diff options
| -rw-r--r-- | gn3/db/sample_data.py | 93 |
1 files changed, 57 insertions, 36 deletions
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] |