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"""
Script that sets default resource access masks for use with the DB proxy
Defaults will be:
Owner - omni_gn
Mask - Public/non-confidential: { data: "view",
metadata: "view",
admin: "not-admin" }
Private/confidentia: { data: "no-access",
metadata: "no-access",
admin: "not-admin" }
To run:
./bin/genenetwork2 ~/my_settings.py -c ./wqflask/maintenance/gen_select_dataset.py
"""
import sys
import json
# NEW: Note we prepend the current path - otherwise a guix instance of GN2 may be used instead
sys.path.insert(0, './')
# NEW: import app to avoid a circular dependency on utility.tools
from wqflask import app
from utility import hmac
from utility.tools import SQL_URI
from utility.redis_tools import get_redis_conn, get_user_id, add_resource, get_resources, get_resource_info
Redis = get_redis_conn()
import urllib.parse
from wqflask.database import database_connection
from utility.logger import getLogger
logger = getLogger(__name__)
def parse_db_uri():
"""Converts a database URI to the db name, host name, user name, and password"""
parsed_uri = urllib.parse.urlparse(SQL_URI)
db_conn_info = dict(
db=parsed_uri.path[1:],
host=parsed_uri.hostname,
user=parsed_uri.username,
passwd=parsed_uri.password)
print(db_conn_info)
return db_conn_info
def insert_probeset_resources(cursor, default_owner_id):
current_resources = Redis.hgetall("resources")
cursor.execute(""" SELECT
ProbeSetFreeze.Id, ProbeSetFreeze.Name, ProbeSetFreeze.confidentiality, ProbeSetFreeze.public
FROM
ProbeSetFreeze""")
resource_results = cursor.fetchall()
for i, resource in enumerate(resource_results):
resource_ob = {}
resource_ob['name'] = resource[1]
resource_ob['owner_id'] = default_owner_id
resource_ob['data'] = {"dataset": str(resource[0])}
resource_ob['type'] = "dataset-probeset"
if resource[2] < 1 and resource[3] > 0:
resource_ob['default_mask'] = {"data": "view",
"metadata": "view",
"admin": "not-admin"}
else:
resource_ob['default_mask'] = {"data": "no-access",
"metadata": "no-access",
"admin": "not-admin"}
resource_ob['group_masks'] = {}
add_resource(resource_ob, update=False)
def insert_publish_resources(cursor, default_owner_id):
current_resources = Redis.hgetall("resources")
cursor.execute(""" SELECT
PublishXRef.Id, PublishFreeze.Id, InbredSet.InbredSetCode
FROM
PublishXRef, PublishFreeze, InbredSet, Publication
WHERE
PublishFreeze.InbredSetId = PublishXRef.InbredSetId AND
InbredSet.Id = PublishXRef.InbredSetId AND
Publication.Id = PublishXRef.PublicationId""")
resource_results = cursor.fetchall()
for resource in resource_results:
if resource[2]:
resource_ob = {}
if resource[2]:
resource_ob['name'] = resource[2] + "_" + str(resource[0])
else:
resource_ob['name'] = str(resource[0])
resource_ob['owner_id'] = default_owner_id
resource_ob['data'] = {"dataset": str(resource[1]),
"trait": str(resource[0])}
resource_ob['type'] = "dataset-publish"
resource_ob['default_mask'] = {"data": "view",
"metadata": "view",
"admin": "not-admin"}
resource_ob['group_masks'] = {}
add_resource(resource_ob, update=False)
else:
continue
def insert_geno_resources(cursor, default_owner_id):
current_resources = Redis.hgetall("resources")
cursor.execute(""" SELECT
GenoFreeze.Id, GenoFreeze.ShortName, GenoFreeze.confidentiality
FROM
GenoFreeze""")
resource_results = cursor.fetchall()
for i, resource in enumerate(resource_results):
resource_ob = {}
resource_ob['name'] = resource[1]
if resource[1] == "HET3-ITPGeno":
resource_ob['owner_id'] = "c5ce8c56-78a6-474f-bcaf-7129d97f56ae"
else:
resource_ob['owner_id'] = default_owner_id
resource_ob['data'] = {"dataset": str(resource[0])}
resource_ob['type'] = "dataset-geno"
if resource[2] < 1:
resource_ob['default_mask'] = {"data": "view",
"metadata": "view",
"admin": "not-admin"}
else:
resource_ob['default_mask'] = {"data": "no-access",
"metadata": "no-access",
"admin": "not-admin"}
resource_ob['group_masks'] = {}
add_resource(resource_ob, update=False)
def insert_resources(default_owner_id):
current_resources = get_resources()
print("START")
insert_publish_resources(cursor, default_owner_id)
print("AFTER PUBLISH")
insert_geno_resources(cursor, default_owner_id)
print("AFTER GENO")
insert_probeset_resources(cursor, default_owner_id)
print("AFTER PROBESET")
def main(cursor):
"""Generates and outputs (as json file) the data for the main dropdown menus on the home page"""
Redis.delete("resources")
owner_id = "c5ce8c56-78a6-474f-bcaf-7129d97f56ae"
insert_resources(owner_id)
if __name__ == '__main__':
with database_connection() as conn:
with conn.cursor() as cursor:
main(cursor)
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