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-rw-r--r--gn3/db/sample_data.py40
1 files changed, 7 insertions, 33 deletions
diff --git a/gn3/db/sample_data.py b/gn3/db/sample_data.py
index 4d8a14f..4062705 100644
--- a/gn3/db/sample_data.py
+++ b/gn3/db/sample_data.py
@@ -1,7 +1,6 @@
"""Module containing functions that work with sample data"""
from typing import Any, Tuple, Dict, Callable
-import re
import MySQLdb
from gn3.csvcmp import extract_strain_name
@@ -63,45 +62,20 @@ def get_trait_csv_sample_data(
conn: Any, trait_name: int, phenotype_id: int
) -> str:
"""Fetch a trait and return it as a csv string"""
- case_attr_columns = set()
- csv_data: Dict = {}
with conn.cursor() as cursor:
cursor.execute("""
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'
+ifnull(ps.error, 'x'), ',', ifnull(ns.count, 'x')) AS 'Data'
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""", (trait_name, phenotype_id))
- for data in cursor.fetchall():
- if data[1] == "x":
- csv_data[data[0]] = None
- else:
- sample, case_attr, value = [
- re.sub(r"(\\n|\\r|\\t|\\)", "", x).strip()
- for x in [data[0], data[1], data[2]]
- ]
- if not csv_data.get(sample):
- csv_data[sample] = {}
- csv_data[sample][case_attr] = value
- case_attr_columns.add(case_attr)
- if not case_attr_columns:
- return "Strain Name,Value,SE,Count\n" + "\n".join(csv_data.keys())
- columns = sorted(case_attr_columns)
- csv = "Strain Name,Value,SE,Count," + ",".join(columns) + "\n"
- for key, _value in csv_data.items():
- if not _value:
- csv += key + (len(case_attr_columns) * ",x") + "\n"
- else:
- vals = [str(_value.get(column, "x")) for column in columns]
- csv += key + "," + ",".join(vals) + "\n"
- return csv
- return "No Sample Data Found"
+WHERE px.Id = %s AND px.PhenotypeId = %s ORDER BY st.Name""",
+ (trait_name, phenotype_id))
+ if not (data := cursor.fetchall()):
+ return "No Sample Data Found"
+ return "Strain Name,Value,SE,Count\n" + \
+ "\n".join([el[0] for el in data])
def get_sample_data_ids(