diff options
Diffstat (limited to 'scripts')
| -rw-r--r-- | scripts/load_phenotypes_to_db.py | 36 |
1 files changed, 18 insertions, 18 deletions
diff --git a/scripts/load_phenotypes_to_db.py b/scripts/load_phenotypes_to_db.py index fdfab4c..d3d9f5a 100644 --- a/scripts/load_phenotypes_to_db.py +++ b/scripts/load_phenotypes_to_db.py @@ -242,12 +242,12 @@ def load_data(conn: mysqldb.Connection, job: dict) -> int: conn, _species["SpeciesId"], _population["Id"])} # b. Save all the data items (DataIds are vibes), return new IDs logger.info("Saving new phenotypes data.") - data = save_pheno_data(conn=conn, - dataidmap=dataidmap, - pheno_name2id=pheno_name2id, - samples=samples, - control_data=_control_data, - filesdir=_outdir) + _num_data_rows = save_pheno_data(conn=conn, + dataidmap=dataidmap, + pheno_name2id=pheno_name2id, + samples=samples, + control_data=_control_data, + filesdir=_outdir) # 4. Cross-reference Phenotype, Publication, and PublishData in PublishXRef logger.info("Cross-referencing new phenotypes to their data and publications.") xrefs = cross_reference_phenotypes_publications_and_data( @@ -255,19 +255,19 @@ def load_data(conn: mysqldb.Connection, job: dict) -> int: # 5. If standard errors and N exist, save them too # (use IDs returned in `3. b.` above). logger.info("Saving new phenotypes standard errors.") - _data_se = save_phenotypes_se(conn=conn, - dataidmap=dataidmap, - pheno_name2id=pheno_name2id, - samples=samples, - control_data=_control_data, - filesdir=_outdir) + _num_se_rows = save_phenotypes_se(conn=conn, + dataidmap=dataidmap, + pheno_name2id=pheno_name2id, + samples=samples, + control_data=_control_data, + filesdir=_outdir) logger.info("Saving new phenotypes sample counts.") - _data_n = save_phenotypes_n(conn=conn, - dataidmap=dataidmap, - pheno_name2id=pheno_name2id, - samples=samples, - control_data=_control_data, - filesdir=_outdir) + _num_n_rows = save_phenotypes_n(conn=conn, + dataidmap=dataidmap, + pheno_name2id=pheno_name2id, + samples=samples, + control_data=_control_data, + filesdir=_outdir) # 6. If entirely new data, update authorisations (break this down) logger.info("Updating authorisation.") update_auth(_token, _species, _population, _dataset, _phenos) |