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# pylint: disable=[R0902, R0903]
"""This contains all the necessary functions that access the phenotypes from
the db"""
from dataclasses import dataclass
from typing import Optional
@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"
}
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