"""Database and utility functions for phenotypes."""
from typing import Optional

import MySQLdb as mdb
from MySQLdb.cursors import 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 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."""
    #TODO: This query isn't exactly right, it misses some data.
    # — Phenotype -> PublishXRef -> PublishData -> Strain -> PublishFreeze
    _query = ("SELECT pxr.*, pd.*, str.* FROM PublishFreeze AS pf "
              "INNER JOIN PublishXRef AS pxr ON pf.InbredSetId=pxr.InbredSetId "
              "INNER JOIN PublishData AS pd ON pxr.DataId=pd.Id "
              "INNER JOIN Strain AS str ON pd.StrainId=str.Id "
              "WHERE pf.InbredSetId=%s AND pf.Id=%s "
              "ORDER BY pxr.DataId ASC, str.Id ASC") + (
                  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 phenotypes_se(conn: mdb.Connection, dataset_id: int) -> tuple[dict, ...]:
    """Fetch the standard errors for the phenotypes."""
    return tuple()


def phenotypes_sample_counts(conn: mdb.Connection, dataset_id: int) -> tuple[dict, ...]:
    """Fetch the standard errors for the phenotypes."""
    return tuple()