CLI runtime overrides

Author: mlin

WDL/CLI.py

@@ -877,20 +877,26 @@ def runner_input(
         name, s_value = buf
 
         # find corresponding input declaration
-        try:
-            decl = available_inputs[name]
-        except KeyError:
+        decl = available_inputs.get(name)
+
+        if not decl:
+            # allow arbitrary runtime/hints overrides
+            nmparts = name.split(".")
+            runtime_idx = next(
+                (i for i, term in enumerate(nmparts) if term in ("runtime", "hints")), -1
+            )
+            if runtime_idx >= 0 and len(nmparts) > (runtime_idx + 1):
+                decl = available_inputs.get(".".join(nmparts[:runtime_idx] + ["_runtime"]))
+
+        if not decl:
             runner_input_help(target)
             raise Error.InputError(f"No such input to {target.name}: {buf[0]}")
 
         # create a Value based on the expected type
         v = runner_input_value(s_value, decl.type, downloadable, root)
 
         # insert value into input_env
-        try:
-            existing = input_env[name]
-        except KeyError:
-            existing = None
+        existing = input_env.get(name)
         if existing:
             if isinstance(v, Value.Array):
                 assert isinstance(existing, Value.Array) and v.type.coerces(existing.type)
@@ -1053,6 +1059,17 @@ def runner_input_value(s_value, ty, downloadable, root):
         return Value.Array(
             ty.item_type, [runner_input_value(s_value, ty.item_type, downloadable, root)]
         )
+    if isinstance(ty, Type.Any):
+        # infer dynamically-typed runtime/hints overrides
+        try:
+            return Value.Int(int(s_value))
+        except ValueError:
+            pass
+        try:
+            return Value.Float(float(s_value))
+        except ValueError:
+            pass
+        return Value.String(s_value)
     raise Error.InputError(
         "No command-line support yet for inputs of type {}; workaround: specify in JSON file with --input".format(
             str(ty)

WDL/Env.py

@@ -105,6 +105,16 @@ def resolve_binding(self, name: str) -> Binding[T]:
                 return b
         raise KeyError()
 
+    def get(self, name: str, default: Optional[T] = None) -> Optional[T]:
+        """
+        Look up a bound value by name, returning the default value or ``None`` if there's no such
+        binding.
+        """
+        try:
+            return self.resolve_binding(name).value
+        except KeyError:
+            return default
+
     def resolve(self, name: str) -> T:
         """
         Look up a bound value by name. Equivalently, ``env[name]``

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 72
+plan tests 74
 
 $miniwdl run_self_test
 is "$?" "0" "run_self_test"
@@ -202,7 +202,7 @@ is "$?" "0" "failer2000 try3 iwuzhere"
 
 
 cat << 'EOF' > multitask.wdl
-version 1.0
+version development
 workflow multi {
     call first
 }
@@ -219,16 +219,20 @@ task first {
 task second {
     command {
         echo -n two
+        cp /etc/issue issue
     }
     output {
         String msg = read_string(stdout())
+        File issue = "issue"
     }
 }
 EOF
 
-$miniwdl run multitask.wdl --task second
+$miniwdl run multitask.wdl runtime.docker=ubuntu:20.10 --task second
 is "$?" "0" "multitask"
 is "$(jq -r '.["second.msg"]' _LAST/outputs.json)" "two" "multitask stdout & _LAST"
+grep -q 20.10 _LAST/out/issue/issue
+is "$?" "0" "override runtime.docker"
 
 cat << 'EOF' > mv_input_file.wdl
 version 1.0
@@ -261,28 +265,33 @@ workflow w {
     }
     output {
         Int dsz = round(size(t.files))
+        File issue = t.issue
     }
 }
 task t {
     input {
         Directory d
     }
     command <<<
+        cp /etc/issue issue
         mkdir outdir
         find ~{d} -type f | xargs -i{} cp {} outdir/
     >>>
     output {
         Array[File] files = glob("outdir/*")
+        File issue = "issue"
     }
 }
 EOF
 
 mkdir -p indir/subdir
 echo alice > indir/alice.txt
 echo bob > indir/subdir/bob.txt
-$miniwdl run dir_io.wdl d=indir
+$miniwdl run dir_io.wdl d=indir t.runtime.docker=ubuntu:20.10
 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"
 
 cat << 'EOF' > uri_inputs.json
 {