diff options
Diffstat (limited to 'scripts/phenotypes/delete_phenotypes.py')
| -rw-r--r-- | scripts/phenotypes/delete_phenotypes.py | 30 |
1 files changed, 26 insertions, 4 deletions
diff --git a/scripts/phenotypes/delete_phenotypes.py b/scripts/phenotypes/delete_phenotypes.py index 028f061..461f3ec 100644 --- a/scripts/phenotypes/delete_phenotypes.py +++ b/scripts/phenotypes/delete_phenotypes.py @@ -24,12 +24,15 @@ 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: - try: - _ids += (int(infile.readline().strip()),) - except TypeError: - pass + for line in infile.readlines(): + try: + _ids += (int(line.strip()),) + except TypeError: + pass return _ids @@ -125,16 +128,27 @@ 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.") + if args.xref_ids_file is not None: + print("Deleting temporary file: ", end="") + args.xref_ids_file.unlink() + print("OK.") + return 0 except AssertionError: logger.error( @@ -143,6 +157,14 @@ if __name__ == "__main__": "and also specify to 'DELETE-ALL' phenotypes in the " "population, we have no way of knowing what it is you want.") return 1 + except requests.exceptions.HTTPError as _exc: + resp = _exc.response + resp_data = resp.json() + logger.debug("%s: %s", + resp_data["error"], + resp_data["error_description"], + exc_info=True) + return 1 except Exception as _exc:# pylint: disable=[broad-exception-caught] logger.debug("Failed while attempting to delete phenotypes.", exc_info=True) |