allow expression in the inputBinding.position

Author: mr-c

cwltool/builder.py

@@ -195,6 +195,7 @@ def bind_input(self,
                    discover_secondaryFiles,  # type: bool
                    lead_pos=None,            # type: Optional[Union[int, List[int]]]
                    tail_pos=None,            # type: Optional[List[int]]
+                   cwl_version=None          # type: Optional[Text]
                   ):  # type: (...) -> List[MutableMapping[Text, Any]]
 
         if tail_pos is None:
@@ -211,7 +212,12 @@ def bind_input(self,
 
             bp = list(aslist(lead_pos))
             if "position" in binding:
-                bp.extend(aslist(binding["position"]))
+                position = binding["position"]
+                if isinstance(position, str) and cwl_version != "v1.0":
+                    binding['position'] = self.do_eval(position, context=datum)
+                    bp.append(binding['position'])
+                else:
+                    bp.extend(aslist(binding['position']))
             else:
                 bp.append(0)
             bp.extend(aslist(tail_pos))

cwltool/process.py

@@ -703,9 +703,13 @@ def inc(d):  # type: (List[int]) -> None
                           tmpdir,
                           stagedir)
 
+        cwl_version = self.metadata.get(
+            "http://commonwl.org/cwltool#original_cwlVersion", None)
+
         bindings.extend(builder.bind_input(
             self.inputs_record_schema, job,
-            discover_secondaryFiles=getdefault(runtime_context.toplevel, False)))
+            discover_secondaryFiles=getdefault(runtime_context.toplevel, False),
+            cwl_version=cwl_version))
 
         if self.tool.get("baseCommand"):
             for index, command in enumerate(aslist(self.tool["baseCommand"])):
@@ -722,7 +726,12 @@ def inc(d):  # type: (List[int]) -> None
                 if isinstance(arg, MutableMapping):
                     arg = copy.deepcopy(arg)
                     if arg.get("position"):
-                        arg["position"] = [arg["position"], i]
+                        position = arg.get("position")
+                        if isinstance(position, str) and cwl_version != "v1.0":
+                            position = builder.do_eval(position)
+                            if position is None:
+                                position = 0
+                        arg["position"] = [position, i]
                     else:
                         arg["position"] = [0, i]
                     bindings.append(arg)