fix #549 (#1135)

Author: mr-c

cwltool/workflow.py

@@ -672,15 +672,19 @@ def __init__(self,
                         param["type"] = "Any"
                         param["not_connected"] = True
                     else:
+                        if isinstance(step_entry, Mapping):
+                            step_entry_name = step_entry['id']
+                        else:
+                            step_entry_name = step_entry
                         validation_errors.append(
                             SourceLine(self.tool["out"], index).makeError(
                                 "Workflow step output '%s' does not correspond to"
-                                % shortname(step_entry))
+                                % shortname(step_entry_name))
                             + "\n" + SourceLine(self.embedded_tool.tool, "outputs").makeError(
                                 "  tool output (expected '%s')" % (
                                     "', '".join(
                                         [shortname(tool_entry["id"]) for tool_entry in
-                                         self.embedded_tool.tool[toolfield]]))))
+                                         self.embedded_tool.tool['outputs']]))))
                 param["id"] = inputid
                 param.lc.line = toolpath_object[stepfield].lc.data[index][0]
                 param.lc.col = toolpath_object[stepfield].lc.data[index][1]

tests/checker_wf/broken-wf3.cwl

@@ -0,0 +1,45 @@
+#!/usr/bin/env cwl-runner
+class: Workflow
+cwlVersion: v1.0
+requirements:
+  ScatterFeatureRequirement: {}
+  MultipleInputFeatureRequirement: {}
+  StepInputExpressionRequirement: {}
+inputs:
+  letters0:
+    type: [string, int]
+    default: "a0"
+  letters1:
+    type: string[]
+    default: ["a1", "b1"]
+  letters2:
+    type: [string, int]
+    default: "a2"
+  letters3:
+    type: string[]
+    default: ["a3", "b3"]
+  letters4:
+    type: string
+    default: "a4"
+  letters5:
+    type: string[]
+    default: ["a5", "b5", "c5"]
+
+outputs:
+  all:
+    type: File
+    outputSource: cat/txt
+
+steps:
+  - id: embedded
+    run: functional-wf.cwl
+    in: []
+    out:
+     - id: All
+  - id: cat
+    run: cat.cwl
+    in:
+      - id: cat_in
+        source:
+         - embedded/All
+    out: [txt]

tests/test_examples.py

@@ -659,6 +659,9 @@ def test_static_checker():
     with pytest.raises(schema_salad.validate.ValidationException):
         factory.make(get_data("tests/checker_wf/broken-wf2.cwl"))
 
+    with pytest.raises(schema_salad.validate.ValidationException):
+        factory.make(get_data("tests/checker_wf/broken-wf3.cwl"))
+
 
 def test_var_spool_cwl_checker1():
     """Confirm that references to /var/spool/cwl are caught."""