1 files changed, 0 insertions, 153 deletions
diff --git a/wqflask/maintenance/set_resource_defaults.py b/wqflask/maintenance/set_resource_defaults.py
deleted file mode 100644
index cebe33c0..00000000
--- a/wqflask/maintenance/set_resource_defaults.py
+++ /dev/null
@@ -1,153 +0,0 @@
-"""
-
-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 get_setting
-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
-
-
-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(get_setting("SQL_URI")) as conn:
-        with conn.cursor() as cursor:
-            main(cursor)