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-rw-r--r--gn3/db/traits.py39
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,