Unverified Commit 9a88c21e authored by Marius van den Beek's avatar Marius van den Beek Committed by GitHub
Browse files

Merge pull request #14108 from mvdbeek/probably_fix_test_delete_cancels_job_test 

Fix deleting jobs when deleting datasets
parents 8aceb264 0be561d6

lib/galaxy/managers/datasets.py

+8 −5
Original line number Diff line number Diff line
@@ -270,7 +270,7 @@ class DatasetAssociationManager( 
        """

        super().delete(item, flush=flush)

        if stop_job:

            self.stop_creating_job(item)

            self.stop_creating_job(item, flush=flush)

        return item



    def purge(self, dataset_assoc, flush=True):
@@ -281,13 +281,14 @@ class DatasetAssociationManager( 
        # TODO: this check may belong in the controller

        self.dataset_manager.error_unless_dataset_purge_allowed()



        # We need to ignore a potential flush=False here and force the flush

        # We need to ignore a potential flush=False here if jobs are not tracked in the database,

        # so that job cleanup associated with stop_creating_job will see

        # the dataset as purged.

        super().purge(dataset_assoc, flush=True)

        flush_required = not self.app.config.track_jobs_in_database

        super().purge(dataset_assoc, flush=flush or flush_required)



        # stop any jobs outputing the dataset_assoc

        self.stop_creating_job(dataset_assoc)

        self.stop_creating_job(dataset_assoc, flush=True)



        # more importantly, purge underlying dataset as well

        if dataset_assoc.dataset.user_can_purge:
@@ -310,7 +311,7 @@ class DatasetAssociationManager( 
            break

        return job



    def stop_creating_job(self, dataset_assoc):

    def stop_creating_job(self, dataset_assoc, flush=False):

        """

        Stops an dataset_assoc's creating job if all the job's other outputs are deleted.

        """
@@ -330,6 +331,8 @@ class DatasetAssociationManager( 
                    job.mark_deleted(track_jobs_in_database)

                    if not track_jobs_in_database:

                        self.app.job_manager.stop(job)

                    if flush:

                        self.session().flush()

                    return True

        return False

lib/galaxy/webapps/galaxy/controllers/dataset.py

+1 −2
Original line number Diff line number Diff line
@@ -876,8 +876,7 @@ class DatasetInterface(BaseUIController, UsesAnnotations, UsesItemRatings, UsesE 
            hda.mark_deleted()

            hda.clear_associated_files()

            trans.log_event(f"Dataset id {str(id)} marked as deleted")

            self.hda_manager.stop_creating_job(hda)

            trans.sa_session.flush()

            self.hda_manager.stop_creating_job(hda, flush=True)

        except Exception:

            msg = f"HDA deletion failed (encoded: {dataset_id}, decoded: {id})"

            log.exception(msg)

lib/galaxy/webapps/galaxy/services/history_contents.py

+4 −2
Original line number Diff line number Diff line
@@ -1097,10 +1097,12 @@ class HistoriesContentsService(ServiceBase, ServesExportStores, ConsumesModelSto 
        return hdas



    def __deserialize_dataset(self, trans, hda, payload: Dict[str, Any]):

        self.hda_deserializer.deserialize(hda, payload, user=trans.user, trans=trans)

        # TODO: when used in batch it would be a lot faster if we set flush=false

        # and the caller flushes only at the end or when a given chunk size is reached.

        self.hda_deserializer.deserialize(hda, payload, user=trans.user, trans=trans, flush=True)

        # TODO: this should be an effect of deleting the hda

        if payload.get("deleted", False):

            self.hda_manager.stop_creating_job(hda)

            self.hda_manager.stop_creating_job(hda, flush=True)



    def __index_legacy(

        self,

lib/galaxy_test/api/test_datasets.py

+25 −26
Original line number Diff line number Diff line
@@ -301,12 +301,7 @@ class DatasetsApiTestCase(ApiTestCase): 


    @skip_without_tool("cat_data_and_sleep")

    def test_delete_cancels_job(self):

        with self.dataset_populator.test_history() as history_id:

            hda_id = self.dataset_populator.new_dataset(history_id)["id"]

            self.dataset_populator.wait_for_history_jobs(history_id)

            active_jobs = self.dataset_populator.active_history_jobs(history_id)

            assert not active_jobs



        hda_id = self.dataset_populator.new_dataset(self.history_id)["id"]

        inputs = {

            "input1": {"src": "hda", "id": hda_id},

            "sleep_time": 10,
@@ -314,19 +309,23 @@ class DatasetsApiTestCase(ApiTestCase): 
        run_response = self.dataset_populator.run_tool_raw(

            "cat_data_and_sleep",

            inputs,

                history_id,

            self.history_id,

        ).json()

            queued_id = run_response["outputs"][0]["id"]

            active_jobs = self.dataset_populator.active_history_jobs(history_id)

            assert active_jobs

        output_hda_id = run_response["outputs"][0]["id"]

        job_id = run_response["jobs"][0]["id"]



        job_details = self.dataset_populator.get_job_details(job_id).json()

        assert job_details["state"] in ("new", "queued", "running"), job_details



        # Use stop_job to cancel the creating job

            delete_response = self.dataset_populator.delete_dataset(history_id, queued_id, stop_job=True)

        delete_response = self.dataset_populator.delete_dataset(self.history_id, output_hda_id, stop_job=True)

        self._assert_status_code_is_ok(delete_response)

        deleted_hda = delete_response.json()

        assert deleted_hda["deleted"], deleted_hda



        # The job should be cancelled

            active_jobs = self.dataset_populator.active_history_jobs(history_id)

            assert not active_jobs, "Job was not cancelled"

        deleted_job_details = self.dataset_populator.get_job_details(job_id).json()

        assert deleted_job_details["state"] in ("deleting", "deleted"), deleted_job_details



    def test_delete_batch(self):

        num_datasets = 4