Apply rename PJA to collection outputs including $ replacements.

Update PJA collection test to test HDCA is renamed also.

lib/galaxy/jobs/actions/post.py

@@ -85,6 +85,20 @@ class RenameDatasetAction(DefaultJobAction):
     name = "RenameDatasetAction"
     verbose_name = "Rename Dataset"
 
+    @classmethod
+    def execute_on_mapped_over(cls, app, sa_session, action, step_outputs, replacement_dict):
+        # Prevent renaming a dataset to the empty string.
+        if action.action_arguments and action.action_arguments.get('newname', ''):
+            new_name = action.action_arguments['newname']
+
+            if replacement_dict:
+                for k, v in replacement_dict.items():
+                    new_name = new_name.replace("${%s}" % k, v)
+
+            for name, step_output in step_outputs.items():
+                if action.output_name == '' or name == action.output_name:
+                    step_output.name = new_name
+
     @classmethod
     def execute(cls, app, sa_session, action, job, replacement_dict):
         # Prevent renaming a dataset to the empty string.
@@ -380,8 +394,13 @@ class ActionBox(object):
                       'ColumnSetAction', 'EmailAction',
                       'DeleteIntermediatesAction', 'TagDatasetAction',
                       'RemoveTagDatasetAction']
+    # Actions that can be applied ahead of the job execution while workflow is still
+    # being scheduled and jobs created.
     immediate_actions = ['ChangeDatatypeAction', 'RenameDatasetAction',
                          'TagDatasetAction', 'RemoveTagDatasetAction']
+    # Actions that will be applied to implicit mapped over collection outputs and not
+    # just individual outputs when steps include mapped over tools and implicit collection outputs.
+    mapped_over_output_actions = ['RenameDatasetAction']
 
     @classmethod
     def get_short_str(cls, action):
@@ -412,6 +431,11 @@ class ActionBox(object):
                 pass
         return npd
 
+    @classmethod
+    def execute_on_mapped_over(cls, app, sa_session, pja, step_outputs, replacement_dict=None):
+        if pja.action_type in ActionBox.actions:
+            ActionBox.actions[pja.action_type].execute_on_mapped_over(app, sa_session, pja, step_outputs, replacement_dict)
+
     @classmethod
     def execute(cls, app, sa_session, pja, job, replacement_dict=None):
         if pja.action_type in ActionBox.actions:

lib/galaxy/workflow/modules.py

@@ -932,7 +932,7 @@ class ToolModule(WorkflowModule):
             step_outputs = dict(execution_tracker.output_datasets)
             step_outputs.update(execution_tracker.output_collections)
         progress.set_step_outputs(invocation_step, step_outputs, already_persisted=not invocation_step.is_new)
-
+        self._handle_mapped_over_post_job_actions(step, step_outputs, invocation.replacement_dict)
         if execution_tracker.execution_errors:
             message = "Failed to create one or more job(s) for workflow step."
             raise Exception(message)
@@ -971,6 +971,18 @@ class ToolModule(WorkflowModule):
         visit_input_values(tool.inputs, step.state.inputs, callback)
         return collections_to_match
 
+    def _effective_post_job_actions(self, step):
+        effective_post_job_actions = step.post_job_actions[:]
+        for key, value in self.runtime_post_job_actions.items():
+            effective_post_job_actions.append(self.__to_pja(key, value, None))
+        return effective_post_job_actions
+
+    def _handle_mapped_over_post_job_actions(self, step, step_outputs, replacement_dict):
+        effective_post_job_actions = self._effective_post_job_actions(step)
+        for pja in effective_post_job_actions:
+            if pja.action_type in ActionBox.immediate_actions:
+                ActionBox.execute_on_mapped_over(self.trans.app, self.trans.sa_session, pja, step_outputs, replacement_dict)
+
     def _handle_post_job_actions(self, step, job, replacement_dict):
         # Create new PJA associations with the created job, to be run on completion.
         # PJA Parameter Replacement (only applies to immediate actions-- rename specifically, for now)
@@ -979,9 +991,7 @@ class ToolModule(WorkflowModule):
         # Combine workflow and runtime post job actions into the effective post
         # job actions for this execution.
         flush_required = False
-        effective_post_job_actions = step.post_job_actions[:]
-        for key, value in self.runtime_post_job_actions.items():
-            effective_post_job_actions.append(self.__to_pja(key, value, None))
+        effective_post_job_actions = self._effective_post_job_actions(step)
         for pja in effective_post_job_actions:
             if pja.action_type in ActionBox.immediate_actions:
                 ActionBox.execute(self.trans.app, self.trans.sa_session, pja, job, replacement_dict)

test/api/test_workflows.py

@@ -2029,6 +2029,11 @@ test_data:
         content = self.dataset_populator.get_history_dataset_details(history_id, hid=4, wait=True, assert_ok=True)
         name = content["name"]
         assert name == "my new name", name
+        assert content["history_content_type"] == "dataset"
+        content = self.dataset_populator.get_history_collection_details(history_id, hid=3, wait=True, assert_ok=True)
+        name = content["name"]
+        assert content["history_content_type"] == "dataset_collection", content
+        assert name == "my new name", name
 
     @skip_without_tool("create_2")
     def test_run_rename_multiple_outputs(self):