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# pylint: disable=[R0902, R0903]
"""Module that exposes common db operations"""
from typing import Optional, Dict, Any
from dataclasses import dataclass, asdict, astuple
from typing_extensions import Protocol
from MySQLdb import escape_string
from gn3.db.phenotypes import Phenotype
from gn3.db.phenotypes import PublishXRef
from gn3.db.phenotypes import Publication
from gn3.db.phenotypes import phenotype_mapping
from gn3.db.phenotypes import publish_x_ref_mapping
from gn3.db.phenotypes import publication_mapping
TABLEMAP = {
"Phenotype": phenotype_mapping,
"PublishXRef": publish_x_ref_mapping,
"Publication": publication_mapping,
}
DATACLASSMAP = {
"Phenotype": Phenotype,
"PublishXRef": PublishXRef,
"Publication": Publication,
}
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"""
if not (any(astuple(data)) and any(astuple(where))):
return None
sql = f"UPDATE {table} SET "
sql += ", ".join(f"{TABLEMAP[table].get(k)} "
f"= '{escape_string(str(v)).decode('utf-8')}'" for
k, v in asdict(data).items()
if v is not None and k in TABLEMAP[table])
sql += " WHERE "
sql += "AND ".join(f"{TABLEMAP[table].get(k)} = "
f"'{escape_string(str(v)).decode('utf-8')}'" for
k, v in asdict(where).items()
if v is not None and k in TABLEMAP[table])
with conn.cursor() as cursor:
cursor.execute(sql)
return cursor.rowcount
def fetchone(conn: Any,
table: str,
where: Dataclass) -> Optional[Dataclass]:
"""Run a SELECT on a table. Returns only one result!"""
if not any(astuple(where)):
return None
sql = f"SELECT * FROM {table} "
sql += "WHERE "
sql += "AND ".join(f"{TABLEMAP[table].get(k)} = "
f"'{escape_string(str(v)).decode('utf-8')}'" for
k, v in asdict(where).items()
if v is not None and k in TABLEMAP[table])
with conn.cursor() as cursor:
cursor.execute(sql)
return DATACLASSMAP[table](*cursor.fetchone())
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