Merge branch 'release_23.0' into dev

lib/galaxy/job_execution/actions/post.py

@@ -55,11 +55,13 @@ class EmailAction(DefaultJobAction):
         try:
             frm = app.config.email_from
             history_id_encoded = app.security.encode_id(job.history_id)
-            invocation_id_encoded = app.security.encode_id(job.workflow_invocation_step.workflow_invocation_id)
+            link_invocation = None
+            if job.workflow_invocation_step:
+                invocation_id_encoded = app.security.encode_id(job.workflow_invocation_step.workflow_invocation_id)
+                link_invocation = (
+                    f"{app.config.galaxy_infrastructure_url}/workflows/invocations/report?id={invocation_id_encoded}"
+                )
             link = f"{app.config.galaxy_infrastructure_url}/histories/view?id={history_id_encoded}"
-            link_invocation = (
-                f"{app.config.galaxy_infrastructure_url}/workflows/invocations/report?id={invocation_id_encoded}"
-            )
             if frm is None:
                 if action.action_arguments and "host" in action.action_arguments:
                     host = action.action_arguments["host"]
@@ -70,7 +72,8 @@ class EmailAction(DefaultJobAction):
             subject = f"Galaxy job completion notification from history '{job.history.name}'"
             outdata = ",\n".join(ds.dataset.display_name() for ds in job.output_datasets)
             body = f"Your Galaxy job generating dataset(s):\n\n{outdata}\n\nis complete as of {datetime.datetime.now().strftime('%I:%M')}. Click the link below to access your data: \n{link}"
-            body += f"\n\nWorkflow Invocation Report:\n{link_invocation}"
+            if link_invocation:
+                body += f"\n\nWorkflow Invocation Report:\n{link_invocation}"
             send_mail(frm, to, subject, body, app.config)
         except Exception as e:
             log.error("EmailAction PJA Failed, exception: %s", unicodify(e))

lib/galaxy/tools/__init__.py

@@ -3578,7 +3578,7 @@ class SortTool(DatabaseOperationTool):
         sorttype = incoming["sort_type"]["sort_type"]
         new_elements = {}
         elements = hdca.collection.elements
-        presort_elements = []
+        presort_elements = None
         if sorttype == "alpha":
             presort_elements = [(dce.element_identifier, dce) for dce in elements]
         elif sorttype == "numeric":
@@ -3603,7 +3603,7 @@ class SortTool(DatabaseOperationTool):
         else:
             raise Exception(f"Unknown sort_type '{sorttype}'")
 
-        if presort_elements:
+        if presort_elements is not None:
             sorted_elements = [x[1] for x in sorted(presort_elements, key=lambda x: x[0])]
 
         for dce in sorted_elements:

lib/galaxy_test/api/test_workflows.py

@@ -6108,6 +6108,44 @@ input:
         put_response = self._update_workflow(workflow_id, workflow_object)
         assert put_response.status_code == 200
 
+    def test_empty_collection_sort(self, history_id):
+        self._run_workflow(
+            """class: GalaxyWorkflow
+inputs:
+  input: collection
+  filter_file: data
+steps:
+  filter_collection:
+    tool_id: __FILTER_FROM_FILE__
+    in:
+       input: input
+       how|filter_source: filter_file
+  sort_collection_1:
+    tool_id: __SORTLIST__
+    in:
+      input: filter_collection/output_filtered
+  sort_collection_2:
+    tool_id: __SORTLIST__
+    in:
+      input: filter_collection/output_discarded
+  merge_collection:
+    tool_id: __MERGE_COLLECTION__
+    in:
+      inputs_0|input: sort_collection_1/output
+      inputs_1|input: sort_collection_2/output
+test_data:
+  input:
+    collection_type: list
+    elements:
+      - identifier: i1
+        content: "0"
+  filter_file: i1
+""",
+            history_id=history_id,
+            wait=True,
+            assert_ok=True,
+        )
+
     @skip_without_tool("random_lines1")
     def test_run_replace_params_over_default_delayed(self):
         with self.dataset_populator.test_history() as history_id: