diff options
Diffstat (limited to 'wqflask/maintenance/set_resource_defaults.py')
| -rw-r--r-- | wqflask/maintenance/set_resource_defaults.py | 171 |
1 files changed, 171 insertions, 0 deletions
diff --git a/wqflask/maintenance/set_resource_defaults.py b/wqflask/maintenance/set_resource_defaults.py new file mode 100644 index 00000000..0f472494 --- /dev/null +++ b/wqflask/maintenance/set_resource_defaults.py @@ -0,0 +1,171 @@ +""" + +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 MySQLdb + +import urllib.parse + +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(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(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(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(default_owner_id) + print("AFTER PUBLISH") + insert_geno_resources(default_owner_id) + print("AFTER GENO") + insert_probeset_resources(default_owner_id) + print("AFTER PROBESET") + + +def main(): + """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__': + Conn = MySQLdb.Connect(**parse_db_uri()) + Cursor = Conn.cursor() + main() |