diff options
| -rw-r--r-- | scripts/load_phenotypes_to_db.py | 37 | ||||
| -rw-r--r-- | uploader/phenotypes/views.py | 13 |
2 files changed, 29 insertions, 21 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) diff --git a/uploader/phenotypes/views.py b/uploader/phenotypes/views.py index 97bcafe..8e47242 100644 --- a/uploader/phenotypes/views.py +++ b/uploader/phenotypes/views.py @@ -374,10 +374,15 @@ def process_phenotypes_individual_files(error_uri): bundlepath = Path(app.config["UPLOAD_FOLDER"], f"{str(uuid.uuid4()).replace('-', '')}.zip") with ZipFile(bundlepath,mode="w") as zfile: - for rqtlkey, formkey in (("phenocovar", "phenotype-descriptions"), - ("pheno", "phenotype-data"), - ("phenose", "phenotype-se"), - ("phenonum", "phenotype-n")): + for rqtlkey, formkey, _type in ( + ("phenocovar", "phenotype-descriptions", "mandatory"), + ("pheno", "phenotype-data", "mandatory"), + ("phenose", "phenotype-se", "optional"), + ("phenonum", "phenotype-n", "optional")): + if _type == "optional" and not bool(form.get(formkey)): + # skip if an optional key does not exist. + continue + cdata[f"{rqtlkey}_transposed"] = ( (form.get(f"{formkey}-transposed") or "off") == "on") |