10827 static checker fix (#435)

* Fix check_types when sinktype is Any and add tests
* Change error message from 'sink has linkMerge' to 'source has linkMerge'
* Fix issue #437 and add test: check_types bug when linkMerge is merge_flattened and srctype is a list

Author: lijiayong

cwltool/workflow.py

@@ -97,7 +97,7 @@ def match_types(sinktype, src, iid, inputobj, linkMerge, valueFrom):
 
 
 def check_types(srctype, sinktype, linkMerge, valueFrom):
-    # type: (Union[List[Text],Text], Union[List[Text],Text], Text, Text) -> Text
+    # type: (Any, Any, Text, Text) -> Text
     """Check if the source and sink types are "pass", "warning", or "exception".
     """
 
@@ -110,18 +110,25 @@ def check_types(srctype, sinktype, linkMerge, valueFrom):
             return "warning"
         else:
             return "exception"
+    elif linkMerge == "merge_nested":
+        return check_types({"items": srctype, "type": "array"}, sinktype, None, None)
+    elif linkMerge == "merge_flattened":
+        return check_types(merge_flatten_type(srctype), sinktype, None, None)
     else:
-        if not isinstance(sinktype, dict):
-            return "exception"
-        elif linkMerge == "merge_nested":
-            return check_types(srctype, sinktype["items"], None, None)
-        elif linkMerge == "merge_flattened":
-            if not isinstance(srctype, dict):
-                return check_types(srctype, sinktype["items"], None, None)
-            else:
-                return check_types(srctype, sinktype, None, None)
-        else:
-            raise WorkflowException(u"Unrecognized linkMerge enum '%s'" % linkMerge)
+        raise WorkflowException(u"Unrecognized linkMerge enu_m '%s'" % linkMerge)
+
+
+def merge_flatten_type(src):
+    # type: (Any) -> Any
+    """Return the merge flattened type of the source type
+    """
+
+    if isinstance(src, list):
+        return [merge_flatten_type(t) for t in src]
+    elif isinstance(src, dict) and src.get("type") == "array":
+        return src
+    else:
+        return {"items": src, "type": "array"}
 
 
 def can_assign_src_to_sink(src, sink, strict=False):  # type: (Any, Any, bool) -> bool
@@ -581,7 +588,7 @@ def static_checker(workflow_inputs, workflow_outputs, step_inputs, step_outputs)
             "  with sink '%s' of type %s"
             % (shortname(sink["id"]), json.dumps(sink["type"])))
         if linkMerge:
-            msg += "\n" + SourceLine(sink).makeError("  sink has linkMerge method %s" % linkMerge)
+            msg += "\n" + SourceLine(sink).makeError("  source has linkMerge method %s" % linkMerge)
         warning_msgs.append(msg)
     for exception in exceptions:
         src = exception.src
@@ -594,7 +601,7 @@ def static_checker(workflow_inputs, workflow_outputs, step_inputs, step_outputs)
             "  with sink '%s' of type %s"
             % (shortname(sink["id"]), json.dumps(sink["type"])))
         if linkMerge:
-            msg += "\n" + SourceLine(sink).makeError("  sink has linkMerge method %s" % linkMerge)
+            msg += "\n" + SourceLine(sink).makeError("  source has linkMerge method %s" % linkMerge)
         exception_msgs.append(msg)
 
     for sink in step_inputs:

tests/test_examples.py

@@ -421,6 +421,12 @@ def test_typecheck(self):
             linkMerge="merge_nested", valueFrom=None),
             "exception")
 
+        # check linkMerge: merge_nested and sinktype is "Any"
+        self.assertEquals(cwltool.workflow.check_types(
+            ['string', 'int'], "Any",
+            linkMerge="merge_nested", valueFrom=None),
+            "pass")
+
         # check linkMerge: merge_flattened
         self.assertEquals(cwltool.workflow.check_types(
             ['string', 'int'],
@@ -458,6 +464,24 @@ def test_typecheck(self):
             linkMerge="merge_flattened", valueFrom=None),
             "exception")
 
+        # check linkMerge: merge_flattened and sinktype is "Any"
+        self.assertEquals(cwltool.workflow.check_types(
+            ['string', 'int'], "Any",
+            linkMerge="merge_flattened", valueFrom=None),
+            "pass")
+
+        self.assertEquals(cwltool.workflow.check_types(
+            {'items': ['string', 'int'], 'type': 'array'}, "Any",
+            linkMerge="merge_flattened", valueFrom=None),
+            "pass")
+
+        # check linkMerge: merge_flattened when srctype is a list
+        self.assertEquals(cwltool.workflow.check_types(
+            [{'items': 'string', 'type': 'array'}],
+            {'items': 'string', 'type': 'array'},
+            linkMerge="merge_flattened", valueFrom=None),
+            "pass")
+
         # check valueFrom
         self.assertEquals(cwltool.workflow.check_types(
             {'items': ['File', 'int'], 'type': 'array'},