diff options
Diffstat (limited to 'gn3')
| -rw-r--r-- | gn3/db/traits.py | 39 |
1 files changed, 23 insertions, 16 deletions
diff --git a/gn3/db/traits.py b/gn3/db/traits.py index f82beb0..5013844 100644 --- a/gn3/db/traits.py +++ b/gn3/db/traits.py @@ -80,23 +80,30 @@ def export_trait_data( def get_trait_csv_sample_data(conn: Any, - trait_name: int, phenotype_id: int): + trait_name: int, phenotype_id: int) -> str: """Fetch a trait and return it as a csv string""" - def __float_strip(num_str): - if str(num_str)[-2:] == ".0": - return str(int(num_str)) - return str(num_str) - def __process_for_csv__(record): - return ",".join([ - __float_strip(record[key]) if record[key] is not None 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) - + __query = ("SELECT concat(st.Name, ',', ifnull(pd.value, 'x'), ',', " + "ifnull(ps.error, 'x'), ',', ifnull(ns.count, 'x')) as 'Data' " + "ifnull(ca.Name, 'x') as 'CaseAttr', " + "ifnull(cxref.value, 'x') as 'Value' " + "FROM PublishFreeze pf " + "JOIN PublishXRef px ON px.InbredSetId = pf.InbredSetId " + "JOIN PublishData pd ON pd.Id = px.DataId " + "JOIN Strain st ON pd.StrainId = st.Id " + "LEFT JOIN PublishSE ps ON ps.DataId = pd.Id " + "AND ps.StrainId = pd.StrainId " + "LEFT JOIN NStrain ns ON ns.DataId = pd.Id " + "AND ns.StrainId = pd.StrainId " + "LEFT JOIN CaseAttributeXRefNew cxref ON " + "(cxref.InbredSetId = px.InbredSetId AND " + "cxref.StrainId = st.Id) " + "LEFT JOIN CaseAttribute ca ON ca.Id = cxref.CaseAttributeId" + "WHERE px.Id = %s AND px.PhenotypeId = %s ORDER BY st.Name") + with conn.cursor() as cursor: + cursor.execute(__query, (trait_name, phenotype_id)) + return ("Strain Name,Value,SE,Count\n" + + "\n".join(map(lambda x:x[0], cursor.fetchall()))) + return "No Sample Data Found" def update_sample_data(conn: Any, #pylint: disable=[R0913] trait_name: str, |