Unverified Commit 03eca7cc authored by mvdbeek's avatar mvdbeek
Browse files

Fix handling of collecting discovered but purged outputs

parent 435a8cd3

lib/galaxy/job_execution/output_collect.py

+10 −2
Original line number Diff line number Diff line
@@ -521,6 +521,7 @@ def collect_primary_datasets(job_context: Union[JobContext, SessionlessJobContex 
                outdata.designation = designation

                outdata.dataset.external_filename = None  # resets filename_override

                # Move data from temp location to dataset location

                if not outdata.dataset.purged:

                    job_context.object_store.update_from_file(outdata.dataset, file_name=filename, create=True)

                primary_output_assigned = True

                continue
@@ -554,6 +555,7 @@ def collect_primary_datasets(job_context: Union[JobContext, SessionlessJobContex 
                dataset_attributes=new_primary_datasets_attributes,

                creating_job_id=job_context.get_job_id() if job_context else None,

                storage_callbacks=storage_callbacks,

                purged=outdata.dataset.purged,

            )

            # Associate new dataset with job

            job_context.add_output_dataset_association(f"__new_primary_file_{name}|{designation}__", primary_data)
@@ -563,7 +565,13 @@ def collect_primary_datasets(job_context: Union[JobContext, SessionlessJobContex 
        if primary_output_assigned:

            outdata.name = new_outdata_name

            outdata.init_meta()

            if not outdata.dataset.purged:

                try:

                    outdata.set_meta()

                except Exception:

                    # We don't want to fail here on a single "bad" discovered dataset

                    log.debug("set meta failed for %s", outdata, exc_info=True)

                    outdata.state = HistoryDatasetAssociation.states.FAILED_METADATA

            outdata.set_peek()

            outdata.discovered = True

            sa_session = job_context.sa_session

lib/galaxy/model/store/discover.py

+6 −1
Original line number Diff line number Diff line
@@ -91,6 +91,7 @@ class ModelPersistenceContext(metaclass=abc.ABCMeta): 
        creating_job_id=None,

        output_name=None,

        storage_callbacks=None,

        purged=False,

    ):

        tag_list = tag_list or []

        sources = sources or []
@@ -190,7 +191,11 @@ class ModelPersistenceContext(metaclass=abc.ABCMeta): 


        if info is not None:

            primary_data.info = info

        if filename:



        if purged:

            primary_data.dataset.purged = True

            primary_data.purged = True

        if filename and not purged:

            if storage_callbacks is None:

                self.finalize_storage(

                    primary_data=primary_data,