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# pylint: disable=[R0902, R0903]
"""This contains all the necessary functions that access the phenotypes from
the db"""
from dataclasses import dataclass, asdict, astuple
from typing import Any, Dict, Optional
from MySQLdb import escape_string
from typing_extensions import Protocol
class Dataclass(Protocol):
"""Type Definition for a Dataclass"""
__dataclass_fields__: Dict
@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
# Mapping from the Phenotype dataclass to the actual column names in the
# database
phenotype_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",
}
@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 PublishXRef dataclass to the actual column names in the
# database
publish_x_ref_mapping = {
"id_": "Id",
"inbred_set_id": "InbredSetId",
"phenotype_id": "PhenotypeId",
"publication_id": "PublicationId",
"data_id": "DataId",
"mean": "mean",
"locus": "locus",
"lrs": "lrs",
"additive": "additive",
"sequence": "sequence",
"comments": "comments",
}
@dataclass(frozen=True)
class Publication:
"""Data Type that represents the table Publication"""
id_: Optional[int] = None
pubmed_id: Optional[int] = None
abstract: Optional[str] = None
authors: Optional[str] = None
title: Optional[str] = None
journal: Optional[str] = None
volume: Optional[str] = None
pages: Optional[str] = None
month: Optional[str] = None
year: Optional[str] = None
publication_mapping = {
"id_": "id",
"PubMed_ID": "pubmed_id",
"Abstract": "abstract",
"Authors": "authors",
"Title": "title",
"Journal": "journal",
"Volume": "volume",
"Pages": "pages",
"Month": "month",
"Year": "year",
}
TABLEMAP = {
"Phenotype": phenotype_mapping,
"PublishXRef": publish_x_ref_mapping,
"Publication": publication_mapping,
}
DATACLASSMAP = {
"Phenotype": Phenotype,
"PublishXRef": PublishXRef,
"Publication": Publication,
}
def update(conn: Any,
table: str,
data: Dataclass,
where: Dataclass) -> Optional[int]:
"""Run an UPDATE on a table"""
if not any(astuple(data) + 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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