diff options
Diffstat (limited to 'scripts/phenotypes')
| -rw-r--r-- | scripts/phenotypes/delete_phenotypes.py | 8 |
1 files changed, 8 insertions, 0 deletions
diff --git a/scripts/phenotypes/delete_phenotypes.py b/scripts/phenotypes/delete_phenotypes.py index e1396f3..1403216 100644 --- a/scripts/phenotypes/delete_phenotypes.py +++ b/scripts/phenotypes/delete_phenotypes.py @@ -24,6 +24,8 @@ def read_xref_ids_file(filepath: Optional[Path]) -> tuple[int, ...]: if filepath is None: return tuple() + logger.debug("Using file '%s' to retrieve XREF IDs for deletion.", + filepath.name) _ids: tuple[int, ...] = tuple() with filepath.open(mode="r") as infile: for line in infile.readlines(): @@ -126,16 +128,22 @@ if __name__ == "__main__": assert not (len(xref_ids) > 0 and args.delete_all) xref_ids = (fetch_all_xref_ids(cursor, args.population_id) if args.delete_all else xref_ids) + logger.debug("Will delete %s phenotypes and related data", + len(xref_ids)) if len(xref_ids) == 0: print("No cross-reference IDs were provided. Aborting.") return 0 + print("Updating authorisations: ", end="") update_auth((args.auth_server_uri, args.auth_token), args.species_id, args.population_id, args.dataset_id, xref_ids) + print("OK.") + print("Deleting the data: ", end="") delete_phenotypes(cursor, args.population_id, xref_ids=xref_ids) + print("OK.") return 0 except AssertionError: logger.error( |