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"""This contains all the necessary functions that are required to add traits
to the published database"""
from typing import Any, Dict, Optional
from dataclasses import dataclass
from typing import Optional
@dataclass(frozen=True)
class riset:
"""Class for keeping track of riset. A riset is a group e.g. rat HSNIH-Palmer,
BXD
"""
name: str
r_id: int
@dataclass(frozen=True)
class webqtlCaseData:
"""Class for keeping track of one case data in one trait"""
value: Optional[float] = None
variance: Optional[float] = None
count: Optional[int] = None # Number of Individuals
def __str__(self):
_str = ""
if self.value:
_str += f"value={self.value:.3f}"
if self.variance:
_str += f" variance={self.variance:.3f}"
if self.count:
_str += " n_data={self.count}"
return _str
def get_riset(data_type: str, name: str, conn: Any):
query, _name, _id = None, None, None
if data_type == "Publish":
query = ("SELECT InbredSet.Name, InbredSet.Id FROM InbredSet, "
"PublishFreeze WHERE PublishFreeze.InbredSetId = "
"InbredSet.Id AND PublishFreeze.Name = '%s'" % name)
elif data_type == "Geno":
query = ("SELECT InbredSet.Name, InbredSet.Id FROM InbredSet, "
"GenoFreeze WHERE GenoFreeze.InbredSetId = "
"InbredSet.Id AND GenoFreeze.Name = '%s'" % name)
elif data_type == "ProbeSet":
query = ("SELECT InbredSet.Name, InbredSet.Id FROM "
"InbredSet, ProbeSetFreeze, ProbeFreeze WHERE "
"ProbeFreeze.InbredSetId = InbredSet.Id AND "
"ProbeFreeze.Id = ProbeSetFreeze.ProbeFreezeId AND "
"ProbeSetFreeze.Name = '%s'" % name)
if query:
with conn.cursor() as cursor:
_name, _id = cursor.fetchone()
if _name == "BXD300":
_name = "BXD"
return riset(_name, _id)
def insert_publication(pubmed_id: int, publication: Optional[Dict],
conn: Any):
"""Creates a new publication record if it's not available"""
sql = ("SELECT Id FROM Publication where "
"PubMed_ID = %d" % pubmed_id)
_id = None
with conn.cursor() as cursor:
cursor.execute(sql)
_id = cursor.fetchone()
if not _id:
# The Publication contains the fields: 'authors', 'title', 'abstract',
# 'journal','volume','pages','month','year'
insert_query = ("INSERT into Publication (%s) Values (%s)" %
(", ".join(publication.keys()),
", ".join(['%s'] * len(publication))))
with conn.cursor() as cursor:
cursor.execute(insert_query, tuple(publication.values()))
def insert_phenotype(phenotype: Optional[Dict], conn: Any):
insert_query = ("INSERT into Phenotype (%s) Values (%s)" %
(", ".join(phenotype.keys()),
", ".join(['%s'] * len(phenotype))))
with conn.cursor() as cursor:
cursor.execute(insert_query, tuple(phenotype.values()))
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