More tests for overrides. Fix bugs.

Author: Peter Amstutz

cwltool/process.py

@@ -424,7 +424,10 @@ def avroize_type(field_type, name_prefix=""):
 
 def get_overrides(metadata, toolid):  # type: (Dict[Text, Any], Text) -> List[Dict[Text, Any]]
     req = []  # type: List[Dict[Text, Any]]
-    for ov in metadata.get("cwl:overrides", []):
+    overrides = metadata.get("cwl:overrides", [])
+    if not isinstance(overrides, list):
+        raise validate.ValidationException("Expected overrides to be a list, but was %s" % type(overrides))
+    for ov in overrides:
         if ov["overrideTarget"] == toolid:
             req.extend(ov["override"])
     return req

cwltool/workflow.py

@@ -681,7 +681,7 @@ def __init__(self, toolpath_object, pos, **kwargs):
                     strict=kwargs.get("strict"),
                     fetcher_constructor=kwargs.get("fetcher_constructor"),
                     resolver=kwargs.get("resolver"),
-                    overrides=kwargs.get("overrides"))
+                    overrides=kwargs.get("metadata", {}).get("overrides"))
         except validate.ValidationException as v:
             raise WorkflowException(
                 u"Tool definition %s failed validation:\n%s" %

tests/override/echo.cwl

@@ -2,6 +2,7 @@ cwlVersion: v1.0
 class: CommandLineTool
 requirements:
   ShellCommandRequirement: {}
+hints:
   EnvVarRequirement:
     envDef:
       MESSAGE: hello1

tests/test_override.py

@@ -42,3 +42,10 @@ def test_overrides(self):
         self.assertEquals(main([get_data('tests/override/echo-job-ov2.yml')],
                                stdout=sio), 0)
         self.assertEquals({"out": "zing hello4"}, json.loads(sio.getvalue()))
+
+        sio = StringIO()
+        self.assertEquals(main(["--overrides", get_data('tests/override/ov2.yml'),
+                                get_data('tests/override/echo-wf.cwl'),
+                                get_data('tests/override/echo-job.yml')],
+                               stdout=sio), 0)
+        self.assertEquals({"out": "zing hello5"}, json.loads(sio.getvalue()))