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
102
103
104
105
106
107
108
|
"""
Link any unlinked InbredSet groups.
"""
import uuid
from pathlib import Path
import click
import gn_auth.auth.db.sqlite3 as authdb
from gn_auth.auth.db import mariadb as biodb
from scripts.migrate_existing_data import sys_admins, admin_group, select_sys_admin
def linked_inbredsets(conn):
"""Fetch all inbredset groups that are linked to the auth system."""
with authdb.cursor(conn) as cursor:
cursor.execute(
"SELECT SpeciesId, InbredSetId FROM linked_inbredset_groups")
return tuple((row["SpeciesId"], row["InbredSetId"])
for row in cursor.fetchall())
def unlinked_inbredsets(conn, linked):
"""Fetch any inbredset groups that are not linked to the auth system."""
with conn.cursor() as cursor:
where_clause = ""
query = "SELECT SpeciesId, InbredSetId, InbredSetName, FullName FROM InbredSet"
if len(linked) > 0:
pholders = ["(%s, %s)"] * len(linked)
where_clause = (f" WHERE (SpeciesId, InbredSetId) "
f"NOT IN ({pholders})")
cursor.execute(query + where_clause,
tuple(arg for sublist in linked for arg in sublist))
return cursor.fetchall()
cursor.execute(query)
return cursor.fetchall()
def link_unlinked(conn, unlinked):
"""Link the unlinked inbredset groups to the auth system."""
params = tuple((str(uuid.uuid4()),) + row for row in unlinked)
with authdb.cursor(conn) as cursor:
cursor.executemany(
"INSERT INTO linked_inbredset_groups VALUES (?, ?, ?, ?, ?)",
params)
return params
def build_resources(conn, new_linked):
"""Build resources for newly linked inbredsets."""
with authdb.cursor(conn) as cursor:
cursor.execute(
"SELECT resource_category_id FROM resource_categories "
"WHERE resource_category_key='inbredset-group'")
category_id = cursor.fetchone()["resource_category_id"]
resources = tuple({
"resource_id": str(uuid.uuid4()),
"resource_name": f"InbredSet: {name}",
"resource_category_id": category_id,
"public": 1,
"data_link_id": datalinkid
} for datalinkid, _sid, _isetid, name, _name in new_linked)
cursor.executemany(
"INSERT INTO resources VALUES "
"(:resource_id, :resource_name, :resource_category_id, :public)",
resources)
cursor.executemany(
"INSERT INTO inbredset_group_resources VALUES "
"(:resource_id, :data_link_id)",
resources)
return resources
def own_resources(conn, group, resources):
"""Link new resources to admin group."""
with authdb.cursor(conn) as cursor:
cursor.executemany(
"INSERT INTO resource_ownership VALUES "
"(:group_id, :resource_id)",
tuple({
"group_id": str(group.group_id),
**resource
} for resource in resources))
return resources
@click.command()
@click.argument("authdbpath") # "Path to the Auth(entic|oris)ation database"
@click.argument("mysqldburi") # "URI to the MySQL database with the biology data"
def run(authdbpath, mysqldburi):
"""Setup command-line arguments."""
if not Path(authdbpath).exists():
print(
f"ERROR: Auth db file `{authdbpath}` does not exist.",
file=sys.stderr)
sys.exit(2)
with (authdb.connection(authdbpath) as authconn,
biodb.database_connection(mysqldburi) as bioconn):
admin = select_sys_admin(sys_admins(authconn))
unlinked = own_resources(
authconn,
admin_group(authconn, admin),
build_resources(
authconn, link_unlinked(
authconn,
unlinked_inbredsets(bioconn, linked_inbredsets(authconn)))))
if __name__ == "__main__":
run() # pylint: disable=[no-value-for-parameter]
|
