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-rw-r--r--wqflask/maintenance/set_resource_defaults.py307
1 files changed, 153 insertions, 154 deletions
diff --git a/wqflask/maintenance/set_resource_defaults.py b/wqflask/maintenance/set_resource_defaults.py
index ba102d9c..344e6a23 100644
--- a/wqflask/maintenance/set_resource_defaults.py
+++ b/wqflask/maintenance/set_resource_defaults.py
@@ -1,155 +1,154 @@
-"""
-
-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()
+"""
+
+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):
+ 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" }
+ 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):
+ resource_ob = {}
+ resource_ob['name'] = resource[1]
+ if resource[1] == "HET3-ITPGeno":
+ resource_ob['owner_id'] = "73a3f093-ca13-4ae0-a179-9a446f709f6e"
+ 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" }
+ 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
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-22 18:16:40 +0000