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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 uploader.db_utils 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)
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)
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)
return {**params, "Id": cursor.lastrowid}
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