diff options
Diffstat (limited to 'wqflask/maintenance')
| -rw-r--r-- | wqflask/maintenance/set_resource_defaults.py | 155 |
1 files changed, 155 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..ba102d9c --- /dev/null +++ b/wqflask/maintenance/set_resource_defaults.py @@ -0,0 +1,155 @@ +"""
+
+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
+
+"""
+
+from __future__ import print_function, division
+
+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.tools import SQL_URI
+from utility.redis_tools import get_redis_conn, get_user_id, add_resource, get_resources
+Redis = get_redis_conn()
+
+import MySQLdb
+
+import urlparse
+
+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 = urlparse.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):
+ if i % 20 == 0:
+ print(i)
+ 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": ["no-access", "view"] }
+ else:
+ resource_ob['default_mask'] = { "data": ["no-access"] }
+ resource_ob['group_masks'] = {}
+
+ add_resource(resource_ob)
+
+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" }
+
+ resource_ob['group_masks'] = {}
+
+ add_resource(resource_ob)
+ 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):
+ if i % 20 == 0:
+ print(i)
+ 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-geno"
+ if resource[2] < 1:
+ resource_ob['default_mask'] = { "data": "view" }
+ else:
+ resource_ob['default_mask'] = { "data": "no-access" }
+ resource_ob['group_masks'] = {}
+
+ add_resource(resource_ob)
+
+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 = get_user_id("email_address", "zachary.a.sloan@gmail.com")
+ insert_resources(owner_id)
+
+if __name__ == '__main__':
+ Conn = MySQLdb.Connect(**parse_db_uri())
+ Cursor = Conn.cursor()
+ main()
\ No newline at end of file |