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"""Handle db interactions for tissue."""
from typing import Union, Optional
import MySQLdb as mdb
from MySQLdb.cursors import DictCursor
def all_tissues(conn: mdb.Connection) -> tuple[dict, ...]:
"""All available tissue."""
with conn.cursor(cursorclass=DictCursor) as cursor:
cursor.execute("SELECT * FROM Tissue ORDER BY TissueName")
return tuple(dict(row) for row in cursor.fetchall())
def tissue_by_id(conn: mdb.Connection, tissueid) -> Optional[dict]:
"""Retrieve a tissue by its ID"""
with conn.cursor(cursorclass=DictCursor) as cursor:
cursor.execute("SELECT * FROM Tissue WHERE Id=%s", (tissueid,))
result = cursor.fetchone()
if bool(result):
return dict(result)
return None
def create_new_tissue(
conn: mdb.Connection,
name: str,
shortname: str,
birnlexid: Optional[str] = None,
birnlexname: Optional[str] = None
) -> dict[str, Union[int, str, None]]:
"""Add a new tissue, organ or biological material to the database."""
with conn.cursor() as cursor:
cursor.execute(
"INSERT INTO "
"Tissue(TissueName, Name, Short_Name, BIRN_lex_ID, BIRN_lex_Name) "
"VALUES (%s, %s, %s, %s, %s)",
(name, name, shortname, birnlexid, birnlexname))
tissueid = cursor.lastrowid
cursor.execute("UPDATE Tissue SET TissueId=%s WHERE Id=%s",
(tissueid, tissueid))
return {
"Id": tissueid,
"TissueId": tissueid,
"TissueName": name,
"Name": name,
"Short_Name": shortname,
"BIRN_lex_ID": birnlexid,
"BIRN_lex_Name": birnlexname
}
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