Handle the case where children processes may define requirements with expressions too (fixing conformance test)

Author: kinow

cwltool/workflow.py

@@ -166,16 +166,42 @@ def job(
         # empty/default inputs of a workflow step).
         #
         # The solution below evaluates the requirements and hints for
-        # the workflow, for each step of the workflow, and for the
-        # embedded tool (command-line or expression tools) of each
-        # step.
+        # the workflow (parent), keeping track of the name of the
+        # requirements and hints. For each step of the workflow and of
+        # the embedded tool (command-line or expression tools) it will
+        # then evaluate the requirements or hints that have the same
+        # name - even though they may be re-evaluated at the step
+        # level (e.g. a workflow defines a requirement resource that
+        # uses inputs.threads_max, and a command-line tool of the same
+        # workflow also defines a requirement with the same name, but
+        # using the command-line tool input values).
         #
         # This prevents evaluation at the step level (i.e. the values
         # were already loaded earlier/eagerly).
         def _fix_hints_and_requirements(
             hints_or_requirements: List[CWLObjectType],
+            requirements_or_hints_to_evaluate: List[str],
         ) -> None:
+            """Internal function to iterate the hints or requirements of steps
+            provided and evaluate the ones that exist in the parent process.
+            """
             for hint_or_requirement in hints_or_requirements:
+                for key, value in hint_or_requirement.items():
+                    if key in requirements_or_hints_to_evaluate:
+                        hint_or_requirement[key] = expression.do_eval(
+                            ex=value,
+                            jobinput=job_order,
+                            requirements=self.requirements,
+                            outdir=runtimeContext.outdir,
+                            tmpdir=runtimeContext.tmpdir,
+                            resources={},
+                            context=None,
+                            timeout=runtimeContext.eval_timeout,
+                        )
+
+        for attr_key in ["hints", "requirements"]:
+            parent_entries = []
+            for hint_or_requirement in getattr(self, attr_key):
                 for key, value in hint_or_requirement.items():
                     hint_or_requirement[key] = expression.do_eval(
                         ex=value,
@@ -187,12 +213,13 @@ def _fix_hints_and_requirements(
                         context=None,
                         timeout=runtimeContext.eval_timeout,
                     )
+                    parent_entries.append(key)
 
-        for key in ["hints", "requirements"]:
-            _fix_hints_and_requirements(getattr(self, key))
             for step in self.steps:
-                _fix_hints_and_requirements(getattr(step, key))
-                _fix_hints_and_requirements(getattr(step.embedded_tool, key))
+                _fix_hints_and_requirements(getattr(step, attr_key), parent_entries)
+                _fix_hints_and_requirements(
+                    getattr(step.embedded_tool, attr_key), parent_entries
+                )
 
         builder = self._init_job(job_order, runtimeContext)