1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
63
64
65
66
67
68
69
70
71
72
73
74
75
76
77
78
79
80
81
82
83
84
85
86
87
88
89
90
91
92
93
94
95
96
97
98
99
100
101
|
"""Handle linking of mRNA Assay data to the Auth(entic|oris)ation system."""
import uuid
from typing import Iterable
from MySQLdb.cursors import DictCursor
from ..checks import authorised_p
from ..groups.models import Group
from ...dictify import dictify
from ...db import sqlite3 as authdb
from ...db import mariadb as gn3db
def linked_mrna_data(conn: authdb.DbConnection) -> Iterable[dict]:
"""Retrieve mRNA Assay data that is linked to user groups."""
with authdb.cursor(conn) as cursor:
cursor.execute("SELECT * FROM linked_mrna_data")
return (dict(row) for row in cursor.fetchall())
@authorised_p(("system:data:link-to-group",),
error_description=(
"You do not have sufficient privileges to link data to (a) "
"group(s)."),
oauth2_scope="profile group resource")
def ungrouped_mrna_data(# pylint: disable=[too-many-arguments]
authconn: authdb.DbConnection, gn3conn: gn3db.DbConnection,
search_query: str, selected: tuple[dict, ...] = tuple(),
limit: int = 10000, offset: int = 0) -> tuple[
dict, ...]:
"""Retrieve mrna data that is not linked to any user group."""
params = tuple(
(row["SpeciesId"], row["InbredSetId"], row["ProbeFreezeId"],
row["ProbeSetFreezeId"])
for row in linked_mrna_data(authconn)) + tuple(
(row["SpeciesId"], row["InbredSetId"], row["ProbeFreezeId"],
row["ProbeSetFreezeId"])
for row in selected)
query = (
"SELECT s.SpeciesId, iset.InbredSetId, iset.InbredSetName, "
"pf.ProbeFreezeId, pf.Name AS StudyName, psf.Id AS ProbeSetFreezeId, "
"psf.Name AS dataset_name, psf.FullName AS dataset_fullname, "
"psf.ShortName AS dataset_shortname "
"FROM Species AS s INNER JOIN InbredSet AS iset "
"ON s.SpeciesId=iset.SpeciesId INNER JOIN ProbeFreeze AS pf "
"ON iset.InbredSetId=pf.InbredSetId INNER JOIN ProbeSetFreeze AS psf "
"ON pf.ProbeFreezeId=psf.ProbeFreezeId ") + (
"WHERE " if (len(params) > 0 or bool(search_query)) else "")
if len(params) > 0:
paramstr = ", ".join(["(%s, %s, %s, %s)"] * len(params))
query = query + (
"(s.SpeciesId, iset.InbredSetId, pf.ProbeFreezeId, psf.Id) "
f"NOT IN ({paramstr}) "
) + ("AND " if bool(search_query) else "")
if bool(search_query):
query = query + (
"CONCAT(pf.Name, psf.Name, ' ', psf.FullName, ' ', psf.ShortName) "
"LIKE %s ")
params = params + ((f"%{search_query}%",),)# type: ignore[operator]
query = query + f"LIMIT {int(limit)} OFFSET {int(offset)}"
with gn3conn.cursor(DictCursor) as cursor:
cursor.execute(
query, tuple(item for sublist in params for item in sublist))
return tuple(row for row in cursor.fetchall())
@authorised_p(
("system:data:link-to-group",),
error_description=(
"You do not have sufficient privileges to link data to (a) "
"group(s)."),
oauth2_scope="profile group resource")
def link_mrna_data(
conn: authdb.DbConnection, group: Group, datasets: dict) -> dict:
"""Link genotye `datasets` to `group`."""
with authdb.cursor(conn) as cursor:
cursor.executemany(
"INSERT INTO linked_mrna_data VALUES "
"(:data_link_id, :group_id, :SpeciesId, :InbredSetId, "
":ProbeFreezeId, :ProbeSetFreezeId, :dataset_name, "
":dataset_fullname, :dataset_shortname) "
"ON CONFLICT "
"(SpeciesId, InbredSetId, ProbeFreezeId, ProbeSetFreezeId) "
"DO NOTHING",
tuple({
"data_link_id": str(uuid.uuid4()),
"group_id": str(group.group_id),
**{
key: value for key,value in dataset.items() if key in (
"SpeciesId", "InbredSetId", "ProbeFreezeId",
"ProbeSetFreezeId", "dataset_fullname", "dataset_name",
"dataset_shortname")
}
} for dataset in datasets))
return {
"description": (
f"Successfully linked {len(datasets)} to group "
f"'{group.group_name}'."),
"group": dictify(group),
"datasets": datasets
}
|
