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| author | Frederick Muriuki Muriithi | 2025-07-01 14:47:39 -0500 |
|---|---|---|
| committer | Frederick Muriuki Muriithi | 2025-07-01 14:47:39 -0500 |
| commit | ffdd133f96202647f9b0e61a8258e16a5445ebd5 (patch) | |
| tree | b59a305e3a6900fc725c16b9183da9394068378c /scripts | |
| parent | 4dc851df38068b98b3e525217978557139578808 (diff) | |
| download | gn-uploader-ffdd133f96202647f9b0e61a8258e16a5445ebd5.tar.gz | |
Ignore any optional files that are not provided.
Diffstat (limited to 'scripts')
| -rw-r--r-- | scripts/load_phenotypes_to_db.py | 37 |
1 files changed, 20 insertions, 17 deletions
diff --git a/scripts/load_phenotypes_to_db.py b/scripts/load_phenotypes_to_db.py index 5ce37f3..08ee558 100644 --- a/scripts/load_phenotypes_to_db.py +++ b/scripts/load_phenotypes_to_db.py @@ -410,23 +410,26 @@ def load_data(conn: mysqldb.Connection, job: dict) -> int: conn, tuple(dataidmap.values())) # 5. If standard errors and N exist, save them too # (use IDs returned in `3. b.` above). - logger.info("Saving new phenotypes standard errors.") - _num_se_rows = save_phenotypes_se(conn=conn, - dataidmap=dataidmap, - pheno_name2id=pheno_name2id, - samples=samples, - control_data=_control_data, - filesdir=_outdir) - logger.info("Saved %s new phenotype standard error rows.", _num_se_rows) - - logger.info("Saving new phenotypes sample counts.") - _num_n_rows = save_phenotypes_n(conn=conn, - dataidmap=dataidmap, - pheno_name2id=pheno_name2id, - samples=samples, - control_data=_control_data, - filesdir=_outdir) - logger.info("Saved %s new phenotype sample counts rows.", _num_n_rows) + if _control_data.get("phenose"): + logger.info("Saving new phenotypes standard errors.") + _num_se_rows = save_phenotypes_se(conn=conn, + dataidmap=dataidmap, + pheno_name2id=pheno_name2id, + samples=samples, + control_data=_control_data, + filesdir=_outdir) + logger.info("Saved %s new phenotype standard error rows.", _num_se_rows) + + if _control_data.get("phenonum"): + logger.info("Saving new phenotypes sample counts.") + _num_n_rows = save_phenotypes_n(conn=conn, + dataidmap=dataidmap, + pheno_name2id=pheno_name2id, + samples=samples, + control_data=_control_data, + filesdir=_outdir) + logger.info("Saved %s new phenotype sample counts rows.", _num_n_rows) + return (_species, _population, _dataset, _xrefs) |