From 59d2d0a8175c4a06c5363a8a3d3addd683ef9a8d Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Tue, 1 Mar 2022 14:14:43 +0300
Subject: Allow deleting case-attribute data during deletion
* gn3/db/sample_data.py (delete_sample_data): Modify this function to allow
deleting case-attribute values.
---
gn3/db/sample_data.py | 93 +++++++++++++++++++++++++++++++--------------------
1 file changed, 57 insertions(+), 36 deletions(-)
(limited to 'gn3/db')
diff --git a/gn3/db/sample_data.py b/gn3/db/sample_data.py
index 708bfd5..06b5767 100644
--- a/gn3/db/sample_data.py
+++ b/gn3/db/sample_data.py
@@ -163,49 +163,70 @@ def update_sample_data(conn: Any, # pylint: disable=[R0913]
def delete_sample_data(conn: Any,
trait_name: str,
- strain_name: str,
+ data: str,
+ csv_header: str,
phenotype_id: int):
"""Given the right parameters, delete sample-data from the relevant
- table."""
- strain_id, data_id, _ = get_sample_data_ids(
+ 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=strain_name)
- deleted_published_data: int = 0
- deleted_se_data: int = 0
- deleted_n_strains: int = 0
-
- with conn.cursor() as cursor:
- # Delete the PublishData table
- try:
- # Only run if the strain_id and data_id exist
- if strain_id and data_id:
- cursor.execute(("DELETE FROM PublishData "
- "WHERE StrainId = %s AND Id = %s")
- % (strain_id, data_id))
- deleted_published_data = cursor.rowcount
-
- # Delete the PublishSE table
- cursor.execute(("DELETE FROM PublishSE "
- "WHERE StrainId = %s AND DataId = %s") %
- (strain_id, data_id))
- deleted_se_data = cursor.rowcount
-
- # Delete the NStrain table
- cursor.execute(("DELETE FROM NStrain "
- "WHERE StrainId = %s AND DataId = %s" %
- (strain_id, data_id)))
- deleted_n_strains = cursor.rowcount
- except Exception as e: #pylint: disable=[C0103, W0612]
- conn.rollback()
- raise MySQLdb.Error
- conn.commit()
- cursor.close()
- cursor.close()
+ 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
- return (deleted_published_data,
- deleted_se_data, deleted_n_strains)
+ 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]
--
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