diff options
| -rw-r--r-- | gn3/authentication.py | 4 | ||||
| -rw-r--r-- | gn3/db/traits.py | 47 | ||||
| -rw-r--r-- | tests/unit/db/test_traits.py | 33 |
3 files changed, 53 insertions, 31 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)"), diff --git a/tests/unit/db/test_traits.py b/tests/unit/db/test_traits.py index 4aa9389..75f3d4c 100644 --- a/tests/unit/db/test_traits.py +++ b/tests/unit/db/test_traits.py @@ -202,8 +202,6 @@ class TestTraitsDBFunctions(TestCase): """ # pylint: disable=C0103 db_mock = mock.MagicMock() - - STRAIN_ID_SQL: str = "UPDATE Strain SET Name = %s WHERE Id = %s" PUBLISH_DATA_SQL: str = ( "UPDATE PublishData SET value = %s " "WHERE StrainId = %s AND Id = %s") @@ -216,16 +214,33 @@ class TestTraitsDBFunctions(TestCase): with db_mock.cursor() as cursor: type(cursor).rowcount = 1 + mock_fetchone = mock.MagicMock() + mock_fetchone.return_value = (1, 1) + type(cursor).fetchone = mock_fetchone self.assertEqual(update_sample_data( conn=db_mock, strain_name="BXD11", - strain_id=10, publish_data_id=8967049, - value=18.7, error=2.3, count=2), - (1, 1, 1, 1)) + trait_name="1", + phenotype_id=10, value=18.7, + error=2.3, count=2), + (1, 1, 1)) cursor.execute.assert_has_calls( - [mock.call(STRAIN_ID_SQL, ('BXD11', 10)), - mock.call(PUBLISH_DATA_SQL, (18.7, 10, 8967049)), - mock.call(PUBLISH_SE_SQL, (2.3, 10, 8967049)), - mock.call(N_STRAIN_SQL, (2, 10, 8967049))] + [mock.call('SELECT Strain.Id, PublishData.Id FROM' + ' (PublishData, Strain, PublishXRef, ' + 'PublishFreeze) LEFT JOIN PublishSE ON ' + '(PublishSE.DataId = PublishData.Id ' + 'AND PublishSE.StrainId = ' + 'PublishData.StrainId) LEFT JOIN NStrain ON ' + '(NStrain.DataId = PublishData.Id AND ' + 'NStrain.StrainId = PublishData.StrainId) WHERE ' + 'PublishXRef.InbredSetId = ' + 'PublishFreeze.InbredSetId AND PublishData.Id = ' + 'PublishXRef.DataId AND PublishXRef.Id = 1 AND ' + 'PublishXRef.PhenotypeId = 10 AND ' + 'PublishData.StrainId = Strain.Id AND ' + 'Strain.Name = "BXD11"'), + mock.call(PUBLISH_DATA_SQL, (18.7, 1, 1)), + mock.call(PUBLISH_SE_SQL, (2.3, 1, 1)), + mock.call(N_STRAIN_SQL, (2, 1, 1))] ) def test_set_haveinfo_field(self): |