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# pylint: disable=[R0902, R0903]
"""This contains all the necessary functions that access the phenotypes from
the db"""
from typing import Optional
from dataclasses import dataclass
from MySQLdb.cursors import DictCursor
from gn3.db_utils import Connection as DBConnection
from .query_tools import mapping_to_query_columns
@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_abbreviation: 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_abbreviation": "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",
}
def fetch_trait(conn: DBConnection, dataset_id: int, trait_name: str) -> dict:
"""Fetch phenotype 'traits' by `dataset_id` and `trait_name`."""
query = (
"SELECT "
"pxr.Id AS id_, pxr.Id as trait_name, pxr.PhenotypeId AS phenotype_id, "
"pxr.PublicationId AS publication_id, pxr.DataId AS data_id, "
"pxr.mean, pxr.locus, pxr.LRS as lrs, pxr.additive, "
"pxr.Sequence as sequence, pxr.comments "
"FROM PublishFreeze AS pf INNER JOIN InbredSet AS iset "
"ON pf.InbredSetId=iset.Id "
"INNER JOIN PublishXRef AS pxr ON iset.Id=pxr.InbredSetId "
"WHERE iset.Id=%(dataset_id)s AND pxr.Id=%(trait_name)s")
with conn.cursor(cursorclass=DictCursor) as cursor:
cursor.execute(
query, {"dataset_id": dataset_id, "trait_name": trait_name})
return cursor.fetchone()
def fetch_metadata(conn: DBConnection, phenotype_id: int) -> dict:
"""Get the phenotype metadata by ID."""
with conn.cursor(cursorclass=DictCursor) as cursor:
cols = ', '.join(mapping_to_query_columns(phenotype_mapping))
cursor.execute(
(f"SELECT Id as id, {cols} FROM Phenotype "
"WHERE Id=%(phenotype_id)s"),
{"phenotype_id": phenotype_id})
return cursor.fetchone()
def fetch_publication_by_id(conn: DBConnection, publication_id: int) -> dict:
"""Fetch the publication by its ID."""
with conn.cursor(cursorclass=DictCursor) as cursor:
cols = ', '.join(mapping_to_query_columns(publication_mapping))
cursor.execute(
(f"SELECT Id as id, {cols} FROM Publication "
"WHERE Id=%(publication_id)s"),
{"publication_id": publication_id})
return cursor.fetchone()
def fetch_publication_by_pubmed_id(conn: DBConnection, pubmed_id: int) -> dict:
"""Fetch the publication by its PUBMED ID."""
with conn.cursor(cursorclass=DictCursor) as cursor:
cols = ', '.join(mapping_to_query_columns(publication_mapping))
cursor.execute(
(f"SELECT Id as id, {cols} FROM Publication "
"WHERE PubMed_Id=%(pubmed_id)s"),
{"pubmed_id": pubmed_id})
return cursor.fetchone()
def update_publication(conn, data=dict) -> int:
"""Update the publication with the given data."""
updatable_cols = ", ".join(f"{publication_mapping[col]}=%({col})s"
for col in data
if col not in ("id_", "id"))
if not bool(updatable_cols):
return 0
with conn.cursor(cursorclass=DictCursor) as cursor:
cursor.execute(
f"UPDATE Publication SET {updatable_cols} WHERE Id=%(id_)s", data)
return cursor.rowcount
def update_phenotype(conn, data:dict) -> int:
"""Update the `Phenotype` table with the given data."""
cols = ", ".join(f"{phenotype_mapping[col]}=%({col})s"
for col in data
if col not in ("id_", "id"))
if not bool(cols):
return 0
with conn.cursor(cursorclass=DictCursor) as cursor:
cursor.execute(
f"UPDATE Phenotype SET {cols} WHERE Id=%(id_)s", data)
return cursor.rowcount
def update_cross_reference(conn, dataset_id, trait_name, data:dict) -> int:
"""Update the `PublishXRef` table with data."""
cols = ", ".join(f"{publish_x_ref_mapping[col]}=%({col})s"
for col in data
if (col not in ("id_", "id") and
col in publish_x_ref_mapping))
if not bool(cols):
return 0
with conn.cursor(cursorclass=DictCursor) as cursor:
cursor.execute(
f"UPDATE PublishXRef SET {cols} WHERE "
"Id=%(trait_name)s AND "
"InbredSetId=%(dataset_id)s",
{
"dataset_id": dataset_id,
"trait_name": trait_name,
**data
})
return cursor.rowcount
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