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authorBonfaceKilz2022-01-05 17:01:37 +0300
committerGitHub2022-01-05 17:01:37 +0300
commitbbd088c6aa26549d2e6b063c8d99492cb6fc33f5 (patch)
tree62ed5cae507303a469c040eb47a8b5b70b3a1a93 /gn3/db
parentaf52afa4318feadfa3cd1cc4dcdd3d86907f68a4 (diff)
parent0b1643e87cf4303db3673dcf3cf240aeb4d518cb (diff)
downloadgenenetwork3-bbd088c6aa26549d2e6b063c8d99492cb6fc33f5.tar.gz
Merge pull request #69 from genenetwork/fix/check-for-duplicates-before-deletions-or-insertions
Fix/check for duplicates before deletions or insertions
Diffstat (limited to 'gn3/db')
-rw-r--r--gn3/db/traits.py47
1 files changed, 29 insertions, 18 deletions
diff --git a/gn3/db/traits.py b/gn3/db/traits.py
index 68b6059..338b320 100644
--- a/gn3/db/traits.py
+++ b/gn3/db/traits.py
@@ -110,7 +110,6 @@ def get_trait_csv_sample_data(conn: Any,
def update_sample_data(conn: Any, #pylint: disable=[R0913]
-
trait_name: str,
strain_name: str,
phenotype_id: int,
@@ -203,25 +202,30 @@ def delete_sample_data(conn: Any,
"AND Strain.Name = \"%s\"") % (trait_name,
phenotype_id,
str(strain_name)))
- strain_id, data_id = cursor.fetchone()
- cursor.execute(("DELETE FROM PublishData "
+ # Check if it exists if the data was already deleted:
+ if _result := cursor.fetchone():
+ strain_id, data_id = _result
+
+ # 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]
+ % (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()
@@ -254,6 +258,13 @@ def insert_sample_data(conn: Any, #pylint: disable=[R0913]
(strain_name,))
strain_id = cursor.fetchone()
+ # Return early if an insert already exists!
+ cursor.execute("SELECT Id FROM PublishData where Id = %s "
+ "AND StrainId = %s",
+ (data_id, strain_id))
+ if cursor.fetchone(): # This strain already exists
+ return (0, 0, 0)
+
# Insert the PublishData table
cursor.execute(("INSERT INTO PublishData (Id, StrainId, value)"
"VALUES (%s, %s, %s)"),