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"""Database and utility functions for phenotypes."""
from typing import Optional
from functools import reduce
from datetime import datetime
import MySQLdb as mdb
from MySQLdb.cursors import Cursor, DictCursor
from flask import current_app as app
from gn_libs.mysqldb import debug_query
def datasets_by_population(
conn: mdb.Connection,
species_id: int,
population_id: int
) -> tuple[dict, ...]:
"""Retrieve all of a population's phenotype studies."""
with conn.cursor(cursorclass=DictCursor) as cursor:
cursor.execute(
"SELECT s.SpeciesId, pf.* FROM Species AS s "
"INNER JOIN InbredSet AS iset ON s.Id=iset.SpeciesId "
"INNER JOIN PublishFreeze AS pf ON iset.Id=pf.InbredSetId "
"WHERE s.Id=%s AND iset.Id=%s;",
(species_id, population_id))
return tuple(dict(row) for row in cursor.fetchall())
def dataset_by_id(conn: mdb.Connection,
species_id: int,
population_id: int,
dataset_id: int) -> dict:
"""Fetch dataset details by identifier"""
with conn.cursor(cursorclass=DictCursor) as cursor:
cursor.execute(
"SELECT s.SpeciesId, pf.* FROM Species AS s "
"INNER JOIN InbredSet AS iset ON s.Id=iset.SpeciesId "
"INNER JOIN PublishFreeze AS pf ON iset.Id=pf.InbredSetId "
"WHERE s.Id=%s AND iset.Id=%s AND pf.Id=%s",
(species_id, population_id, dataset_id))
return dict(cursor.fetchone())
def phenotypes_count(conn: mdb.Connection,
population_id: int,
dataset_id: int) -> int:
"""Count the number of phenotypes in the dataset."""
with conn.cursor(cursorclass=DictCursor) as cursor:
cursor.execute(
"SELECT COUNT(*) AS total_phenos FROM Phenotype AS pheno "
"INNER JOIN PublishXRef AS pxr ON pheno.Id=pxr.PhenotypeId "
"INNER JOIN PublishFreeze AS pf ON pxr.InbredSetId=pf.InbredSetId "
"WHERE pxr.InbredSetId=%s AND pf.Id=%s",
(population_id, dataset_id))
return int(cursor.fetchone()["total_phenos"])
def dataset_phenotypes(conn: mdb.Connection,
population_id: int,
dataset_id: int,
offset: int = 0,
limit: Optional[int] = None) -> tuple[dict, ...]:
"""Fetch the actual phenotypes."""
_query = (
"SELECT pheno.*, pxr.Id, ist.InbredSetCode FROM Phenotype AS pheno "
"INNER JOIN PublishXRef AS pxr ON pheno.Id=pxr.PhenotypeId "
"INNER JOIN PublishFreeze AS pf ON pxr.InbredSetId=pf.InbredSetId "
"INNER JOIN InbredSet AS ist ON pf.InbredSetId=ist.Id "
"WHERE pxr.InbredSetId=%s AND pf.Id=%s") + (
f" LIMIT {limit} OFFSET {offset}" if bool(limit) else "")
with conn.cursor(cursorclass=DictCursor) as cursor:
cursor.execute(_query, (population_id, dataset_id))
debug_query(cursor, app.logger)
return tuple(dict(row) for row in cursor.fetchall())
def __phenotype_se__(cursor: Cursor,
species_id: int,
population_id: int,
dataset_id: int,
xref_id: str) -> dict:
"""Fetch standard-error values (if they exist) for a phenotype."""
_sequery = (
"SELECT pxr.Id AS xref_id, pxr.DataId, str.Id AS StrainId, pse.error, nst.count "
"FROM Phenotype AS pheno "
"INNER JOIN PublishXRef AS pxr ON pheno.Id=pxr.PhenotypeId "
"INNER JOIN PublishSE AS pse ON pxr.DataId=pse.DataId "
"INNER JOIN NStrain AS nst ON pse.DataId=nst.DataId "
"INNER JOIN Strain AS str ON nst.StrainId=str.Id "
"INNER JOIN StrainXRef AS sxr ON str.Id=sxr.StrainId "
"INNER JOIN PublishFreeze AS pf ON sxr.InbredSetId=pf.InbredSetId "
"INNER JOIN InbredSet AS iset ON pf.InbredSetId=iset.InbredSetId "
"WHERE (str.SpeciesId, pxr.InbredSetId, pf.Id, pxr.Id)=(%s, %s, %s, %s)")
cursor.execute(_sequery,
(species_id, population_id, dataset_id, xref_id))
return {(row["DataId"], row["StrainId"]): {
"xref_id": row["xref_id"],
"DataId": row["DataId"],
"error": row["error"],
"count": row["count"]
} for row in cursor.fetchall()}
def __organise_by_phenotype__(pheno, row):
"""Organise disparate data rows into phenotype 'objects'."""
_pheno = pheno.get(row["Id"])
return {
**pheno,
row["Id"]: {
"Id": row["Id"],
"Pre_publication_description": row["Pre_publication_description"],
"Post_publication_description": row["Post_publication_description"],
"Original_description": row["Original_description"],
"Units": row["Units"],
"Pre_publication_abbreviation": row["Pre_publication_abbreviation"],
"Post_publication_abbreviation": row["Post_publication_abbreviation"],
"xref_id": row["pxr.Id"],
"data": {
**(_pheno["data"] if bool(_pheno) else {}),
(row["DataId"], row["StrainId"]): {
"DataId": row["DataId"],
"mean": row["mean"],
"Locus": row["Locus"],
"LRS": row["LRS"],
"additive": row["additive"],
"Sequence": row["Sequence"],
"comments": row["comments"],
"value": row["value"],
"StrainName": row["Name"],
"StrainName2": row["Name2"],
"StrainSymbol": row["Symbol"],
"StrainAlias": row["Alias"]
}
}
}
}
def __merge_pheno_data_and_se__(data, sedata) -> dict:
"""Merge phenotype data with the standard errors."""
return {
key: {**value, **sedata.get(key, {})}
for key, value in data.items()
}
def phenotype_by_id(
conn: mdb.Connection,
species_id: int,
population_id: int,
dataset_id: int,
xref_id
) -> Optional[dict]:
"""Fetch a specific phenotype."""
_dataquery = ("SELECT pheno.*, pxr.*, pd.*, str.*, iset.InbredSetCode "
"FROM Phenotype AS pheno "
"INNER JOIN PublishXRef AS pxr ON pheno.Id=pxr.PhenotypeId "
"INNER JOIN PublishData AS pd ON pxr.DataId=pd.Id "
"INNER JOIN Strain AS str ON pd.StrainId=str.Id "
"INNER JOIN StrainXRef AS sxr ON str.Id=sxr.StrainId "
"INNER JOIN PublishFreeze AS pf ON sxr.InbredSetId=pf.InbredSetId "
"INNER JOIN InbredSet AS iset ON pf.InbredSetId=iset.InbredSetId "
"WHERE "
"(str.SpeciesId, pxr.InbredSetId, pf.Id, pxr.Id)=(%s, %s, %s, %s)")
with conn.cursor(cursorclass=DictCursor) as cursor:
cursor.execute(_dataquery,
(species_id, population_id, dataset_id, xref_id))
_pheno: dict = reduce(__organise_by_phenotype__, cursor.fetchall(), {})
if bool(_pheno) and len(_pheno.keys()) == 1:
_pheno = tuple(_pheno.values())[0]
return {
**_pheno,
"data": tuple(__merge_pheno_data_and_se__(
_pheno["data"],
__phenotype_se__(cursor,
species_id,
population_id,
dataset_id,
xref_id)).values())
}
if bool(_pheno) and len(_pheno.keys()) > 1:
raise Exception(
"We found more than one phenotype with the same identifier!")
return None
def phenotypes_data(conn: mdb.Connection,
population_id: int,
dataset_id: int,
offset: int = 0,
limit: Optional[int] = None) -> tuple[dict, ...]:
"""Fetch the data for the phenotypes."""
# — Phenotype -> PublishXRef -> PublishData -> Strain -> StrainXRef -> PublishFreeze
_query = ("SELECT pheno.*, pxr.*, pd.*, str.*, iset.InbredSetCode "
"FROM Phenotype AS pheno "
"INNER JOIN PublishXRef AS pxr ON pheno.Id=pxr.PhenotypeId "
"INNER JOIN PublishData AS pd ON pxr.DataId=pd.Id "
"INNER JOIN Strain AS str ON pd.StrainId=str.Id "
"INNER JOIN StrainXRef AS sxr ON str.Id=sxr.StrainId "
"INNER JOIN PublishFreeze AS pf ON sxr.InbredSetId=pf.InbredSetId "
"INNER JOIN InbredSet AS iset ON pf.InbredSetId=iset.InbredSetId "
"WHERE pxr.InbredSetId=%s AND pf.Id=%s") + (
f" LIMIT {limit} OFFSET {offset}" if bool(limit) else "")
with conn.cursor(cursorclass=DictCursor) as cursor:
cursor.execute(_query, (population_id, dataset_id))
debug_query(cursor, app.logger)
return tuple(dict(row) for row in cursor.fetchall())
def save_new_dataset(cursor: Cursor,
population_id: int,
dataset_name: str,
dataset_fullname: str,
dataset_shortname: str) -> dict:
"""Create a new phenotype dataset."""
params = {
"population_id": population_id,
"dataset_name": dataset_name,
"dataset_fullname": dataset_fullname,
"dataset_shortname": dataset_shortname,
"created": datetime.now().date().isoformat(),
"public": 2,
"confidentiality": 0,
"users": None
}
cursor.execute(
"INSERT INTO PublishFreeze(Name, FullName, ShortName, CreateTime, "
"public, InbredSetId, confidentiality, AuthorisedUsers) "
"VALUES(%(dataset_name)s, %(dataset_fullname)s, %(dataset_shortname)s, "
"%(created)s, %(public)s, %(population_id)s, %(confidentiality)s, "
"%(users)s)",
params)
debug_query(cursor, app.logger)
return {**params, "Id": cursor.lastrowid}
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