, Type.Any(), "_requirements"))
 
         for decl in reversed(self.inputs if self.inputs is not None else self.postinputs):
             ans = ans.bind(decl.name, decl)

WDL/__init__.py

@@ -244,17 +244,29 @@ def values_from_json(
             else:
                 key2parts = key2.split(".")
 
-                runtime_idx = next(
-                    (i for i, term in enumerate(key2parts) if term in ("runtime",)), -1
-                )
+                for override in (
+                    "requirements",
+                    "runtime",
+                ):
+                    runtime_idx = next(
+                        (i for i, term in enumerate(key2parts) if term == override),
+                        -1,
+                    )
+                    if (
+                        runtime_idx >= 0
+                        and len(key2parts) > (runtime_idx + 1)
+                        and ".".join(key2parts[:runtime_idx] + ["_" + override]) in available
+                    ):
+                        # allow arbitrary keys for runtime
+                        ty = Type.Any()
+
                 if (
-                    runtime_idx >= 0
-                    and len(key2parts) > (runtime_idx + 1)
-                    and ".".join(key2parts[:runtime_idx] + ["_runtime"]) in available
+                    not ty
+                    and len(key2parts) == 3
+                    and key2parts[0]
+                    and key2parts[1]
+                    and key2parts[2]
                 ):
-                    # allow arbitrary keys for runtime
-                    ty = Type.Any()
-                elif len(key2parts) == 3 and key2parts[0] and key2parts[1] and key2parts[2]:
                     # attempt to simplify <call>.<subworkflow>.<input> from old Cromwell JSON
                     key2 = ".".join([key2parts[0], key2parts[2]])
                     if key2 in available:

WDL/runtime/task.py

@@ -501,6 +501,8 @@ def _eval_task_runtime(
         runtime_values[key] = expr.eval(env, stdlib)
     for b in inputs.enter_namespace("runtime"):
         runtime_values[b.name] = b.value  # input overrides
+    for b in inputs.enter_namespace("requirements"):
+        runtime_values[b.name] = b.value
     logger.debug(_("runtime values", **dict((key, str(v)) for key, v in runtime_values.items())))
 
     # have container implementation validate & postprocess into container.runtime_values

tests/runner.t

@@ -11,7 +11,7 @@ source tests/bash-tap/bash-tap-bootstrap
 export PYTHONPATH="$SOURCE_DIR:$PYTHONPATH"
 miniwdl="python3 -m WDL"
 
-plan tests 97
+plan tests 99
 
 $miniwdl run_self_test
 is "$?" "0" "run_self_test"
@@ -372,6 +372,10 @@ is "$?" "0" "directory input"
 is `jq -r '.["w.dsz"]' _LAST/outputs.json` "10" "use of directory input"
 grep -q 20.10 _LAST/out/issue/issue
 is "$?" "0" "override t.runtime.docker"
+$miniwdl run dir_io.wdl d=indir t.requirements.docker=ubuntu:24.04
+is "$?" "0" "directory input 2"
+grep -q 24.04 _LAST/out/issue/issue
+is "$?" "0" "override t.requirements.docker"
 
 cat << 'EOF' > uri_inputs.json
 {

tests/test_7runner.py

@@ -751,7 +751,7 @@ def test_runtime_override(self):
             input {
                 String who
             }
-            call t {
+            call t as tc {
                 input:
                     who = who
             }
@@ -775,9 +775,46 @@ def test_runtime_override(self):
         """
         outp = self._run(wdl, {
             "who": "Alice",
-            "t.runtime.container": ["ubuntu:20.10"]
+            "tc.runtime.container": ["ubuntu:20.10"]
+        })
+        assert "20.10" in outp["tc.issue"]
+
+        outp = self._run(wdl, {
+            "who": "Alice",
+            "tc.requirements.container": ["ubuntu:24.04"]
+        })
+        assert "24.04" in outp["tc.issue"]
+
+    def test_task_named_requirements(self):
+        # "requirements" became a keyword in WDL 1.2, so before that a task or one of its inputs
+        # could be named "requirements" -- ensure that still works as expected
+        wdl = """
+        version 1.1
+        workflow w {
+            call requirements
+        }
+        task requirements {
+            input {
+                Int requirements = 21
+            }
+            command {}
+            output {
+                Int result = requirements
+            }
+            runtime {
+                docker: "ubuntu:24.04"
+            }
+        }
+        """
+        outp = self._run(wdl, {
+            "requirements.requirements": 42
         })
-        assert "20.10" in outp["t.issue"]
+        assert outp["requirements.result"] == 42
+
+        with self.assertRaises(WDL.Error.InputError):
+            outp = self._run(wdl, {
+                "requirements.requirements": "bogus"
+            })
 
 
 class MiscRegressionTests(RunnerTestCase):