Only pass formal params (#765)

* Only pass formal parameters to workflow step.

Parameters which are connected to the workflow step but do not
correspond to a parameter of the tool run by the step should not
appear in the input object.

* Add static checker warning for connections that don't correspond to
tool input parameter.

Author: tetron

cwltool/checker.py

@@ -67,6 +67,8 @@ def can_assign_src_to_sink(src, sink, strict=False):  # type: (Any, Any, bool) -
     if src == "Any" or sink == "Any":
         return True
     if isinstance(src, dict) and isinstance(sink, dict):
+        if sink.get("not_connected") and strict:
+            return False
         if src["type"] == "array" and sink["type"] == "array":
             return can_assign_src_to_sink(src["items"], sink["items"], strict)
         elif src["type"] == "record" and sink["type"] == "record":
@@ -127,8 +129,8 @@ def _rec_fields(rec):  # type: (Dict[Text, Any]) -> Dict[Text, Any]
             return False
     return True
 
-def static_checker(workflow_inputs, workflow_outputs, step_inputs, step_outputs):
-    # type: (List[Dict[Text, Any]], List[Dict[Text, Any]], List[Dict[Text, Any]], List[Dict[Text, Any]]) -> None
+def static_checker(workflow_inputs, workflow_outputs, step_inputs, step_outputs, param_to_step):
+    # type: (List[Dict[Text, Any]], List[Dict[Text, Any]], List[Dict[Text, Any]], List[Dict[Text, Any]], Dict[Text, Dict[Text, Any]]) -> None
     """Check if all source and sink types of a workflow are compatible before run time.
     """
 
@@ -165,6 +167,13 @@ def static_checker(workflow_inputs, workflow_outputs, step_inputs, step_outputs)
                     "source '%s' does not include secondaryFiles." % (shortname(src["id"])))
             msg4 = SourceLine(src, "id").makeError("To fix, add secondaryFiles: %s to definition of '%s'." % (sink.get("secondaryFiles"), shortname(src["id"])))
             msg = SourceLine(sink).makeError("%s\n%s" % (msg1, bullets([msg2, msg3, msg4], "  ")))
+        elif sink.get("not_connected"):
+            msg = SourceLine(sink, "type").makeError(
+                "'%s' is not an input parameter of %s, expected %s"
+                % (shortname(sink["id"]), param_to_step[sink["id"]]["run"],
+                   ", ".join(shortname(s["id"])
+                             for s in param_to_step[sink["id"]]["inputs"]
+                             if not s.get("not_connected"))))
         else:
             msg = SourceLine(src, "type").makeError(
                 "Source '%s' of type %s may be incompatible"

cwltool/workflow.py

@@ -446,12 +446,15 @@ def __init__(self, toolpath_object, **kwargs):
 
         step_inputs = []  # type: List[Any]
         step_outputs = []  # type: List[Any]
+        param_to_step = {}  # type: Dict[Text, Dict[Text, Any]]
         for step in self.steps:
             step_inputs.extend(step.tool["inputs"])
             step_outputs.extend(step.tool["outputs"])
+            for s in step.tool["inputs"]:
+                param_to_step[s["id"]] = step.tool
 
         if kwargs.get("do_validate", True):
-            static_checker(workflow_inputs, workflow_outputs, step_inputs, step_outputs)
+            static_checker(workflow_inputs, workflow_outputs, step_inputs, step_outputs, param_to_step)
 
 
     def job(self,
@@ -539,6 +542,7 @@ def __init__(self, toolpath_object, pos, **kwargs):
                 if not found:
                     if stepfield == "in":
                         param["type"] = "Any"
+                        param["not_connected"] = True
                     else:
                         validation_errors.append(
                             SourceLine(self.tool["out"], n).makeError(
@@ -629,7 +633,8 @@ def job(self,
         for i in self.tool["inputs"]:
             p = i["id"]
             field = shortname(p)
-            job_order[field] = job_order[i["id"]]
+            if not i.get("not_connected"):
+                job_order[field] = job_order[i["id"]]
             del job_order[i["id"]]
 
         try: