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| -rw-r--r-- | gn3/db/traits.py | 26 |
1 files changed, 26 insertions, 0 deletions
diff --git a/gn3/db/traits.py b/gn3/db/traits.py index a773fb2..ec4fa5a 100644 --- a/gn3/db/traits.py +++ b/gn3/db/traits.py @@ -1 +1,27 @@ +"""This class contains functions relating to trait data manipulation""" +from typing import Any + + +def get_trait_csv_sample_data(conn: Any, + trait_name: int, phenotype_id: int): + """Fetch a trait and return it as a csv string""" + sql = ("SELECT Strain.Id, PublishData.Id, 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 Id, Publish Data Id,Strain Name,Value,SE,Count"] with conn.cursor() as cursor: + cursor.execute(sql, (trait_name, phenotype_id,)) + for record in cursor.fetchall(): + csv_data.append(",".join([str(val) if val else "x" + for val in record])) + return "\n".join(csv_data) |