Merge github.com:genenetwork/genenetwork2 into acenteno

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()