# pylint: disable=[R0902, R0903] """Module that exposes common db operations""" import logging from dataclasses import asdict, astuple from typing import Any, Dict, List, Optional, Generator, Tuple, Union from typing_extensions import Protocol from gn3.db.metadata_audit import MetadataAudit from gn3.db.probesets import Probeset from gn3.db.phenotypes import Phenotype from gn3.db.phenotypes import Publication from gn3.db.phenotypes import PublishXRef from gn3.db.metadata_audit import metadata_audit_mapping from gn3.db.probesets import probeset_mapping from gn3.db.phenotypes import phenotype_mapping from gn3.db.phenotypes import publication_mapping from gn3.db.phenotypes import publish_x_ref_mapping logger = logging.getLogger(__name__) TABLEMAP = { "Phenotype": phenotype_mapping, "ProbeSet": probeset_mapping, "Publication": publication_mapping, "PublishXRef": publish_x_ref_mapping, "metadata_audit": metadata_audit_mapping, } DATACLASSMAP = { "Phenotype": Phenotype, "ProbeSet": Probeset, "Publication": Publication, "PublishXRef": PublishXRef, "metadata_audit": MetadataAudit, } class Dataclass(Protocol): """Type Definition for a Dataclass""" __dataclass_fields__: Dict def update(conn: Any, table: str, data: Dataclass, where: Dataclass) -> Optional[int]: """Run an UPDATE on a table""" logger.warning( "DEPRECATION WARNING: The function `%s.update` is deprecated and will " "be removed soon. **DO NOT** use it, and remove all references to it " "from your code.", __name__) if not (any(astuple(data)) and any(astuple(where))): return None data_ = {k: v for k, v in asdict(data).items() if v is not None and k in TABLEMAP[table]} where_ = {k: v for k, v in asdict(where).items() if v is not None and k in TABLEMAP[table]} sql = f"UPDATE {table} SET " sql += ", ".join(f"{TABLEMAP[table].get(k)} " "= %s" for k in data_.keys()) sql += " WHERE " sql += " AND ".join(f"{TABLEMAP[table].get(k)} = " "%s" for k in where_.keys()) with conn.cursor() as cursor: cursor.execute(sql, tuple(data_.values()) + tuple(where_.values())) conn.commit() return cursor.rowcount def diff_from_dict(old: Dict, new: Dict) -> Dict: """Construct a new dict with a specific structure that contains the difference between the 2 dicts in the structure: diff_from_dict({"id": 1, "data": "a"}, {"id": 2, "data": "b"}) Should return: {"id": {"old": 1, "new": 2}, "data": {"old": "a", "new": "b"}} """ dict_ = {} for key in old.keys(): dict_[key] = {"old": old[key], "new": new[key]} return dict_