Adding all the authentication stuff

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