Improve error message for invalid outputs and add tests

Author: Anton Khodak

cwltool/load_tool.py

@@ -20,7 +20,7 @@
 from avro.schema import Names
 from ruamel.yaml.comments import CommentedMap, CommentedSeq
 from schema_salad.ref_resolver import ContextType, Fetcher, Loader, file_uri
-from schema_salad.sourceline import cmap
+from schema_salad.sourceline import cmap, SourceLine
 from schema_salad.validate import ValidationException
 
 from . import process, update
@@ -125,7 +125,9 @@ def _convert_stdstreams_to_files(workflowobj):
         if workflowobj.get('class') == 'CommandLineTool':
             for out in workflowobj.get('outputs', []):
                 if type(out) is not CommentedMap:
-                    raise ValidationException("Output '%s' is not valid" % out)
+                    with SourceLine(workflowobj, "outputs", ValidationException, _logger.isEnabledFor(logging.DEBUG)):
+                        raise ValidationException("Output '%s' is not a valid CWL type, "
+                                                  "check the outputs section of your tool" % out)
                 for streamtype in ['stdout', 'stderr']:
                     if out.get('type') == streamtype:
                         if 'outputBinding' in out:

tests/test_examples.py

@@ -514,6 +514,19 @@ def test_lifting(self):
             echo = f.make(get_data("tests/test_bad_outputs_wf.cwl"))
             self.assertEqual(echo(inp="foo"), {"out": "foo\n"})
 
+    def test_malformed_outputs(self):
+        # check that tool validation fails if one of the outputs is not a valid CWL type
+        f = cwltool.factory.Factory()
+        with self.assertRaises(schema_salad.validate.ValidationException):
+            echo = f.make(get_data("tests/wf/malformed_outputs.cwl"))
+            echo()
+
+    def test_separate_without_prefix(self):
+        # check that setting 'separate = false' on an inputBinding without prefix does not fail the workflow
+        f = cwltool.factory.Factory()
+        echo = f.make(get_data("tests/wf/separate_without_prefix.cwl"))
+        self.assertEqual(echo(), {"output": "string\n"})
+
 
     def test_checker(self):
         # check that the static checker raises exception when a source type

tests/wf/malformed_outputs.cwl

@@ -0,0 +1,8 @@
+cwlVersion: v1.0
+class: CommandLineTool
+baseCommand: echo
+
+inputs:
+  []
+outputs:
+  -

tests/wf/separate_without_prefix.cwl

@@ -0,0 +1,22 @@
+cwlVersion: v1.0
+class: CommandLineTool
+baseCommand: echo
+
+inputs:
+  src:
+    type: string
+    default:
+      string
+    inputBinding:
+      position: 1
+      separate: false
+
+stdout: output.txt
+
+outputs:
+  output:
+    type: string
+    outputBinding:
+      glob: output.txt
+      loadContents: true
+      outputEval: $(self[0].contents)