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| author | Frederick Muriuki Muriithi | 2025-12-03 12:35:05 -0600 |
|---|---|---|
| committer | Frederick Muriuki Muriithi | 2025-12-03 12:35:05 -0600 |
| commit | d461596b55086310717dc30f6816f6ae452a61bd (patch) | |
| tree | 319c3e8eb0a3e592d6d0f32d48af6e3c75c724f7 | |
| parent | 7cf30517630a1b3ffa50b3eb4f1e9304924d964a (diff) | |
| download | gn-uploader-d461596b55086310717dc30f6816f6ae452a61bd.tar.gz | |
Fix exitcode: Ensure correct exit code is returned.
| -rw-r--r-- | scripts/run_qtlreaper.py | 5 |
1 files changed, 3 insertions, 2 deletions
diff --git a/scripts/run_qtlreaper.py b/scripts/run_qtlreaper.py index 764ee70..c3aef5d 100644 --- a/scripts/run_qtlreaper.py +++ b/scripts/run_qtlreaper.py @@ -109,6 +109,7 @@ def save_qtl_values_to_db(conn, qtls: dict): def dispatch(args: Namespace) -> int: """Dispatch the actual logic.""" + exitcode = 1 with mysqldb.database_connection(args.db_uri) as conn: try: population = population_by_species_and_id(conn, args.species_id, args.population_id) @@ -166,7 +167,7 @@ def dispatch(args: Namespace) -> int: _traitsfile.unlink() _qtlreaper_main_output.unlink() logger.info("Successfully computed p values for %s traits.", len(_traitsdata)) - return 0 + exitcode = 0 except FileNotFoundError as fnf: logger.error(", ".join(fnf.args), exc_info=False) except AssertionError as aserr: @@ -175,7 +176,7 @@ def dispatch(args: Namespace) -> int: logger.debug("Type of exception: %s", type(_exc)) logger.error("General exception!", exc_info=True) finally: - return 1 + return exitcode # python3 -m scripts.run_qtlreaper "mysql://webqtlout:webqtlout@127.0.0.1:3307/db_webqtl" 1 1 /home/frederick/genotype_files/genotype /tmp/qc_app_files/qtlreaper --loglevel debug |