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# pylint: disable=[R0902]
"""This contains all the necessary functions that access the phenotypes from
the db"""
from dataclasses import dataclass, asdict, astuple
from typing import Any, Optional
from MySQLdb import escape_string
@dataclass(frozen=True)
class Phenotype:
"""Data Type that represents a Phenotype"""
id_: Optional[int] = None
pre_pub_description: Optional[str] = None
post_pub_description: Optional[str] = None
original_description: Optional[str] = None
units: Optional[str] = None
pre_pub_abbrevition: Optional[str] = None
post_pub_abbreviation: Optional[str] = None
lab_code: Optional[str] = None
submitter: Optional[str] = None
owner: Optional[str] = None
authorized_users: Optional[str] = None
@dataclass(frozen=True)
class PublishXRef:
"""Data Type that represents the table PublishXRef"""
id_: Optional[int] = None
inbred_set_id: Optional[str] = None
phenotype_id: Optional[int] = None
publication_id: Optional[str] = None
data_id: Optional[int] = None
mean: Optional[float] = None
locus: Optional[str] = None
lrs: Optional[float] = None
additive: Optional[float] = None
sequence: Optional[int] = None
comments: Optional[str] = None
# Mapping from the Phenotype dataclass to the actual column names in the
# database
phenotype_column_mapping = {
"id_": "id",
"pre_pub_description": "Pre_publication_description",
"post_pub_description": "Post_publication_description",
"original_description": "Original_description",
"units": "Units",
"pre_pub_abbrevition": "Pre_publication_abbreviation",
"post_pub_abbreviation": "Post_publication_abbreviation",
"lab_code": "Lab_code",
"submitter": "Submitter",
"owner": "Owner",
"authorized_users": "Authorized_Users",
}
def update_phenotype(conn: Any,
data: Phenotype,
where: Phenotype) -> Optional[int]:
"""Update phenotype metadata with DATA that depends on the WHERE clause"""
if not any(astuple(data) + astuple(where)):
return None
sql = "UPDATE Phenotype SET "
sql += ", ".join(f"{phenotype_column_mapping.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 phenotype_column_mapping)
sql += " WHERE "
sql += "AND ".join(f"{phenotype_column_mapping.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 phenotype_column_mapping)
with conn.cursor() as cursor:
cursor.execute(sql)
return cursor.rowcount
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