# 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 wqflask.database import Connection as DBConnection


@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",
}


@dataclass(frozen=True)
class Probeset:
    """Data Type that represents a Probeset"""
    id_: Optional[int] = None
    name: Optional[str] = None
    symbol: Optional[str] = None
    description: Optional[str] = None
    probe_target_description: Optional[str] = None
    chr_: Optional[str] = None
    mb: Optional[float] = None  # pylint: disable=C0103
    alias: Optional[str] = None
    geneid: Optional[str] = None
    homologeneid: Optional[str] = None
    unigeneid: Optional[str] = None
    omim: Optional[str] = None
    refseq_transcriptid: Optional[str] = None
    blatseq: Optional[str] = None
    targetseq: Optional[str] = None
    strand_probe: Optional[str] = None
    probe_set_target_region: Optional[str] = None
    probe_set_specificity: Optional[float] = None
    probe_set_blat_score: Optional[float] = None
    probe_set_blat_mb_start: Optional[float] = None
    probe_set_blat_mb_end: Optional[float] = None
    probe_set_strand: Optional[str] = None
    probe_set_note_by_rw: Optional[str] = None
    flag: Optional[str] = None


# Mapping from the Phenotype dataclass to the actual column names in the
# database
probeset_mapping = {
    "id_": "Id",
    "name": "Name",
    "symbol": "symbol",
    "description": "description",
    "probe_target_description": "Probe_Target_Description",
    "chr_": "Chr",
    "mb": "Mb",
    "alias": "alias",
    "geneid": "GeneId",
    "homologeneid": "HomoloGeneID",
    "unigeneid": "UniGeneId",
    "omim": "OMIM",
    "refseq_transcriptid": "RefSeq_TranscriptId",
    "blatseq": "BlatSeq",
    "targetseq": "TargetSeq",
    "strand_probe": "Strand_Probe",
    "probe_set_target_region": "Probe_set_target_region",
    "probe_set_specificity": "Probe_set_specificity",
    "probe_set_blat_score": "Probe_set_BLAT_score",
    "probe_set_blat_mb_start": "Probe_set_Blat_Mb_start",
    "probe_set_blat_mb_end": "Probe_set_Blat_Mb_end",
    "probe_set_strand": "Probe_set_strand",
    "probe_set_note_by_rw": "Probe_set_Note_by_RW",
    "flag": "flag"
}

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 pf.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()