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"""Functions for accessing the database relating to datasets."""
import MySQLdb as mdb
from MySQLdb.cursors import DictCursor
def geno_datasets_by_species_and_population(
conn: mdb.Connection,
speciesid: int,
populationid: int) -> tuple[dict, ...]:
"""Retrieve all genotypes datasets by species and population"""
with conn.cursor(cursorclass=DictCursor) as cursor:
cursor.execute(
"SELECT gf.* FROM InbredSet AS iset INNER JOIN GenoFreeze AS gf "
"ON iset.InbredSetId=gf.InbredSetId "
"WHERE iset.SpeciesId=%(sid)s AND iset.InbredSetId=%(pid)s",
{"sid": speciesid, "pid": populationid})
return tuple(dict(row) for row in cursor.fetchall())
def geno_dataset_by_id(conn: mdb.Connection, dataset_id: int) -> dict:
"""Retrieve genotype dataset by ID"""
with conn.cursor(cursorclass=DictCursor) as cursor:
cursor.execute("SELECT * FROM GenoFreeze WHERE Id=%s",
(dataset_id,))
return dict(cursor.fetchone())
def probeset_studies_by_species_and_population(
conn: mdb.Connection,
speciesid: int,
populationid: int) -> tuple[dict, ...]:
"""Retrieve all probesets"""
with conn.cursor(cursorclass=DictCursor) as cursor:
cursor.execute(
"SELECT pf.* FROM InbredSet AS iset INNER JOIN ProbeFreeze AS pf "
"ON iset.InbredSetId=pf.InbredSetId "
"WHERE iset.SpeciesId=%(sid)s AND iset.InbredSetId=%(pid)s",
{"sid": speciesid, "pid": populationid})
return tuple(dict(row) for row in cursor.fetchall())
def probeset_datasets_by_study(conn: mdb.Connection,
studyid: int) -> tuple[dict, ...]:
"""Retrieve all probeset databases by study."""
with conn.cursor(cursorclass=DictCursor) as cursor:
cursor.execute("SELECT * FROM ProbeSetFreeze WHERE ProbeFreezeId=%s",
(studyid,))
return tuple(dict(row) for row in cursor.fetchall())
def probe_study_by_id(conn: mdb.Connection, studyid: int) -> dict:
"""Retrieve ProbeSet study by ID"""
with conn.cursor(cursorclass=DictCursor) as cursor:
cursor.execute("SELECT * FROM ProbeFreeze WHERE Id=%s",
(studyid,))
return dict(cursor.fetchone())
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