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| author | BonfaceKilz | 2022-01-05 17:01:37 +0300 |
|---|---|---|
| committer | GitHub | 2022-01-05 17:01:37 +0300 |
| commit | bbd088c6aa26549d2e6b063c8d99492cb6fc33f5 (patch) | |
| tree | 62ed5cae507303a469c040eb47a8b5b70b3a1a93 /gn3 | |
| parent | af52afa4318feadfa3cd1cc4dcdd3d86907f68a4 (diff) | |
| parent | 0b1643e87cf4303db3673dcf3cf240aeb4d518cb (diff) | |
| download | genenetwork3-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')
| -rw-r--r-- | gn3/authentication.py | 4 | ||||
| -rw-r--r-- | gn3/db/traits.py | 47 |
2 files changed, 29 insertions, 22 deletions
diff --git a/gn3/authentication.py b/gn3/authentication.py index 4aedacd..d0b35bc 100644 --- a/gn3/authentication.py +++ b/gn3/authentication.py @@ -163,8 +163,4 @@ def create_group(conn: Redis, group_name: Optional[str], } conn.hset("groups", group_id, json.dumps(group)) return group - # This might break stuff, but it fixes the linting error regarding - # inconsistent return types. - # @BonfaceKilz please review this and replace with appropriate return and - # remove these comments. return None 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)"), |