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from gn3.csvcmp import extract_strain_name
from typing import Any, Tuple, Union
import MySQLdb
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"""
__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")
case_attr_columns = set()
csv_data = {}
with conn.cursor() as cursor:
cursor.execute(__query, (trait_name, phenotype_id))
for data in cursor.fetchall():
if data[1] == "x":
csv_data[data[0]] = None
else:
sample, case_attr, value = data[0], data[1], data[2]
if not csv_data.get(sample):
csv_data[sample] = {}
csv_data[sample][case_attr] = None if value == "x" else value
case_attr_columns.add(case_attr)
if not case_attr_columns:
return ("Strain Name,Value,SE,Count\n" +
"\n".join(csv_data.keys()))
else:
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"
def get_sample_data_ids(conn: Any, publishxref_id: int,
phenotype_id: int,
strain_name: str) -> Tuple:
strain_id, publishdata_id, inbredset_id = None, None, None
with conn.cursor() as cursor:
cursor.execute("SELECT st.id, pd.Id, pf.InbredSetId "
"FROM PublishData pd "
"JOIN Strain st ON pd.StrainId = st.Id "
"JOIN PublishXRef px ON px.DataId = pd.Id "
"JOIN PublishFreeze pf ON pf.InbredSetId "
"= px.InbredSetId WHERE px.Id = %s "
"AND px.PhenotypeId = %s AND st.Name = %s",
(publishxref_id, phenotype_id, strain_name))
if _result := cursor.fetchone():
strain_id, publishdata_id, inbredset_id = _result
if not all([strain_id, publishdata_id, inbredset_id]):
# Applies for data to be inserted:
cursor.execute("SELECT DataId, InbredSetId FROM PublishXRef "
"WHERE Id = %s AND PhenotypeId = %s",
(publishxref_id, phenotype_id))
publishdata_id, inbredset_id = cursor.fetchone()
cursor.execute("SELECT Id FROM Strain WHERE Name = %s",
(strain_name,))
strain_id = cursor.fetchone()
return (strain_id, publishdata_id, inbredset_id)
def update_sample_data(conn: Any, # pylint: disable=[R0913]
trait_name: str,
strain_name: str,
phenotype_id: int,
value: Union[int, float, str],
error: Union[int, float, str],
count: Union[int, str]):
"""Given the right parameters, update sample-data from the relevant
table."""
strain_id, data_id, _ = get_sample_data_ids(
conn=conn, publishxref_id=trait_name,
phenotype_id=phenotype_id, strain_name=strain_name)
updated_published_data: int = 0
updated_se_data: int = 0
updated_n_strains: int = 0
with conn.cursor() as cursor:
# Update the PublishData table
if value == "x":
cursor.execute(("DELETE FROM PublishData "
"WHERE StrainId = %s AND Id = %s")
% (strain_id, data_id))
updated_published_data = cursor.rowcount
else:
cursor.execute(("UPDATE PublishData SET value = %s "
"WHERE StrainId = %s AND Id = %s"),
(value, strain_id, data_id))
updated_published_data = cursor.rowcount
if not updated_published_data:
cursor.execute(
"SELECT * FROM "
"PublishData WHERE StrainId = "
"%s AND Id = %s" % (strain_id, data_id))
if not cursor.fetchone():
cursor.execute(("INSERT INTO PublishData (Id, StrainId, "
" value) VALUES (%s, %s, %s)") %
(data_id, strain_id, value))
updated_published_data = cursor.rowcount
# Update the PublishSE table
if error == "x":
cursor.execute(("DELETE FROM PublishSE "
"WHERE StrainId = %s AND DataId = %s") %
(strain_id, data_id))
updated_se_data = cursor.rowcount
else:
cursor.execute(("UPDATE PublishSE SET error = %s "
"WHERE StrainId = %s AND DataId = %s"),
(None if error == "x" else error,
strain_id, data_id))
updated_se_data = cursor.rowcount
if not updated_se_data:
cursor.execute(
"SELECT * FROM "
"PublishSE WHERE StrainId = "
"%s AND DataId = %s" % (strain_id, data_id))
if not cursor.fetchone():
cursor.execute(("INSERT INTO PublishSE (StrainId, DataId, "
" error) VALUES (%s, %s, %s)") %
(strain_id, data_id,
None if error == "x" else error))
updated_se_data = cursor.rowcount
# Update the NStrain table
if count == "x":
cursor.execute(("DELETE FROM NStrain "
"WHERE StrainId = %s AND DataId = %s" %
(strain_id, data_id)))
updated_n_strains = cursor.rowcount
else:
cursor.execute(("UPDATE NStrain SET count = %s "
"WHERE StrainId = %s AND DataId = %s"),
(count, strain_id, data_id))
updated_n_strains = cursor.rowcount
if not updated_n_strains:
cursor.execute(
"SELECT * FROM "
"NStrain WHERE StrainId = "
"%s AND DataId = %s" % (strain_id, data_id))
if not cursor.fetchone():
cursor.execute(("INSERT INTO NStrain "
"(StrainId, DataId, count) "
"VALUES (%s, %s, %s)") %
(strain_id, data_id, count))
updated_n_strains = cursor.rowcount
return (updated_published_data,
updated_se_data, updated_n_strains)
def delete_sample_data(conn: Any,
trait_name: str,
data: str,
csv_header: str,
phenotype_id: int):
"""Given the right parameters, delete sample-data from the relevant
tables."""
def __delete_data(conn, table):
if value and value != "x":
_map = {
"PublishData": "StrainId = %s AND Id = %s",
"PublishSE": "StrainId = %s AND DataId = %s",
"NStrain": "StrainId = %s AND DataId = %s",
}
with conn.cursor() as cursor:
cursor.execute((f"DELETE FROM {table} "
f"WHERE {_map.get(table)}"),
(strain_id, data_id))
return cursor.rowcount
return 0
def __delete_case_attribute(conn, strain_id,
case_attr, inbredset_id):
if value != "x":
with conn.cursor() as cursor:
cursor.execute(
("DELETE FROM CaseAttributeXRefNew "
"WHERE StrainId = "
"(SELECT CaseAttributeId FROM "
f"CaseAttribute WHERE NAME = %s) "
"AND InbredSetId = %s"),
(strain_id, case_attr, inbredset_id)
)
return cursor.rowcount
return 0
strain_id, data_id, inbredset_id = get_sample_data_ids(
conn=conn, publishxref_id=trait_name,
phenotype_id=phenotype_id,
strain_name=extract_strain_name(csv_header, data))
none_case_attrs = {
"Strain Name": lambda: 0,
"Value": lambda: __delete_data(conn, "PublishData"),
"SE": lambda: __delete_data(conn, "PublishSE"),
"Count": lambda: __delete_data(conn, "NStrain"),
}
count = 0
try:
for header, value in zip(csv_header.split(","), data.split(",")):
header = header.strip()
value = value.strip()
if header in none_case_attrs:
count += none_case_attrs.get(header)()
else:
count += __delete_case_attribute(
conn=conn,
strain_id=strain_id,
case_attr=header,
inbredset_id=inbredset_id)
except Exception as e: # pylint: disable=[C0103, W0612]
conn.rollback()
raise MySQLdb.Error
conn.commit()
return count
def insert_sample_data(conn: Any, # pylint: disable=[R0913]
trait_name: str,
data: str,
csv_header: str,
phenotype_id: int):
"""Given the right parameters, insert sample-data to the relevant table.
"""
def __insert_data(conn, table, value):
if value and value != "x":
_map = {
"PublishData": "(StrainId, Id, value)",
"PublishSE": "(StrainId, DataId, error)",
"NStrain": "(StrainId, DataId, count)",
}
_query = (f"INSERT INTO {table} "
f"{_map.get(table)} "
f"VALUES %s %s %s")
with conn.cursor() as cursor:
cursor.execute((f"INSERT INTO {table} "
f"{_map.get(table)} "
f"VALUES (%s, %s, %s)"),
(strain_id, data_id, value))
return cursor.rowcount
return 0
def __insert_case_attribute(conn, strain_id,
case_attr, value, inbredset_id):
if value != "x":
with conn.cursor() as cursor:
cursor.execute(
(f"INSERT INTO CaseAttributeXRefNew "
"StrainId, CaseAttributeId, Value, InbredSetId "
"VALUES ("
f"{strain_id}, "
"(SELECT CaseAttributeId FROM "
f"CaseAttribute WHERE NAME = %s), "
"%s)" , (strain_id, case_attr, value, inbredset_id)))
return cursor.rowcount
return 0
strain_id, data_id, inbredset_id = get_sample_data_ids(
conn=conn, publishxref_id=trait_name,
phenotype_id=phenotype_id,
strain_name=extract_strain_name(csv_header, data))
none_case_attrs = {
"Strain Name": lambda _: 0,
"Value": lambda x: __insert_data(conn, "PublishData", x),
"SE": lambda x: __insert_data(conn, "PublishSE", x),
"Count": lambda x: __insert_data(conn, "NStrain", x),
}
try:
count = 0
for header, value in zip(csv_header.split(","), data.split(",")):
header = header.strip()
value = value.strip()
if header in none_case_attrs:
count += none_case_attrs.get(header)(value)
else:
count += __insert_case_attribute(
conn=conn,
strain_id=strain_id,
case_attr=header,
value=value,
inbredset_id=inbredset_id)
return count
except Exception as e: # pylint: disable=[C0103, W0612]
conn.rollback()
raise MySQLdb.Error
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