Merge branch 'release_24.0' into release_24.1

lib/galaxy/managers/jobs.py

@@ -286,7 +286,7 @@ def get_accessible_job(self, trans: ProvidesUserContext, decoded_job_id) -> Job:
 
     def stop(self, job, message=None):
         if not job.finished:
-            job.mark_deleted(self.app.config.track_jobs_in_database)
+            job.mark_deleted(self.app.config.track_jobs_in_database, message)
             session = self.app.model.session
             with transaction(session):
                 session.commit()

lib/galaxy/model/__init__.py

@@ -1880,7 +1880,7 @@ def mark_stopped(self, track_jobs_in_database=False):
         else:
             self.state = Job.states.STOPPED
 
-    def mark_deleted(self, track_jobs_in_database=False):
+    def mark_deleted(self, track_jobs_in_database=False, message=None):
         """
         Mark this job as deleted, and mark any output datasets as discarded.
         """
@@ -1891,7 +1891,8 @@ def mark_deleted(self, track_jobs_in_database=False):
             self.state = Job.states.DELETING
         else:
             self.state = Job.states.DELETED
-        self.info = "Job output deleted by user before job completed."
+        info = message or "Job output deleted by user before job completed."
+        self.info = info
         for jtoda in self.output_datasets:
             output_hda = jtoda.dataset
             output_hda.deleted = True
@@ -1901,7 +1902,7 @@ def mark_deleted(self, track_jobs_in_database=False):
                 shared_hda.deleted = True
                 shared_hda.blurb = "deleted"
                 shared_hda.peek = "Job deleted"
-                shared_hda.info = "Job output deleted by user before job completed"
+                shared_hda.info = info
 
     def mark_failed(self, info="Job execution failed", blurb=None, peek=None):
         """
@@ -4905,11 +4906,16 @@ def display_name(self):
     def display_info(self):
         return self.datatype.display_info(self)
 
-    def get_converted_files_by_type(self, file_type):
+    def get_converted_files_by_type(self, file_type, include_errored=False):
         for assoc in self.implicitly_converted_datasets:
             if not assoc.deleted and assoc.type == file_type:
                 item = assoc.dataset or assoc.dataset_ldda
-                if not item.deleted and item.state in Dataset.valid_input_states:
+                valid_states = (
+                    (Dataset.states.ERROR, *Dataset.valid_input_states)
+                    if include_errored
+                    else Dataset.valid_input_states
+                )
+                if not item.deleted and item.state in valid_states:
                     return item
         return None
 
@@ -4924,7 +4930,7 @@ def get_converted_dataset_deps(self, trans, target_ext):
             depends_list = []
         return {dep: self.get_converted_dataset(trans, dep) for dep in depends_list}
 
-    def get_converted_dataset(self, trans, target_ext, target_context=None, history=None):
+    def get_converted_dataset(self, trans, target_ext, target_context=None, history=None, include_errored=False):
         """
         Return converted dataset(s) if they exist, along with a dict of dependencies.
         If not converted yet, do so and return None (the first time). If unconvertible, raise exception.
@@ -4936,7 +4942,7 @@ def get_converted_dataset(self, trans, target_ext, target_context=None, history=
         converted_dataset = self.get_metadata_dataset(target_ext)
         if converted_dataset:
             return converted_dataset
-        converted_dataset = self.get_converted_files_by_type(target_ext)
+        converted_dataset = self.get_converted_files_by_type(target_ext, include_errored=include_errored)
         if converted_dataset:
             return converted_dataset
         deps = {}
@@ -5160,7 +5166,8 @@ def convert_dataset(self, trans, target_type):
 
         # Get converted dataset; this will start the conversion if necessary.
         try:
-            converted_dataset = self.get_converted_dataset(trans, target_type)
+            # Include errored datasets here, we let user chose to retry or view error
+            converted_dataset = self.get_converted_dataset(trans, target_type, include_errored=True)
         except NoConverterException:
             return self.conversion_messages.NO_CONVERTER
         except ConverterDependencyException as dep_error:

lib/galaxy_test/api/test_jobs.py

@@ -1062,6 +1062,24 @@ def test_delete_job(self, history_id):
         self._assert_status_code_is(empty_search_response, 200)
         assert len(empty_search_response.json()) == 0
 
+    @pytest.mark.require_new_history
+    def test_delete_job_with_message(self, history_id):
+        input_dataset_id = self.__history_with_ok_dataset(history_id)
+        inputs = json.dumps({"input1": {"src": "hda", "id": input_dataset_id}})
+        search_payload = self._search_payload(history_id=history_id, tool_id="cat1", inputs=inputs)
+        # create a job
+        tool_response = self._post("tools", data=search_payload).json()
+        job_id = tool_response["jobs"][0]["id"]
+        output_dataset_id = tool_response["outputs"][0]["id"]
+        # delete the job with message
+        expected_message = "test message"
+        delete_job_response = self._delete(f"jobs/{job_id}", data={"message": expected_message}, json=True)
+        self._assert_status_code_is(delete_job_response, 200)
+        # Check the output dataset is deleted and the info field contains the message
+        dataset_details = self._get(f"histories/{history_id}/contents/{output_dataset_id}").json()
+        assert dataset_details["deleted"] is True
+        assert dataset_details["misc_info"] == expected_message
+
     @pytest.mark.require_new_history
     def test_destination_params(self, history_id):
         dataset_id = self.__history_with_ok_dataset(history_id)