diff options
| -rw-r--r-- | gn3/db/traits.py | 29 |
1 files changed, 9 insertions, 20 deletions
diff --git a/gn3/db/traits.py b/gn3/db/traits.py index 338b320..9554be2 100644 --- a/gn3/db/traits.py +++ b/gn3/db/traits.py @@ -86,26 +86,15 @@ def get_trait_csv_sample_data(conn: Any, if str(num_str)[-2:] == ".0": return str(int(num_str)) return str(num_str) - sql = ("SELECT DISTINCT Strain.Name, PublishData.value, " - "PublishSE.error, NStrain.count FROM " - "(PublishData, Strain, PublishXRef, PublishFreeze) " - "LEFT JOIN PublishSE ON " - "(PublishSE.DataId = PublishData.Id AND " - "PublishSE.StrainId = PublishData.StrainId) " - "LEFT JOIN NStrain ON (NStrain.DataId = PublishData.Id AND " - "NStrain.StrainId = PublishData.StrainId) WHERE " - "PublishXRef.InbredSetId = PublishFreeze.InbredSetId AND " - "PublishData.Id = PublishXRef.DataId AND " - "PublishXRef.Id = %s AND PublishXRef.PhenotypeId = %s " - "AND PublishData.StrainId = Strain.Id Order BY Strain.Name") - csv_data = ["Strain Name,Value,SE,Count"] - with conn.cursor() as cursor: - cursor.execute(sql, (trait_name, phenotype_id,)) - for record in cursor.fetchall(): - (strain_name, value, error, count) = record - csv_data.append( - ",".join([__float_strip(val) if val else "x" - for val in (strain_name, value, error, count)])) + def __process_for_csv__(record): + return ",".join([ + __float_strip(record[key]) if record[key] else "x" + for key in ("sample_name", "value", "se_error", "nstrain")]) + csv_data = ["Strain Name,Value,SE,Count"] + [ + __process_for_csv__(record) for record in + retrieve_publish_trait_data( + {"trait_name": trait_name, "db": {"dataset_id": phenotype_id}}, + conn)] return "\n".join(csv_data) |