Merge branch 'release_20.05' into release_20.09

lib/galaxy/tools/parameters/wrapped_json.py

@@ -94,10 +94,13 @@ def _json_wrap_input(input, value_wrapper, profile, handle_files="skip"):
     elif input_type == "boolean":
         json_value = _cast_if_not_none(value_wrapper, bool)
     elif input_type == "select":
-        if input.multiple and packaging.version.parse(str(profile)) >= packaging.version.parse('20.05'):
-            json_value = [_ for _ in _cast_if_not_none(value_wrapper.value, list)]
-        else:
+        if packaging.version.parse(str(profile)) < packaging.version.parse('20.05'):
             json_value = _cast_if_not_none(value_wrapper, str)
+        else:
+            if input.multiple:
+                json_value = [str(_) for _ in _cast_if_not_none(value_wrapper.value, list)]
+            else:
+                json_value = _cast_if_not_none(value_wrapper.value, str)
     elif input_type == "data_column":
         # value is a SelectToolParameterWrapper()
         if input.multiple:

lib/galaxy/webapps/galaxy/api/workflows.py

@@ -245,7 +245,8 @@ class WorkflowsAPIController(BaseAPIController, UsesStoredWorkflowMixin, UsesAnn
 
         Lists all versions of this workflow.
         """
-        stored_workflow = self.workflow_manager.get_stored_accessible_workflow(trans, workflow_id, **kwds)
+        instance = util.string_as_bool(kwds.get("instance", "false"))
+        stored_workflow = self.workflow_manager.get_stored_accessible_workflow(trans, workflow_id, by_stored_id=not instance)
         return [{'version': i, 'update_time': str(w.update_time), 'steps': len(w.steps)} for i, w in enumerate(reversed(stored_workflow.workflows))]
 
     @expose_api

test/functional/tools/inputs_as_json.xml

@@ -27,8 +27,8 @@ if test_case == "1":
     assert_equals(as_dict["inttest"], 12456)
     assert_equals(as_dict["floattest"], 6.789)
     assert_equals(as_dict["radio_select"], "a_radio")
-    assert_equals(as_dict["optional_select"], None)
-    assert_equals(as_dict["optional_multiple_select"], [])
+    assert_equals(as_dict["optional_select"], "None")
+    assert_equals(as_dict["optional_multiple_select"], "None")
     assert_equals(as_dict["repeat"][0]["r"], "000000")
     assert_equals(as_dict["repeat"][1]["r"], "FFFFFF")
     assert_equals(as_dict["cond"]["more_text"], "fdefault")
@@ -43,7 +43,7 @@ elif test_case == "2":
     assert_equals(as_dict["floattest"], 1.0)
     assert_equals(as_dict["radio_select"], "a_radio")
     assert_equals(as_dict["optional_select"], "a")
-    assert_equals(as_dict["optional_multiple_select"], ['a', 'b'])
+    assert_equals(as_dict["optional_multiple_select"], 'a,b')
     assert_equals(as_dict["repeat"][0]["r"], "000000")
     assert_equals(as_dict["cond"]["cond_test"], "second")
     assert_equals(as_dict["cond"]["more_text"], "sdefault")

test/functional/tools/inputs_as_json_profile.xml

@@ -1,7 +1,7 @@
 <!-- test if profile version of inputs json generation works, i.e.
      - multiple selects get comma separated string (lists >= 20.05)
      - empty optional selects get "None" ([] >= 20.05) -->
-<tool id="inputs_as_json" name="inputs_as_json" profile="20.01" version="1.0.0">
+<tool id="inputs_as_json_profile" name="inputs_as_json_profile" profile="20.05" version="1.0.0">
     <command detect_errors="exit_code"><![CDATA[
         cat inputs.json &&
         python $check_inputs inputs.json $test_case
@@ -30,8 +30,8 @@ if test_case == "1":
     assert_equals(as_dict["inttest"], 12456)
     assert_equals(as_dict["floattest"], 6.789)
     assert_equals(as_dict["radio_select"], "a_radio")
-    assert_equals(as_dict["optional_select"], "None")
-    assert_equals(as_dict["optional_multiple_select"], "None")
+    assert_equals(as_dict["optional_select"], None)
+    assert_equals(as_dict["optional_multiple_select"], [])
     assert_equals(as_dict["repeat"][0]["r"], "000000")
     assert_equals(as_dict["repeat"][1]["r"], "FFFFFF")
     assert_equals(as_dict["cond"]["more_text"], "fdefault")
@@ -46,7 +46,7 @@ elif test_case == "2":
     assert_equals(as_dict["floattest"], 1.0)
     assert_equals(as_dict["radio_select"], "a_radio")
     assert_equals(as_dict["optional_select"], "a")
-    assert_equals(as_dict["optional_multiple_select"], 'a,b')
+    assert_equals(as_dict["optional_multiple_select"], ['a', 'b'])
     assert_equals(as_dict["repeat"][0]["r"], "000000")
     assert_equals(as_dict["cond"]["cond_test"], "second")
     assert_equals(as_dict["cond"]["more_text"], "sdefault")