From a302a2b0ac0e7c0f26a0d063c3f2b057f61d47f1 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 5 Jun 2020 16:52:56 -0500
Subject: Commiting other current group/resource management code, plus the new
 files

---
 wqflask/utility/authentication_tools.py | 46 +++++++++++++++++++++++++++++++++
 1 file changed, 46 insertions(+)
 create mode 100644 wqflask/utility/authentication_tools.py

(limited to 'wqflask/utility/authentication_tools.py')

diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py
new file mode 100644
index 00000000..537881a5
--- /dev/null
+++ b/wqflask/utility/authentication_tools.py
@@ -0,0 +1,46 @@
+from __future__ import absolute_import, print_function, division
+
+import json
+import requests
+
+from base import data_set
+
+from utility import hmac
+from utility.redis_tools import get_redis_conn, get_resource_info, get_resource_id
+
+from flask import Flask, g, redirect, url_for
+
+import logging
+logger = logging.getLogger(__name__ )
+
+def check_resource_availability(dataset, trait_id=None):
+    resource_id = get_resource_id(dataset, trait_id)
+
+    if resource_id:
+        the_url = "http://localhost:8080/available?resource={}&user={}".format(resource_id, g.user_session.user_id)
+        try:
+            response = json.loads(requests.get(the_url).content)['data']
+        except:
+            resource_info = get_resource_info(resource_id)
+            response = resource_info['default_mask']['data']
+
+        if 'view' in response:
+            return True
+        else:
+            return redirect(url_for("no_access_page"))
+
+    return True
+
+def check_owner(dataset=None, trait_id=None, resource_id=None):
+    if resource_id:
+        resource_info = get_resource_info(resource_id)
+        if g.user_session.user_id == resource_info['owner_id']:
+            return resource_id
+    else:
+        resource_id = get_resource_id(dataset, trait_id)
+        if resource_id:
+            resource_info = get_resource_info(resource_id)
+            if g.user_session.user_id == resource_info['owner_id']:
+                return resource_id
+
+    return False
\ No newline at end of file
-- 
cgit v1.2.3


From ea47eb228b1224ea83e3f50a056bf715b3bf5ec6 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 17 Jun 2020 14:49:40 -0500
Subject: Adding all the authentication stuff

---
 wqflask/base/data_set.py                           |  36 +--
 wqflask/base/trait.py                              |   5 +-
 wqflask/maintenance/set_resource_defaults.py       | 307 ++++++++++-----------
 wqflask/utility/authentication_tools.py            | 132 ++++++---
 wqflask/utility/redis_tools.py                     |  67 ++++-
 wqflask/wqflask/docs.py                            |   4 +-
 wqflask/wqflask/group_manager.py                   | 220 ++++++++++-----
 wqflask/wqflask/resource_manager.py                | 204 +++++++++-----
 .../wqflask/static/new/javascript/group_manager.js |  74 ++---
 .../static/new/javascript/search_results.js        |   1 -
 .../templates/admin/change_resource_owner.html     | 116 ++++++++
 wqflask/wqflask/templates/admin/create_group.html  | 178 ++++++------
 wqflask/wqflask/templates/admin/group_manager.html |  18 +-
 .../wqflask/templates/admin/manage_resource.html   | 200 ++++++++------
 .../wqflask/templates/admin/search_for_groups.html | 198 ++++++++-----
 .../templates/admin/select_group_to_add.html       |  54 ----
 .../templates/admin/set_group_privileges.html      | 102 +++++++
 wqflask/wqflask/templates/admin/view_group.html    | 238 ++++++++++++++++
 wqflask/wqflask/templates/base.html                |   5 +
 .../wqflask/templates/set_group_privileges.html    |  77 ++++++
 wqflask/wqflask/templates/show_trait_details.html  |   4 +-
 wqflask/wqflask/views.py                           |   2 +-
 22 files changed, 1516 insertions(+), 726 deletions(-)
 create mode 100644 wqflask/wqflask/templates/admin/change_resource_owner.html
 delete mode 100644 wqflask/wqflask/templates/admin/select_group_to_add.html
 create mode 100644 wqflask/wqflask/templates/admin/set_group_privileges.html
 create mode 100644 wqflask/wqflask/templates/admin/view_group.html
 create mode 100644 wqflask/wqflask/templates/set_group_privileges.html

(limited to 'wqflask/utility/authentication_tools.py')

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 1457ba8d..92dc8615 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -486,25 +486,18 @@ class DatasetGroup(object):
 
 def datasets(group_name, this_group = None):
     key = "group_dataset_menu:v2:" + group_name
-    logger.debug("key is2:", key)
     dataset_menu = []
-    logger.debug("[tape4] webqtlConfig.PUBLICTHRESH:", webqtlConfig.PUBLICTHRESH)
-    logger.debug("[tape4] type webqtlConfig.PUBLICTHRESH:", type(webqtlConfig.PUBLICTHRESH))
     the_results = fetchall('''
          (SELECT '#PublishFreeze',PublishFreeze.FullName,PublishFreeze.Name
           FROM PublishFreeze,InbredSet
           WHERE PublishFreeze.InbredSetId = InbredSet.Id
             and InbredSet.Name = '%s'
-            and PublishFreeze.public > %s
-            and PublishFreeze.confidentiality < 1
           ORDER BY PublishFreeze.Id ASC)
          UNION
          (SELECT '#GenoFreeze',GenoFreeze.FullName,GenoFreeze.Name
           FROM GenoFreeze, InbredSet
           WHERE GenoFreeze.InbredSetId = InbredSet.Id
-            and InbredSet.Name = '%s'
-            and GenoFreeze.public > %s
-            and GenoFreeze.confidentiality < 1)
+            and InbredSet.Name = '%s')
          UNION
          (SELECT Tissue.Name, ProbeSetFreeze.FullName,ProbeSetFreeze.Name
           FROM ProbeSetFreeze, ProbeFreeze, InbredSet, Tissue
@@ -512,12 +505,10 @@ def datasets(group_name, this_group = None):
             and ProbeFreeze.TissueId = Tissue.Id
             and ProbeFreeze.InbredSetId = InbredSet.Id
             and InbredSet.Name like %s
-            and ProbeSetFreeze.public > %s
-            and ProbeSetFreeze.confidentiality < 1
           ORDER BY Tissue.Name, ProbeSetFreeze.OrderList DESC)
-        ''' % (group_name, webqtlConfig.PUBLICTHRESH,
-              group_name, webqtlConfig.PUBLICTHRESH,
-              "'" + group_name + "'", webqtlConfig.PUBLICTHRESH))
+        ''' % (group_name,
+              group_name,
+              "'" + group_name + "'"))
 
     sorted_results = sorted(the_results, key=lambda kv: kv[0])
 
@@ -637,29 +628,25 @@ class DataSet(object):
 
         """
 
-
         try:
             if self.type == "ProbeSet":
                 query_args = tuple(escape(x) for x in (
-                    str(webqtlConfig.PUBLICTHRESH),
                     self.name,
                     self.name,
                     self.name))
 
                 self.id, self.name, self.fullname, self.shortname, self.data_scale, self.tissue = fetch1("""
-SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, ProbeSetFreeze.FullName, ProbeSetFreeze.ShortName, ProbeSetFreeze.DataScale, Tissue.Name
-FROM ProbeSetFreeze, ProbeFreeze, Tissue
-WHERE ProbeSetFreeze.public > %s
-AND ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id
-AND ProbeFreeze.TissueId = Tissue.Id
-AND (ProbeSetFreeze.Name = '%s' OR ProbeSetFreeze.FullName = '%s' OR ProbeSetFreeze.ShortName = '%s')
+    SELECT ProbeSetFreeze.Id, ProbeSetFreeze.Name, ProbeSetFreeze.FullName, ProbeSetFreeze.ShortName, ProbeSetFreeze.DataScale, Tissue.Name
+    FROM ProbeSetFreeze, ProbeFreeze, Tissue
+    WHERE ProbeSetFreeze.ProbeFreezeId = ProbeFreeze.Id
+    AND ProbeFreeze.TissueId = Tissue.Id
+    AND (ProbeSetFreeze.Name = '%s' OR ProbeSetFreeze.FullName = '%s' OR ProbeSetFreeze.ShortName = '%s')
                 """ % (query_args),"/dataset/"+self.name+".json",
             lambda r: (r["id"],r["name"],r["full_name"],r["short_name"],r["data_scale"],r["tissue"])
                 )
             else:
                 query_args = tuple(escape(x) for x in (
                     (self.type + "Freeze"),
-                    str(webqtlConfig.PUBLICTHRESH),
                     self.name,
                     self.name,
                     self.name))
@@ -668,9 +655,8 @@ AND (ProbeSetFreeze.Name = '%s' OR ProbeSetFreeze.FullName = '%s' OR ProbeSetFre
                 self.id, self.name, self.fullname, self.shortname = fetchone("""
                         SELECT Id, Name, FullName, ShortName
                         FROM %s
-                        WHERE public > %s AND
-                             (Name = '%s' OR FullName = '%s' OR ShortName = '%s')
-                  """ % (query_args))
+                        WHERE (Name = '%s' OR FullName = '%s' OR ShortName = '%s')
+                    """ % (query_args))
 
         except TypeError:
             logger.debug("Dataset {} is not yet available in GeneNetwork.".format(self.name))
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 2a945588..7700ecd5 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -46,9 +46,10 @@ def create_trait(**kw):
             else:
                 permitted = check_resource_availability(dataset)
 
-    if permitted:
+    if permitted != "no-access":
         the_trait = GeneralTrait(**kw)
         if the_trait.dataset.type != "Temp":
+
             the_trait = retrieve_trait_info(the_trait, the_trait.dataset, get_qtl_info=kw.get('get_qtl_info'))
         return the_trait
     else:
@@ -383,7 +384,6 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
     if dataset.type == 'Publish':
         the_url = "http://localhost:8080/run-action?resource={}&user={}&branch=data&action=view".format(resource_id, g.user_session.user_id)
     else:
-
         the_url = "http://localhost:8080/run-action?resource={}&user={}&branch=data&action=view&trait={}".format(resource_id, g.user_session.user_id, trait.name)
 
     try:
@@ -424,7 +424,6 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
             logger.sql(query)
             trait_info = g.db.execute(query).fetchone()
 
-
         #XZ, 05/08/2009: Xiaodong add this block to use ProbeSet.Id to find the probeset instead of just using ProbeSet.Name
         #XZ, 05/08/2009: to avoid the problem of same probeset name from different platforms.
         elif dataset.type == 'ProbeSet':
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
diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py
index 537881a5..07ceacc0 100644
--- a/wqflask/utility/authentication_tools.py
+++ b/wqflask/utility/authentication_tools.py
@@ -1,46 +1,86 @@
-from __future__ import absolute_import, print_function, division
-
-import json
-import requests
-
-from base import data_set
-
-from utility import hmac
-from utility.redis_tools import get_redis_conn, get_resource_info, get_resource_id
-
-from flask import Flask, g, redirect, url_for
-
-import logging
-logger = logging.getLogger(__name__ )
-
-def check_resource_availability(dataset, trait_id=None):
-    resource_id = get_resource_id(dataset, trait_id)
-
-    if resource_id:
-        the_url = "http://localhost:8080/available?resource={}&user={}".format(resource_id, g.user_session.user_id)
-        try:
-            response = json.loads(requests.get(the_url).content)['data']
-        except:
-            resource_info = get_resource_info(resource_id)
-            response = resource_info['default_mask']['data']
-
-        if 'view' in response:
-            return True
-        else:
-            return redirect(url_for("no_access_page"))
-
-    return True
-
-def check_owner(dataset=None, trait_id=None, resource_id=None):
-    if resource_id:
-        resource_info = get_resource_info(resource_id)
-        if g.user_session.user_id == resource_info['owner_id']:
-            return resource_id
-    else:
-        resource_id = get_resource_id(dataset, trait_id)
-        if resource_id:
-            resource_info = get_resource_info(resource_id)
-            if g.user_session.user_id == resource_info['owner_id']:
-                return resource_id
-
-    return False
\ No newline at end of file
+from __future__ import absolute_import, print_function, division
+
+import json
+import requests
+
+from base import data_set
+
+from utility import hmac
+from utility.redis_tools import get_redis_conn, get_resource_info, get_resource_id
+
+from flask import Flask, g, redirect, url_for
+
+import logging
+logger = logging.getLogger(__name__ )
+
+def check_resource_availability(dataset, trait_id=None):
+    resource_id = get_resource_id(dataset, trait_id)
+
+    response = None
+    if resource_id:
+        resource_info = get_resource_info(resource_id)
+
+        the_url = "http://localhost:8080/available?resource={}&user={}".format(resource_id, g.user_session.user_id)
+        try:
+            response = json.loads(requests.get(the_url).content)['data']
+        except:
+            response = resource_info['default_mask']['data']
+
+        if 'edit' in response:
+            return "edit"
+        elif 'view' in response:
+            return "view"
+        else:
+            return "no-access"
+
+    return False
+
+def check_admin(resource_id=None):
+
+    return "not-admin"
+
+    # ZS: commented out until proxy can return this
+    # the_url = "http://localhost:8080/available?resource={}&user={}".format(resource_id, g.user_session.user_id)
+    # try:
+    #     response = json.loads(requests.get(the_url).content)
+    # except:
+    #     response = resource_info['default_mask']['admin']
+
+    # if 'edit-admins' in response:
+    #     return "edit-admins"
+    # elif 'edit-access' in response:
+    #     return "edit-access"
+    # else:
+    #     return "not-admin"
+
+def check_owner(dataset=None, trait_id=None, resource_id=None):
+    if resource_id:
+        resource_info = get_resource_info(resource_id)
+        if g.user_session.user_id == resource_info['owner_id']:
+            return resource_id
+    else:
+        resource_id = get_resource_id(dataset, trait_id)
+        if resource_id:
+            resource_info = get_resource_info(resource_id)
+            if g.user_session.user_id == resource_info['owner_id']:
+                return resource_id
+
+    return False
+
+def check_owner_or_admin(dataset=None, trait_id=None, resource_id=None):
+    if resource_id:
+        resource_info = get_resource_info(resource_id)
+        if g.user_session.user_id == resource_info['owner_id']:
+            return [resource_id, "owner"]
+        else:
+            return [resource_id, check_admin(resource_id)]
+    else:
+        resource_id = get_resource_id(dataset, trait_id)
+        if resource_id:
+            resource_info = get_resource_info(resource_id)
+            if g.user_session.user_id == resource_info['owner_id']:
+                return [resource_id, "owner"]
+            else:
+                return [resource_id, check_admin(resource_id)]
+
+    return [resource_id, "not-admin"]
\ No newline at end of file
diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py
index bc30a0af..c6d221ff 100644
--- a/wqflask/utility/redis_tools.py
+++ b/wqflask/utility/redis_tools.py
@@ -16,7 +16,7 @@ from utility.logger import getLogger
 logger = getLogger(__name__)
 
 def get_redis_conn():
-    Redis = redis.StrictRedis(port=6380)
+    Redis = redis.StrictRedis(port=6379)
     return Redis
 
 Redis = get_redis_conn()
@@ -51,6 +51,27 @@ def get_user_by_unique_column(column_name, column_value):
 
     return item_details
 
+def get_users_like_unique_column(column_name, column_value):
+    """
+    Like previous function, but this only checks if the input is a subset of a field and can return multiple results
+    """
+    matched_users = []
+
+    if column_value != "":
+        user_list = Redis.hgetall("users")
+        if column_name != "user_id":
+            for key in user_list:
+                user_ob = json.loads(user_list[key])
+                if column_name in user_ob:
+                    if column_value in user_ob[column_name]:
+                        matched_users.append(user_ob)
+        else:
+            matched_users.append(json.loads(user_list[column_value]))
+
+    return matched_users
+
+# def search_users_by_unique_column(column_name, column_value):
+
 def set_user_attribute(user_id, column_name, column_value):
     user_info = json.loads(Redis.hget("users", user_id))
     user_info[column_name] = column_value
@@ -142,6 +163,28 @@ def get_group_by_unique_column(column_name, column_value):
 
     return matched_groups
 
+def get_groups_like_unique_column(column_name, column_value):
+    """
+    Like previous function, but this only checks if the input is a subset of a field and can return multiple results
+    """
+    matched_groups = []
+
+    if column_value != "":
+        group_list = Redis.hgetall("groups")
+        if column_name != "group_id":
+            for key in group_list:
+                group_info = json.loads(group_list[key])
+                if column_name == "admins" or column_name == "members": #ZS: Since these fields are lists, search in the list
+                    if column_value in group_info[column_name]:
+                        matched_groups.append(group_info)
+                else:
+                    if column_name in group_info:
+                        if column_value in group_info[column_name]:
+                            matched_groups.append(group_info)
+        else:
+            matched_groups.append(json.loads(group_list[column_value]))
+
+    return matched_groups
 
 def create_group(admin_user_ids, member_user_ids = [], group_name = "Default Group Name"):
     group_id = str(uuid.uuid4())
@@ -192,9 +235,13 @@ def add_users_to_group(user_id, group_id, user_emails = [], admins = False): #ZS
 
 def remove_users_from_group(user_id, users_to_remove_ids, group_id, user_type = "members"): #ZS: User type is because I assume admins can remove other admins
     group_info = get_group_info(group_id)
+
     if user_id in group_info["admins"]:
+        users_to_remove_set = set(users_to_remove_ids)
+        if user_type == "admins" and user_id in users_to_remove_set: #ZS: Make sure an admin can't remove themselves from a group, since I imagine we don't want groups to be able to become admin-less
+            users_to_remove_set.remove(user_id)
         group_users = set(group_info[user_type])
-        group_users -= set(users_to_remove_ids)
+        group_users -= users_to_remove_set
         group_info[user_type] = list(group_users)
         group_info["changed_timestamp"] = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p')
         Redis.hset("groups", group_id, json.dumps(group_info))
@@ -232,7 +279,6 @@ def get_resource_info(resource_id):
     return json.loads(resource_info)
 
 def add_resource(resource_info):
-
     if 'trait' in resource_info['data']:
         resource_id = hmac.hmac_creation('{}:{}:{}'.format(str(resource_info['type']), str(resource_info['data']['dataset']), str(resource_info['data']['trait'])))
     else:
@@ -241,3 +287,18 @@ def add_resource(resource_info):
     Redis.hset("resources", resource_id, json.dumps(resource_info))
 
     return resource_info
+
+def add_access_mask(resource_id, group_id, access_mask):
+    the_resource = get_resource_info(resource_id)
+    the_resource['group_masks'][group_id] = access_mask
+
+    Redis.hset("resources", resource_id, json.dumps(the_resource))
+
+    return the_resource
+
+def change_resource_owner(resource_id, new_owner_id):
+    the_resource= get_resource_info(resource_id)
+    the_resource['owner_id'] = new_owner_id
+
+    Redis.delete("resource")
+    Redis.hset("resources", resource_id, json.dumps(the_resource))
\ No newline at end of file
diff --git a/wqflask/wqflask/docs.py b/wqflask/wqflask/docs.py
index 0187f32e..78407e22 100644
--- a/wqflask/wqflask/docs.py
+++ b/wqflask/wqflask/docs.py
@@ -1,5 +1,7 @@
 from __future__ import absolute_import, print_function, division
 
+import codecs
+
 from flask import g
 
 from utility.logger import getLogger
@@ -20,7 +22,7 @@ class Docs(object):
             self.content = ""
         else:
             self.title = result[0]
-            self.content = result[1]
+            self.content = result[1].encode("latin1")
 
         self.editable = "false"
         # ZS: Removing option to edit to see if text still gets vandalized
diff --git a/wqflask/wqflask/group_manager.py b/wqflask/wqflask/group_manager.py
index f41ae56d..9afc016b 100644
--- a/wqflask/wqflask/group_manager.py
+++ b/wqflask/wqflask/group_manager.py
@@ -1,77 +1,145 @@
-
-from __future__ import print_function, division, absolute_import
-
-from flask import (Flask, g, render_template, url_for, request, make_response,
-                   redirect, flash)
-
-from wqflask import app
-from wqflask.user_login import send_verification_email
-
-from utility.redis_tools import get_user_groups, get_group_info, create_group, delete_group, add_users_to_group, remove_users_from_group, \
-                                change_group_name, save_verification_code, check_verification_code, get_user_by_unique_column
-
-from utility.logger import getLogger
-logger = getLogger(__name__)
-
-@app.route("/groups/manage", methods=('GET', 'POST'))
-def manage_groups():
-   params = request.form if request.form else request.args
-   if "add_new_group" in params:
-      return redirect(url_for('add_group'))
-   else:
-      admin_groups, user_groups = get_user_groups(g.user_session.user_id)
-      return render_template("admin/group_manager.html", admin_groups=admin_groups, user_groups=user_groups)
-
-@app.route("/groups/remove", methods=('POST',))
-def remove_groups():
-   group_ids_to_remove = request.form['selected_group_ids']
-   for group_id in group_ids_to_remove.split(":"):
-      delete_group(g.user_session.user_id, group_id)
-
-   return redirect(url_for('manage_groups'))
-
-@app.route("/groups/create", methods=('GET', 'POST'))
-def add_group():
-   params = request.form if request.form else request.args
-   if "group_name" in params:
-      member_user_ids = set()
-      admin_user_ids = set()
-      admin_user_ids.add(g.user_session.user_id) #ZS: Always add the user creating the group as an admin
-      if "admin_emails" in params:
-         admin_emails = params['admin_emails_to_add'].split(",")
-         for email in admin_emails:
-            user_details = get_user_by_unique_column("email_address", email)
-            if user_details:
-               admin_user_ids.add(user_details['user_id'])
-         #send_group_invites(params['group_id'], user_email_list = admin_emails, user_type="admins")
-      if "user_emails" in params:
-         member_emails = params['member_emails_to_add'].split(",")
-         for email in member_emails:
-            user_details = get_user_by_unique_column("email_address", email)
-            if user_details:
-               member_user_ids.add(user_details['user_id'])
-         #send_group_invites(params['group_id'], user_email_list = user_emails, user_type="members")
-
-      create_group(list(admin_user_ids), list(member_user_ids), params['group_name'])
-      return redirect(url_for('manage_groups'))
-   else:
-      return render_template("admin/create_group.html")
-
-#ZS: Will integrate this later, for now just letting users be added directly
-def send_group_invites(group_id, user_email_list = [], user_type="members"):
-   for user_email in user_email_list:
-      user_details = get_user_by_unique_column("email_address", user_email)
-      if user_details:
-         group_info = get_group_info(group_id)
-         #ZS: Probably not necessary since the group should normally always exist if group_id is being passed here,
-         #    but it's technically possible to hit it if Redis is cleared out before submitting the new users or something
-         if group_info:
-            #ZS: Don't add user if they're already an admin or if they're being added a regular user and are already a regular user,
-            #    but do add them if they're a regular user and are added as an admin
-            if (user_details['user_id'] in group_info['admins']) or \
-               ((user_type == "members") and (user_details['user_id'] in group_info['members'])):
-               continue
-            else:
-               send_verification_email(user_details, template_name = "email/group_verification.txt", key_prefix = "verification_code", subject = "You've been invited to join a GeneNetwork user group")
-
+
+from __future__ import print_function, division, absolute_import
+
+from flask import (Flask, g, render_template, url_for, request, make_response,
+                   redirect, flash)
+
+from wqflask import app
+from wqflask.user_login import send_verification_email
+
+from utility.redis_tools import get_user_groups, get_group_info, create_group, delete_group, add_users_to_group, remove_users_from_group, \
+                                change_group_name, save_verification_code, check_verification_code, get_user_by_unique_column, get_resources, get_resource_info
+
+from utility.logger import getLogger
+logger = getLogger(__name__)
+
+@app.route("/groups/manage", methods=('GET', 'POST'))
+def manage_groups():
+   params = request.form if request.form else request.args
+   if "add_new_group" in params:
+      return redirect(url_for('add_group'))
+   else:
+      admin_groups, user_groups = get_user_groups(g.user_session.user_id)
+      return render_template("admin/group_manager.html", admin_groups=admin_groups, user_groups=user_groups)
+
+@app.route("/groups/view", methods=('GET', 'POST'))
+def view_group():
+   params = request.form if request.form else request.args
+   group_id = params['id']
+   group_info = get_group_info(group_id)
+   admins_info = []
+   user_is_admin = False
+   if g.user_session.user_id in group_info['admins']:
+      user_is_admin = True
+   for user_id in group_info['admins']:
+      if user_id:
+         user_info = get_user_by_unique_column("user_id", user_id)
+         admins_info.append(user_info)
+   members_info = []
+   for user_id in group_info['members']:
+      if user_id:
+         user_info = get_user_by_unique_column("user_id", user_id)
+         members_info.append(user_info)
+
+   #ZS: This whole part might not scale well with many resources
+   resources_info  = []
+   all_resources = get_resources()
+   for resource_id in all_resources:
+      resource_info = get_resource_info(resource_id)
+      group_masks = resource_info['group_masks']
+      if group_id in group_masks:
+         this_resource = {}
+         privileges = group_masks[group_id]
+         this_resource['id'] = resource_id
+         this_resource['name'] = resource_info['name']
+         this_resource['data'] = privileges['data']
+         this_resource['metadata'] = privileges['metadata']
+         this_resource['admin'] = privileges['admin']
+         resources_info.append(this_resource)
+
+   return render_template("admin/view_group.html", group_info=group_info, admins=admins_info, members=members_info, user_is_admin=user_is_admin, resources=resources_info)
+
+@app.route("/groups/remove", methods=('POST',))
+def remove_groups():
+   group_ids_to_remove = request.form['selected_group_ids']
+   for group_id in group_ids_to_remove.split(":"):
+      delete_group(g.user_session.user_id, group_id)
+
+   return redirect(url_for('manage_groups'))
+
+@app.route("/groups/remove_users", methods=('POST',))
+def remove_users():
+   group_id = request.form['group_id']
+   admin_ids_to_remove = request.form['selected_admin_ids']
+   member_ids_to_remove = request.form['selected_member_ids']
+
+   remove_users_from_group(g.user_session.user_id, admin_ids_to_remove.split(":"), group_id, user_type="admins")
+   remove_users_from_group(g.user_session.user_id, member_ids_to_remove.split(":"), group_id, user_type="members")
+
+   return redirect(url_for('view_group', id=group_id))
+
+@app.route("/groups/add_<path:user_type>", methods=('POST',))
+def add_users(user_type='members'):
+   group_id = request.form['group_id']
+   if user_type == "admins":
+      user_emails = request.form['admin_emails_to_add'].split(",")
+      add_users_to_group(g.user_session.user_id, group_id, user_emails, admins = True)
+   elif user_type == "members":
+      user_emails = request.form['member_emails_to_add'].split(",")
+      add_users_to_group(g.user_session.user_id, group_id, user_emails, admins = False)
+
+   return redirect(url_for('view_group', id=group_id))
+
+@app.route("/groups/change_name", methods=('POST',))
+def change_name():
+   group_id = request.form['group_id']
+   new_name = request.form['new_name']
+   group_info = change_group_name(g.user_session.user_id, group_id, new_name)
+
+   return new_name
+
+@app.route("/groups/create", methods=('GET', 'POST'))
+def add_or_edit_group():
+   params = request.form if request.form else request.args
+   if "group_name" in params:
+      member_user_ids = set()
+      admin_user_ids = set()
+      admin_user_ids.add(g.user_session.user_id) #ZS: Always add the user creating the group as an admin
+      if "admin_emails_to_add" in params:
+         admin_emails = params['admin_emails_to_add'].split(",")
+         for email in admin_emails:
+            user_details = get_user_by_unique_column("email_address", email)
+            if user_details:
+               admin_user_ids.add(user_details['user_id'])
+         #send_group_invites(params['group_id'], user_email_list = admin_emails, user_type="admins")
+      if "member_emails_to_add" in params:
+         member_emails = params['member_emails_to_add'].split(",")
+         for email in member_emails:
+            user_details = get_user_by_unique_column("email_address", email)
+            if user_details:
+               member_user_ids.add(user_details['user_id'])
+         #send_group_invites(params['group_id'], user_email_list = user_emails, user_type="members")
+
+      create_group(list(admin_user_ids), list(member_user_ids), params['group_name'])
+      return redirect(url_for('manage_groups'))
+   else:
+      return render_template("admin/create_group.html")
+
+#ZS: Will integrate this later, for now just letting users be added directly
+def send_group_invites(group_id, user_email_list = [], user_type="members"):
+   for user_email in user_email_list:
+      user_details = get_user_by_unique_column("email_address", user_email)
+      if user_details:
+         group_info = get_group_info(group_id)
+         #ZS: Probably not necessary since the group should normally always exist if group_id is being passed here,
+         #    but it's technically possible to hit it if Redis is cleared out before submitting the new users or something
+         if group_info:
+            #ZS: Don't add user if they're already an admin or if they're being added a regular user and are already a regular user,
+            #    but do add them if they're a regular user and are added as an admin
+            if (user_details['user_id'] in group_info['admins']) or \
+               ((user_type == "members") and (user_details['user_id'] in group_info['members'])):
+               continue
+            else:
+               send_verification_email(user_details, template_name = "email/group_verification.txt", key_prefix = "verification_code", subject = "You've been invited to join a GeneNetwork user group")
+
 #@app.route()
\ No newline at end of file
diff --git a/wqflask/wqflask/resource_manager.py b/wqflask/wqflask/resource_manager.py
index 7d88b8ed..0f9f5c9d 100644
--- a/wqflask/wqflask/resource_manager.py
+++ b/wqflask/wqflask/resource_manager.py
@@ -1,72 +1,134 @@
-from __future__ import print_function, division, absolute_import
-
-from flask import (Flask, g, render_template, url_for, request, make_response,
-                   redirect, flash)
-
-from wqflask import app
-
-from utility.authentication_tools import check_owner
-from utility.redis_tools import get_resource_info, get_group_info, get_group_by_unique_column, get_user_id
-
-from utility.logger import getLogger
-logger = getLogger(__name__)
-
-@app.route("/resources/manage", methods=('GET', 'POST'))
-def view_resource():
-    params = request.form if request.form else request.args
-    if 'resource_id' in request.args:
-        resource_id = request.args['resource_id']
-        if check_owner(resource_id=resource_id):
-            resource_info = get_resource_info(resource_id)
-            group_masks = resource_info['group_masks']
-            group_masks_with_names = get_group_names(group_masks)
-            default_mask = resource_info['default_mask']['data']
-            return render_template("admin/manage_resource.html", resource_id = resource_id, resource_info=resource_info, default_mask=default_mask, group_masks=group_masks_with_names)
-        else:
-            return redirect(url_for("no_access_page"))
-        
-@app.route("/resources/add_group", methods=('POST',))
-def add_group_to_resource():
-    resource_id = request.form['resource_id']
-    if check_owner(resource_id=resource_id):
-        if all(key in request.form for key in ('group_id', 'group_name', 'user_name', 'user_email')):
-            group_list = []
-            if request.form['group_id'] != "":
-                the_group = get_group_info(request.form['group_id'])
-                if the_group:
-                    group_list.append(the_group)
-            if request.form['group_name'] != "":
-                matched_groups = get_group_by_unique_column("name", request.form['group_name'])
-                for group in matched_groups:
-                    group_list.append(group)
-            if request.form['user_name'] != "":
-                user_id = get_user_id("user_name", request.form['user_name'])
-                if user_id:
-                    matched_groups = get_group_by_unique_column("admins", user_id)
-                    matched_groups += get_group_by_unique_column("members", user_id)
-                    for group in matched_groups:
-                        group_list.append(group)
-            if request.form['user_email'] != "":
-                user_id = get_user_id("email_address", request.form['user_email'])
-                if user_id:
-                    matched_groups = get_group_by_unique_column("admins", user_id)
-                    matched_groups += get_group_by_unique_column("members", user_id)
-                    for group in matched_groups:
-                        group_list.append(group)
-            return render_template("admin/select_group_to_add.html", group_list=group_list, resource_id = resource_id)
-        elif 'selected_group' in request.form:
-            group_id = request.form['selected_group']
-            return render_template("admin/set_group_privileges.html", resource_id = resource_id, group_id = group_id)
-        else:
-            return render_template("admin/search_for_groups.html", resource_id = resource_id)
-    else:
-        return redirect(url_for("no_access_page"))
-
-def get_group_names(group_masks):
-    group_masks_with_names = {}
-    for group_id, group_mask in group_masks.iteritems():
-        this_mask = group_mask
-        group_name = get_group_info(group_id)['name']
-        this_mask['name'] = group_name
-    
+from __future__ import print_function, division, absolute_import
+
+import json
+
+from flask import (Flask, g, render_template, url_for, request, make_response,
+                   redirect, flash)
+
+from wqflask import app
+
+from utility.authentication_tools import check_owner_or_admin
+from utility.redis_tools import get_resource_info, get_group_info, get_groups_like_unique_column, get_user_id, get_user_by_unique_column, get_users_like_unique_column, add_access_mask, add_resource, change_resource_owner
+
+from utility.logger import getLogger
+logger = getLogger(__name__)
+
+@app.route("/resources/manage", methods=('GET', 'POST'))
+def manage_resource():
+    params = request.form if request.form else request.args
+    if 'resource_id' in request.args:
+        resource_id = request.args['resource_id']
+        admin_status = check_owner_or_admin(resource_id=resource_id)[1]
+
+        resource_info = get_resource_info(resource_id)
+        group_masks = resource_info['group_masks']
+        group_masks_with_names = get_group_names(group_masks)
+        default_mask = resource_info['default_mask']['data']
+        owner_id = resource_info['owner_id']
+        owner_info = get_user_by_unique_column("user_id", owner_id)
+
+        if 'name' in owner_info:
+            owner_display_name = owner_info['full_name']
+        elif 'user_name' in owner_info:
+            owner_display_name = owner_info['user_name']
+        elif 'email_address' in owner_info:
+            owner_display_name = owner_info['email_address']
+        else:
+            owner_display_name = None
+
+        return render_template("admin/manage_resource.html", owner_name = owner_display_name, resource_id = resource_id, resource_info=resource_info, default_mask=default_mask, group_masks=group_masks_with_names, admin_status=admin_status)
+
+@app.route("/search_for_users", methods=('POST',))
+def search_for_user():
+    params = request.form
+    user_list = []
+    user_list += get_users_like_unique_column("full_name", params['user_name'])
+    user_list += get_users_like_unique_column("email_address", params['user_email'])
+
+    return json.dumps(user_list)
+
+@app.route("/search_for_groups", methods=('POST',))
+def search_for_groups():
+    params = request.form
+    group_list = []
+    group_list += get_groups_like_unique_column("id", params['group_id'])
+    group_list += get_groups_like_unique_column("name", params['group_name'])
+
+    user_list = []
+    user_list += get_users_like_unique_column("full_name", params['user_name'])
+    user_list += get_users_like_unique_column("email_address", params['user_email'])
+    for user in user_list:
+        group_list += get_groups_like_unique_column("admins", user['user_id'])
+        group_list += get_groups_like_unique_column("members", user['user_id'])
+
+    return json.dumps(group_list)
+
+@app.route("/resources/change_owner", methods=('POST',))
+def change_owner():
+    resource_id = request.form['resource_id']
+    if 'new_owner' in request.form:
+        admin_status = check_owner_or_admin(resource_id=resource_id)[1]
+        if admin_status == "owner":
+            new_owner_id = request.form['new_owner']
+            change_resource_owner(resource_id, new_owner_id)
+            flash("The resource's owner has beeen changed.", "alert-info")
+            return redirect(url_for("manage_resource", resource_id=resource_id))
+        else:
+            flash("You lack the permissions to make this change.", "error")
+            return redirect(url_for("manage_resource", resource_id=resource_id))
+    else:
+        return render_template("admin/change_resource_owner.html", resource_id = resource_id)
+
+@app.route("/resources/change_default_privileges", methods=('POST',))
+def change_default_privileges():
+    resource_id = request.form['resource_id']
+    admin_status = check_owner_or_admin(resource_id=resource_id)
+    if admin_status == "owner" or admin_status == "edit-admins":
+        resource_info = get_resource_info(resource_id)
+        default_mask = resource_info['default_mask']
+        if request.form['open_to_public'] == "True":
+            default_mask['data'] = 'view'
+        else:
+            default_mask['data'] = 'no-access'
+        resource_info['default_mask'] = default_mask
+        add_resource(resource_info)
+        flash("Your changes have been saved.", "alert-info")
+        return redirect(url_for("manage_resource", resource_id=resource_id))
+    else:
+        return redirect(url_for("no_access_page"))
+
+@app.route("/resources/add_group", methods=('POST',))
+def add_group_to_resource():
+    resource_id = request.form['resource_id']
+    admin_status = check_owner_or_admin(resource_id=resource_id)[1]
+    if admin_status == "owner" or admin_status == "edit-admins" or admin_status == "edit-access":
+        if 'selected_group' in request.form:
+            group_id = request.form['selected_group']
+            resource_info = get_resource_info(resource_id)
+            default_privileges = resource_info['default_mask']
+            return render_template("admin/set_group_privileges.html", resource_id = resource_id, group_id = group_id, default_privileges = default_privileges)
+        elif all(key in request.form for key in ('data_privilege', 'metadata_privilege', 'admin_privilege')):
+            group_id = request.form['group_id']
+            group_name = get_group_info(group_id)['name']
+            access_mask = {
+                'data': request.form['data_privilege'],
+                'metadata': request.form['metadata_privilege'],
+                'admin': request.form['admin_privilege']
+            }
+            add_access_mask(resource_id, group_id, access_mask)
+            flash("Privileges have been added for group {}.".format(group_name), "alert-info")
+            return redirect(url_for("manage_resource", resource_id=resource_id))
+        else:
+            return render_template("admin/search_for_groups.html", resource_id = resource_id)
+    else:
+        return redirect(url_for("no_access_page"))
+
+def get_group_names(group_masks):
+    group_masks_with_names = {}
+    for group_id, group_mask in group_masks.iteritems():
+        this_mask = group_mask
+        group_name = get_group_info(group_id)['name']
+        this_mask['name'] = group_name
+        group_masks_with_names[group_id] = this_mask
+    
     return group_masks_with_names
\ No newline at end of file
diff --git a/wqflask/wqflask/static/new/javascript/group_manager.js b/wqflask/wqflask/static/new/javascript/group_manager.js
index 5e82d104..4c172cbf 100644
--- a/wqflask/wqflask/static/new/javascript/group_manager.js
+++ b/wqflask/wqflask/static/new/javascript/group_manager.js
@@ -1,38 +1,38 @@
-$('#add_to_admins').click(function() {
-    add_emails('admin')
-})
-
-$('#add_to_members').click(function() {
-    add_emails('member')
-})
-
-$('#clear_admins').click(function(){
-    clear_emails('admin')
-})
-
-$('#clear_members').click(function(){
-    clear_emails('member')
-})
-
-
-function add_emails(user_type){
-    var email_address = $('input[name=user_email]').val();
-    var email_list_string = $('input[name=' + user_type + '_emails_to_add]').val()
-    console.log(email_list_string)
-    if (email_list_string == ""){
-        var email_set = new Set();
-    } else {
-        var email_set = new Set(email_list_string.split(","))
-    }
-    email_set.add(email_address)
-
-    $('input[name=' + user_type + '_emails_to_add]').val(Array.from(email_set).join(','))
-
-    var emails_display_string = Array.from(email_set).join('\n')
-    $('.added_' + user_type + 's').val(emails_display_string)
-}
-
-function clear_emails(user_type){
-    $('input[name=' + user_type + '_emails_to_add]').val("")
-    $('.added_' + user_type + 's').val("")
+$('#add_to_admins').click(function() {
+    add_emails('admin')
+})
+
+$('#add_to_members').click(function() {
+    add_emails('member')
+})
+
+$('#clear_admins').click(function(){
+    clear_emails('admin')
+})
+
+$('#clear_members').click(function(){
+    clear_emails('member')
+})
+
+
+function add_emails(user_type){
+    var email_address = $('input[name=user_email]').val();
+    var email_list_string = $('input[name=' + user_type + '_emails_to_add]').val().trim()
+    console.log(email_list_string)
+    if (email_list_string == ""){
+        var email_set = new Set();
+    } else {
+        var email_set = new Set(email_list_string.split(","))
+    }
+    email_set.add(email_address)
+
+    $('input[name=' + user_type + '_emails_to_add]').val(Array.from(email_set).join(','))
+
+    var emails_display_string = Array.from(email_set).join('\n')
+    $('.added_' + user_type + 's').val(emails_display_string)
+}
+
+function clear_emails(user_type){
+    $('input[name=' + user_type + '_emails_to_add]').val("")
+    $('.added_' + user_type + 's').val("")
 }
\ No newline at end of file
diff --git a/wqflask/wqflask/static/new/javascript/search_results.js b/wqflask/wqflask/static/new/javascript/search_results.js
index 8fa698b4..115dac13 100644
--- a/wqflask/wqflask/static/new/javascript/search_results.js
+++ b/wqflask/wqflask/static/new/javascript/search_results.js
@@ -296,7 +296,6 @@ $(function() {
   $("#deselect_all").click(deselect_all);
   $("#invert").click(invert);
   $("#add").click(add);
-  $("#remove").click(remove);
   $("#submit_bnw").click(submit_bnw);
   $("#export_traits").click(export_traits);
   $('.trait_checkbox, .btn').click(change_buttons);
diff --git a/wqflask/wqflask/templates/admin/change_resource_owner.html b/wqflask/wqflask/templates/admin/change_resource_owner.html
new file mode 100644
index 00000000..ae9409b0
--- /dev/null
+++ b/wqflask/wqflask/templates/admin/change_resource_owner.html
@@ -0,0 +1,116 @@
+{% extends "base.html" %}
+{% block title %}Resource Manager{% endblock %}
+{% block css %}
+    <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
+    <link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
+{% endblock %}
+{% block content %}
+<!-- Start of body -->
+    <div class="container">
+        <div class="page-header">
+            <h1>Search for user to assign ownership to:</h1>
+        </div>
+        <form id="change_owner_form" action="/resources/change_owner" method="POST">
+            <input type="hidden" name="resource_id" value="{{ resource_id }}">
+            <div style="min-width: 600px; max-width: 800px;">
+                <fieldset>
+                    <div class="form-horizontal" style="width: 900px;">
+                        <div style="margin-bottom: 30px;">
+                            <h2>Search for user by either name or e-mail:</h2>
+                        </div>
+                        <div class="form-group" style="padding-left: 20px;">
+                            <label for="user_name" class="col-xs-3" style="float: left; font-size: 18px;">User's Name:</label>
+                            <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
+                                <input name="user_name" type="text" value="">
+                            </div>
+                        </div>
+                        <div class="form-group" style="padding-left: 20px;">
+                            <label for="user_email" class="col-xs-3" style="float: left; font-size: 18px;">User's E-mail:</label>
+                            <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
+                                <input name="user_email" type="text" value="">
+                            </div>
+                        </div>
+                        <div class="form-group" style="padding-left: 20px;">
+                            <label class="col-xs-3" style="float: left; font-size: 18px;"></label>
+                            <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
+                                <button type="button" id="find_users" class="btn btn-primary">Search</button>
+                                <button style="margin-left: 20px; display: none;" type="submit" id="submit_new_owner" class="btn btn-success">Assign Ownership to Selected User</button>
+                            </div>
+                        </div>
+                    </div>
+                </fieldset>
+                <hr>
+                <div id="user_results">
+                </div>
+            </div>
+        </form>
+    </div>
+
+<!-- End of body -->
+
+{% endblock %}
+
+{% block js %}
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
+
+    <script language="javascript">
+        $('#find_users').click(function() {
+            $.ajax({
+                method: "POST",
+                url: "/search_for_users",
+                data: {
+                    user_name: $('input[name=user_name]').val(),
+                    user_email: $('input[name=user_email]').val()
+                },
+                success: populate_users
+            });
+        })
+
+        populate_users = function(json_user_list){
+            var user_list = JSON.parse(json_user_list)
+
+            var the_html = ""
+            if (user_list.length > 0){
+                the_html += "<table id='users_table' style='padding-top: 10px; width: 100%;' class='table-hover table-striped cell-border'>";
+                the_html += "<thead><tr><th></th><th>Index</th><th>Name</th><th>E-mail Address</th><th>Organization</th></tr></thead>";
+                the_html += "<tbody>";
+                for (_i = 0, _len = user_list.length; _i < _len; _i++) {
+                    this_user = user_list[_i]
+                    the_html += "<tr>";
+                    the_html += "<td align='center' class='select_user'><input type='radio' name='new_owner' value='" + this_user.user_id + "'></td>";
+                    the_html += "<td>" + (_i + 1).toString() + "</td>"
+                    if ("full_name" in this_user) {
+                        the_html += "<td>" + this_user.full_name + "</td>";
+                    } else {
+                        the_html += "<td>N/A</td>"
+                    }
+                    if ("email_address" in this_user) {
+                        the_html += "<td>" + this_user.email_address + "</td>";
+                    } else {
+                        the_html += "<td>N/A</td>"
+                    }
+                    if ("organization" in this_user) {
+                        the_html += "<td>" + this_user.organization + "</td>";
+                    } else {
+                        the_html += "<td>N/A</td>"
+                    }
+                    the_html += "</tr>"
+                }
+                the_html += "</tbody>";
+                the_html += "</table>";
+            } else {
+                the_html = "<span>No users were found matching the entered criteria.</span>"
+            }
+
+            $('#user_results').html(the_html)
+            if (user_list.length > 0){
+                $('#users_table').dataTable({
+                    'order': [[1, "asc" ]],
+                    'sDom': 'tr'
+                });
+                $('input[name=select_user]:eq(0)').prop("checked", true)
+                $('#submit_new_owner').css("display", "inline-block")
+            }
+        }
+    </script>
+{% endblock %}
diff --git a/wqflask/wqflask/templates/admin/create_group.html b/wqflask/wqflask/templates/admin/create_group.html
index 55c3fa0b..5a6929fb 100644
--- a/wqflask/wqflask/templates/admin/create_group.html
+++ b/wqflask/wqflask/templates/admin/create_group.html
@@ -1,89 +1,89 @@
-{% extends "base.html" %}
-{% block title %}Group Manager{% endblock %}
-{% block content %}
-<!-- Start of body -->
-    <div class="container">
-        <div class="page-header">
-            <h1>Create Group</h1>
-        </div>
-        <form action="/groups/create" method="POST">
-            <input type="hidden" name="admin_emails_to_add" value="">
-            <input type="hidden" name="member_emails_to_add" value="">
-            <fieldset>
-                <div class="form-horizontal" style="width: 900px; margin-bottom: 50px;">
-                    <div class="form-group" style="padding-left: 20px;">
-                        <label for="group_name" class="col-xs-3" style="float: left; font-size: 18px;">Group Name:</label>
-                        <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
-                            <div class="col-xs-12">
-                                <input name="group_name" type="text" style="width:100%;"></input>
-                            </div>
-                        </div>
-                    </div>
-                    <div class="form-group" style="padding-left: 20px;">
-                        <label for="user_email" class="col-xs-3" style="float: left; font-size: 18px;">Add User Email:</label>
-                        <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
-                            <div class="col-xs-12">
-                                <input name="user_email" type="text" style="width:100%;"></input>
-                            </div>
-                        </div>
-                    </div>
-                    <div class="form-group" style="padding-left: 20px;">
-                        <label class="col-xs-3"></label>
-                        <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
-                            <div class="col-xs-6">
-                                <button type="button" id="add_to_admins" class="btn btn-default">Add to Admins</button>
-                            </div>
-                            <div class="col-xs-6">
-                                <button type="button" id="add_to_members" class="btn btn-default">Add to Members</button>
-                            </div>
-                        </div>
-                    </div>
-                    <div class="form-group" style="padding-left: 20px;">
-                        <label class="col-xs-3" style="font-size: 18px;">Members to be added:</label>
-                        <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
-                            <div class="col-xs-6">
-                                <textarea rows="8" cols="60" readonly placeholder="No users added" style="overflow-y: scroll; resize: none; width: 200px;" class="added_admins"></textarea>
-                            </div>
-                            <div class="col-xs-6">
-                                <textarea rows="8" cols="60" readonly placeholder="No users added" style="overflow-y: scroll; resize: none; width: 200px;" class="added_members"></textarea>
-                            </div>
-                        </div>
-                    </div>
-                    <div class="form-group" style="padding-left: 20px;">
-                        <label class="col-xs-3"></label>
-                        <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
-                            <div class="col-xs-6">
-                                <button type="button" id="clear_admins" class="btn btn-default">Clear</button>
-                            </div>
-                            <div class="col-xs-6">
-                                <button type="button" id="clear_members" class="btn btn-default">Clear</button>
-                            </div>
-                        </div>
-                    </div>
-                    <div class="form-group" style="padding-left: 20px;">
-                        <label for="create_group" class="col-xs-3" style="float: left; font-size: 18px;"></label>
-                        <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
-                            <div class="col-xs-6">
-                                <button type="button" id="create_group" class="btn btn-primary">Create Group</button>
-                            </div>
-                        </div>
-                    </div>
-                </div>
-            </fieldset>
-        </form>
-    </div>
-
-
-
-<!-- End of body -->
-
-{% endblock %}
-
-{% block js %}
-    <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/javascript/group_manager.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
-
-    <script type="text/javascript" charset="utf-8">
-    </script>
-{% endblock %}
+{% extends "base.html" %}
+{% block title %}Group Manager{% endblock %}
+{% block content %}
+<!-- Start of body -->
+    <div class="container">
+        <div class="page-header">
+            <h1>Create Group</h1>
+        </div>
+        <form action="/groups/create" method="POST">
+            <input type="hidden" name="admin_emails_to_add" value="">
+            <input type="hidden" name="member_emails_to_add" value="">
+            <fieldset>
+                <div class="form-horizontal" style="width: 900px; margin-bottom: 50px;">
+                    <div class="form-group" style="padding-left: 20px;">
+                        <label for="group_name" class="col-xs-3" style="float: left; font-size: 18px;">Group Name:</label>
+                        <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
+                            <div class="col-xs-12">
+                                <input name="group_name" type="text" style="width:100%;"></input>
+                            </div>
+                        </div>
+                    </div>
+                    <div class="form-group" style="padding-left: 20px;">
+                        <label for="user_email" class="col-xs-3" style="float: left; font-size: 18px;">Add User Email:</label>
+                        <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
+                            <div class="col-xs-12">
+                                <input name="user_email" type="text" style="width:100%;"></input>
+                            </div>
+                        </div>
+                    </div>
+                    <div class="form-group" style="padding-left: 20px;">
+                        <label class="col-xs-3"></label>
+                        <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
+                            <div class="col-xs-6">
+                                <button type="button" id="add_to_admins" class="btn btn-default">Add to Admins</button>
+                            </div>
+                            <div class="col-xs-6">
+                                <button type="button" id="add_to_members" class="btn btn-default">Add to Members</button>
+                            </div>
+                        </div>
+                    </div>
+                    <div class="form-group" style="padding-left: 20px;">
+                        <label class="col-xs-3" style="font-size: 18px;">Members to be added:</label>
+                        <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
+                            <div class="col-xs-6">
+                                <textarea rows="8" cols="60" readonly placeholder="No users added" style="overflow-y: scroll; resize: none; width: 200px;" class="added_admins"></textarea>
+                            </div>
+                            <div class="col-xs-6">
+                                <textarea rows="8" cols="60" readonly placeholder="No users added" style="overflow-y: scroll; resize: none; width: 200px;" class="added_members"></textarea>
+                            </div>
+                        </div>
+                    </div>
+                    <div class="form-group" style="padding-left: 20px;">
+                        <label class="col-xs-3"></label>
+                        <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
+                            <div class="col-xs-6">
+                                <button type="button" id="clear_admins" class="btn btn-default">Clear</button>
+                            </div>
+                            <div class="col-xs-6">
+                                <button type="button" id="clear_members" class="btn btn-default">Clear</button>
+                            </div>
+                        </div>
+                    </div>
+                    <div class="form-group" style="padding-left: 20px;">
+                        <label for="create_group" class="col-xs-3" style="float: left; font-size: 18px;"></label>
+                        <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
+                            <div class="col-xs-6">
+                                <button type="submit" id="create_group" class="btn btn-primary">Create Group</button>
+                            </div>
+                        </div>
+                    </div>
+                </div>
+            </fieldset>
+        </form>
+    </div>
+
+
+
+<!-- End of body -->
+
+{% endblock %}
+
+{% block js %}
+    <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/new/javascript/group_manager.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
+
+    <script type="text/javascript" charset="utf-8">
+    </script>
+{% endblock %}
diff --git a/wqflask/wqflask/templates/admin/group_manager.html b/wqflask/wqflask/templates/admin/group_manager.html
index 23d8205a..70d55684 100644
--- a/wqflask/wqflask/templates/admin/group_manager.html
+++ b/wqflask/wqflask/templates/admin/group_manager.html
@@ -23,7 +23,7 @@
                 <br>
                 <button type="submit" name="add_new_group" class="btn btn-primary">Create a new group</button>
                 {% else %}
-                <div><h3>Admin Groups</h3></div>
+                <div style="margin-top: 20px;"><h2>Admin Groups</h2></div>
                 <hr>
                 {% if admin_groups|length == 0 %}
                 <h4>You currently aren't the administrator of any groups.</h4>
@@ -45,8 +45,8 @@
                         <tr>
                             <td><input type="checkbox" name="group_id" value="{{ group.id }}"></td>
                             <td align="right">{{ loop.index }}</td>
-                            <td>{{ group.name }}</td>
-                            <td align="right">{{ group.admins|length + group.users|length }}</td>
+                            <td><a href="/groups/view?id={{ group.id }}">{{ group.name }}</a></td>
+                            <td align="right">{{ group.admins|length + group.members|length }}</td>
                             <td>{{ group.created_timestamp }}</td>
                             <td>{{ group.changed_timestamp }}</td>
                             <td>{{ group.id }}</td>
@@ -58,7 +58,7 @@
             </div>
             <hr>
             <div style="min-width: 800px; max-width: 1000px;">
-                <div><h3>User Groups</h3></div>
+                <div><h2>User Groups</h2></div>
                 <hr>
                 {% if user_groups|length == 0 %}
                 <h4>You currently aren't a member of any groups.</h4>
@@ -80,7 +80,7 @@
                             <td><input type="checkbox" name="read" value="{{ group.id }}"></td>
                             <td>{{ loop.index }}</td>
                             <td>{{ group.name }}</td>
-                            <td>{{ group.admins|length + group.users|length }}</td>
+                            <td>{{ group.admins|length + group.members|length }}</td>
                             <td>{{ group.created_timestamp }}</td>
                             <td>{{ group.changed_timestamp }}</td>
                         </tr>
@@ -103,10 +103,14 @@
     <script type="text/javascript" charset="utf-8">
         $(document).ready( function () {
             {% if admin_groups|length != 0 %}
-            $('#admin_groups').dataTable();
+            $('#admin_groups').dataTable({
+                'sDom': 'tr'
+            });
             {% endif %}
             {% if user_groups|length != 0 %}
-            $('#user_groups').dataTable();
+            $('#user_groups').dataTable({
+                'sDom': 'tr'
+            });
             {% endif %}
             submit_special = function(url) {
                 $("#groups_form").attr("action", url);
diff --git a/wqflask/wqflask/templates/admin/manage_resource.html b/wqflask/wqflask/templates/admin/manage_resource.html
index a47f47ad..0b12eaae 100644
--- a/wqflask/wqflask/templates/admin/manage_resource.html
+++ b/wqflask/wqflask/templates/admin/manage_resource.html
@@ -1,92 +1,108 @@
-{% extends "base.html" %}
-{% block title %}Resource Manager{% endblock %}
-{% block content %}
-<!-- Start of body -->
-    <div class="container">
-        <div class="page-header">
-            <h1>Resource Manager</h1>
-        </div>
-        <form id="manage_resource" action="/resources/manage" method="POST">
-            <input type="hidden" name="resource_id" value="{{ resource_id }}">
-            <div class="col-xs-6" style="min-width: 600px; max-width: 800px;">
-                <fieldset>
-                    <div class="form-horizontal" style="width: 900px; margin-bottom: 50px;">
-                        <div class="form-group" style="padding-left: 20px;">
-                            <label for="group_name" class="col-xs-3" style="float: left; font-size: 18px;">Resource Name:</label>
-                            <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
-                                {{ resource_info.name }}
-                            </div>
-                        </div>
-                        <div class="form-group" style="padding-left: 20px;">
-                            <label for="user_email" class="col-xs-3" style="float: left; font-size: 18px;">Open to Public:</label>
-                            <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
-                                <label class="radio-inline">
-                                    <input type="radio" name="default_mask" value="True" checked="">
-                                    Yes
-                                </label>
-                                <label class="radio-inline">
-                                    <input type="radio" name="default_mask" value="False">
-                                    No
-                            </label>
-                            </div>
-                        </div>
-                        <div class="form-group" style="padding-left: 20px;">
-                            <label class="col-xs-3" style="float: left; font-size: 18px;"></label>
-                            <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
-                                <button id="save_changes" class="btn btn-primary">Save Changes</button>
-                            </div>
-                        </div>
-                    </div>
-                </fieldset>
-            </div>
-            <div class="col-xs-6" style="min-width: 600px; max-width: 800px;">
-                <button id="add_group_to_resource" class="btn btn-primary" style="margin-bottom: 30px;" data-url="/resources/add_group">Add Group</button>
-                <br>
-                {% if group_masks|length > 0 %}
-                <h3>Current Group Permissions</h3>
-                <table>
-                    <thead>
-                        <tr>
-                            <th>Name</th>
-                            <th>Data</th>
-                            <th>Metadata</th>
-                            <th>Admin</th>
-                        </tr>
-                    </thead>
-                    <tbody>
-                        {% for key, value in group_masks.iteritems() %}
-                        <tr>
-                            <td>{{ value.name }}</td>
-                            <td>{{ value.data }}</td>
-                            <td>{{ value.metadata }}</td>
-                            <td>{{ value.admin }}</td>
-                        </tr>
-                        {% endfor %}
-                    </tbody>
-                </table>
-                {% else %}
-                <h3>No groups are currently added to this resource.</h3>
-                {% endif %}
-            </div>
-        </form>
-    </div>
-
-
-
-<!-- End of body -->
-
-{% endblock %}
-
-{% block js %}
-    <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/javascript/group_manager.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
-
-    <script type="text/javascript" charset="utf-8">
-        $('#add_group_to_resource').click(function(){
-            url = $(this).data("url");
-            $('#manage_resource').attr("action", url)
-            $('#manage_resource').submit()
-        })
-    </script>
-{% endblock %}
+{% extends "base.html" %}
+{% block title %}Resource Manager{% endblock %}
+{% block css %}
+    <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
+    <link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
+{% endblock %}
+{% block content %}
+<!-- Start of body -->
+    <div class="container">
+        {{ flash_me() }}
+        <div class="page-header" style="display: inline-block;">
+            <h1>Resource Manager</h1>
+            <h3>{% if owner_name is not none %}Current Owner: {{ owner_name }}{% endif %} {% if admin_status == "owner" %}<button id="change_owner" class="btn btn-danger" data-url="/resources/change_owner" style="margin-left: 20px;">Change Owner</button>{% endif %}</h3>
+        </div>
+        <form id="manage_resource" action="/resources/manage" method="POST">
+            <input type="hidden" name="resource_id" value="{{ resource_id }}">
+            <div style="min-width: 600px; max-width: 800px;">
+                <fieldset>
+                    <div class="form-horizontal" style="width: 900px; margin-bottom: 50px;">
+                        <div class="form-group" style="padding-left: 20px;">
+                            <label for="group_name" class="col-xs-3" style="float: left; font-size: 18px;">Resource Name:</label>
+                            <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
+                                {{ resource_info.name }}
+                            </div>
+                        </div>
+                        {% if admin_status == "owner" %}
+                        <div class="form-group" style="padding-left: 20px;">
+                            <label for="user_email" class="col-xs-3" style="float: left; font-size: 18px;">Open to Public:</label>
+                            <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
+                                <label class="radio-inline">
+                                    <input type="radio" name="open_to_public" value="True" {% if default_mask != 'no-access' %}checked{% endif %}>
+                                    Yes
+                                </label>
+                                <label class="radio-inline">
+                                    <input type="radio" name="open_to_public" value="False" {% if default_mask == 'no-access' %}checked{% endif %}>
+                                    No
+                            </label>
+                            </div>
+                        </div>
+                        <div class="form-group" style="padding-left: 20px;">
+                            <label class="col-xs-3" style="float: left; font-size: 18px;"></label>
+                            <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
+                                <button id="save_changes" class="btn btn-primary" data-url="/resources/change_default_privileges">Save Changes</button>
+                            </div>
+                        </div>
+                        {% endif %}
+                    </div>
+                </fieldset>
+            </div>
+            {% if admin_status == "owner" or admin_status == "edit-admins" or admin_status == "edit-access" %}
+            <div style="min-width: 600px; max-width: 800px;">
+                <hr>
+                <button id="add_group_to_resource" class="btn btn-primary" style="margin-bottom: 30px;" data-url="/resources/add_group">Add Group</button>
+                <br>
+                {% if group_masks|length > 0 %}
+                <h2>Current Group Permissions</h2>
+                <hr>
+                <table id="groups_table" class="table-hover table-striped cell-border">
+                    <thead>
+                        <tr>
+                            <th>Name</th>
+                            <th>Data</th>
+                            <th>Metadata</th>
+                            <th>Admin</th>
+                        </tr>
+                    </thead>
+                    <tbody>
+                        {% for key, value in group_masks.iteritems() %}
+                        <tr>
+                            <td>{{ value.name }}</td>
+                            <td>{{ value.data }}</td>
+                            <td>{{ value.metadata }}</td>
+                            <td>{{ value.admin }}</td>
+                        </tr>
+                        {% endfor %}
+                    </tbody>
+                </table>
+                {% else %}
+                <h3>No groups are currently added to this resource.</h3>
+                {% endif %}
+            </div>
+            {% endif %}
+        </form>
+    </div>
+
+
+
+<!-- End of body -->
+
+{% endblock %}
+
+{% block js %}
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
+
+    <script type="text/javascript" charset="utf-8">
+        $('#add_group_to_resource, #save_changes, #change_owner').click(function(){
+            url = $(this).data("url");
+            $('#manage_resource').attr("action", url)
+            $('#manage_resource').submit()
+        })
+
+        {% if group_masks|length > 0 %}
+        $('#groups_table').dataTable({
+            'sDom': 'tr',
+        });
+        {% endif %}
+    </script>
+{% endblock %}
diff --git a/wqflask/wqflask/templates/admin/search_for_groups.html b/wqflask/wqflask/templates/admin/search_for_groups.html
index 89eb11dd..f304a172 100644
--- a/wqflask/wqflask/templates/admin/search_for_groups.html
+++ b/wqflask/wqflask/templates/admin/search_for_groups.html
@@ -1,64 +1,134 @@
-{% extends "base.html" %}
-{% block title %}Resource Manager{% endblock %}
-{% block content %}
-<!-- Start of body -->
-    <div class="container">
-        <div class="page-header">
-            <h1>Find Groups</h1>
-        </div>
-        <form id="find_groups" action="/resources/add_group" method="POST">
-            <input type="hidden" name="resource_id" value="{{ resource_id }}">
-            <div style="min-width: 600px; max-width: 800px;">
-                <fieldset>
-                    <div class="form-horizontal" style="width: 900px;">
-                        <div style="margin-bottom: 30px;">
-                            <h2>Search by:</h2>
-                        </div>
-                        <div class="form-group" style="padding-left: 20px;">
-                            <label for="group_name" class="col-xs-3" style="float: left; font-size: 18px;">Group ID:</label>
-                            <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
-                                <input name="group_id" type="text" value="">
-                            </div>
-                        </div>
-                        <div class="form-group" style="padding-left: 20px;">
-                            <label for="group_name" class="col-xs-3" style="float: left; font-size: 18px;">Group Name:</label>
-                            <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
-                                <input name="group_name" type="text" value="">
-                            </div>
-                        </div>
-                        <div class="form-group" style="padding-left: 20px;">
-                            <label for="user_name" class="col-xs-3" style="float: left; font-size: 18px;">User Name:</label>
-                            <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
-                                <input name="user_name" type="text" value="">
-                            </div>
-                        </div>
-                        <div class="form-group" style="padding-left: 20px;">
-                            <label for="user_email" class="col-xs-3" style="float: left; font-size: 18px;">User E-mail:</label>
-                            <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
-                                <input name="user_email" type="text" value="">
-                            </div>
-                        </div>
-                        <div class="form-group" style="padding-left: 20px;">
-                            <label class="col-xs-3" style="float: left; font-size: 18px;"></label>
-                            <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
-                                <button type="submit" id="find_groups" class="btn btn-primary">Search</button>
-                            </div>
-                        </div>
-                    </div>
-                </fieldset>
-            </div>
-        </form>
-    </div>
-
-<!-- End of body -->
-
-{% endblock %}
-
-{% block js %}
-    <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/new/javascript/group_manager.js"></script>
-    <script language="javascript" type="text/javascript" src="/static/packages/underscore/underscore-min.js"></script>
-
-    <script type="text/javascript" charset="utf-8">
-    </script>
-{% endblock %}
+{% extends "base.html" %}
+{% block title %}Resource Manager{% endblock %}
+{% block css %}
+    <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
+    <link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
+{% endblock %}
+{% block content %}
+<!-- Start of body -->
+    <div class="container">
+        <div class="page-header">
+            <h1>Find Groups</h1>
+        </div>
+        <form id="add_group" action="/resources/add_group" method="POST">
+            <input type="hidden" name="resource_id" value="{{ resource_id }}">
+            <div style="min-width: 600px; max-width: 800px;">
+                <fieldset>
+                    <div class="form-horizontal" style="width: 900px;">
+                        <div style="margin-bottom: 30px;">
+                            <h2>Search by:</h2>
+                        </div>
+                        <div class="form-group" style="padding-left: 20px;">
+                            <label for="group_name" class="col-xs-3" style="float: left; font-size: 18px;">Group ID:</label>
+                            <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
+                                <input name="group_id" type="text" value="">
+                            </div>
+                        </div>
+                        <div class="form-group" style="padding-left: 20px;">
+                            <label for="group_name" class="col-xs-3" style="float: left; font-size: 18px;">Group Name:</label>
+                            <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
+                                <input name="group_name" type="text" value="">
+                            </div>
+                        </div>
+                        <div class="form-group" style="padding-left: 20px;">
+                            <label for="user_name" class="col-xs-3" style="float: left; font-size: 18px;">User Name:</label>
+                            <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
+                                <input name="user_name" type="text" value="">
+                            </div>
+                        </div>
+                        <div class="form-group" style="padding-left: 20px;">
+                            <label for="user_email" class="col-xs-3" style="float: left; font-size: 18px;">User E-mail:</label>
+                            <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
+                                <input name="user_email" type="text" value="">
+                            </div>
+                        </div>
+                        <div class="form-group" style="padding-left: 20px;">
+                            <label class="col-xs-3" style="float: left; font-size: 18px;"></label>
+                            <div class="controls input-append col-xs-9" style="display: flex; padding-left: 20px; float: left;">
+                                <button type="button" id="find_groups" class="btn btn-primary">Search</button>
+                                <button style="margin-left: 20px; display: none;" type="submit" id="submit_group" class="btn btn-success">Add Privileges for Selected Group</button>
+                            </div>
+                        </div>
+                    </div>
+                </fieldset>
+                <hr>
+                <div id="group_results">
+                </div>
+            </div>
+        </form>
+    </div>
+
+<!-- End of body -->
+
+{% endblock %}
+
+{% block js %}
+    <script language="javascript" type="text/javascript" src="/static/new/packages/DataTables/js/jquery.js"></script>
+    <script language="javascript" type="text/javascript" src="/static/new/javascript/group_manager.js"></script>
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
+
+    <script type="text/javascript" charset="utf-8">
+
+        $('#find_groups').click(function() {
+            $.ajax({
+                method: "POST",
+                url: "/search_for_groups",
+                data: {
+                    group_id: $('input[name=group_id]').val(),
+                    group_name: $('input[name=group_name]').val(),
+                    user_name: $('input[name=user_name]').val(),
+                    user_email: $('input[name=user_email]').val()
+                },
+                success: populate_groups
+            });
+        })
+
+        populate_groups = function(json_group_list){
+            console.log(json_group_list)
+            var group_list = JSON.parse(json_group_list)
+
+            var the_html = ""
+            if (group_list.length > 0){
+                the_html += "<table id='groups_table' style='padding-top: 10px; width: 100%;' class='table-hover table-striped cell-border'>";
+                the_html += "<thead><tr><th></th><th>Index</th><th>Name</th><th># Admins</th><th># Members</th></tr></thead>";
+                the_html += "<tbody>";
+                for (_i = 0, _len = group_list.length; _i < _len; _i++) {
+                    this_group = group_list[_i]
+                    the_html += "<tr>";
+                    the_html += "<td align='center' class='select_group'><input type='radio' name='selected_group' value='" + this_group.id + "'></td>";
+                    the_html += "<td>" + (_i + 1).toString() + "</td>"
+                    if ("name" in this_group) {
+                        the_html += "<td>" + this_group.name + "</td>";
+                    } else {
+                        the_html += "<td>N/A</td>"
+                    }
+                    if ("admins" in this_group) {
+                        the_html += "<td>" + this_group.admins.length + "</td>";
+                    } else {
+                        the_html += "<td>0</td>"
+                    }
+                    if ("members" in this_group) {
+                        the_html += "<td>" + this_group.members.length + "</td>";
+                    } else {
+                        the_html += "<td>0</td>"
+                    }
+                    the_html += "</tr>"
+                }
+                the_html += "</tbody>";
+                the_html += "</table>";
+            } else {
+                the_html = "<span>No groups were found matching the entered criteria.</span>"
+            }
+
+            $('#group_results').html(the_html)
+            if (group_list.length > 0){
+                $('#groups_table').dataTable({
+                    'order': [[1, "asc" ]],
+                    'sDom': 'tr'
+                });
+                $('input[name=selected_group]:eq(0)').prop("checked", true)
+                $('#submit_group').css("display", "inline-block")
+            }
+        }
+    </script>
+{% endblock %}
diff --git a/wqflask/wqflask/templates/admin/select_group_to_add.html b/wqflask/wqflask/templates/admin/select_group_to_add.html
deleted file mode 100644
index df70fb2f..00000000
--- a/wqflask/wqflask/templates/admin/select_group_to_add.html
+++ /dev/null
@@ -1,54 +0,0 @@
-{% extends "base.html" %}
-{% block title %}Matched Groups{% endblock %}
-{% block css %}
-    <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
-    <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.dataTables.css">
-    <link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
-{% endblock %}
-{% block content %}
-<!-- Start of body -->
-    <div class="container">
-        <h1>The following groups were found:</h1>
-        <br>
-        <form id="add_groups">
-            <input type="hidden" name="resource_id" value="{{ resource_id }}">
-            <div id="groups_list" style="min-width: 600px; max-width: 800px;">
-                {% if group_list|length > 0 %}
-                <button type="submit" class="btn btn-primary" style="margin-bottom: 40px;">Add Selected Group</button>
-                <table id="groups_table" class="table-hover table-striped cell-border" style="float: left;">
-                    <thead>
-                        <tr>
-                            <th></th>
-                            <th>Name</th>
-                            <th>Created</th>
-                            <th>Last Changed</th>
-                        </tr>
-                    </thead>
-                    <tbody>
-                    {% for group in group_list %}
-                        <tr>
-                            <td align="center" style="padding: 0px;"><input type="radio" name="selected_group" VALUE="{{ group.id }}"></td>
-                            <td>{% if 'name' in group %}{{ group.name }}{% else %}N/A{% endif %}</td>
-                            <td>{% if 'created_timestamp' in group %}{{ group.created_timestamp }}{% else %}N/A{% endif %}</td>
-                            <td>{% if 'changed_timestamp' in group %}{{ group.changed_timestamp }}{% else %}N/A{% endif %}</td>
-                        </tr>
-                    {% endfor %}
-                    </tbody>
-                </table>
-                {% else %}
-                <h2>No matching groups were found.</h2>
-                {% endif %}
-            </div>
-        </form>
-    </div>
-
-<!-- End of body -->
-
-{% endblock %}
-
-{% block js %}
-    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
-    <script>
-        $('#groups_table').dataTable();
-    </script>
-{% endblock %}
diff --git a/wqflask/wqflask/templates/admin/set_group_privileges.html b/wqflask/wqflask/templates/admin/set_group_privileges.html
new file mode 100644
index 00000000..bc52788f
--- /dev/null
+++ b/wqflask/wqflask/templates/admin/set_group_privileges.html
@@ -0,0 +1,102 @@
+{% extends "base.html" %}
+{% block title %}Set Group Privileges{% endblock %}
+{% block css %}
+    <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
+    <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.dataTables.css">
+    <link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
+{% endblock %}
+{% block content %}
+<!-- Start of body -->
+    <div class="container">
+        <h1>Group Privileges</h1>
+        <br>
+        <form id="set_group_privileges" action="/resources/add_group" method="POST">
+            <input type="hidden" name="resource_id" value="{{ resource_id }}">
+            <input type="hidden" name="group_id" value="{{ group_id }}">
+            <div style="min-width: 600px; max-width: 800px;">
+                <button type="submit" class="btn btn-primary" style="margin-bottom: 10px;">Add Group</button>
+                <hr>
+                <h2>Data and Metadata Privileges</h2>
+                <table id="data_privileges_table" class="table-hover table-striped cell-border" style="float: left;">
+                    <thead>
+                        <tr>
+                            <th></th>
+                            <th>No-Access</th>
+                            <th>View</th>
+                            <th>Edit</th>
+                        </tr>
+                    </thead>
+                    <tbody>
+                        <tr>
+                            <td>Data:</td>
+                            {% if 'data' in default_privileges %}
+                            <td align="center" style="padding: 0px;"><input type="radio" name="data_privilege" VALUE="no-access" {% if default_privileges.data == "no-access" %}checked{% endif %}></td>
+                            <td align="center" style="padding: 0px;"><input type="radio" name="data_privilege" VALUE="view" {% if default_privileges.data == "view" %}checked{% endif %}></td>
+                            <td align="center" style="padding: 0px;"><input type="radio" name="data_privilege" VALUE="edit" {% if default_privileges.data == "edit" %}checked{% endif %}></td>
+                            {% else %}
+                            <td align="center" style="padding: 0px;"><input type="radio" name="data_privilege" VALUE="no-access" checked></td>
+                            <td align="center" style="padding: 0px;"><input type="radio" name="data_privilege" VALUE="view"></td>
+                            <td align="center" style="padding: 0px;"><input type="radio" name="data_privilege" VALUE="edit"></td>
+                            {% endif %}
+                        </tr>
+                        <tr>
+                            <td>Metadata:</td>
+                            {% if 'metadata' in default_privileges %}
+                            <td align="center" style="padding: 0px;"><input type="radio" name="metadata_privilege" VALUE="no-access" {% if default_privileges.metadata == "no-access" %}checked{% endif %}></td>
+                            <td align="center" style="padding: 0px;"><input type="radio" name="metadata_privilege" VALUE="view" {% if default_privileges.metadata == "view" %}checked{% endif %}></td>
+                            <td align="center" style="padding: 0px;"><input type="radio" name="metadata_privilege" VALUE="edit" {% if default_privileges.metadata[-1] == "edit" %}checked{% endif %}></td>
+                            {% else %}
+                            <td align="center" style="padding: 0px;"><input type="radio" name="metadata_privilege" VALUE="no-access" checked></td>
+                            <td align="center" style="padding: 0px;"><input type="radio" name="metadata_privilege" VALUE="view"></td>
+                            <td align="center" style="padding: 0px;"><input type="radio" name="metadata_privilege" VALUE="edit"></td>
+                            {% endif %}
+                        </tr>
+                    </tbody>
+                </table>
+                <hr>
+                <h2>Admin Privileges</h2>
+                <table id="admin_privileges_table" class="table-hover table-striped cell-border" style="float: left;">
+                    <thead>
+                        <tr>
+                            <th></th>
+                            <th>Not Admin</th>
+                            <th>Edit Access</th>
+                            <th>Edit Admins</th>
+                        </tr>
+                    </thead>
+                    <tbody>
+                        <tr>
+                            <td>Admin:</td>
+                            {% if 'admin' in default_privileges %}
+                            <td align="center" style="padding: 0px;"><input type="radio" name="admin_privilege" VALUE="not-admin" {% if default_privileges.admin == "not-admin" %}checked{% endif %}></td>
+                            <td align="center" style="padding: 0px;"><input type="radio" name="admin_privilege" VALUE="edit-access" {% if default_privileges.admin == "edit-access" %}checked{% endif %}></td>
+                            <td align="center" style="padding: 0px;"><input type="radio" name="admin_privilege" VALUE="edit-admins" {% if default_privileges.admin == "edit-admins" %}checked{% endif %}></td>
+                            {% else %}
+                            <td align="center" style="padding: 0px;"><input type="radio" name="admin_privilege" VALUE="not-admin" checked></td>
+                            <td align="center" style="padding: 0px;"><input type="radio" name="admin_privilege" VALUE="edit-access"></td>
+                            <td align="center" style="padding: 0px;"><input type="radio" name="admin_privilege" VALUE="edit-admins"></td>
+                            {% endif %}
+                        </tr>
+                    </tbody>
+                </table>
+            </div>
+        </form>
+    </div>
+
+<!-- End of body -->
+
+{% endblock %}
+
+{% block js %}
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
+    <script>
+        $('#data_privileges_table').dataTable({
+            'sDom': 'tr',
+            'bSort': false
+        });
+        $('#admin_privileges_table').dataTable({
+            'sDom': 'tr',
+            'bSort': false
+        });
+    </script>
+{% endblock %}
diff --git a/wqflask/wqflask/templates/admin/view_group.html b/wqflask/wqflask/templates/admin/view_group.html
new file mode 100644
index 00000000..b797cd70
--- /dev/null
+++ b/wqflask/wqflask/templates/admin/view_group.html
@@ -0,0 +1,238 @@
+{% extends "base.html" %}
+{% block title %}View and Edit Group{% endblock %}
+{% block css %}
+    <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
+    <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.dataTables.css">
+    <link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
+{% endblock %}
+{% block content %}
+<!-- Start of body -->
+    <div class="container">
+        <div class="page-header">
+            <h1>
+                <span id="group_name">{{ group_info.name }}</span>
+                <input type="text" name="new_group_name" style="font-size: 20px; display: none; width: 500px;" class="form-control" placeholder="{{ group_info.name }}"> 
+                <button class="btn btn-default" style="display: inline;" id="change_group_name">Change Group Name</button>
+            </h1>
+            {% if user_is_admin == true %}
+            <div style="display: inline;">
+                <button type="button" id="remove_users" class="btn btn-danger" data-url="/groups/remove_users">Remove Selected Users from Group</button>
+            </div>
+            {% endif %}
+        </div>
+        <form id="group_form" action="/groups/view" method="POST">
+            <input type="hidden" name="group_id" value="{{ group_info.id }}">
+            <input type="hidden" name="selected_admin_ids" value="">
+            <input type="hidden" name="selected_member_ids" value="">
+            <div class="row">
+            <div id="groups_div" class="col-xs-6" style="margin-right: 30px; min-width: 600px; max-width: 800px;">
+                <div>
+                    <div style="margin-top: 20px;"><h2>Admins</h2></div>
+                    <hr>
+                    <table id="group_admins" class="table-hover table-striped cell-border" style="float: left;">
+                        <thead>
+                            <tr>
+                                <th></th>
+                                <th>Index</th>
+                                <th>Name</th>
+                                <th>Email Address</th>
+                                <th>Organization</th>
+                            </tr>
+                        </thead>
+                        <tbody>
+                            {% for admin in admins %}
+                            <tr>
+                                <td style="text-align: center; padding: 0px 10px 2px 10px;"><input type="checkbox" name="admin_id" value="{{ admin.user_id }}"></td>
+                                <td align="right">{{ loop.index }}</td>
+                                <td>{% if 'full_name' in admin %}{{ admin.full_name }}{% else %}N/A{% endif %}</td>
+                                <td>{% if 'email_address' in admin %}{{ admin.email_address }}{% else %}N/A{% endif %}</td>
+                                <td>{% if 'organization' in admin %}{{ admin.organization }}{% else %}N/A{% endif %}</td>
+                            </tr>
+                            {% endfor %}
+                        </tbody>
+                    </table>
+                    {% if user_is_admin == true %}
+                    <div style="margin-top: 20px;">
+                            <span>E-mail of user to add to admins (multiple e-mails can be added separated by commas):</span>
+                            <input type="text" size="60" name="admin_emails_to_add" placeholder="Enter E-mail(s)" value="">
+                    </div>
+                    <div style="margin-bottom: 30px; margin-top: 20px;">
+                        <button type="button" id="add_admins" class="btn btn-primary" data-usertype="admin" data-url="/groups/add_admins">Add Admin(s)</button>
+                    </div>
+                    {% endif %}
+                </div>
+                <hr>
+                <div>
+                    {% if members|length > 0 %}
+                    <div><h2>Members</h2></div>
+                    <hr>
+                    <table id="group_members" class="table-hover table-striped cell-border" style="float: left;">
+                        <thead>
+                            <tr>
+                                <th></th>
+                                <th>Index</th>
+                                <th>Name</th>
+                                <th>Email Address</th>
+                                <th>Organization</th>
+                            </tr>
+                        </thead>
+                        <tbody>
+                            {% for member in members %}
+                            <tr>
+                                <td style="text-align: center; padding: 0px 10px 2px 10px;"><input type="checkbox" name="member_id" value="{{ member.user_id }}"></td>
+                                <td align="right">{{ loop.index }}</td>
+                                <td>{% if 'full_name' in member %}{{ member.full_name }}{% else %}N/A{% endif %}</td>
+                                <td>{% if 'email_address' in member %}{{ member.email_address }}{% else %}N/A{% endif %}</td>
+                                <td>{% if 'organization' in member %}{{ member.organization }}{% else %}N/A{% endif %}</td>
+                            </tr>
+                            {% endfor %}
+                        </tbody>
+                    </table>
+                    {% if user_is_admin == true %}
+                    <div style="margin-top: 20px;">
+                            <span>E-mail of user to add to members (multiple e-mails can be added separated by commas):</span>
+                            <input type="text" size="60" name="member_emails_to_add" placeholder="Enter E-mail(s)" value="">
+                    </div>
+                    <div style="margin-bottom: 30px; margin-top: 20px;">
+                        <button type="button" id="add_members" class="btn btn-primary" data-usertype="member" data-url="/groups/add_members">Add Member(s)</button>
+                    </div>
+                    {% endif %}
+                    {% else %}
+                    There are currently no members in this group.
+                    {% endif %}
+                </div>
+            </div>
+            <div id="resources_div" class="col-xs-6" style="border-left: 1px solid #eee; margin-right: 30px; min-width: 600px; max-width: 800px;">
+                <div style="margin-top: 20px;"><h2>Resources</h2></div>
+                <hr>
+                {% if resources|length > 0 %}
+                <table id="resources" class="table-hover table-striped cell-border" style="float: left;">
+                    <thead>
+                        <tr>
+                            <th>Index</th>
+                            <th>Name</th>
+                            <th>Data</th>
+                            <th>Metadata</th>
+                            <th>Admin</th>
+                        </tr>
+                    </thead>
+                    <tbody>
+                        {% for resource in resources %}
+                        <tr>
+                            <td align="right">{{ loop.index }}</td>
+                            <td>{% if 'name' in resource %}<a href="/resources/manage?resource_id={{ resource.id }}">{{ resource.name }}</a>{% else %}N/A{% endif %}</td>
+                            <td>{% if 'data' in resource %}{{ resource.data }}{% else %}N/A{% endif %}</td>
+                            <td>{% if 'metadata' in resource %}{{ resource.metadata }}{% else %}N/A{% endif %}</td>
+                            <td>{% if 'admin' in resource %}{{ resource.admin }}{% else %}N/A{% endif %}</td>
+                        </tr>
+                        {% endfor %}
+                    </tbody>
+                </table>
+                {% else %}
+                There are currently no resources associated with this group.
+                {% endif %}
+            </div>
+            </div>
+        </form>
+    </div>
+
+<!-- End of body -->
+
+{% endblock %}
+
+{% block js %}
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
+
+    <script type="text/javascript" charset="utf-8">
+        $(document).ready( function () {
+            $('#group_admins').dataTable({
+                'order': [[1, "asc" ]],
+                'columns': [
+                    { "type": "natural", "width": "25px"},
+                    { "type": "natural", "width": "30px" },
+                    { "type": "natural", "width": "150px" },
+                    { "type": "natural" },
+                    { "type": "natural" }
+                ],
+                'sDom': 'tr'
+            });
+            {% if members|length > 0 %}
+            $('#group_members').dataTable({
+                'order': [[1, "asc" ]],
+                'columns': [
+                    { "type": "natural", "width": "25px"},
+                    { "type": "natural", "width": "30px" },
+                    { "type": "natural", "width": "150px" },
+                    { "type": "natural" },
+                    { "type": "natural" }
+                ],
+                'sDom': 'tr'
+            });
+            {% endif %}
+            {% if resources|length > 0 %}
+            $('#resources').dataTable({
+                'order': [[0, "asc" ]],
+                'columns': [
+                    { "type": "natural", "width": "30px" },
+                    { "type": "natural", "width": "150px" },
+                    { "type": "natural" },
+                    { "type": "natural" },
+                    { "type": "natural" }
+                ],
+                'sDom': 'tr'
+            });
+            {% endif %}
+
+            $('#resources_div').css('height', $('#groups_div').css('height'))
+
+            submit_special = function(url) {
+                $("#group_form").attr("action", url);
+                return $("#group_form").submit();
+            };
+
+            $("#remove_users").on("click", function() {
+                url = $(this).data("url");
+                admins = [];
+                $("input[name=admin_id]:checked").each(function() {
+                    admins.push($(this).val());
+                });
+                admins_string = admins.join(":")
+                $("input[name=selected_admin_ids]").val(admins_string)
+
+                members = [];
+                $("input[name=member_id]:checked").each(function() {
+                    members.push($(this).val());
+                });
+                members_string = members.join(":")
+                $("input[name=selected_member_ids]").val(members_string)
+                return submit_special(url)
+            });
+
+            $("#add_admins, #add_members").on("click", function() {
+                url = $(this).data("url");
+                return submit_special(url)
+            });
+
+            $("#change_group_name").on("click", function() {
+                if ($('input[name=new_group_name]').css('display') == 'none') {
+                    $('input[name=new_group_name]').css('display', 'inline');
+                    $('#group_name').css('display', 'none');
+                } else {
+                    new_name = $('input[name=new_group_name]').val()
+                    $.ajax({
+                        type: "POST",
+                        url: "/groups/change_name",
+                        data: {
+                            group_id: $('input[name=group_id]').val(),
+                            new_name: new_name
+                        }
+                    });
+                    $('input[name=new_group_name]').css('display', 'none');
+                    $('input[name=group_name]').val(new_name);
+                    $('#group_name').text(new_name)
+                    $('#group_name').css('display', 'inline');
+                }
+            });
+        });
+    </script>
+{% endblock %}
diff --git a/wqflask/wqflask/templates/base.html b/wqflask/wqflask/templates/base.html
index 07c1b48e..262d9ee5 100644
--- a/wqflask/wqflask/templates/base.html
+++ b/wqflask/wqflask/templates/base.html
@@ -94,6 +94,11 @@
                             <a id="login_in" href="/n/login">Sign in</a>
                             {% endif %}
                         </li>
+                        {% if g.user_session.logged_in %}
+                        <li class="">
+                            <a id="manage_groups" title="Manage Groups" href="/groups/manage">Manage Groups</a>
+                        </li>
+                        {% endif %}
                         {% endif %}
                         <!--
                         <li style="margin-left: 20px;">
diff --git a/wqflask/wqflask/templates/set_group_privileges.html b/wqflask/wqflask/templates/set_group_privileges.html
new file mode 100644
index 00000000..98b0cc12
--- /dev/null
+++ b/wqflask/wqflask/templates/set_group_privileges.html
@@ -0,0 +1,77 @@
+{% extends "base.html" %}
+{% block title %}Set Group Privileges{% endblock %}
+{% block css %}
+    <link rel="stylesheet" type="text/css" href="{{ url_for('css', filename='DataTables/css/jquery.dataTables.css') }}" />
+    <link rel="stylesheet" type="text/css" href="/static/new/packages/DataTables/extensions/buttons.dataTables.css">
+    <link rel="stylesheet" type="text/css" href="/static/new/css/show_trait.css" />
+{% endblock %}
+{% block content %}
+<!-- Start of body -->
+    <div class="container">
+        <h1>Group Privileges</h1>
+        <br>
+        <form id="set_group_privileges">
+            <input type="hidden" name="resource_id" value="{{ resource_id }}">
+            <div style="min-width: 600px; max-width: 800px;">
+                <button type="submit" class="btn btn-primary" style="margin-bottom: 40px;">Add Group</button>
+                <hr>
+                <h2>Data and Metadata Privileges</h2>
+                <table id="data_privileges_table" class="table-hover table-striped cell-border" style="float: left;">
+                    <thead>
+                        <tr>
+                            <th></th>
+                            <th>No-Access</th>
+                            <th>View</th>
+                            <th>Edit</th>
+                        </tr>
+                    </thead>
+                    <tbody>
+                        <tr>
+                            <td>Data:</td>
+                            <td align="center" style="padding: 0px;"><input type="radio" name="data_privilege" VALUE="no-access" checked></td>
+                            <td align="center" style="padding: 0px;"><input type="radio" name="data_privilege" VALUE="view"></td>
+                            <td align="center" style="padding: 0px;"><input type="radio" name="data_privilege" VALUE="edit"></td>
+                        </tr>
+                        <tr>
+                            <td>Metadata:</td>
+                            <td align="center" style="padding: 0px;"><input type="radio" name="metadata_privilege" VALUE="no-access" checked></td>
+                            <td align="center" style="padding: 0px;"><input type="radio" name="metadata_privilege" VALUE="view"></td>
+                            <td align="center" style="padding: 0px;"><input type="radio" name="metadata_privilege" VALUE="edit"></td>
+                        </tr>
+                    </tbody>
+                </table>
+                <hr>
+                <h2>Admin Privileges</h2>
+                <table id="admin_privileges_table" class="table-hover table-striped cell-border" style="float: left;">
+                    <thead>
+                        <tr>
+                            <th></th>
+                            <th>Not Admin</th>
+                            <th>Edit Access</th>
+                            <th>Edit Admins</th>
+                        </tr>
+                    </thead>
+                    <tbody>
+                        <tr>
+                            <td>Admin:</td>
+                            <td align="center" style="padding: 0px;"><input type="radio" name="admin_privilege" VALUE="not-admin" checked></td>
+                            <td align="center" style="padding: 0px;"><input type="radio" name="admin_privilege" VALUE="edit-access"></td>
+                            <td align="center" style="padding: 0px;"><input type="radio" name="admin_privilege" VALUE="edit-admins"></td>
+                        </tr>
+                    </tbody>
+                </table>
+            </div>
+        </form>
+    </div>
+
+<!-- End of body -->
+
+{% endblock %}
+
+{% block js %}
+    <script language="javascript" type="text/javascript" src="{{ url_for('js', filename='DataTables/js/jquery.dataTables.min.js') }}"></script>
+    <script>
+        $('#data_privileges_table').dataTable();
+        $('#admin_privileges_table').dataTable();
+    </script>
+{% endblock %}
diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html
index 5c315878..5e0bae79 100644
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -248,8 +248,8 @@
         <a target="_blank" href="http://gn1.genenetwork.org/webqtl/main.py?cmd=show&db={{ this_trait.dataset.name }}&probeset={{ this_trait.name }}">
         <button type="button" id="view_in_gn1" class="btn btn-primary" title="View Trait in GN1">View in GN1</button>
         </a>
-        {% if resource_id %}
-        <a target="_blank" href="./resources/manage?resource_id={{ resource_id }}">
+        {% if admin_status[1] == "owner" or admin_status[1] == "edit-admins" or admin_status[1] == "edit-access" %}
+        <a target="_blank" href="./resources/manage?resource_id={{ admin_status[0] }}">
             <button type="button" id="edit_resource" class="btn btn-success" title="Edit Resource">Edit</button>
         </a>
         {% endif %}
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index ee827ba3..dc431aa9 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -102,7 +102,7 @@ def check_access_permissions():
             else:
                 available = check_resource_availability(dataset)
 
-            if not available:
+            if available == "no-access":
                 return redirect(url_for("no_access_page"))
 
 @app.teardown_appcontext
-- 
cgit v1.2.3


From fcb3cb1105cf2a1d97c1a08fa636b118ed231ffa Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 17 Jun 2020 16:28:15 -0500
Subject: A user's id is now set as a parameter if it doesn't already exist

---
 wqflask/maintenance/set_resource_defaults.py       |  8 +++---
 wqflask/utility/authentication_tools.py            | 30 ++++++++++++----------
 wqflask/utility/redis_tools.py                     |  4 +++
 wqflask/wqflask/group_manager.py                   |  4 +--
 wqflask/wqflask/templates/admin/group_manager.html | 16 +++++++-----
 5 files changed, 36 insertions(+), 26 deletions(-)

(limited to 'wqflask/utility/authentication_tools.py')

diff --git a/wqflask/maintenance/set_resource_defaults.py b/wqflask/maintenance/set_resource_defaults.py
index 344e6a23..0c221bbf 100644
--- a/wqflask/maintenance/set_resource_defaults.py
+++ b/wqflask/maintenance/set_resource_defaults.py
@@ -27,8 +27,9 @@ 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
+from utility.redis_tools import get_redis_conn, get_user_id, add_resource, get_resources, get_resource_info
 Redis = get_redis_conn()
 
 import MySQLdb
@@ -117,7 +118,7 @@ def insert_geno_resources(default_owner_id):
         resource_ob = {}
         resource_ob['name'] = resource[1]
         if resource[1] == "HET3-ITPGeno":
-            resource_ob['owner_id'] = "73a3f093-ca13-4ae0-a179-9a446f709f6e"
+            resource_ob['owner_id'] = "c5ce8c56-78a6-474f-bcaf-7129d97f56ae"
         else:
             resource_ob['owner_id'] = default_owner_id
         resource_ob['data'] = { "dataset" : str(resource[0]) }
@@ -145,7 +146,8 @@ def main():
 
     Redis.delete("resources")
 
-    owner_id = get_user_id("email_address", "zachary.a.sloan@gmail.com")
+    owner_id = "c5ce8c56-78a6-474f-bcaf-7129d97f56ae"
+
     insert_resources(owner_id)
 
 if __name__ == '__main__':
diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py
index 07ceacc0..dfa0e2d9 100644
--- a/wqflask/utility/authentication_tools.py
+++ b/wqflask/utility/authentication_tools.py
@@ -7,6 +7,7 @@ from base import data_set
 
 from utility import hmac
 from utility.redis_tools import get_redis_conn, get_resource_info, get_resource_id
+Redis = get_redis_conn()
 
 from flask import Flask, g, redirect, url_for
 
@@ -14,8 +15,12 @@ import logging
 logger = logging.getLogger(__name__ )
 
 def check_resource_availability(dataset, trait_id=None):
-    resource_id = get_resource_id(dataset, trait_id)
 
+    #ZS: Check if super-user - we should probably come up with some way to integrate this into the proxy
+    if g.user_session.user_id in Redis.smembers("super_users"):
+        return "edit"
+
+    resource_id = get_resource_id(dataset, trait_id)
     response = None
     if resource_id:
         resource_info = get_resource_info(resource_id)
@@ -68,19 +73,16 @@ def check_owner(dataset=None, trait_id=None, resource_id=None):
     return False
 
 def check_owner_or_admin(dataset=None, trait_id=None, resource_id=None):
-    if resource_id:
-        resource_info = get_resource_info(resource_id)
-        if g.user_session.user_id == resource_info['owner_id']:
-            return [resource_id, "owner"]
-        else:
-            return [resource_id, check_admin(resource_id)]
-    else:
+    if not resource_id:
         resource_id = get_resource_id(dataset, trait_id)
-        if resource_id:
-            resource_info = get_resource_info(resource_id)
-            if g.user_session.user_id == resource_info['owner_id']:
-                return [resource_id, "owner"]
-            else:
-                return [resource_id, check_admin(resource_id)]
+
+    if g.user_session.user_id in Redis.smembers("super_users"):
+        return [resource_id, "owner"]
+
+    resource_info = get_resource_info(resource_id)
+    if g.user_session.user_id == resource_info['owner_id']:
+        return [resource_id, "owner"]
+    else:
+        return [resource_id, check_admin(resource_id)]
 
     return [resource_id, "not-admin"]
\ No newline at end of file
diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py
index c6d221ff..9d09a66b 100644
--- a/wqflask/utility/redis_tools.py
+++ b/wqflask/utility/redis_tools.py
@@ -30,6 +30,7 @@ def is_redis_available():
 
 def get_user_id(column_name, column_value):
     user_list = Redis.hgetall("users")
+    key_list = []
     for key in user_list:
         user_ob = json.loads(user_list[key])
         if column_name in user_ob and user_ob[column_name] == column_value:
@@ -62,6 +63,9 @@ def get_users_like_unique_column(column_name, column_value):
         if column_name != "user_id":
             for key in user_list:
                 user_ob = json.loads(user_list[key])
+                if "user_id" not in user_ob:
+                    set_user_attribute(key, "user_id", key)
+                    user_ob["user_id"] = key
                 if column_name in user_ob:
                     if column_value in user_ob[column_name]:
                         matched_users.append(user_ob)
diff --git a/wqflask/wqflask/group_manager.py b/wqflask/wqflask/group_manager.py
index 9afc016b..24848ed8 100644
--- a/wqflask/wqflask/group_manager.py
+++ b/wqflask/wqflask/group_manager.py
@@ -19,8 +19,8 @@ def manage_groups():
    if "add_new_group" in params:
       return redirect(url_for('add_group'))
    else:
-      admin_groups, user_groups = get_user_groups(g.user_session.user_id)
-      return render_template("admin/group_manager.html", admin_groups=admin_groups, user_groups=user_groups)
+      admin_groups, member_groups = get_user_groups(g.user_session.user_id)
+      return render_template("admin/group_manager.html", admin_groups=admin_groups, member_groups=member_groups)
 
 @app.route("/groups/view", methods=('GET', 'POST'))
 def view_group():
diff --git a/wqflask/wqflask/templates/admin/group_manager.html b/wqflask/wqflask/templates/admin/group_manager.html
index 70d55684..c8ed6851 100644
--- a/wqflask/wqflask/templates/admin/group_manager.html
+++ b/wqflask/wqflask/templates/admin/group_manager.html
@@ -10,18 +10,20 @@
     <div class="container">
         <div class="page-header">
             <h1>Manage Groups</h1>
+            {% if admin_groups|length != 0 or member_groups|length != 0 %}
             <div style="display: inline;">
                 <button type="button" id="create_group" class="btn btn-primary" data-url="/groups/create">Create Group</button>
                 <button type="button" id="remove_groups" class="btn btn-primary" data-url="/groups/remove">Remove Selected Groups</button>
             </div>
+            {% endif %}
         </div>
         <form id="groups_form" action="/groups/manage" method="POST">
             <input type="hidden" name="selected_group_ids" value="">
             <div style="min-width: 800px; max-width: 1000px;">
-                {% if admin_groups|length == 0 and user_groups|length == 0 %}
+                {% if admin_groups|length == 0 and member_groups|length == 0 %}
                 <h4>You currently aren't a member or admin of any groups.</h4>
                 <br>
-                <button type="submit" name="add_new_group" class="btn btn-primary">Create a new group</button>
+                <button type="button" id="create_group" class="btn btn-primary" data-url="/groups/create">Create a new group</button>
                 {% else %}
                 <div style="margin-top: 20px;"><h2>Admin Groups</h2></div>
                 <hr>
@@ -60,10 +62,10 @@
             <div style="min-width: 800px; max-width: 1000px;">
                 <div><h2>User Groups</h2></div>
                 <hr>
-                {% if user_groups|length == 0 %}
+                {% if member_groups|length == 0 %}
                 <h4>You currently aren't a member of any groups.</h4>
                 {% else %}
-                <table id="user_groups" class="table-hover table-striped cell-border" style="float: left;">
+                <table id="member_groups" class="table-hover table-striped cell-border" style="float: left;">
                     <thead>
                         <tr>
                             <th></th>
@@ -75,7 +77,7 @@
                         </tr>
                     </thead>
                     <tbody>
-                        {% for group in user_groups %}
+                        {% for group in member_groups %}
                         <tr>
                             <td><input type="checkbox" name="read" value="{{ group.id }}"></td>
                             <td>{{ loop.index }}</td>
@@ -107,8 +109,8 @@
                 'sDom': 'tr'
             });
             {% endif %}
-            {% if user_groups|length != 0 %}
-            $('#user_groups').dataTable({
+            {% if member_groups|length != 0 %}
+            $('#member_groups').dataTable({
                 'sDom': 'tr'
             });
             {% endif %}
-- 
cgit v1.2.3


From 75802ed1f9e5d955987bf5f5eb78a9cb120116ec Mon Sep 17 00:00:00 2001
From: zsloan
Date: Sat, 20 Jun 2020 17:33:22 -0500
Subject: Added some admin functionality and fixed issue with temp traits

---
 wqflask/base/trait.py                        | 17 ++++--
 wqflask/base/webqtlConfig.py                 |  4 ++
 wqflask/maintenance/set_resource_defaults.py | 20 +++++--
 wqflask/utility/authentication_tools.py      | 79 +++++++++++++++-------------
 wqflask/wqflask/resource_manager.py          |  6 +--
 wqflask/wqflask/views.py                     | 20 ++++---
 6 files changed, 90 insertions(+), 56 deletions(-)

(limited to 'wqflask/utility/authentication_tools.py')

diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 7700ecd5..c2b8b910 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -42,11 +42,11 @@ def create_trait(**kw):
 
         if kw.get('dataset_name') != "Temp":
             if dataset.type == 'Publish':
-                permitted = check_resource_availability(dataset, kw.get('name'))
+                permissions = check_resource_availability(dataset, kw.get('name'))
             else:
-                permitted = check_resource_availability(dataset)
+                permissions = check_resource_availability(dataset)
 
-    if permitted != "no-access":
+    if "view" in permissions['data']:
         the_trait = GeneralTrait(**kw)
         if the_trait.dataset.type != "Temp":
 
@@ -382,9 +382,16 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
 
     resource_id = get_resource_id(dataset, trait.name)
     if dataset.type == 'Publish':
-        the_url = "http://localhost:8080/run-action?resource={}&user={}&branch=data&action=view".format(resource_id, g.user_session.user_id)
+        the_url = "http://localhost:8081/run-action?resource={}&user={}&branch=data&action=view".format(resource_id, g.user_session.user_id)
     else:
-        the_url = "http://localhost:8080/run-action?resource={}&user={}&branch=data&action=view&trait={}".format(resource_id, g.user_session.user_id, trait.name)
+        the_url = "http://localhost:8081/run-action?resource={}&user={}&branch=data&action=view&trait={}".format(resource_id, g.user_session.user_id, trait.name)
+
+    response = requests.get(the_url).content
+    if response.strip() == "no-access":
+        trait.view = False
+        return trait
+    else:
+        trait_info = json.loads(response)
 
     try:
         response = requests.get(the_url).content
diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py
index 55407123..3d86bc22 100644
--- a/wqflask/base/webqtlConfig.py
+++ b/wqflask/base/webqtlConfig.py
@@ -17,6 +17,10 @@ DEBUG = 1
 #USER privilege
 USERDICT = {'guest':1,'user':2, 'admin':3, 'root':4}
 
+#Set privileges
+SUPER_PRIVILEGES = {'data': ['no-access', 'view', 'edit'], 'metadata': ['no-access', 'view', 'edit'], 'admin': ['not-admin', 'edit-access', 'edit-admins']}
+DEFAULT_PRIVILEGES = {'data': ['no-access', 'view'], 'metadata': ['no-access', 'view'], 'admin': ['not-admin']}
+
 #minimum number of informative strains
 KMININFORMATIVE = 5
 
diff --git a/wqflask/maintenance/set_resource_defaults.py b/wqflask/maintenance/set_resource_defaults.py
index 0c221bbf..ddb3b17b 100644
--- a/wqflask/maintenance/set_resource_defaults.py
+++ b/wqflask/maintenance/set_resource_defaults.py
@@ -68,9 +68,13 @@ def insert_probeset_resources(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" }
+            resource_ob['default_mask'] = { "data": "view",
+                                            "metadata": "view",
+                                            "admin": "not-admin"}
         else:
-            resource_ob['default_mask'] = { "data": "no-access" }
+            resource_ob['default_mask'] = { "data": "no-access",
+                                            "metadata": "no-access",
+                                            "admin": "not-admin"}
         resource_ob['group_masks'] = {}
 
         add_resource(resource_ob)
@@ -98,7 +102,9 @@ def insert_publish_resources(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['default_mask'] = { "data": "view",
+                                            "metadata": "view",
+                                            "admin": "not-admin"}
 
             resource_ob['group_masks'] = {}
 
@@ -124,9 +130,13 @@ def insert_geno_resources(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" }
+            resource_ob['default_mask'] = { "data": "view",
+                                            "metadata": "view",
+                                            "admin": "not-admin"}
         else:
-            resource_ob['default_mask'] = { "data": "no-access" }
+            resource_ob['default_mask'] = { "data": "no-access",
+                                            "metadata": "no-access",
+                                            "admin": "not-admin"}
         resource_ob['group_masks'] = {}
 
         add_resource(resource_ob)
diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py
index dfa0e2d9..6c88949b 100644
--- a/wqflask/utility/authentication_tools.py
+++ b/wqflask/utility/authentication_tools.py
@@ -3,7 +3,7 @@ from __future__ import absolute_import, print_function, division
 import json
 import requests
 
-from base import data_set
+from base import data_set, webqtlConfig
 
 from utility import hmac
 from utility.redis_tools import get_redis_conn, get_resource_info, get_resource_id
@@ -18,45 +18,47 @@ def check_resource_availability(dataset, trait_id=None):
 
     #ZS: Check if super-user - we should probably come up with some way to integrate this into the proxy
     if g.user_session.user_id in Redis.smembers("super_users"):
-        return "edit"
+       return webqtlConfig.SUPER_PRIVILEGES
 
-    resource_id = get_resource_id(dataset, trait_id)
     response = None
-    if resource_id:
-        resource_info = get_resource_info(resource_id)
-
-        the_url = "http://localhost:8080/available?resource={}&user={}".format(resource_id, g.user_session.user_id)
-        try:
-            response = json.loads(requests.get(the_url).content)['data']
-        except:
-            response = resource_info['default_mask']['data']
 
-        if 'edit' in response:
-            return "edit"
-        elif 'view' in response:
-            return "view"
-        else:
-            return "no-access"
+    #At least for now assume temporary entered traits are accessible#At least for now assume temporary entered traits are accessible
+    if type(dataset) == str:
+        return webqtlConfig.DEFAULT_PRIVILEGES
+    if dataset.type == "Temp":
+        return webqtlConfig.DEFAULT_PRIVILEGES
 
-    return False
+    resource_id = get_resource_id(dataset, trait_id)
 
-def check_admin(resource_id=None):
+    if resource_id:
+        resource_info = get_resource_info(resource_id)
+    else:
+        return response #ZS: Need to substitute in something that creates the resource in Redis later
 
-    return "not-admin"
+    the_url = "http://localhost:8081/available?resource={}&user={}".format(resource_id, g.user_session.user_id)
+    try:
+        response = json.loads(requests.get(the_url).content)
+    except:
+        response = resource_info['default_mask']
 
-    # ZS: commented out until proxy can return this
-    # the_url = "http://localhost:8080/available?resource={}&user={}".format(resource_id, g.user_session.user_id)
-    # try:
-    #     response = json.loads(requests.get(the_url).content)
-    # except:
-    #     response = resource_info['default_mask']['admin']
+    if response:
+        return response
+    else: #ZS: No idea how this would happen, but just in case
+        return False
 
-    # if 'edit-admins' in response:
-    #     return "edit-admins"
-    # elif 'edit-access' in response:
-    #     return "edit-access"
-    # else:
-    #     return "not-admin"
+def check_admin(resource_id=None):
+    the_url = "http://localhost:8081/available?resource={}&user={}".format(resource_id, g.user_session.user_id)
+    try:
+        response = json.loads(requests.get(the_url).content)['admin']
+    except:
+        response = resource_info['default_mask']['admin']
+
+    if 'edit-admins' in response:
+        return "edit-admins"
+    elif 'edit-access' in response:
+        return "edit-access"
+    else:
+        return "not-admin"
 
 def check_owner(dataset=None, trait_id=None, resource_id=None):
     if resource_id:
@@ -74,15 +76,18 @@ def check_owner(dataset=None, trait_id=None, resource_id=None):
 
 def check_owner_or_admin(dataset=None, trait_id=None, resource_id=None):
     if not resource_id:
-        resource_id = get_resource_id(dataset, trait_id)
+        if dataset.type == "Temp":
+            return "not-admin"
+        else:
+            resource_id = get_resource_id(dataset, trait_id)
 
     if g.user_session.user_id in Redis.smembers("super_users"):
-        return [resource_id, "owner"]
+        return "owner"
 
     resource_info = get_resource_info(resource_id)
     if g.user_session.user_id == resource_info['owner_id']:
-        return [resource_id, "owner"]
+        return "owner"
     else:
-        return [resource_id, check_admin(resource_id)]
+        return check_admin(resource_id)
 
-    return [resource_id, "not-admin"]
\ No newline at end of file
+    return "not-admin"
\ No newline at end of file
diff --git a/wqflask/wqflask/resource_manager.py b/wqflask/wqflask/resource_manager.py
index 0f9f5c9d..39a07310 100644
--- a/wqflask/wqflask/resource_manager.py
+++ b/wqflask/wqflask/resource_manager.py
@@ -18,7 +18,7 @@ def manage_resource():
     params = request.form if request.form else request.args
     if 'resource_id' in request.args:
         resource_id = request.args['resource_id']
-        admin_status = check_owner_or_admin(resource_id=resource_id)[1]
+        admin_status = check_owner_or_admin(resource_id=resource_id)
 
         resource_info = get_resource_info(resource_id)
         group_masks = resource_info['group_masks']
@@ -67,7 +67,7 @@ def search_for_groups():
 def change_owner():
     resource_id = request.form['resource_id']
     if 'new_owner' in request.form:
-        admin_status = check_owner_or_admin(resource_id=resource_id)[1]
+        admin_status = check_owner_or_admin(resource_id=resource_id)
         if admin_status == "owner":
             new_owner_id = request.form['new_owner']
             change_resource_owner(resource_id, new_owner_id)
@@ -100,7 +100,7 @@ def change_default_privileges():
 @app.route("/resources/add_group", methods=('POST',))
 def add_group_to_resource():
     resource_id = request.form['resource_id']
-    admin_status = check_owner_or_admin(resource_id=resource_id)[1]
+    admin_status = check_owner_or_admin(resource_id=resource_id)
     if admin_status == "owner" or admin_status == "edit-admins" or admin_status == "edit-access":
         if 'selected_group' in request.form:
             group_id = request.form['selected_group']
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index dc431aa9..bc01839b 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -96,13 +96,21 @@ def check_access_permissions():
             pass
     else:
         if 'dataset' in request.args:
-            dataset = create_dataset(request.args['dataset'])
-            if 'trait_id' in request.args:
-                available = check_resource_availability(dataset, request.args['trait_id'])
+            if request.args['dataset'] == "Temp":
+                permissions = check_resource_availability("Temp")
             else:
-                available = check_resource_availability(dataset)
-
-            if available == "no-access":
+                dataset = create_dataset(request.args['dataset'])
+
+                if dataset.type == "Temp":
+                    permissions = False
+                if 'trait_id' in request.args:
+                    permissions = check_resource_availability(dataset, request.args['trait_id'])
+                elif dataset.type != "Publish":
+                    permissions = check_resource_availability(dataset)
+                else:
+                    return None
+
+            if 'view' not in permissions['data']:
                 return redirect(url_for("no_access_page"))
 
 @app.teardown_appcontext
-- 
cgit v1.2.3


From 51417c06061246bc92be89db198b3e74e7126035 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Sat, 20 Jun 2020 17:47:38 -0500
Subject: Fixed ports for proxy (though I need to add the port to global
 variables) and also simplified the check_owner_or_admin function a little

---
 wqflask/base/trait.py                             | 4 ++--
 wqflask/utility/authentication_tools.py           | 4 ++--
 wqflask/wqflask/show_trait/show_trait.py          | 3 ++-
 wqflask/wqflask/templates/show_trait_details.html | 4 ++--
 4 files changed, 8 insertions(+), 7 deletions(-)

(limited to 'wqflask/utility/authentication_tools.py')

diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index c2b8b910..0e26ca2c 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -382,9 +382,9 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
 
     resource_id = get_resource_id(dataset, trait.name)
     if dataset.type == 'Publish':
-        the_url = "http://localhost:8081/run-action?resource={}&user={}&branch=data&action=view".format(resource_id, g.user_session.user_id)
+        the_url = "http://localhost:8080/run-action?resource={}&user={}&branch=data&action=view".format(resource_id, g.user_session.user_id)
     else:
-        the_url = "http://localhost:8081/run-action?resource={}&user={}&branch=data&action=view&trait={}".format(resource_id, g.user_session.user_id, trait.name)
+        the_url = "http://localhost:8080/run-action?resource={}&user={}&branch=data&action=view&trait={}".format(resource_id, g.user_session.user_id, trait.name)
 
     response = requests.get(the_url).content
     if response.strip() == "no-access":
diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py
index 6c88949b..06b2854a 100644
--- a/wqflask/utility/authentication_tools.py
+++ b/wqflask/utility/authentication_tools.py
@@ -35,7 +35,7 @@ def check_resource_availability(dataset, trait_id=None):
     else:
         return response #ZS: Need to substitute in something that creates the resource in Redis later
 
-    the_url = "http://localhost:8081/available?resource={}&user={}".format(resource_id, g.user_session.user_id)
+    the_url = "http://localhost:8080/available?resource={}&user={}".format(resource_id, g.user_session.user_id)
     try:
         response = json.loads(requests.get(the_url).content)
     except:
@@ -47,7 +47,7 @@ def check_resource_availability(dataset, trait_id=None):
         return False
 
 def check_admin(resource_id=None):
-    the_url = "http://localhost:8081/available?resource={}&user={}".format(resource_id, g.user_session.user_id)
+    the_url = "http://localhost:8080/available?resource={}&user={}".format(resource_id, g.user_session.user_id)
     try:
         response = json.loads(requests.get(the_url).content)['admin']
     except:
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index ed4ff0ad..4698807a 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -72,7 +72,8 @@ class ShowTrait(object):
                                            cellid=None)
             self.trait_vals = Redis.get(self.trait_id).split()
 
-        self.admin_status = check_owner_or_admin(self.dataset, self.trait_id)
+        self.resource_id = get_resource_id(self.dataset, self.trait_id)
+        self.admin_status = check_owner_or_admin(resource_id=self.resource_id)
 
         #ZS: Get verify/rna-seq link URLs
         try:
diff --git a/wqflask/wqflask/templates/show_trait_details.html b/wqflask/wqflask/templates/show_trait_details.html
index 5e0bae79..965c0340 100644
--- a/wqflask/wqflask/templates/show_trait_details.html
+++ b/wqflask/wqflask/templates/show_trait_details.html
@@ -248,8 +248,8 @@
         <a target="_blank" href="http://gn1.genenetwork.org/webqtl/main.py?cmd=show&db={{ this_trait.dataset.name }}&probeset={{ this_trait.name }}">
         <button type="button" id="view_in_gn1" class="btn btn-primary" title="View Trait in GN1">View in GN1</button>
         </a>
-        {% if admin_status[1] == "owner" or admin_status[1] == "edit-admins" or admin_status[1] == "edit-access" %}
-        <a target="_blank" href="./resources/manage?resource_id={{ admin_status[0] }}">
+        {% if admin_status == "owner" or admin_status == "edit-admins" or admin_status == "edit-access" %}
+        <a target="_blank" href="./resources/manage?resource_id={{ resource_id }}">
             <button type="button" id="edit_resource" class="btn btn-success" title="Edit Resource">Edit</button>
         </a>
         {% endif %}
-- 
cgit v1.2.3


From 645c07b98aae9508e8a0aeedd8eaca815d5daf54 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 24 Jun 2020 17:13:45 -0500
Subject: Temporary partial fix to issue of resources without info; need to add
 something that automatically inserts resources with default privileges

---
 wqflask/base/trait.py                            | 12 ++++--------
 wqflask/utility/authentication_tools.py          | 11 +++++++----
 wqflask/utility/redis_tools.py                   |  5 ++++-
 wqflask/wqflask/correlation/show_corr_results.py |  7 +++----
 wqflask/wqflask/templates/correlation_page.html  |  4 ++++
 5 files changed, 22 insertions(+), 17 deletions(-)

(limited to 'wqflask/utility/authentication_tools.py')

diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 0e26ca2c..7fc016f3 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -386,13 +386,6 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
     else:
         the_url = "http://localhost:8080/run-action?resource={}&user={}&branch=data&action=view&trait={}".format(resource_id, g.user_session.user_id, trait.name)
 
-    response = requests.get(the_url).content
-    if response.strip() == "no-access":
-        trait.view = False
-        return trait
-    else:
-        trait_info = json.loads(response)
-
     try:
         response = requests.get(the_url).content
         if response.strip() == "no-access":
@@ -402,7 +395,10 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
             trait_info = json.loads(response)
     except:
         resource_info = get_resource_info(resource_id)
-        default_permissions = resource_info['default_mask']['data']
+        if resource_info:
+            default_permissions = resource_info['default_mask']['data']
+        else:
+            default_permissions = webqtlConfig.DEFAULT_PRIVILEGES
         if 'view' not in default_permissions:
             trait.view = False
             return trait
diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py
index 06b2854a..f9028f32 100644
--- a/wqflask/utility/authentication_tools.py
+++ b/wqflask/utility/authentication_tools.py
@@ -32,6 +32,8 @@ def check_resource_availability(dataset, trait_id=None):
 
     if resource_id:
         resource_info = get_resource_info(resource_id)
+        if not resource_info:
+            return webqtlConfig.DEFAULT_PRIVILEGES
     else:
         return response #ZS: Need to substitute in something that creates the resource in Redis later
 
@@ -85,9 +87,10 @@ def check_owner_or_admin(dataset=None, trait_id=None, resource_id=None):
         return "owner"
 
     resource_info = get_resource_info(resource_id)
-    if g.user_session.user_id == resource_info['owner_id']:
-        return "owner"
-    else:
-        return check_admin(resource_id)
+    if resource_info:
+        if g.user_session.user_id == resource_info['owner_id']:
+            return "owner"
+        else:
+            return check_admin(resource_id)
 
     return "not-admin"
\ No newline at end of file
diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py
index 9d09a66b..8a5f95ee 100644
--- a/wqflask/utility/redis_tools.py
+++ b/wqflask/utility/redis_tools.py
@@ -280,7 +280,10 @@ def get_resource_id(dataset, trait_id=None):
 
 def get_resource_info(resource_id):
     resource_info = Redis.hget("resources", resource_id)
-    return json.loads(resource_info)
+    if resource_info:
+        return json.loads(resource_info)
+    else:
+        return None
 
 def add_resource(resource_info):
     if 'trait' in resource_info['data']:
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index 7eab7184..bc2912f2 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -200,8 +200,6 @@ class CorrelationResults(object):
 
             for _trait_counter, trait in enumerate(self.correlation_data.keys()[:self.return_number]):
                 trait_object = create_trait(dataset=self.target_dataset, name=trait, get_qtl_info=True, get_sample_info=False)
-                if not trait_object:
-                    continue
 
                 if self.target_dataset.type == "ProbeSet" or self.target_dataset.type == "Geno":
                     #ZS: Convert trait chromosome to an int for the location range option
@@ -237,9 +235,8 @@ class CorrelationResults(object):
                         trait_object.tissue_pvalue = tissue_corr_data[trait][2]
                     elif self.corr_type == "lit":
                         trait_object.lit_corr = lit_corr_data[trait][1]
-                    self.correlation_results.append(trait_object)
 
-            self.target_dataset.get_trait_info(self.correlation_results, self.target_dataset.group.species)
+                    self.correlation_results.append(trait_object)
 
             if self.corr_type != "lit" and self.dataset.type == "ProbeSet" and self.target_dataset.type == "ProbeSet":
                 self.do_lit_correlation_for_trait_list()
@@ -498,6 +495,8 @@ def do_bicor(this_trait_vals, target_trait_vals):
 def generate_corr_json(corr_results, this_trait, dataset, target_dataset, for_api = False):
     results_list = []
     for i, trait in enumerate(corr_results):
+        if trait.view == False:
+            continue
         results_dict = {}
         if not for_api:
             results_dict['checkbox'] = "<INPUT TYPE='checkbox' NAME='searchResult' class='checkbox trait_checkbox' style='padding-right: 0px;' VALUE='" + hmac.hmac_creation('{}:{}'.format(trait.name, trait.dataset.name)) + "'>"
diff --git a/wqflask/wqflask/templates/correlation_page.html b/wqflask/wqflask/templates/correlation_page.html
index f429948d..3d750bea 100644
--- a/wqflask/wqflask/templates/correlation_page.html
+++ b/wqflask/wqflask/templates/correlation_page.html
@@ -169,7 +169,11 @@
                         <TD data-export="N/A">N/A</TD>
                         {% endif %}
                         <td data-export="{{ trait.description_display }}">{% if trait.description_display|length > 70 %}{{ trait.description_display[:70] }}...{% else %}{{ trait.description_display }}{% endif %}</td>
+                        {% if trait.authors %}
                         <td data-export="{{ trait.authors }}">{% if trait.authors.split(',') > 6 %}{{ trait.authors.split(',')[:6]|join(', ') }}, et al.{% else %}{{ trait.authors }}{% endif %}</td>
+                        {% else %}
+                        <TD data-export="N/A">N/A</TD>
+                        {% endif %}
                         <td data-export="{{ trait.pubmed_text }}">
                             <a href="{{ trait.pubmed_link }}">
                                 {{ trait.pubmed_text }}
-- 
cgit v1.2.3


From 81c35e99a7ff808bf2fcf1f5e19631adf07d42e8 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 22 Jul 2020 17:46:37 -0500
Subject: It should add new resources to Redis automatically now

---
 wqflask/utility/authentication_tools.py | 61 +++++++++++++++++++++++++--------
 wqflask/utility/redis_tools.py          |  5 +--
 2 files changed, 47 insertions(+), 19 deletions(-)

(limited to 'wqflask/utility/authentication_tools.py')

diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py
index f9028f32..ed7462d1 100644
--- a/wqflask/utility/authentication_tools.py
+++ b/wqflask/utility/authentication_tools.py
@@ -6,7 +6,7 @@ import requests
 from base import data_set, webqtlConfig
 
 from utility import hmac
-from utility.redis_tools import get_redis_conn, get_resource_info, get_resource_id
+from utility.redis_tools import get_redis_conn, get_resource_info, get_resource_id, add_resource
 Redis = get_redis_conn()
 
 from flask import Flask, g, redirect, url_for
@@ -16,13 +16,7 @@ logger = logging.getLogger(__name__ )
 
 def check_resource_availability(dataset, trait_id=None):
 
-    #ZS: Check if super-user - we should probably come up with some way to integrate this into the proxy
-    if g.user_session.user_id in Redis.smembers("super_users"):
-       return webqtlConfig.SUPER_PRIVILEGES
-
-    response = None
-
-    #At least for now assume temporary entered traits are accessible#At least for now assume temporary entered traits are accessible
+    #At least for now assume temporary entered traits are accessible
     if type(dataset) == str:
         return webqtlConfig.DEFAULT_PRIVILEGES
     if dataset.type == "Temp":
@@ -33,9 +27,13 @@ def check_resource_availability(dataset, trait_id=None):
     if resource_id:
         resource_info = get_resource_info(resource_id)
         if not resource_info:
-            return webqtlConfig.DEFAULT_PRIVILEGES
-    else:
-        return response #ZS: Need to substitute in something that creates the resource in Redis later
+            resource_info = add_new_resource(dataset, trait_id)
+
+    #ZS: Check if super-user - we should probably come up with some way to integrate this into the proxy
+    if g.user_session.user_id in Redis.smembers("super_users"):
+       return webqtlConfig.SUPER_PRIVILEGES
+
+    response = None
 
     the_url = "http://localhost:8080/available?resource={}&user={}".format(resource_id, g.user_session.user_id)
     try:
@@ -43,10 +41,43 @@ def check_resource_availability(dataset, trait_id=None):
     except:
         response = resource_info['default_mask']
 
-    if response:
-        return response
-    else: #ZS: No idea how this would happen, but just in case
-        return False
+    return response
+
+def add_new_resource(dataset, trait_id=None):
+    resource_ob = {
+        'owner_id'    : webqtlConfig.DEFAULT_OWNER_ID,
+        'default_mask': webqtlConfig.DEFAULT_PRIVILEGES,
+        'group_masks' : {}
+    }
+
+    if dataset.type == "Publish":
+        resource_ob['name'] = get_group_code(dataset) + "_" + str(trait_id)
+        resource_ob['data'] = {
+            'dataset': dataset.id,
+            'trait'  : trait_id
+        }
+        resource_ob['type'] = 'dataset-publish'
+    elif dataset.type == "Geno":
+        resource_ob['name'] = dataset.name
+        resource_ob['data'] = {
+            'dataset': dataset.id
+        }
+        resource_ob['type'] = 'dataset-geno'
+    else:
+        resource_ob['name'] = dataset.name
+        resource_ob['data'] = {
+            'dataset': dataset.id
+        }
+        resource_ob['type'] = 'dataset-probeset'
+
+    resource_info = add_resource(resource_ob, update=False)
+
+    return resource_info
+
+def get_group_code(dataset):
+    results = g.db.execute("SELECT InbredSetCode from InbredSet where Name='{}'".format(dataset.group.name)).fetchone()
+
+    return results[0]
 
 def check_admin(resource_id=None):
     the_url = "http://localhost:8080/available?resource={}&user={}".format(resource_id, g.user_session.user_id)
diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py
index 6c912a23..1377a564 100644
--- a/wqflask/utility/redis_tools.py
+++ b/wqflask/utility/redis_tools.py
@@ -264,17 +264,14 @@ def get_resources():
     return resource_list
 
 def get_resource_id(dataset, trait_id=None):
+    resource_id = False
     if dataset.type == "Publish":
         if trait_id:
             resource_id = hmac.hmac_creation("{}:{}:{}".format('dataset-publish', dataset.id, trait_id))
-        else:
-            return False
     elif dataset.type == "ProbeSet":
         resource_id = hmac.hmac_creation("{}:{}".format('dataset-probeset', dataset.id))
     elif dataset.type == "Geno":
         resource_id = hmac.hmac_creation("{}:{}".format('dataset-geno', dataset.id))
-    else:
-        return False
 
     return resource_id
 
-- 
cgit v1.2.3


From 91e52482071ce90acf3607597de2ae79e298fd67 Mon Sep 17 00:00:00 2001
From: Pjotr Prins
Date: Sat, 25 Jul 2020 16:25:14 +0100
Subject: The variable is never defined, so let's default to "none"

---
 wqflask/utility/authentication_tools.py | 5 +++--
 1 file changed, 3 insertions(+), 2 deletions(-)

(limited to 'wqflask/utility/authentication_tools.py')

diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py
index ed7462d1..9a2a5ccd 100644
--- a/wqflask/utility/authentication_tools.py
+++ b/wqflask/utility/authentication_tools.py
@@ -45,7 +45,7 @@ def check_resource_availability(dataset, trait_id=None):
 
 def add_new_resource(dataset, trait_id=None):
     resource_ob = {
-        'owner_id'    : webqtlConfig.DEFAULT_OWNER_ID,
+        'owner_id'    : "none", # webqtlConfig.DEFAULT_OWNER_ID,
         'default_mask': webqtlConfig.DEFAULT_PRIVILEGES,
         'group_masks' : {}
     }
@@ -84,6 +84,7 @@ def check_admin(resource_id=None):
     try:
         response = json.loads(requests.get(the_url).content)['admin']
     except:
+        logger.debug(resource_info)
         response = resource_info['default_mask']['admin']
 
     if 'edit-admins' in response:
@@ -124,4 +125,4 @@ def check_owner_or_admin(dataset=None, trait_id=None, resource_id=None):
         else:
             return check_admin(resource_id)
 
-    return "not-admin"
\ No newline at end of file
+    return "not-admin"
-- 
cgit v1.2.3


From 317d7a78930ecf4be8ec80bd688c14baa8852f04 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Wed, 29 Jul 2020 18:50:08 -0500
Subject: Fixed error that occured for new resources in check_admin *
 wqflask/utility/authentication_tools.py: the code forgot to get resource_info
 when a resource wasn't in Redis yet, causing an error when it was referenced,
 so I added a line getting the resource info (and also a couple comments for
 other lines related to authentication)

---
 wqflask/utility/authentication_tools.py | 6 +++---
 1 file changed, 3 insertions(+), 3 deletions(-)

(limited to 'wqflask/utility/authentication_tools.py')

diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py
index 9a2a5ccd..ece7022c 100644
--- a/wqflask/utility/authentication_tools.py
+++ b/wqflask/utility/authentication_tools.py
@@ -24,9 +24,9 @@ def check_resource_availability(dataset, trait_id=None):
 
     resource_id = get_resource_id(dataset, trait_id)
 
-    if resource_id:
+    if resource_id: #ZS: This should never be false, but it's technically possible if a non-Temp dataset somehow had a type other than Publish/ProbeSet/Geno
         resource_info = get_resource_info(resource_id)
-        if not resource_info:
+        if not resource_info: #ZS: If resource isn't already in redis, add it with default privileges
             resource_info = add_new_resource(dataset, trait_id)
 
     #ZS: Check if super-user - we should probably come up with some way to integrate this into the proxy
@@ -84,7 +84,7 @@ def check_admin(resource_id=None):
     try:
         response = json.loads(requests.get(the_url).content)['admin']
     except:
-        logger.debug(resource_info)
+        resource_info = get_resource_info(resource_id)
         response = resource_info['default_mask']['admin']
 
     if 'edit-admins' in response:
-- 
cgit v1.2.3


From 3aaa28ea762c496eeb84e09e45194e3fd2a51673 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Wed, 19 Aug 2020 03:45:49 +0300
Subject: Make Python more idiomatic

Run `2to3-3.8 -f idioms -w .`

See: <https://docs.python.org/2/library/2to3.html#2to3fixer-idioms>
---
 scripts/maintenance/readProbeSetMean_v7.py | 6 ++----
 scripts/maintenance/readProbeSetSE_v7.py   | 6 ++----
 wqflask/base/data_set.py                   | 4 ++--
 wqflask/utility/authentication_tools.py    | 2 +-
 wqflask/utility/svg.py                     | 2 +-
 wqflask/wqflask/ctl/ctl_analysis.py        | 2 +-
 wqflask/wqflask/show_trait/SampleList.py   | 2 +-
 wqflask/wqflask/show_trait/show_trait.py   | 2 +-
 wqflask/wqflask/user_login.py              | 2 +-
 9 files changed, 12 insertions(+), 16 deletions(-)

(limited to 'wqflask/utility/authentication_tools.py')

diff --git a/scripts/maintenance/readProbeSetMean_v7.py b/scripts/maintenance/readProbeSetMean_v7.py
index 97767715..864b4e08 100755
--- a/scripts/maintenance/readProbeSetMean_v7.py
+++ b/scripts/maintenance/readProbeSetMean_v7.py
@@ -80,8 +80,7 @@ while line:
 	if kj%100000 == 0:
 		print(('checked ',kj,' lines'))
 
-GeneList = list(map(string.lower, GeneList))
-GeneList.sort()
+GeneList = sorted(map(string.lower, GeneList))
 	
 if isCont==0:
 	sys.exit(0)
@@ -148,9 +147,8 @@ for item in results:
 	
 print(Names)
 
-Names = list(map(string.lower, Names))
+Names = sorted(map(string.lower, Names))
 
-Names.sort() # -- Fixed the lower case problem of ProbeSets affx-mur_b2_at  doesn't exist --#
 
 
 ##---- compare genelist with names ----##
diff --git a/scripts/maintenance/readProbeSetSE_v7.py b/scripts/maintenance/readProbeSetSE_v7.py
index 833c3f5f..20a846a4 100755
--- a/scripts/maintenance/readProbeSetSE_v7.py
+++ b/scripts/maintenance/readProbeSetSE_v7.py
@@ -91,8 +91,7 @@ while line:
     if kj % 100000 == 0:
         print(('checked ', kj, ' lines'))
 
-GeneList = list(map(string.lower, GeneList))
-GeneList.sort()
+GeneList = sorted(map(string.lower, GeneList))
 
 if isCont == 0:
     sys.exit(0)
@@ -158,8 +157,7 @@ results = db.fetchall()
 Names = []
 for item in results:
     Names.append(item[0])
-    Names = list(map(string.lower, Names))
-    Names.sort()  # -- Fixed the lower case problem of ProbeSets affx-mur_b2_at  doesn't exist --#
+    Names = sorted(map(string.lower, Names))
 
 ##---- compare genelist with names ----##
 x = y = 0
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index b0119b58..06e1c551 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -254,7 +254,7 @@ class Markers(object):
         logger.debug("length of self.markers:", len(self.markers))
         logger.debug("length of p_values:", len(p_values))
 
-        if type(p_values) is list:
+        if isinstance(p_values, list):
             # THIS IS only needed for the case when we are limiting the number of p-values calculated
             # if len(self.markers) > len(p_values):
             #    self.markers = self.markers[:len(p_values)]
@@ -270,7 +270,7 @@ class Markers(object):
                     marker['lod_score'] = -math.log10(marker['p_value'])
                     # Using -log(p) for the LRS; need to ask Rob how he wants to get LRS from p-values
                     marker['lrs_value'] = -math.log10(marker['p_value']) * 4.61
-        elif type(p_values) is dict:
+        elif isinstance(p_values, dict):
             filtered_markers = []
             for marker in self.markers:
                 #logger.debug("marker[name]", marker['name'])
diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py
index ece7022c..bc03eb55 100644
--- a/wqflask/utility/authentication_tools.py
+++ b/wqflask/utility/authentication_tools.py
@@ -17,7 +17,7 @@ logger = logging.getLogger(__name__ )
 def check_resource_availability(dataset, trait_id=None):
 
     #At least for now assume temporary entered traits are accessible
-    if type(dataset) == str:
+    if isinstance(dataset, str):
         return webqtlConfig.DEFAULT_PRIVILEGES
     if dataset.type == "Temp":
         return webqtlConfig.DEFAULT_PRIVILEGES
diff --git a/wqflask/utility/svg.py b/wqflask/utility/svg.py
index 872f22fe..874ada9d 100644
--- a/wqflask/utility/svg.py
+++ b/wqflask/utility/svg.py
@@ -332,7 +332,7 @@ class SVGelement:
                 f.write('\n'+'\t'*(level+2)+line)
             f.write('\n'+'\t'*(level+1)+']]>\n')
         if self.text:
-            if type(self.text) == type(''):  # If the text is only text
+            if isinstance(self.text, type('')):  # If the text is only text
                 f.write(_escape(str(self.text)))
             else:  # If the text is a spannedtext class
                 f.write(str(self.text))
diff --git a/wqflask/wqflask/ctl/ctl_analysis.py b/wqflask/wqflask/ctl/ctl_analysis.py
index f0be7a98..e58a7b87 100644
--- a/wqflask/wqflask/ctl/ctl_analysis.py
+++ b/wqflask/wqflask/ctl/ctl_analysis.py
@@ -175,7 +175,7 @@ class CTL(object):
         sys.stdout.flush()
 
         # Create the interactive graph for cytoscape visualization (Nodes and Edges)
-        if not type(significant) == ri.RNULLType:
+        if not isinstance(significant, ri.RNULLType):
           for x in range(len(significant[0])):
             logger.debug(significant[0][x], significant[1][x], significant[2][x])     # Debug to console
             tsS = significant[0][x].split(':')                                        # Source
diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py
index ad78ebcc..21ba7f63 100644
--- a/wqflask/wqflask/show_trait/SampleList.py
+++ b/wqflask/wqflask/show_trait/SampleList.py
@@ -43,7 +43,7 @@ class SampleList(object):
         for counter, sample_name in enumerate(sample_names, 1):
             sample_name = sample_name.replace("_2nd_", "")
 
-            if type(self.this_trait) is list: #ZS: self.this_trait will be a list if it is a Temp trait
+            if isinstance(self.this_trait, list): #ZS: self.this_trait will be a list if it is a Temp trait
                 if counter <= len(self.this_trait) and str(self.this_trait[counter-1]).upper() != 'X':
                     sample = webqtlCaseData.webqtlCaseData(name=sample_name, value=float(self.this_trait[counter-1]))
                 else:
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index c156e61b..65899ab2 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -625,7 +625,7 @@ def get_categorical_variables(this_trait, sample_list):
 
 def get_genotype_scales(genofiles):
     geno_scales = {}
-    if type(genofiles) is list:
+    if isinstance(genofiles, list):
         for the_file in genofiles:
             file_location = the_file['location']
             geno_scales[file_location] = get_scales_from_genofile(file_location)
diff --git a/wqflask/wqflask/user_login.py b/wqflask/wqflask/user_login.py
index cfee0079..04672b45 100644
--- a/wqflask/wqflask/user_login.py
+++ b/wqflask/wqflask/user_login.py
@@ -193,7 +193,7 @@ def login():
             if user_details:
                 submitted_password = params['password']
                 pwfields = user_details['password']
-                if type(pwfields) is str:
+                if isinstance(pwfields, str):
                     pwfields = json.loads(pwfields)
                 encrypted_pass_fields = encode_password(pwfields, submitted_password)
                 password_match = pbkdf2.safe_str_cmp(encrypted_pass_fields['password'], pwfields['password'])
-- 
cgit v1.2.3


From 303e4b71c2172da5be19c84d4be5a062329ac013 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Wed, 26 Aug 2020 19:12:33 +0300
Subject: Remove "from __future__ import new_feature" statements

See: <https://docs.python.org/2/library/2to3.html#2to3fixer-future>
---
 test/requests/link_checker.py                      |  1 -
 test/requests/main_web_functionality.py            | 22 ++++++++++++----------
 test/requests/mapping_tests.py                     |  1 -
 test/requests/navigation_tests.py                  |  1 -
 test/requests/test-website.py                      |  2 +-
 webtests/browser_run.py                            |  4 +---
 webtests/correlation_matrix_test.py                |  2 --
 webtests/correlation_test.py                       |  2 --
 webtests/marker_regression_test.py                 |  2 --
 webtests/show_trait_js_test.py                     |  2 --
 webtests/test_runner.py                            |  4 +---
 wqflask/base/data_set.py                           |  1 -
 wqflask/base/mrna_assay_tissue_data.py             |  4 +---
 wqflask/base/species.py                            |  4 +---
 wqflask/base/trait.py                              |  2 --
 wqflask/maintenance/convert_dryad_to_bimbam.py     |  3 +--
 wqflask/maintenance/convert_geno_to_bimbam.py      |  3 +--
 wqflask/maintenance/gen_select_dataset.py          | 10 +---------
 .../maintenance/generate_kinship_from_bimbam.py    |  3 +--
 .../maintenance/generate_probesetfreeze_file.py    |  2 --
 wqflask/maintenance/geno_to_json.py                |  3 +--
 wqflask/maintenance/get_group_samplelists.py       |  2 --
 wqflask/maintenance/print_benchmark.py             |  4 +---
 wqflask/maintenance/quantile_normalize.py          |  7 +------
 wqflask/maintenance/set_resource_defaults.py       |  4 +---
 wqflask/utility/Plot.py                            |  2 --
 wqflask/utility/after.py                           |  4 +---
 wqflask/utility/authentication_tools.py            |  2 --
 wqflask/utility/benchmark.py                       |  2 --
 wqflask/utility/chunks.py                          |  2 --
 wqflask/utility/db_tools.py                        |  2 --
 wqflask/utility/gen_geno_ob.py                     |  4 +---
 wqflask/utility/genofile_parser.py                 |  1 -
 wqflask/utility/helper_functions.py                |  2 --
 wqflask/utility/hmac.py                            |  4 +---
 wqflask/utility/redis_tools.py                     |  4 +---
 wqflask/utility/temp_data.py                       |  1 -
 wqflask/wqflask/__init__.py                        |  2 --
 wqflask/wqflask/api/correlation.py                 |  4 +---
 wqflask/wqflask/api/gen_menu.py                    |  2 --
 wqflask/wqflask/api/mapping.py                     |  2 --
 wqflask/wqflask/api/router.py                      |  4 +---
 wqflask/wqflask/collect.py                         |  3 ---
 .../comparison_bar_chart/comparison_bar_chart.py   |  1 -
 wqflask/wqflask/correlation/corr_scatter_plot.py   |  4 +---
 .../wqflask/correlation/correlation_functions.py   |  4 +---
 wqflask/wqflask/correlation/show_corr_results.py   |  2 --
 .../wqflask/correlation_matrix/show_corr_matrix.py |  2 --
 wqflask/wqflask/do_search.py                       |  2 --
 wqflask/wqflask/docs.py                            |  4 +---
 wqflask/wqflask/export_traits.py                   |  4 +---
 wqflask/wqflask/external_tools/send_to_bnw.py      |  4 +---
 .../wqflask/external_tools/send_to_geneweaver.py   |  4 +---
 .../wqflask/external_tools/send_to_webgestalt.py   |  4 +---
 wqflask/wqflask/group_manager.py                   |  5 +----
 wqflask/wqflask/gsearch.py                         |  2 --
 wqflask/wqflask/heatmap/heatmap.py                 |  2 --
 wqflask/wqflask/interval_analyst/GeneUtil.py       |  2 --
 wqflask/wqflask/marker_regression/run_mapping.py   |  4 +---
 wqflask/wqflask/model.py                           |  4 +---
 wqflask/wqflask/network_graph/network_graph.py     |  2 --
 wqflask/wqflask/news.py                            |  1 -
 wqflask/wqflask/parser.py                          |  2 --
 wqflask/wqflask/resource_manager.py                |  4 +---
 wqflask/wqflask/search_results.py                  |  2 --
 wqflask/wqflask/send_mail.py                       |  2 --
 wqflask/wqflask/show_trait/SampleList.py           |  2 --
 wqflask/wqflask/show_trait/export_trait_data.py    |  4 +---
 wqflask/wqflask/show_trait/show_trait.py           |  2 --
 wqflask/wqflask/snp_browser/snp_browser.py         |  2 --
 wqflask/wqflask/submit_bnw.py                      |  4 +---
 wqflask/wqflask/update_search_results.py           |  2 --
 wqflask/wqflask/user_login.py                      |  4 +---
 wqflask/wqflask/user_manager.py                    |  2 --
 wqflask/wqflask/user_session.py                    |  2 --
 wqflask/wqflask/views.py                           |  2 --
 76 files changed, 45 insertions(+), 190 deletions(-)

(limited to 'wqflask/utility/authentication_tools.py')

diff --git a/test/requests/link_checker.py b/test/requests/link_checker.py
index 5e16a5cd..949a33c8 100644
--- a/test/requests/link_checker.py
+++ b/test/requests/link_checker.py
@@ -1,4 +1,3 @@
-from __future__ import print_function
 import re
 import requests
 from lxml.html import parse
diff --git a/test/requests/main_web_functionality.py b/test/requests/main_web_functionality.py
index d070dab9..78030307 100644
--- a/test/requests/main_web_functionality.py
+++ b/test/requests/main_web_functionality.py
@@ -1,9 +1,7 @@
-from __future__ import print_function
-import re
 import requests
 from lxml.html import parse
 from link_checker import check_page
-from requests.exceptions import ConnectionError
+
 
 def check_home(url):
     doc = parse(url).getroot()
@@ -11,20 +9,23 @@ def check_home(url):
     assert(search_button[0].value == "Search")
     print("OK")
 
+
 def check_search_page(host):
     data = dict(
-        species="mouse"
-        , group="BXD"
-        , type="Hippocampus mRNA"
-        , dataset="HC_M2_0606_P"
-        , search_terms_or=""
-        , search_terms_and="MEAN=(15 16) LRS=(23 46)")
+        species="mouse",
+        group="BXD",
+        type="Hippocampus mRNA",
+        dataset="HC_M2_0606_P",
+        search_terms_or="",
+        search_terms_and="MEAN=(15 16) LRS=(23 46)")
     result = requests.get(host+"/search", params=data)
     found = result.text.find("records are shown below")
     assert(found >= 0)
     assert(result.status_code == 200)
     print("OK")
-    check_traits_page(host, "/show_trait?trait_id=1435395_s_at&dataset=HC_M2_0606_P")
+    check_traits_page(host, ("/show_trait?trait_id=1435395_"
+                             "s_at&dataset=HC_M2_0606_P"))
+
 
 def check_traits_page(host, traits_url):
     doc = parse(host+traits_url).getroot()
@@ -33,6 +34,7 @@ def check_traits_page(host, traits_url):
     print("OK")
     check_page(host, host+traits_url)
 
+
 def check_main_web_functionality(args_obj, parser):
     print("")
     print("Checking main web functionality...")
diff --git a/test/requests/mapping_tests.py b/test/requests/mapping_tests.py
index 5748a2a3..19b22c21 100644
--- a/test/requests/mapping_tests.py
+++ b/test/requests/mapping_tests.py
@@ -1,4 +1,3 @@
-from __future__ import print_function
 import re
 import copy
 import json
diff --git a/test/requests/navigation_tests.py b/test/requests/navigation_tests.py
index eda27324..6b91c1fd 100644
--- a/test/requests/navigation_tests.py
+++ b/test/requests/navigation_tests.py
@@ -1,4 +1,3 @@
-from __future__ import print_function
 import re
 import requests
 from lxml.html import parse
diff --git a/test/requests/test-website.py b/test/requests/test-website.py
index f90d1843..8bfb47c2 100755
--- a/test/requests/test-website.py
+++ b/test/requests/test-website.py
@@ -3,7 +3,7 @@
 #   env GN2_PROFILE=/home/wrk/opt/gn-latest ./bin/genenetwork2 ./etc/default_settings.py -c ../test/requests/test-website.py http://localhost:5003
 #
 # Mostly to pick up the Guix GN2_PROFILE and python modules
-from __future__ import print_function
+
 import argparse
 from link_checker import check_links
 from link_checker import check_packaged_js_files
diff --git a/webtests/browser_run.py b/webtests/browser_run.py
index 2ec299c5..7ee540b7 100644
--- a/webtests/browser_run.py
+++ b/webtests/browser_run.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, division, print_function
-
 __all__ = ('sleep', 'testmod', 'test')
 
 from doctest import testmod
@@ -71,4 +69,4 @@ class Test(object):
 
 
 
-test = Test()
\ No newline at end of file
+test = Test()
diff --git a/webtests/correlation_matrix_test.py b/webtests/correlation_matrix_test.py
index 8529c265..97114890 100644
--- a/webtests/correlation_matrix_test.py
+++ b/webtests/correlation_matrix_test.py
@@ -65,8 +65,6 @@ text: 0.608\n71
 
 """
 
-from __future__ import absolute_import, division, print_function
-
 from browser_run import *
 
 testmod()
diff --git a/webtests/correlation_test.py b/webtests/correlation_test.py
index aad3a69f..311bb847 100644
--- a/webtests/correlation_test.py
+++ b/webtests/correlation_test.py
@@ -44,8 +44,6 @@ text: 1.000
 
 """
 
-from __future__ import absolute_import, division, print_function
-
 from browser_run import *
 
 testmod()
diff --git a/webtests/marker_regression_test.py b/webtests/marker_regression_test.py
index c4f76f53..9b4a4acb 100644
--- a/webtests/marker_regression_test.py
+++ b/webtests/marker_regression_test.py
@@ -48,8 +48,6 @@ text: 11.511
 
 """
 
-from __future__ import absolute_import, division, print_function
-
 from browser_run import *
 
 testmod()
diff --git a/webtests/show_trait_js_test.py b/webtests/show_trait_js_test.py
index 0fd2c16c..34ffd3b7 100644
--- a/webtests/show_trait_js_test.py
+++ b/webtests/show_trait_js_test.py
@@ -35,8 +35,6 @@ style: display: none;
 
 """
 
-from __future__ import absolute_import, division, print_function
-
 from browser_run import *
 
 testmod()
diff --git a/webtests/test_runner.py b/webtests/test_runner.py
index ef6d0d69..b5b590a6 100644
--- a/webtests/test_runner.py
+++ b/webtests/test_runner.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, division, print_function
-
 import unittest
 import doctest
 import glob
@@ -25,4 +23,4 @@ def main():
     runner.run(suite)
     
 if __name__ == '__main__':
-    main()
\ No newline at end of file
+    main()
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 39a8a2ed..8ac7a279 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -18,7 +18,6 @@
 #
 # This module is used by GeneNetwork project (www.genenetwork.org)
 
-from __future__ import absolute_import, print_function, division
 from db.call import fetchall, fetchone, fetch1
 from utility.logger import getLogger
 from utility.tools import USE_GN_SERVER, USE_REDIS, flat_files, flat_file_exists, GN2_BASE_URL
diff --git a/wqflask/base/mrna_assay_tissue_data.py b/wqflask/base/mrna_assay_tissue_data.py
index 6fec5dcd..33ce12bd 100644
--- a/wqflask/base/mrna_assay_tissue_data.py
+++ b/wqflask/base/mrna_assay_tissue_data.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, print_function, division
-
 import collections
 
 from flask import g
@@ -92,4 +90,4 @@ class MrnaAssayTissueData(object):
                 else:
                     symbol_values_dict[result.Symbol.lower()].append(result.value)
 
-        return symbol_values_dict
\ No newline at end of file
+        return symbol_values_dict
diff --git a/wqflask/base/species.py b/wqflask/base/species.py
index 6d99af65..e3f1bc4a 100644
--- a/wqflask/base/species.py
+++ b/wqflask/base/species.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, print_function, division
-
 import collections
 
 from flask import Flask, g
@@ -59,4 +57,4 @@ class Chromosomes(object):
         results = g.db.execute(query).fetchall()
 
         for item in results:
-            self.chromosomes[item.OrderId] = IndChromosome(item.Name, item.Length)
\ No newline at end of file
+            self.chromosomes[item.OrderId] = IndChromosome(item.Name, item.Length)
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 09c41fa7..b20efd2a 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, division, print_function
-
 import os
 import string
 import resource
diff --git a/wqflask/maintenance/convert_dryad_to_bimbam.py b/wqflask/maintenance/convert_dryad_to_bimbam.py
index e833b395..12ce35e9 100644
--- a/wqflask/maintenance/convert_dryad_to_bimbam.py
+++ b/wqflask/maintenance/convert_dryad_to_bimbam.py
@@ -6,7 +6,6 @@ Convert data dryad files to a BIMBAM _geno and _snps file
 
 """
 
-from __future__ import print_function, division, absolute_import
 import sys
 sys.path.append("..")
 
@@ -67,4 +66,4 @@ def convert_dryad_to_bimbam(filename):
 
 if __name__=="__main__":
     input_filename = "/home/zas1024/cfw_data/" + sys.argv[1] + ".txt"
-    convert_dryad_to_bimbam(input_filename)
\ No newline at end of file
+    convert_dryad_to_bimbam(input_filename)
diff --git a/wqflask/maintenance/convert_geno_to_bimbam.py b/wqflask/maintenance/convert_geno_to_bimbam.py
index 528b98cf..d49742f2 100644
--- a/wqflask/maintenance/convert_geno_to_bimbam.py
+++ b/wqflask/maintenance/convert_geno_to_bimbam.py
@@ -9,7 +9,6 @@ code
 
 """
 
-from __future__ import print_function, division, absolute_import
 import sys
 sys.path.append("..")
 import os
@@ -187,4 +186,4 @@ if __name__=="__main__":
     #convertob = ConvertGenoFile("/home/zas1024/gene/genotype_files/genotypes/SRxSHRSPF2.geno", "/home/zas1024/gene/genotype_files/new_genotypes/SRxSHRSPF2.json")
     #convertob.convert()
     ConvertGenoFile.process_all(Old_Geno_Directory, New_Geno_Directory)
-    #ConvertGenoFiles(Geno_Directory)
\ No newline at end of file
+    #ConvertGenoFiles(Geno_Directory)
diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py
index fd65a52a..544e2fd1 100644
--- a/wqflask/maintenance/gen_select_dataset.py
+++ b/wqflask/maintenance/gen_select_dataset.py
@@ -30,14 +30,6 @@ It needs to be run manually when database has been changed. Run it as
 #
 # This module is used by GeneNetwork project (www.genenetwork.org)
 
-from __future__ import print_function, division
-
-#from flask import config
-#
-#cdict = {}
-#config = config.Config(cdict).from_envvar('WQFLASK_SETTINGS')
-#print("cdict is:", cdict)
-
 import sys
 
 # NEW: Note we prepend the current path - otherwise a guix instance of GN2 may be used instead
@@ -319,4 +311,4 @@ def _test_it():
 if __name__ == '__main__':
     Conn = MySQLdb.Connect(**parse_db_uri())
     Cursor = Conn.cursor()
-    main()
\ No newline at end of file
+    main()
diff --git a/wqflask/maintenance/generate_kinship_from_bimbam.py b/wqflask/maintenance/generate_kinship_from_bimbam.py
index b53f5dda..60257b28 100644
--- a/wqflask/maintenance/generate_kinship_from_bimbam.py
+++ b/wqflask/maintenance/generate_kinship_from_bimbam.py
@@ -8,7 +8,6 @@ and uses GEMMA to generate their corresponding kinship/relatedness matrix file
 
 """
 
-from __future__ import print_function, division, absolute_import
 import sys
 sys.path.append("..")
 import os
@@ -58,4 +57,4 @@ if __name__=="__main__":
     Bimbam_Directory = """/export/local/home/zas1024/genotype_files/genotype/bimbam/"""
     GenerateKinshipMatrices.process_all(Geno_Directory, Bimbam_Directory)
     
-    #./gemma -g /home/zas1024/genotype_files/genotype/bimbam/BXD_geno.txt -p /home/zas1024/genotype_files/genotype/bimbam/BXD_pheno.txt -gk 1 -o BXD
\ No newline at end of file
+    #./gemma -g /home/zas1024/genotype_files/genotype/bimbam/BXD_geno.txt -p /home/zas1024/genotype_files/genotype/bimbam/BXD_pheno.txt -gk 1 -o BXD
diff --git a/wqflask/maintenance/generate_probesetfreeze_file.py b/wqflask/maintenance/generate_probesetfreeze_file.py
index 4231cc7c..b1e41e9a 100644
--- a/wqflask/maintenance/generate_probesetfreeze_file.py
+++ b/wqflask/maintenance/generate_probesetfreeze_file.py
@@ -1,7 +1,5 @@
 #!/usr/bin/python
 
-from __future__ import absolute_import, print_function, division
-
 import sys
 
 # sys.path.insert(0, "..") - why?
diff --git a/wqflask/maintenance/geno_to_json.py b/wqflask/maintenance/geno_to_json.py
index 9579812a..7e7fd241 100644
--- a/wqflask/maintenance/geno_to_json.py
+++ b/wqflask/maintenance/geno_to_json.py
@@ -9,7 +9,6 @@ code
 
 """
 
-from __future__ import print_function, division, absolute_import
 import sys
 sys.path.append("..")
 import os
@@ -194,4 +193,4 @@ if __name__=="__main__":
     ConvertGenoFile.process_all(Old_Geno_Directory, New_Geno_Directory)
     #ConvertGenoFiles(Geno_Directory)
     
-    #process_csv(Input_File, Output_File)
\ No newline at end of file
+    #process_csv(Input_File, Output_File)
diff --git a/wqflask/maintenance/get_group_samplelists.py b/wqflask/maintenance/get_group_samplelists.py
index fb22898a..3f9d0278 100644
--- a/wqflask/maintenance/get_group_samplelists.py
+++ b/wqflask/maintenance/get_group_samplelists.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, print_function, division
-
 import os
 import glob
 import gzip
diff --git a/wqflask/maintenance/print_benchmark.py b/wqflask/maintenance/print_benchmark.py
index ae327cf3..b24ce4f1 100644
--- a/wqflask/maintenance/print_benchmark.py
+++ b/wqflask/maintenance/print_benchmark.py
@@ -1,7 +1,5 @@
 #!/usr/bin/python
 
-from __future__ import absolute_import, print_function, division
-
 import time
 
 from pprint import pformat as pf
@@ -40,4 +38,4 @@ def new_main():
     print(pf(TheCounter.Counters))
 
 if __name__ == '__main__':
-    new_main()
\ No newline at end of file
+    new_main()
diff --git a/wqflask/maintenance/quantile_normalize.py b/wqflask/maintenance/quantile_normalize.py
index 4d6e03bf..701b2b50 100644
--- a/wqflask/maintenance/quantile_normalize.py
+++ b/wqflask/maintenance/quantile_normalize.py
@@ -1,10 +1,5 @@
-from __future__ import absolute_import, print_function, division
-
 import sys
 sys.path.insert(0, './')
-
-
-
 import MySQLdb
 import urllib.parse
 
@@ -126,4 +121,4 @@ if __name__ == '__main__':
         }
     )
 
-    print(response)
\ No newline at end of file
+    print(response)
diff --git a/wqflask/maintenance/set_resource_defaults.py b/wqflask/maintenance/set_resource_defaults.py
index abd5416c..4177c124 100644
--- a/wqflask/maintenance/set_resource_defaults.py
+++ b/wqflask/maintenance/set_resource_defaults.py
@@ -16,8 +16,6 @@ To run:
 
 """
 
-from __future__ import print_function, division
-
 import sys
 import json
 
@@ -163,4 +161,4 @@ def main():
 if __name__ == '__main__':
     Conn = MySQLdb.Connect(**parse_db_uri())
     Cursor = Conn.cursor()
-    main()
\ No newline at end of file
+    main()
diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py
index 48a5c7ba..61f408d2 100644
--- a/wqflask/utility/Plot.py
+++ b/wqflask/utility/Plot.py
@@ -24,8 +24,6 @@
 #
 # Last updated by GeneNetwork Core Team 2010/10/20
 
-from __future__ import print_function
-
 from PIL import ImageColor
 from PIL import ImageDraw
 from PIL import ImageFont
diff --git a/wqflask/utility/after.py b/wqflask/utility/after.py
index b628a0a4..06091ecb 100644
--- a/wqflask/utility/after.py
+++ b/wqflask/utility/after.py
@@ -1,5 +1,3 @@
-from __future__ import print_function, division, absolute_import
-
 """
 See: http://flask.pocoo.org/docs/patterns/deferredcallbacks/#deferred-callbacks
 
@@ -13,4 +11,4 @@ def after_this_request(f):
     if not hasattr(g, 'after_request_callbacks'):
         g.after_request_callbacks = []
     g.after_request_callbacks.append(f)
-    return f
\ No newline at end of file
+    return f
diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py
index bc03eb55..0e499180 100644
--- a/wqflask/utility/authentication_tools.py
+++ b/wqflask/utility/authentication_tools.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, print_function, division
-
 import json
 import requests
 
diff --git a/wqflask/utility/benchmark.py b/wqflask/utility/benchmark.py
index 221e5151..ea5a0ab6 100644
--- a/wqflask/utility/benchmark.py
+++ b/wqflask/utility/benchmark.py
@@ -1,5 +1,3 @@
-from __future__ import print_function, division, absolute_import
-
 import collections
 import inspect
 import time
diff --git a/wqflask/utility/chunks.py b/wqflask/utility/chunks.py
index d91b9bf4..9a7db102 100644
--- a/wqflask/utility/chunks.py
+++ b/wqflask/utility/chunks.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, print_function, division
-
 import math
 import time
 
diff --git a/wqflask/utility/db_tools.py b/wqflask/utility/db_tools.py
index 4034f39c..92bde505 100644
--- a/wqflask/utility/db_tools.py
+++ b/wqflask/utility/db_tools.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, print_function, division
-
 from MySQLdb import escape_string as escape
 
 def create_in_clause(items):
diff --git a/wqflask/utility/gen_geno_ob.py b/wqflask/utility/gen_geno_ob.py
index ae42f834..81085ffe 100644
--- a/wqflask/utility/gen_geno_ob.py
+++ b/wqflask/utility/gen_geno_ob.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, division, print_function
-
 import utility.logger
 logger = utility.logger.getLogger(__name__ )
 
@@ -178,4 +176,4 @@ class Locus(object):
                 if allele in list(geno_table.keys()):
                     self.genotype.append(geno_table[allele])
                 else: #ZS: Some genotype appears that isn't specified in the metadata, make it unknown
-                    self.genotype.append("U")
\ No newline at end of file
+                    self.genotype.append("U")
diff --git a/wqflask/utility/genofile_parser.py b/wqflask/utility/genofile_parser.py
index af306731..0b736176 100644
--- a/wqflask/utility/genofile_parser.py
+++ b/wqflask/utility/genofile_parser.py
@@ -1,7 +1,6 @@
 # CTL analysis for GN2
 # Author / Maintainer: Danny Arends <Danny.Arends@gmail.com>
 
-from __future__ import print_function, division, absolute_import
 import sys
 import os
 import glob
diff --git a/wqflask/utility/helper_functions.py b/wqflask/utility/helper_functions.py
index 107c9ec6..7eb7f013 100644
--- a/wqflask/utility/helper_functions.py
+++ b/wqflask/utility/helper_functions.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, print_function, division
-
 from base import data_set
 from base.trait import create_trait
 from base.species import TheSpecies
diff --git a/wqflask/utility/hmac.py b/wqflask/utility/hmac.py
index b08be97e..73e28790 100644
--- a/wqflask/utility/hmac.py
+++ b/wqflask/utility/hmac.py
@@ -1,5 +1,3 @@
-from __future__ import print_function, division, absolute_import
-
 import hmac
 import hashlib
 
@@ -37,4 +35,4 @@ def url_for_hmac(endpoint, **values):
     return url + combiner + "hm=" + hm
 
 app.jinja_env.globals.update(url_for_hmac=url_for_hmac,
-                             data_hmac=data_hmac)
\ No newline at end of file
+                             data_hmac=data_hmac)
diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py
index 1377a564..13ac5cfe 100644
--- a/wqflask/utility/redis_tools.py
+++ b/wqflask/utility/redis_tools.py
@@ -1,5 +1,3 @@
-from __future__ import print_function, division, absolute_import
-
 import uuid
 import simplejson as json
 import datetime
@@ -306,4 +304,4 @@ def change_resource_owner(resource_id, new_owner_id):
     the_resource['owner_id'] = new_owner_id
 
     Redis.delete("resource")
-    Redis.hset("resources", resource_id, json.dumps(the_resource))
\ No newline at end of file
+    Redis.hset("resources", resource_id, json.dumps(the_resource))
diff --git a/wqflask/utility/temp_data.py b/wqflask/utility/temp_data.py
index 2f2726c6..4144ae00 100644
--- a/wqflask/utility/temp_data.py
+++ b/wqflask/utility/temp_data.py
@@ -1,4 +1,3 @@
-from __future__ import print_function, division, absolute_import
 from redis import Redis
 
 import simplejson as json
diff --git a/wqflask/wqflask/__init__.py b/wqflask/wqflask/__init__.py
index d729aef5..e73f833f 100644
--- a/wqflask/wqflask/__init__.py
+++ b/wqflask/wqflask/__init__.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, division, print_function
-
 import sys
 import jinja2
 
diff --git a/wqflask/wqflask/api/correlation.py b/wqflask/wqflask/api/correlation.py
index eb05645e..7da13121 100644
--- a/wqflask/wqflask/api/correlation.py
+++ b/wqflask/wqflask/api/correlation.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, division, print_function
-
 import collections
 
 import scipy
@@ -234,4 +232,4 @@ def init_corr_params(start_vars):
         'return_count' : return_count
     }
 
-    return corr_params
\ No newline at end of file
+    return corr_params
diff --git a/wqflask/wqflask/api/gen_menu.py b/wqflask/wqflask/api/gen_menu.py
index 41966f78..1dcafe1f 100644
--- a/wqflask/wqflask/api/gen_menu.py
+++ b/wqflask/wqflask/api/gen_menu.py
@@ -1,5 +1,3 @@
-from __future__ import print_function, division
-
 from flask import g
 
 
diff --git a/wqflask/wqflask/api/mapping.py b/wqflask/wqflask/api/mapping.py
index 92c27c9b..d59a69df 100644
--- a/wqflask/wqflask/api/mapping.py
+++ b/wqflask/wqflask/api/mapping.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, division, print_function
-
 import string
 
 from base import data_set
diff --git a/wqflask/wqflask/api/router.py b/wqflask/wqflask/api/router.py
index 5f9b81b8..acf7ce4a 100644
--- a/wqflask/wqflask/api/router.py
+++ b/wqflask/wqflask/api/router.py
@@ -1,7 +1,5 @@
 # GN2 API
 
-from __future__ import absolute_import, division, print_function
-
 import os, io, csv, json, datetime, requests, yaml
 import zlib
 from zipfile import ZipFile, ZIP_DEFLATED
@@ -966,4 +964,4 @@ def get_group_id(group_name):
     if group_id:
         return group_id[0]
     else:
-        return None
\ No newline at end of file
+        return None
diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py
index 06c00930..15383603 100644
--- a/wqflask/wqflask/collect.py
+++ b/wqflask/wqflask/collect.py
@@ -1,6 +1,3 @@
-from __future__ import print_function, division, absolute_import
-
-
 import os
 import hashlib
 import datetime
diff --git a/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py b/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py
index 16832621..92de6073 100644
--- a/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py
+++ b/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py
@@ -18,7 +18,6 @@
 #
 # This module is used by GeneNetwork project (www.genenetwork.org)
 
-from __future__ import absolute_import, print_function, division
 from pprint import pformat as pf
 
 from base.trait import create_trait
diff --git a/wqflask/wqflask/correlation/corr_scatter_plot.py b/wqflask/wqflask/correlation/corr_scatter_plot.py
index 57a8d85f..929cd2c9 100644
--- a/wqflask/wqflask/correlation/corr_scatter_plot.py
+++ b/wqflask/wqflask/correlation/corr_scatter_plot.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, print_function, division
-
 import math
 
 from flask import g
@@ -130,4 +128,4 @@ def get_intercept_coords(slope, intercept, x_range, y_range):
     intercept_coords.append([x1, y1])
     intercept_coords.append([x2, y2])
 
-    return intercept_coords
\ No newline at end of file
+    return intercept_coords
diff --git a/wqflask/wqflask/correlation/correlation_functions.py b/wqflask/wqflask/correlation/correlation_functions.py
index abaa212f..b883e361 100644
--- a/wqflask/wqflask/correlation/correlation_functions.py
+++ b/wqflask/wqflask/correlation/correlation_functions.py
@@ -24,8 +24,6 @@
 #
 # Last updated by NL 2011/03/23
 
-from __future__ import absolute_import, print_function, division
-
 import math
 import rpy2.robjects
 import string
@@ -114,4 +112,4 @@ def get_trait_symbol_and_tissue_values(symbol_list=None):
     tissue_data = MrnaAssayTissueData(gene_symbols=symbol_list)
 
     if len(tissue_data.gene_symbols):
-        return tissue_data.get_symbol_values_pairs()
\ No newline at end of file
+        return tissue_data.get_symbol_values_pairs()
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index 5ced30b6..e5b87c6a 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -18,8 +18,6 @@
 #
 # This module is used by GeneNetwork project (www.genenetwork.org)
 
-from __future__ import absolute_import, print_function, division
-
 import collections
 import json
 import scipy
diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
index bd5aca1f..7b4bda31 100644
--- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
+++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
@@ -18,8 +18,6 @@
 #
 # This module is used by GeneNetwork project (www.genenetwork.org)
 
-from __future__ import absolute_import, print_function, division
-
 import datetime
 import math
 import numpy as np
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index cc9c1860..de8e1e78 100644
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -1,5 +1,3 @@
-from __future__ import print_function, division
-
 import string
 import requests
 import json
diff --git a/wqflask/wqflask/docs.py b/wqflask/wqflask/docs.py
index 78407e22..8628b81d 100644
--- a/wqflask/wqflask/docs.py
+++ b/wqflask/wqflask/docs.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, print_function, division
-
 import codecs
 
 from flask import g
@@ -42,4 +40,4 @@ def update_text(start_vars):
             sql = "UPDATE Docs SET content='{0}' WHERE entry='{1}';".format(content, start_vars['entry_type'])
             g.db.execute(sql)
     except:
-        pass
\ No newline at end of file
+        pass
diff --git a/wqflask/wqflask/export_traits.py b/wqflask/wqflask/export_traits.py
index 2f4e9aac..3a886537 100644
--- a/wqflask/wqflask/export_traits.py
+++ b/wqflask/wqflask/export_traits.py
@@ -1,5 +1,3 @@
-from __future__ import print_function, division
-
 import csv
 import xlsxwriter
 import io 
@@ -140,4 +138,4 @@ def sort_traits_by_group(trait_list=[]):
 
         traits_by_group[trait.dataset.group.name].append(trait)
 
-    return traits_by_group
\ No newline at end of file
+    return traits_by_group
diff --git a/wqflask/wqflask/external_tools/send_to_bnw.py b/wqflask/wqflask/external_tools/send_to_bnw.py
index 68efd10d..efa17f05 100644
--- a/wqflask/wqflask/external_tools/send_to_bnw.py
+++ b/wqflask/wqflask/external_tools/send_to_bnw.py
@@ -18,8 +18,6 @@
 #
 # This module is used by GeneNetwork project (www.genenetwork.org)
 
-from __future__ import absolute_import, print_function, division
-
 from base.trait import GeneralTrait
 from utility import helper_functions, corr_result_helpers
 
@@ -69,4 +67,4 @@ class SendToBNW(object):
             if has_none:
                 continue
             self.form_value += ",".join(str(cell) for cell in row)
-            self.form_value += ";"
\ No newline at end of file
+            self.form_value += ";"
diff --git a/wqflask/wqflask/external_tools/send_to_geneweaver.py b/wqflask/wqflask/external_tools/send_to_geneweaver.py
index 9844bab4..93164233 100644
--- a/wqflask/wqflask/external_tools/send_to_geneweaver.py
+++ b/wqflask/wqflask/external_tools/send_to_geneweaver.py
@@ -18,8 +18,6 @@
 #
 # This module is used by GeneNetwork project (www.genenetwork.org)
 
-from __future__ import absolute_import, print_function, division
-
 import string
 
 from flask import Flask, g
@@ -109,4 +107,4 @@ def test_chip(trait_list):
                 chip_name = '%s_NA' % result[0]
                 return chip_name
 
-    return chip_name
\ No newline at end of file
+    return chip_name
diff --git a/wqflask/wqflask/external_tools/send_to_webgestalt.py b/wqflask/wqflask/external_tools/send_to_webgestalt.py
index 30ca024f..b255ba95 100644
--- a/wqflask/wqflask/external_tools/send_to_webgestalt.py
+++ b/wqflask/wqflask/external_tools/send_to_webgestalt.py
@@ -18,8 +18,6 @@
 #
 # This module is used by GeneNetwork project (www.genenetwork.org)
 
-from __future__ import absolute_import, print_function, division
-
 import string
 
 from flask import Flask, g
@@ -123,4 +121,4 @@ def gen_gene_id_list(trait_list):
         trait_name_list.append(trait.name)
         retrieve_trait_info(trait, trait.dataset)
         gene_id_list.append(str(trait.geneid))
-    return trait_name_list, gene_id_list
\ No newline at end of file
+    return trait_name_list, gene_id_list
diff --git a/wqflask/wqflask/group_manager.py b/wqflask/wqflask/group_manager.py
index 24848ed8..e6079c3e 100644
--- a/wqflask/wqflask/group_manager.py
+++ b/wqflask/wqflask/group_manager.py
@@ -1,6 +1,3 @@
-
-from __future__ import print_function, division, absolute_import
-
 from flask import (Flask, g, render_template, url_for, request, make_response,
                    redirect, flash)
 
@@ -142,4 +139,4 @@ def send_group_invites(group_id, user_email_list = [], user_type="members"):
             else:
                send_verification_email(user_details, template_name = "email/group_verification.txt", key_prefix = "verification_code", subject = "You've been invited to join a GeneNetwork user group")
 
-#@app.route()
\ No newline at end of file
+#@app.route()
diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py
index c65a1415..6d797a29 100644
--- a/wqflask/wqflask/gsearch.py
+++ b/wqflask/wqflask/gsearch.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, print_function, division
-
 import json
 
 from flask import Flask, g
diff --git a/wqflask/wqflask/heatmap/heatmap.py b/wqflask/wqflask/heatmap/heatmap.py
index 1f1cdb90..cca5a4fc 100644
--- a/wqflask/wqflask/heatmap/heatmap.py
+++ b/wqflask/wqflask/heatmap/heatmap.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, print_function, division
-
 import string
 import os
 import random
diff --git a/wqflask/wqflask/interval_analyst/GeneUtil.py b/wqflask/wqflask/interval_analyst/GeneUtil.py
index a39e5d0f..17c8ccbf 100644
--- a/wqflask/wqflask/interval_analyst/GeneUtil.py
+++ b/wqflask/wqflask/interval_analyst/GeneUtil.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, print_function, division
-
 import string
 
 from flask import Flask, g
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index 67512bc6..7ae84b16 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, print_function, division
-
 from base.trait import GeneralTrait
 from base import data_set  #import create_dataset
 
@@ -711,4 +709,4 @@ def get_perm_strata(this_trait, sample_list, categorical_vars, used_samples):
     list_to_numbers = [d[x] for x in perm_strata_strings]
     perm_strata = list_to_numbers
 
-    return perm_strata
\ No newline at end of file
+    return perm_strata
diff --git a/wqflask/wqflask/model.py b/wqflask/wqflask/model.py
index a135761c..772f74e4 100644
--- a/wqflask/wqflask/model.py
+++ b/wqflask/wqflask/model.py
@@ -1,5 +1,3 @@
-from __future__ import print_function, division, absolute_import
-
 import uuid
 import datetime
 
@@ -168,4 +166,4 @@ def display_collapsible(number):
 
 def user_uuid():
     """Unique cookie for a user"""
-    user_uuid = request.cookies.get('user_uuid')
\ No newline at end of file
+    user_uuid = request.cookies.get('user_uuid')
diff --git a/wqflask/wqflask/network_graph/network_graph.py b/wqflask/wqflask/network_graph/network_graph.py
index 2a4c4a93..70e5dd58 100644
--- a/wqflask/wqflask/network_graph/network_graph.py
+++ b/wqflask/wqflask/network_graph/network_graph.py
@@ -18,8 +18,6 @@
 #
 # This module is used by GeneNetwork project (www.genenetwork.org)
 
-from __future__ import absolute_import, print_function, division
-
 import scipy
 import simplejson as json
 from pprint import pformat as pf
diff --git a/wqflask/wqflask/news.py b/wqflask/wqflask/news.py
index 20319756..0675ec4b 100644
--- a/wqflask/wqflask/news.py
+++ b/wqflask/wqflask/news.py
@@ -1,4 +1,3 @@
-from __future__ import absolute_import, print_function, division
 from flask import g
 
 class News(object):
diff --git a/wqflask/wqflask/parser.py b/wqflask/wqflask/parser.py
index 1ca5ecff..472dd30e 100644
--- a/wqflask/wqflask/parser.py
+++ b/wqflask/wqflask/parser.py
@@ -17,8 +17,6 @@ be acceptable.]
 
 """
 
-from __future__ import print_function, division
-
 import re
 
 from pprint import pformat as pf
diff --git a/wqflask/wqflask/resource_manager.py b/wqflask/wqflask/resource_manager.py
index 6b3e00fb..e883d5da 100644
--- a/wqflask/wqflask/resource_manager.py
+++ b/wqflask/wqflask/resource_manager.py
@@ -1,5 +1,3 @@
-from __future__ import print_function, division, absolute_import
-
 import json
 
 from flask import (Flask, g, render_template, url_for, request, make_response,
@@ -131,4 +129,4 @@ def get_group_names(group_masks):
         this_mask['name'] = group_name
         group_masks_with_names[group_id] = this_mask
     
-    return group_masks_with_names
\ No newline at end of file
+    return group_masks_with_names
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index c07a7670..f6c677a8 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, print_function, division
-
 import re
 import uuid
 from math import *
diff --git a/wqflask/wqflask/send_mail.py b/wqflask/wqflask/send_mail.py
index bf5d0dd8..86e8a558 100644
--- a/wqflask/wqflask/send_mail.py
+++ b/wqflask/wqflask/send_mail.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, division, print_function
-
 import datetime
 import time
 
diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py
index f17e825e..6fcf7cec 100644
--- a/wqflask/wqflask/show_trait/SampleList.py
+++ b/wqflask/wqflask/show_trait/SampleList.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, print_function, division
-
 from flask import Flask, g
 
 from base import webqtlCaseData
diff --git a/wqflask/wqflask/show_trait/export_trait_data.py b/wqflask/wqflask/show_trait/export_trait_data.py
index 68c3ad7d..2d76b935 100644
--- a/wqflask/wqflask/show_trait/export_trait_data.py
+++ b/wqflask/wqflask/show_trait/export_trait_data.py
@@ -1,5 +1,3 @@
-from __future__ import print_function, division
-
 import simplejson as json
 
 from pprint import pformat as pf
@@ -71,4 +69,4 @@ def cmp_samples(a, b):
         else:
             return 1
     else:
-        return -1
\ No newline at end of file
+        return -1
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 6a74cada..e93b0289 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, print_function, division
-
 import string
 import os
 import datetime
diff --git a/wqflask/wqflask/snp_browser/snp_browser.py b/wqflask/wqflask/snp_browser/snp_browser.py
index b3d26caf..0db7e1fe 100644
--- a/wqflask/wqflask/snp_browser/snp_browser.py
+++ b/wqflask/wqflask/snp_browser/snp_browser.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, print_function, division
-
 from flask import Flask, g, url_for
 
 import string
diff --git a/wqflask/wqflask/submit_bnw.py b/wqflask/wqflask/submit_bnw.py
index 59e60dfd..a0e84c8c 100644
--- a/wqflask/wqflask/submit_bnw.py
+++ b/wqflask/wqflask/submit_bnw.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, print_function, division
-
 from base.trait import GeneralTrait
 from base import data_set
 from utility import helper_functions
@@ -8,4 +6,4 @@ import utility.logger
 logger = utility.logger.getLogger(__name__ )
 
 def get_bnw_input(start_vars):
-    logger.debug("BNW VARS:", start_vars)
\ No newline at end of file
+    logger.debug("BNW VARS:", start_vars)
diff --git a/wqflask/wqflask/update_search_results.py b/wqflask/wqflask/update_search_results.py
index 68bea9d6..672f95b1 100644
--- a/wqflask/wqflask/update_search_results.py
+++ b/wqflask/wqflask/update_search_results.py
@@ -1,5 +1,3 @@
-from __future__ import absolute_import, print_function, division
-
 import json
 
 from flask import Flask, g
diff --git a/wqflask/wqflask/user_login.py b/wqflask/wqflask/user_login.py
index 04672b45..10cb7319 100644
--- a/wqflask/wqflask/user_login.py
+++ b/wqflask/wqflask/user_login.py
@@ -1,5 +1,3 @@
-from __future__ import print_function, division, absolute_import
-
 import os
 import hashlib
 import datetime
@@ -470,4 +468,4 @@ def register():
 
 @app.errorhandler(401)
 def unauthorized(error):
-    return redirect(url_for('login'))
\ No newline at end of file
+    return redirect(url_for('login'))
diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py
index 3c41e2b8..24191a15 100644
--- a/wqflask/wqflask/user_manager.py
+++ b/wqflask/wqflask/user_manager.py
@@ -1,5 +1,3 @@
-from __future__ import print_function, division, absolute_import
-
 import os
 import hashlib
 import datetime
diff --git a/wqflask/wqflask/user_session.py b/wqflask/wqflask/user_session.py
index 71c31c57..c1f38396 100644
--- a/wqflask/wqflask/user_session.py
+++ b/wqflask/wqflask/user_session.py
@@ -1,5 +1,3 @@
-from __future__ import print_function, division, absolute_import
-
 import datetime
 import time
 import uuid
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 83d5202e..b0489e64 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -2,8 +2,6 @@
 #
 # Main routing table for GN2
 
-from __future__ import absolute_import, division, print_function
-
 import traceback # for error page
 import os        # for error gifs
 import random    # for random error gif
-- 
cgit v1.2.3


From 70dbeeb5832711ed5271434e482c18bc7ea095b8 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Thu, 27 Aug 2020 03:28:43 +0300
Subject: Add check for empty group_code when adding a new resource

* wqflask/utility/authentication_tools.py(add_new_resource): If group_code is
"None", an error is thrown when you try to: `group_code + "_" + str(trait_id)`
---
 wqflask/utility/authentication_tools.py | 6 ++++--
 1 file changed, 4 insertions(+), 2 deletions(-)

(limited to 'wqflask/utility/authentication_tools.py')

diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py
index 0e499180..73c39399 100644
--- a/wqflask/utility/authentication_tools.py
+++ b/wqflask/utility/authentication_tools.py
@@ -49,7 +49,10 @@ def add_new_resource(dataset, trait_id=None):
     }
 
     if dataset.type == "Publish":
-        resource_ob['name'] = get_group_code(dataset) + "_" + str(trait_id)
+        group_code = get_group_code(dataset)
+        if group_code is None:
+            group_code = ""
+        resource_ob['name'] = group_code + "_" + str(trait_id)
         resource_ob['data'] = {
             'dataset': dataset.id,
             'trait'  : trait_id
@@ -74,7 +77,6 @@ def add_new_resource(dataset, trait_id=None):
 
 def get_group_code(dataset):
     results = g.db.execute("SELECT InbredSetCode from InbredSet where Name='{}'".format(dataset.group.name)).fetchone()
-
     return results[0]
 
 def check_admin(resource_id=None):
-- 
cgit v1.2.3


From dba31ef2aa9e3f89621848fdb79b915dbd3c56e2 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Sat, 29 Aug 2020 13:47:52 -0500
Subject: Fixed issue where exporting traits would throw an error if a
 dataset's group didn't have an InbredSetCode set in the DB *
 wqflask/utility/authentication_tools.py - Changed get_group_code to return an
 empty string instead of None if InbredSetCode doesn't exist for a dataset
 group * wqflask/wqflask/views.py - Changed zipped export filename to
 "export_(datetime)" instead of "collection_(datetime)" since this export can
 occur from both the collection page and the global search page

---
 wqflask/utility/authentication_tools.py | 6 ++++--
 wqflask/wqflask/views.py                | 2 +-
 2 files changed, 5 insertions(+), 3 deletions(-)

(limited to 'wqflask/utility/authentication_tools.py')

diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py
index ece7022c..3553b92b 100644
--- a/wqflask/utility/authentication_tools.py
+++ b/wqflask/utility/authentication_tools.py
@@ -76,8 +76,10 @@ def add_new_resource(dataset, trait_id=None):
 
 def get_group_code(dataset):
     results = g.db.execute("SELECT InbredSetCode from InbredSet where Name='{}'".format(dataset.group.name)).fetchone()
-
-    return results[0]
+    if results[0]:
+        return results[0]
+    else:
+        return ""
 
 def check_admin(resource_id=None):
     the_url = "http://localhost:8080/available?resource={}&user={}".format(resource_id, g.user_session.user_id)
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index a898de43..91d1a279 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -419,7 +419,7 @@ def export_traits_csv():
     if len(file_list) > 1:
         now = datetime.datetime.now()
         time_str = now.strftime('%H:%M_%d%B%Y')
-        filename = "collection_{}".format(time_str)
+        filename = "export_{}".format(time_str)
         memory_file = StringIO.StringIO()
         with ZipFile(memory_file, mode='w', compression=ZIP_DEFLATED) as zf:
             for the_file in file_list:
-- 
cgit v1.2.3


From 90475fed0b2d1bd192a641bd417f6dfef79653d0 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Mon, 31 Aug 2020 20:34:31 +0300
Subject: Remove typo at beginning of line

* wqflask/utility/authentication_tools.py: Remove accidental char at beginning
of line.
---
 wqflask/utility/authentication_tools.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

(limited to 'wqflask/utility/authentication_tools.py')

diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py
index 68bbb276..c52ebafa 100644
--- a/wqflask/utility/authentication_tools.py
+++ b/wqflask/utility/authentication_tools.py
@@ -88,7 +88,7 @@ def check_admin(resource_id=None):
         response = json.loads(requests.get(the_url).content)['admin']
     except:
         resource_info = get_resource_info(resource_id)
-l        response = resource_info['default_mask']['admin']
+        response = resource_info['default_mask']['admin']
 
     if 'edit-admins' in response:
         return "edit-admins"
-- 
cgit v1.2.3


From af0ca059da29391db9b1dfca0fe96883ce95f72f Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Tue, 15 Sep 2020 23:43:09 +0300
Subject: Remove unnecessary if branch

* wqflask/utility/authentication_tools.py
(check_resource_availability): Combine if statements into one boolean
check in one if branch.
---
 wqflask/utility/authentication_tools.py | 4 +---
 1 file changed, 1 insertion(+), 3 deletions(-)

(limited to 'wqflask/utility/authentication_tools.py')

diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py
index 3553b92b..954f55fc 100644
--- a/wqflask/utility/authentication_tools.py
+++ b/wqflask/utility/authentication_tools.py
@@ -17,9 +17,7 @@ logger = logging.getLogger(__name__ )
 def check_resource_availability(dataset, trait_id=None):
 
     #At least for now assume temporary entered traits are accessible
-    if type(dataset) == str:
-        return webqtlConfig.DEFAULT_PRIVILEGES
-    if dataset.type == "Temp":
+    if type(dataset) == str or dataset.type == "Temp":
         return webqtlConfig.DEFAULT_PRIVILEGES
 
     resource_id = get_resource_id(dataset, trait_id)
-- 
cgit v1.2.3


From 23521ad683beaaff200743cb37dec68cd19cc2d5 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Wed, 16 Sep 2020 00:06:04 +0300
Subject: Apply pep8

* wqflask/utility/authentication_tools.py: Apply pep8 formatting to
file.
---
 wqflask/utility/authentication_tools.py | 37 ++++++++++++++++++++-------------
 1 file changed, 23 insertions(+), 14 deletions(-)

(limited to 'wqflask/utility/authentication_tools.py')

diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py
index 954f55fc..239b08e3 100644
--- a/wqflask/utility/authentication_tools.py
+++ b/wqflask/utility/authentication_tools.py
@@ -1,4 +1,6 @@
 from __future__ import absolute_import, print_function, division
+import logging
+from flask import Flask, g, redirect, url_for
 
 import json
 import requests
@@ -9,31 +11,31 @@ from utility import hmac
 from utility.redis_tools import get_redis_conn, get_resource_info, get_resource_id, add_resource
 Redis = get_redis_conn()
 
-from flask import Flask, g, redirect, url_for
 
-import logging
-logger = logging.getLogger(__name__ )
+logger = logging.getLogger(__name__)
+
 
 def check_resource_availability(dataset, trait_id=None):
 
-    #At least for now assume temporary entered traits are accessible
+    # At least for now assume temporary entered traits are accessible
     if type(dataset) == str or dataset.type == "Temp":
         return webqtlConfig.DEFAULT_PRIVILEGES
 
     resource_id = get_resource_id(dataset, trait_id)
 
-    if resource_id: #ZS: This should never be false, but it's technically possible if a non-Temp dataset somehow had a type other than Publish/ProbeSet/Geno
+    if resource_id:  # ZS: This should never be false, but it's technically possible if a non-Temp dataset somehow had a type other than Publish/ProbeSet/Geno
         resource_info = get_resource_info(resource_id)
-        if not resource_info: #ZS: If resource isn't already in redis, add it with default privileges
+        if not resource_info:  # ZS: If resource isn't already in redis, add it with default privileges
             resource_info = add_new_resource(dataset, trait_id)
 
-    #ZS: Check if super-user - we should probably come up with some way to integrate this into the proxy
+    # ZS: Check if super-user - we should probably come up with some way to integrate this into the proxy
     if g.user_session.user_id in Redis.smembers("super_users"):
-       return webqtlConfig.SUPER_PRIVILEGES
+        return webqtlConfig.SUPER_PRIVILEGES
 
     response = None
 
-    the_url = "http://localhost:8080/available?resource={}&user={}".format(resource_id, g.user_session.user_id)
+    the_url = "http://localhost:8080/available?resource={}&user={}".format(
+        resource_id, g.user_session.user_id)
     try:
         response = json.loads(requests.get(the_url).content)
     except:
@@ -41,18 +43,19 @@ def check_resource_availability(dataset, trait_id=None):
 
     return response
 
+
 def add_new_resource(dataset, trait_id=None):
     resource_ob = {
-        'owner_id'    : "none", # webqtlConfig.DEFAULT_OWNER_ID,
+        'owner_id': "none",  # webqtlConfig.DEFAULT_OWNER_ID,
         'default_mask': webqtlConfig.DEFAULT_PRIVILEGES,
-        'group_masks' : {}
+        'group_masks': {}
     }
 
     if dataset.type == "Publish":
         resource_ob['name'] = get_group_code(dataset) + "_" + str(trait_id)
         resource_ob['data'] = {
             'dataset': dataset.id,
-            'trait'  : trait_id
+            'trait': trait_id
         }
         resource_ob['type'] = 'dataset-publish'
     elif dataset.type == "Geno":
@@ -72,15 +75,19 @@ def add_new_resource(dataset, trait_id=None):
 
     return resource_info
 
+
 def get_group_code(dataset):
-    results = g.db.execute("SELECT InbredSetCode from InbredSet where Name='{}'".format(dataset.group.name)).fetchone()
+    results = g.db.execute("SELECT InbredSetCode from InbredSet where Name='{}'".format(
+        dataset.group.name)).fetchone()
     if results[0]:
         return results[0]
     else:
         return ""
 
+
 def check_admin(resource_id=None):
-    the_url = "http://localhost:8080/available?resource={}&user={}".format(resource_id, g.user_session.user_id)
+    the_url = "http://localhost:8080/available?resource={}&user={}".format(
+        resource_id, g.user_session.user_id)
     try:
         response = json.loads(requests.get(the_url).content)['admin']
     except:
@@ -94,6 +101,7 @@ def check_admin(resource_id=None):
     else:
         return "not-admin"
 
+
 def check_owner(dataset=None, trait_id=None, resource_id=None):
     if resource_id:
         resource_info = get_resource_info(resource_id)
@@ -108,6 +116,7 @@ def check_owner(dataset=None, trait_id=None, resource_id=None):
 
     return False
 
+
 def check_owner_or_admin(dataset=None, trait_id=None, resource_id=None):
     if not resource_id:
         if dataset.type == "Temp":
-- 
cgit v1.2.3


From f4a8789a5f28e1527d4c801b40176f47aa44146c Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Thu, 17 Sep 2020 17:16:28 +0300
Subject: Apply pep8

* wqflask/base/trait.py: Apply pep8.
* wqflask/utility/authentication_tools.py: Ditto.
---
 wqflask/base/trait.py                   | 192 +++++++++++++++++++-------------
 wqflask/utility/authentication_tools.py |  32 ++++--
 2 files changed, 134 insertions(+), 90 deletions(-)

(limited to 'wqflask/utility/authentication_tools.py')

diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 6950cf11..548ccc4c 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -1,36 +1,30 @@
-import os
-import string
-import resource
-import codecs
 import requests
-import random
+import simplejson as json
+from wqflask import app
 
 from base import webqtlConfig
 from base.webqtlCaseData import webqtlCaseData
 from base.data_set import create_dataset
-from db import webqtlDatabaseFunction
-from utility import webqtlUtil
 from utility import hmac
 from utility.authentication_tools import check_resource_availability
-from utility.tools import GN2_BASE_URL, GN_VERSION
-from utility.redis_tools import get_redis_conn, get_resource_id, get_resource_info
-Redis = get_redis_conn()
+from utility.tools import GN2_BASE_URL
+from utility.redis_tools import get_redis_conn, get_resource_id
 
-from wqflask import app
-
-import simplejson as json
 from utility.db_tools import escape
-from pprint import pformat as pf
 
-from flask import Flask, g, request, url_for, redirect, make_response, render_template
+from flask import g, request, url_for
 
 from utility.logger import getLogger
-logger = getLogger(__name__ )
+
+logger = getLogger(__name__)
+
+Redis = get_redis_conn()
+
 
 def create_trait(**kw):
-    assert bool(kw.get('dataset')) != bool(kw.get('dataset_name')), "Needs dataset ob. or name";
+    assert bool(kw.get('dataset')) != bool(
+        kw.get('dataset_name')), "Needs dataset ob. or name"
 
-    permitted = True
     if kw.get('name'):
         if kw.get('dataset_name'):
             if kw.get('dataset_name') != "Temp":
@@ -40,18 +34,23 @@ def create_trait(**kw):
 
         if kw.get('dataset_name') != "Temp":
             if dataset.type == 'Publish':
-                permissions = check_resource_availability(dataset, kw.get('name'))
+                permissions = check_resource_availability(
+                    dataset, kw.get('name'))
             else:
                 permissions = check_resource_availability(dataset)
 
     if "view" in permissions['data']:
         the_trait = GeneralTrait(**kw)
         if the_trait.dataset.type != "Temp":
-            the_trait = retrieve_trait_info(the_trait, the_trait.dataset, get_qtl_info=kw.get('get_qtl_info'))
+            the_trait = retrieve_trait_info(
+                the_trait,
+                the_trait.dataset,
+                get_qtl_info=kw.get('get_qtl_info'))
         return the_trait
     else:
         return None
 
+
 class GeneralTrait(object):
     """
     Trait class defines a trait in webqtl, can be either Microarray,
@@ -61,12 +60,17 @@ class GeneralTrait(object):
 
     def __init__(self, get_qtl_info=False, get_sample_info=True, **kw):
         # xor assertion
-        assert bool(kw.get('dataset')) != bool(kw.get('dataset_name')), "Needs dataset ob. or name";
-        self.name = kw.get('name')                 # Trait ID, ProbeSet ID, Published ID, etc.
+        assert bool(kw.get('dataset')) != bool(
+            kw.get('dataset_name')), "Needs dataset ob. or name"
+        # Trait ID, ProbeSet ID, Published ID, etc.
+        self.name = kw.get('name')
         if kw.get('dataset_name'):
             if kw.get('dataset_name') == "Temp":
                 temp_group = self.name.split("_")[2]
-                self.dataset = create_dataset(dataset_name = "Temp", dataset_type = "Temp", group_name = temp_group)
+                self.dataset = create_dataset(
+                    dataset_name="Temp",
+                    dataset_type="Temp",
+                    group_name=temp_group)
             else:
                 self.dataset = create_dataset(kw.get('dataset_name'))
         else:
@@ -74,7 +78,8 @@ class GeneralTrait(object):
         self.cellid = kw.get('cellid')
         self.identification = kw.get('identification', 'un-named trait')
         self.haveinfo = kw.get('haveinfo', False)
-        self.sequence = kw.get('sequence')         # Blat sequence, available for ProbeSet
+        # Blat sequence, available for ProbeSet
+        self.sequence = kw.get('sequence')
         self.data = kw.get('data', {})
         self.view = True
 
@@ -100,9 +105,10 @@ class GeneralTrait(object):
             elif len(name2) == 3:
                 self.dataset, self.name, self.cellid = name2
 
-        # Todo: These two lines are necessary most of the time, but perhaps not all of the time
-        # So we could add a simple if statement to short-circuit this if necessary
-        if get_sample_info != False:
+        # Todo: These two lines are necessary most of the time, but
+        # perhaps not all of the time So we could add a simple if
+        # statement to short-circuit this if necessary
+        if get_sample_info is not False:
             self = retrieve_sample_data(self, self.dataset)
 
     def export_informative(self, include_variance=0):
@@ -116,13 +122,13 @@ class GeneralTrait(object):
         the_vars = []
         sample_aliases = []
         for sample_name, sample_data in list(self.data.items()):
-            if sample_data.value != None:
-                if not include_variance or sample_data.variance != None:
+            if sample_data.value is not None:
+                if not include_variance or sample_data.variance is not None:
                     samples.append(sample_name)
                     vals.append(sample_data.value)
                     the_vars.append(sample_data.variance)
                     sample_aliases.append(sample_data.name2)
-        return  samples, vals, the_vars, sample_aliases
+        return samples, vals, the_vars, sample_aliases
 
     @property
     def description_fmt(self):
@@ -161,12 +167,17 @@ class GeneralTrait(object):
 
         alias = 'Not available'
         if self.symbol:
-            human_response = requests.get(GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.upper())
-            mouse_response = requests.get(GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.capitalize())
-            other_response = requests.get(GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.lower())
+            human_response = requests.get(
+                GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.upper())
+            mouse_response = requests.get(
+                GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.capitalize())
+            other_response = requests.get(
+                GN2_BASE_URL + "gn3/gene/aliases/" + self.symbol.lower())
 
             if human_response and mouse_response and other_response:
-                alias_list = json.loads(human_response.content) + json.loads(mouse_response.content) + json.loads(other_response.content)
+                alias_list = json.loads(human_response.content) + json.loads(
+                    mouse_response.content) + \
+                    json.loads(other_response.content)
 
                 filtered_aliases = []
                 seen = set()
@@ -180,33 +191,34 @@ class GeneralTrait(object):
 
         return alias
 
-
     @property
     def location_fmt(self):
         '''Return a text formatted location
 
-        While we're at it we set self.location in case we need it later (do we?)
+        While we're at it we set self.location in case we need it
+        later (do we?)
 
         '''
 
         if self.chr and self.mb:
-            self.location = 'Chr %s @ %s Mb'  % (self.chr, self.mb)
+            self.location = 'Chr %s @ %s Mb' % (self.chr, self.mb)
         elif self.chr:
             self.location = 'Chr %s @ Unknown position' % (self.chr)
         else:
             self.location = 'Not available'
 
         fmt = self.location
-        ##XZ: deal with direction
+        # XZ: deal with direction
         if self.strand_probe == '+':
             fmt += (' on the plus strand ')
         elif self.strand_probe == '-':
             fmt += (' on the minus strand ')
 
         return fmt
-        
+
+
 def retrieve_sample_data(trait, dataset, samplelist=None):
-    if samplelist == None:
+    if samplelist is None:
         samplelist = []
 
     if dataset.type == "Temp":
@@ -222,16 +234,19 @@ def retrieve_sample_data(trait, dataset, samplelist=None):
             all_samples_ordered = dataset.group.all_samples_ordered()
             for i, item in enumerate(results):
                 try:
-                    trait.data[all_samples_ordered[i]] = webqtlCaseData(all_samples_ordered[i], float(item))
+                    trait.data[all_samples_ordered[i]] = webqtlCaseData(
+                        all_samples_ordered[i], float(item))
                 except:
                     pass
         else:
             for item in results:
                 name, value, variance, num_cases, name2 = item
                 if not samplelist or (samplelist and name in samplelist):
-                    trait.data[name] = webqtlCaseData(*item)   #name, value, variance, num_cases)
+                    # name, value, variance, num_cases)
+                    trait.data[name] = webqtlCaseData(*item)
     return trait
 
+
 @app.route("/trait/get_sample_data")
 def get_sample_data():
     params = request.args
@@ -247,7 +262,8 @@ def get_sample_data():
         trait_dict['group'] = trait_ob.dataset.group.name
         trait_dict['tissue'] = trait_ob.dataset.tissue
         trait_dict['species'] = trait_ob.dataset.group.species
-        trait_dict['url'] = url_for('show_trait_page', trait_id = trait, dataset = dataset)
+        trait_dict['url'] = url_for(
+            'show_trait_page', trait_id=trait, dataset=dataset)
         trait_dict['description'] = trait_ob.description_display
         if trait_ob.dataset.type == "ProbeSet":
             trait_dict['symbol'] = trait_ob.symbol
@@ -257,22 +273,27 @@ def get_sample_data():
                 trait_dict['pubmed_link'] = trait_ob.pubmed_link
             trait_dict['pubmed_text'] = trait_ob.pubmed_text
 
-        return json.dumps([trait_dict, {key: value.value for key, value in list(trait_ob.data.items()) }])
+        return json.dumps([trait_dict, {key: value.value for
+                                        key, value in list(
+                                            trait_ob.data.items())}])
     else:
         return None
-    
+
+
 def jsonable(trait):
     """Return a dict suitable for using as json
 
     Actual turning into json doesn't happen here though"""
 
-    dataset = create_dataset(dataset_name = trait.dataset.name, dataset_type = trait.dataset.type, group_name = trait.dataset.group.name)
-    
+    dataset = create_dataset(dataset_name=trait.dataset.name,
+                             dataset_type=trait.dataset.type,
+                             group_name=trait.dataset.group.name)
+
     if dataset.type == "ProbeSet":
         return dict(name=trait.name,
                     symbol=trait.symbol,
                     dataset=dataset.name,
-                    dataset_name = dataset.shortname,
+                    dataset_name=dataset.shortname,
                     description=trait.description_display,
                     mean=trait.mean,
                     location=trait.location_repr,
@@ -284,7 +305,7 @@ def jsonable(trait):
         if trait.pubmed_id:
             return dict(name=trait.name,
                         dataset=dataset.name,
-                        dataset_name = dataset.shortname,
+                        dataset_name=dataset.shortname,
                         description=trait.description_display,
                         abbreviation=trait.abbreviation,
                         authors=trait.authors,
@@ -297,7 +318,7 @@ def jsonable(trait):
         else:
             return dict(name=trait.name,
                         dataset=dataset.name,
-                        dataset_name = dataset.shortname,
+                        dataset_name=dataset.shortname,
                         description=trait.description_display,
                         abbreviation=trait.abbreviation,
                         authors=trait.authors,
@@ -309,19 +330,20 @@ def jsonable(trait):
     elif dataset.type == "Geno":
         return dict(name=trait.name,
                     dataset=dataset.name,
-                    dataset_name = dataset.shortname,
+                    dataset_name=dataset.shortname,
                     location=trait.location_repr
                     )
     else:
         return dict()
 
+
 def jsonable_table_row(trait, dataset_name, index):
     """Return a list suitable for json and intended to be displayed in a table
 
     Actual turning into json doesn't happen here though"""
 
     dataset = create_dataset(dataset_name)
-    
+
     if dataset.type == "ProbeSet":
         if trait.mean == "":
             mean = "N/A"
@@ -333,11 +355,13 @@ def jsonable_table_row(trait, dataset_name, index):
             additive = "%.3f" % round(float(trait.additive), 2)
         return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + hmac.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">',
                 index,
-                '<a href="/show_trait?trait_id='+str(trait.name)+'&dataset='+dataset.name+'">'+str(trait.name)+'</a>',
+                '<a href="/show_trait?trait_id=' +
+                str(trait.name)+'&dataset='+dataset.name +
+                '">'+str(trait.name)+'</a>',
                 trait.symbol,
                 trait.description_display,
                 trait.location_repr,
-                mean, 
+                mean,
                 trait.LRS_score_repr,
                 trait.LRS_location_repr,
                 additive]
@@ -349,7 +373,9 @@ def jsonable_table_row(trait, dataset_name, index):
         if trait.pubmed_id:
             return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + hmac.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">',
                     index,
-                    '<a href="/show_trait?trait_id='+str(trait.name)+'&dataset='+dataset.name+'">'+str(trait.name)+'</a>',
+                    '<a href="/show_trait?trait_id=' +
+                    str(trait.name)+'&dataset='+dataset.name +
+                    '">'+str(trait.name)+'</a>',
                     trait.description_display,
                     trait.authors,
                     '<a href="' + trait.pubmed_link + '">' + trait.pubmed_text + '</href>',
@@ -359,7 +385,9 @@ def jsonable_table_row(trait, dataset_name, index):
         else:
             return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + hmac.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">',
                     index,
-                    '<a href="/show_trait?trait_id='+str(trait.name)+'&dataset='+dataset.name+'">'+str(trait.name)+'</a>',
+                    '<a href="/show_trait?trait_id=' +
+                    str(trait.name)+'&dataset='+dataset.name +
+                    '">'+str(trait.name)+'</a>',
                     trait.description_display,
                     trait.authors,
                     trait.pubmed_text,
@@ -369,7 +397,9 @@ def jsonable_table_row(trait, dataset_name, index):
     elif dataset.type == "Geno":
         return ['<input type="checkbox" name="searchResult" class="checkbox trait_checkbox" value="' + hmac.data_hmac('{}:{}'.format(str(trait.name), dataset.name)) + '">',
                 index,
-                '<a href="/show_trait?trait_id='+str(trait.name)+'&dataset='+dataset.name+'">'+str(trait.name)+'</a>',
+                '<a href="/show_trait?trait_id=' +
+                str(trait.name)+'&dataset='+dataset.name +
+                '">'+str(trait.name)+'</a>',
                 trait.location_repr]
     else:
         return dict()
@@ -380,14 +410,16 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
 
     resource_id = get_resource_id(dataset, trait.name)
     if dataset.type == 'Publish':
-        the_url = "http://localhost:8080/run-action?resource={}&user={}&branch=data&action=view".format(resource_id, g.user_session.user_id)
+        the_url = "http://localhost:8080/run-action?resource={}&user={}&branch=data&action=view".format(
+            resource_id, g.user_session.user_id)
     else:
-        the_url = "http://localhost:8080/run-action?resource={}&user={}&branch=data&action=view&trait={}".format(resource_id, g.user_session.user_id, trait.name)
+        the_url = "http://localhost:8080/run-action?resource={}&user={}&branch=data&action=view&trait={}".format(
+            resource_id, g.user_session.user_id, trait.name)
 
     try:
         response = requests.get(the_url).content
         trait_info = json.loads(response)
-    except: #ZS: I'm assuming the trait is viewable if the try fails for some reason; it should never reach this point unless the user has privileges, since that's dealt with in create_trait
+    except:  # ZS: I'm assuming the trait is viewable if the try fails for some reason; it should never reach this point unless the user has privileges, since that's dealt with in create_trait
         if dataset.type == 'Publish':
             query = """
                     SELECT
@@ -416,8 +448,8 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
             logger.sql(query)
             trait_info = g.db.execute(query).fetchone()
 
-        #XZ, 05/08/2009: Xiaodong add this block to use ProbeSet.Id to find the probeset instead of just using ProbeSet.Name
-        #XZ, 05/08/2009: to avoid the problem of same probeset name from different platforms.
+        # XZ, 05/08/2009: Xiaodong add this block to use ProbeSet.Id to find the probeset instead of just using ProbeSet.Name
+        # XZ, 05/08/2009: to avoid the problem of same probeset name from different platforms.
         elif dataset.type == 'ProbeSet':
             display_fields_string = ', ProbeSet.'.join(dataset.display_fields)
             display_fields_string = 'ProbeSet.' + display_fields_string
@@ -430,11 +462,11 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
                             ProbeSetFreeze.Name = '%s' AND
                             ProbeSet.Name = '%s'
                     """ % (escape(display_fields_string),
-                        escape(dataset.name),
-                        escape(str(trait.name)))
+                           escape(dataset.name),
+                           escape(str(trait.name)))
             logger.sql(query)
             trait_info = g.db.execute(query).fetchone()
-        #XZ, 05/08/2009: We also should use Geno.Id to find marker instead of just using Geno.Name
+        # XZ, 05/08/2009: We also should use Geno.Id to find marker instead of just using Geno.Name
         # to avoid the problem of same marker name from different species.
         elif dataset.type == 'Geno':
             display_fields_string = ',Geno.'.join(dataset.display_fields)
@@ -448,11 +480,11 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
                             GenoFreeze.Name = '%s' AND
                             Geno.Name = '%s'
                     """ % (escape(display_fields_string),
-                        escape(dataset.name),
-                        escape(trait.name))
+                           escape(dataset.name),
+                           escape(trait.name))
             logger.sql(query)
             trait_info = g.db.execute(query).fetchone()
-        else: #Temp type
+        else:  # Temp type
             query = """SELECT %s FROM %s WHERE Name = %s"""
             logger.sql(query)
             trait_info = g.db.execute(query,
@@ -462,7 +494,7 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
     if trait_info:
         trait.haveinfo = True
         for i, field in enumerate(dataset.display_fields):
-            holder =  trait_info[i]
+            holder = trait_info[i]
             setattr(trait, field, holder)
 
         if dataset.type == 'Publish':
@@ -475,9 +507,9 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
 
             description = trait.post_publication_description
 
-            #If the dataset is confidential and the user has access to confidential
-            #phenotype traits, then display the pre-publication description instead
-            #of the post-publication description
+            # If the dataset is confidential and the user has access to confidential
+            # phenotype traits, then display the pre-publication description instead
+            # of the post-publication description
             if trait.confidential:
                 trait.abbreviation = trait.pre_publication_abbreviation
                 trait.description_display = trait.pre_publication_description
@@ -514,15 +546,17 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
 
             trait.location_repr = 'N/A'
             if trait.chr and trait.mb:
-                trait.location_repr = 'Chr%s: %.6f' % (trait.chr, float(trait.mb))
+                trait.location_repr = 'Chr%s: %.6f' % (
+                    trait.chr, float(trait.mb))
 
         elif dataset.type == "Geno":
             trait.location_repr = 'N/A'
             if trait.chr and trait.mb:
-                trait.location_repr = 'Chr%s: %.6f' % (trait.chr, float(trait.mb))
+                trait.location_repr = 'Chr%s: %.6f' % (
+                    trait.chr, float(trait.mb))
 
         if get_qtl_info:
-            #LRS and its location
+            # LRS and its location
             trait.LRS_score_repr = "N/A"
             trait.LRS_location_repr = "N/A"
             trait.locus = trait.locus_chr = trait.locus_mb = trait.lrs = trait.pvalue = trait.additive = ""
@@ -594,10 +628,12 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
                     trait.locus = trait.lrs = trait.additive = ""
 
             if (dataset.type == 'Publish' or dataset.type == "ProbeSet") and trait.locus_chr != "" and trait.locus_mb != "":
-                trait.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % (trait.locus_chr, float(trait.locus_mb))
+                trait.LRS_location_repr = LRS_location_repr = 'Chr%s: %.6f' % (
+                    trait.locus_chr, float(trait.locus_mb))
                 if trait.lrs != "":
                     trait.LRS_score_repr = LRS_score_repr = '%3.1f' % trait.lrs
     else:
-        raise KeyError(repr(trait.name)+' information is not found in the database.')
-        
+        raise KeyError(repr(trait.name) +
+                       ' information is not found in the database.')
+
     return trait
diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py
index 390ad75a..ce0c0749 100644
--- a/wqflask/utility/authentication_tools.py
+++ b/wqflask/utility/authentication_tools.py
@@ -1,30 +1,37 @@
 import json
 import requests
 
-from base import data_set, webqtlConfig
-
-from utility import hmac
-from utility.redis_tools import get_redis_conn, get_resource_info, get_resource_id, add_resource
-Redis = get_redis_conn()
+from flask import g
+from base import webqtlConfig
 
 
-logger = logging.getLogger(__name__)
+from utility.redis_tools import (get_redis_conn,
+                                 get_resource_info,
+                                 get_resource_id,
+                                 add_resource)
+Redis = get_redis_conn()
 
 
 def check_resource_availability(dataset, trait_id=None):
-
     # At least for now assume temporary entered traits are accessible
     if type(dataset) == str or dataset.type == "Temp":
         return webqtlConfig.DEFAULT_PRIVILEGES
 
     resource_id = get_resource_id(dataset, trait_id)
 
-    if resource_id:  # ZS: This should never be false, but it's technically possible if a non-Temp dataset somehow had a type other than Publish/ProbeSet/Geno
+    # ZS: This should never be false, but it's technically possible if
+    # a non-Temp dataset somehow had a type other than
+    # Publish/ProbeSet/Geno
+    if resource_id:
         resource_info = get_resource_info(resource_id)
-        if not resource_info:  # ZS: If resource isn't already in redis, add it with default privileges
+
+        # ZS: If resource isn't already in redis, add it with default
+        # privileges
+        if not resource_info:
             resource_info = add_new_resource(dataset, trait_id)
 
-    # ZS: Check if super-user - we should probably come up with some way to integrate this into the proxy
+    # ZS: Check if super-user - we should probably come up with some
+    # way to integrate this into the proxy
     if g.user_session.user_id in Redis.smembers("super_users"):
         return webqtlConfig.SUPER_PRIVILEGES
 
@@ -76,8 +83,9 @@ def add_new_resource(dataset, trait_id=None):
 
 
 def get_group_code(dataset):
-    results = g.db.execute("SELECT InbredSetCode from InbredSet where Name='{}'".format(
-        dataset.group.name)).fetchone()
+    results = g.db.execute(
+        "SELECT InbredSetCode from InbredSet where Name='{}'".format(
+            dataset.group.name)).fetchone()
     if results[0]:
         return results[0]
     else:
-- 
cgit v1.2.3


From f1f80b480ea0f71b7ea34f0b23ad136a56e1bc21 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Thu, 18 Feb 2021 18:21:23 +0000
Subject: Changed authentication_tools.py to account for encoding str as bytes
 and dealing with the permissions response either being a list or not a list
 (this should be temporary until I figure out what is going on here)

---
 wqflask/utility/authentication_tools.py | 19 ++++++++++---------
 1 file changed, 10 insertions(+), 9 deletions(-)

(limited to 'wqflask/utility/authentication_tools.py')

diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py
index ce0c0749..786475a8 100644
--- a/wqflask/utility/authentication_tools.py
+++ b/wqflask/utility/authentication_tools.py
@@ -11,7 +11,6 @@ from utility.redis_tools import (get_redis_conn,
                                  add_resource)
 Redis = get_redis_conn()
 
-
 def check_resource_availability(dataset, trait_id=None):
     # At least for now assume temporary entered traits are accessible
     if type(dataset) == str or dataset.type == "Temp":
@@ -32,13 +31,14 @@ def check_resource_availability(dataset, trait_id=None):
 
     # ZS: Check if super-user - we should probably come up with some
     # way to integrate this into the proxy
-    if g.user_session.user_id in Redis.smembers("super_users"):
+    if str.encode(g.user_session.user_id) in Redis.smembers("super_users"):
         return webqtlConfig.SUPER_PRIVILEGES
 
     response = None
 
     the_url = "http://localhost:8080/available?resource={}&user={}".format(
         resource_id, g.user_session.user_id)
+
     try:
         response = json.loads(requests.get(the_url).content)
     except:
@@ -101,12 +101,13 @@ def check_admin(resource_id=None):
         resource_info = get_resource_info(resource_id)
         response = resource_info['default_mask']['admin']
 
-    if 'edit-admins' in response:
-        return "edit-admins"
-    elif 'edit-access' in response:
-        return "edit-access"
-    else:
-        return "not-admin"
+    if type(response) is list:
+        if 'edit-admins' in response:
+            return 'edit_admins'
+        elif 'edit-access' in response:
+            return 'edit-access'
+
+    return response
 
 
 def check_owner(dataset=None, trait_id=None, resource_id=None):
@@ -131,7 +132,7 @@ def check_owner_or_admin(dataset=None, trait_id=None, resource_id=None):
         else:
             resource_id = get_resource_id(dataset, trait_id)
 
-    if g.user_session.user_id in Redis.smembers("super_users"):
+    if str.encode(g.user_session.user_id) in Redis.smembers("super_users"):
         return "owner"
 
     resource_info = get_resource_info(resource_id)
-- 
cgit v1.2.3


From 7004219e51a6053a03ec4a997d759c52ed36bdfe Mon Sep 17 00:00:00 2001
From: zsloan
Date: Tue, 16 Mar 2021 17:10:50 +0000
Subject: Removed unnecessary encoding of user_id from authentication_tools.py

---
 wqflask/utility/authentication_tools.py | 4 ++--
 1 file changed, 2 insertions(+), 2 deletions(-)

(limited to 'wqflask/utility/authentication_tools.py')

diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py
index 786475a8..672b36d5 100644
--- a/wqflask/utility/authentication_tools.py
+++ b/wqflask/utility/authentication_tools.py
@@ -31,7 +31,7 @@ def check_resource_availability(dataset, trait_id=None):
 
     # ZS: Check if super-user - we should probably come up with some
     # way to integrate this into the proxy
-    if str.encode(g.user_session.user_id) in Redis.smembers("super_users"):
+    if g.user_session.user_id in Redis.smembers("super_users"):
         return webqtlConfig.SUPER_PRIVILEGES
 
     response = None
@@ -132,7 +132,7 @@ def check_owner_or_admin(dataset=None, trait_id=None, resource_id=None):
         else:
             resource_id = get_resource_id(dataset, trait_id)
 
-    if str.encode(g.user_session.user_id) in Redis.smembers("super_users"):
+    if g.user_session.user_id in Redis.smembers("super_users"):
         return "owner"
 
     resource_info = get_resource_info(resource_id)
-- 
cgit v1.2.3


From 406eb27859cca232a562c722cbbd37aca2e3be84 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Fri, 30 Apr 2021 12:26:19 +0300
Subject: autopep8: Fix E301,E302,E303,E304,E305,E306

---
 etc/default_settings.py                            | 21 +++----
 wqflask/base/data_set.py                           |  1 -
 wqflask/base/mrna_assay_tissue_data.py             |  1 +
 wqflask/base/species.py                            |  3 +
 wqflask/base/webqtlCaseData.py                     |  3 +-
 wqflask/db/call.py                                 |  4 ++
 wqflask/db/gn_server.py                            |  1 +
 wqflask/db/webqtlDatabaseFunction.py               |  1 +
 wqflask/maintenance/convert_dryad_to_bimbam.py     |  3 +
 wqflask/maintenance/convert_geno_to_bimbam.py      |  4 ++
 wqflask/maintenance/gen_select_dataset.py          |  5 ++
 .../maintenance/generate_kinship_from_bimbam.py    |  1 +
 .../maintenance/generate_probesetfreeze_file.py    |  7 +++
 wqflask/maintenance/geno_to_json.py                |  6 +-
 wqflask/maintenance/get_group_samplelists.py       |  3 +
 wqflask/maintenance/print_benchmark.py             |  4 ++
 wqflask/maintenance/quantile_normalize.py          |  6 ++
 wqflask/maintenance/set_resource_defaults.py       |  7 +++
 wqflask/run_gunicorn.py                            |  2 +
 wqflask/tests/unit/base/test_webqtl_case_data.py   |  1 +
 .../unit/utility/test_authentication_tools.py      |  1 +
 wqflask/tests/unit/utility/test_chunks.py          |  1 +
 .../test_display_mapping_results.py                |  2 +
 .../marker_regression/test_plink_mapping.py        |  3 +-
 .../marker_regression/test_qtlreaper_mapping.py    |  2 +
 .../wqflask/marker_regression/test_rqtl_mapping.py |  2 +-
 wqflask/tests/unit/wqflask/test_collect.py         |  2 +
 .../tests/wqflask/show_trait/test_show_trait.py    |  1 -
 wqflask/utility/Plot.py                            | 13 +++++
 wqflask/utility/__init__.py                        |  2 +
 wqflask/utility/after.py                           |  1 +
 wqflask/utility/authentication_tools.py            |  1 +
 wqflask/utility/benchmark.py                       |  1 +
 wqflask/utility/corestats.py                       |  2 +
 wqflask/utility/elasticsearch_tools.py             |  7 +++
 wqflask/utility/external.py                        |  1 +
 wqflask/utility/gen_geno_ob.py                     |  3 +
 wqflask/utility/genofile_parser.py                 |  1 +
 wqflask/utility/logger.py                          |  3 +
 wqflask/utility/pillow_utils.py                    |  4 ++
 wqflask/utility/startup_config.py                  |  1 +
 wqflask/utility/svg.py                             | 67 +++++++++++++++++++++-
 wqflask/utility/temp_data.py                       |  1 +
 wqflask/utility/tools.py                           | 25 ++++++++
 wqflask/utility/type_checking.py                   |  5 ++
 wqflask/utility/webqtlUtil.py                      |  5 ++
 wqflask/wqflask/__init__.py                        |  1 +
 wqflask/wqflask/api/correlation.py                 |  7 +++
 wqflask/wqflask/api/mapping.py                     |  2 +-
 wqflask/wqflask/api/router.py                      | 20 +++++++
 wqflask/wqflask/collect.py                         |  8 +++
 wqflask/wqflask/correlation/corr_scatter_plot.py   |  1 +
 wqflask/wqflask/correlation/show_corr_results.py   |  4 +-
 .../wqflask/correlation_matrix/show_corr_matrix.py |  3 +
 wqflask/wqflask/ctl/ctl_analysis.py                |  1 +
 wqflask/wqflask/database.py                        |  2 +
 wqflask/wqflask/db_info.py                         |  1 +
 wqflask/wqflask/do_search.py                       | 21 ++++++-
 wqflask/wqflask/docs.py                            |  2 +-
 wqflask/wqflask/export_traits.py                   |  2 +
 wqflask/wqflask/external_tools/send_to_bnw.py      |  1 +
 .../wqflask/external_tools/send_to_geneweaver.py   |  3 +
 .../wqflask/external_tools/send_to_webgestalt.py   |  3 +
 wqflask/wqflask/group_manager.py                   |  9 +++
 wqflask/wqflask/gsearch.py                         |  1 +
 wqflask/wqflask/heatmap/heatmap.py                 |  3 +
 wqflask/wqflask/interval_analyst/GeneUtil.py       |  2 +
 .../marker_regression/display_mapping_results.py   |  9 ---
 wqflask/wqflask/marker_regression/plink_mapping.py |  9 ++-
 .../wqflask/marker_regression/qtlreaper_mapping.py |  5 ++
 wqflask/wqflask/marker_regression/rqtl_mapping.py  | 15 +++++
 wqflask/wqflask/marker_regression/run_mapping.py   |  9 +++
 wqflask/wqflask/model.py                           |  7 ++-
 wqflask/wqflask/network_graph/network_graph.py     |  1 +
 wqflask/wqflask/news.py                            |  1 +
 wqflask/wqflask/parser.py                          |  1 +
 wqflask/wqflask/pbkdf2.py                          |  2 +
 wqflask/wqflask/resource_manager.py                |  7 +++
 wqflask/wqflask/search_results.py                  |  4 ++
 wqflask/wqflask/send_mail.py                       |  3 +-
 wqflask/wqflask/server_side.py                     |  1 -
 wqflask/wqflask/show_trait/SampleList.py           |  1 +
 wqflask/wqflask/show_trait/export_trait_data.py    |  3 +
 wqflask/wqflask/snp_browser/snp_browser.py         |  9 ++-
 wqflask/wqflask/submit_bnw.py                      |  1 +
 wqflask/wqflask/update_search_results.py           |  1 +
 wqflask/wqflask/user_login.py                      | 21 +++++++
 wqflask/wqflask/user_manager.py                    | 38 +++++++++++-
 wqflask/wqflask/user_session.py                    |  6 ++
 89 files changed, 446 insertions(+), 46 deletions(-)

(limited to 'wqflask/utility/authentication_tools.py')

diff --git a/etc/default_settings.py b/etc/default_settings.py
index 27522187..a194b10e 100644
--- a/etc/default_settings.py
+++ b/etc/default_settings.py
@@ -73,23 +73,24 @@ SMTP_PASSWORD = "UNKNOWN"
 
 # ---- Behavioural settings (defaults) note that logger and log levels can
 #      be overridden at the module level and with enviroment settings
-WEBSERVER_MODE  = 'DEV'     # Python webserver mode (DEBUG|DEV|PROD)
+WEBSERVER_MODE = 'DEV'     # Python webserver mode (DEBUG|DEV|PROD)
 WEBSERVER_BRANDING = None   # Set the branding (nyi)
 WEBSERVER_DEPLOY = None     # Deployment specifics (nyi)
-WEBSERVER_URL    = "http://localhost:"+str(SERVER_PORT)+"/" # external URL
+WEBSERVER_URL = "http://localhost:" + str(SERVER_PORT) + "/" # external URL
 
-LOG_LEVEL       = 'WARNING' # Logger mode (DEBUG|INFO|WARNING|ERROR|CRITICAL)
+LOG_LEVEL = 'WARNING' # Logger mode (DEBUG|INFO|WARNING|ERROR|CRITICAL)
 LOG_LEVEL_DEBUG = '0'       # logger.debugf log level (0-5, 5 = show all)
-LOG_SQL         = 'False'   # Log SQL/backend and GN_SERVER calls
+LOG_SQL = 'False'   # Log SQL/backend and GN_SERVER calls
 LOG_SQL_ALCHEMY = 'False'
-LOG_BENCH       = True      # Log bench marks
+LOG_BENCH = True      # Log bench marks
 
-USE_REDIS       = True      # REDIS caching (note that redis will be phased out)
-USE_GN_SERVER   = 'False'   # Use GN_SERVER SQL calls
-HOME            = os.environ['HOME']
+USE_REDIS = True      # REDIS caching (note that redis will be phased out)
+USE_GN_SERVER = 'False'   # Use GN_SERVER SQL calls
+HOME = os.environ['HOME']
 
 # ---- Default locations
-GENENETWORK_FILES   = HOME+"/genotype_files"  # base dir for all static data files
+# base dir for all static data files
+GENENETWORK_FILES = HOME + "/genotype_files"
 
 # ---- Path overrides for Genenetwork - the defaults are normally
 #      picked up from Guix or in the HOME directory
@@ -98,7 +99,7 @@ GENENETWORK_FILES   = HOME+"/genotype_files"  # base dir for all static data fil
 # PRIVATE_FILES = HOME+"/gn2_private_data" # private static data files (unused)
 
 # ---- Local path to JS libraries - for development modules (only)
-JS_GN_PATH = os.environ['HOME']+"/genenetwork/javascript"
+JS_GN_PATH = os.environ['HOME'] + "/genenetwork/javascript"
 
 # ---- GN2 Executables (overwrite for testing only)
 # PLINK_COMMAND = str.strip(os.popen("which plink2").read())
diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 55ab45f5..c14808d6 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -311,7 +311,6 @@ class HumanMarkers(Markers):
                 marker['Mb'] = float(splat[3]) / 1000000
             self.markers.append(marker)
 
-
     def add_pvalues(self, p_values):
         super(HumanMarkers, self).add_pvalues(p_values)
 
diff --git a/wqflask/base/mrna_assay_tissue_data.py b/wqflask/base/mrna_assay_tissue_data.py
index f3264b3d..cbc05738 100644
--- a/wqflask/base/mrna_assay_tissue_data.py
+++ b/wqflask/base/mrna_assay_tissue_data.py
@@ -11,6 +11,7 @@ from utility.db_tools import escape
 from utility.logger import getLogger
 logger = getLogger(__name__)
 
+
 class MrnaAssayTissueData:
 
     def __init__(self, gene_symbols=None):
diff --git a/wqflask/base/species.py b/wqflask/base/species.py
index cf764d72..44f133b5 100644
--- a/wqflask/base/species.py
+++ b/wqflask/base/species.py
@@ -6,6 +6,7 @@ from flask import Flask, g
 from utility.logger import getLogger
 logger = getLogger(__name__)
 
+
 class TheSpecies:
     def __init__(self, dataset=None, species_name=None):
         if species_name != None:
@@ -15,6 +16,7 @@ class TheSpecies:
             self.dataset = dataset
             self.chromosomes = Chromosomes(dataset=self.dataset)
 
+
 class IndChromosome:
     def __init__(self, name, length):
         self.name = name
@@ -25,6 +27,7 @@ class IndChromosome:
         """Chromosome length in megabases"""
         return self.length / 1000000
 
+
 class Chromosomes:
     def __init__(self, dataset=None, species=None):
         self.chromosomes = collections.OrderedDict()
diff --git a/wqflask/base/webqtlCaseData.py b/wqflask/base/webqtlCaseData.py
index aa55470f..2d07ab9d 100644
--- a/wqflask/base/webqtlCaseData.py
+++ b/wqflask/base/webqtlCaseData.py
@@ -28,6 +28,7 @@ import utility.tools
 
 utility.tools.show_settings()
 
+
 class webqtlCaseData:
     """one case data in one trait"""
 
@@ -78,4 +79,4 @@ class webqtlCaseData:
     def display_num_cases(self):
         if self.num_cases is not None:
             return "%s" % self.num_cases
-        return "x"
\ No newline at end of file
+        return "x"
diff --git a/wqflask/db/call.py b/wqflask/db/call.py
index 555878ad..9412b376 100644
--- a/wqflask/db/call.py
+++ b/wqflask/db/call.py
@@ -16,6 +16,7 @@ logger = getLogger(__name__)
 
 # from inspect import stack
 
+
 def fetch1(query, path=None, func=None):
     """Fetch one result as a Tuple using either a SQL query or the URI
 path to GN_SERVER (when USE_GN_SERVER is True). Apply func to
@@ -35,6 +36,7 @@ GN_SERVER result when set (which should return a Tuple)
     else:
         return fetchone(query)
 
+
 def fetchone(query):
     """Return tuple containing one row by calling SQL directly (the
 original fetchone, but with logging)
@@ -46,6 +48,7 @@ original fetchone, but with logging)
             return res.fetchone()
         return logger.sql(query, helper)
 
+
 def fetchall(query):
     """Return row iterator by calling SQL directly (the
 original fetchall, but with logging)
@@ -57,6 +60,7 @@ original fetchall, but with logging)
             return res.fetchall()
         return logger.sql(query, helper)
 
+
 def gn_server(path):
     """Return JSON record by calling GN_SERVER
 
diff --git a/wqflask/db/gn_server.py b/wqflask/db/gn_server.py
index 6c7383d0..f9b01658 100644
--- a/wqflask/db/gn_server.py
+++ b/wqflask/db/gn_server.py
@@ -5,5 +5,6 @@ from db.call import gn_server
 from utility.logger import getLogger
 logger = getLogger(__name__)
 
+
 def menu_main():
     return gn_server("/int/menu/main.json")
diff --git a/wqflask/db/webqtlDatabaseFunction.py b/wqflask/db/webqtlDatabaseFunction.py
index 18ade405..50ac06fd 100644
--- a/wqflask/db/webqtlDatabaseFunction.py
+++ b/wqflask/db/webqtlDatabaseFunction.py
@@ -31,6 +31,7 @@ logger = getLogger(__name__)
 # function: connect to database and return cursor instance
 ###########################################################################
 
+
 def retrieve_species(group):
     """Get the species of a group (e.g. returns string "mouse" on "BXD"
 
diff --git a/wqflask/maintenance/convert_dryad_to_bimbam.py b/wqflask/maintenance/convert_dryad_to_bimbam.py
index 8eab66e8..e417c280 100644
--- a/wqflask/maintenance/convert_dryad_to_bimbam.py
+++ b/wqflask/maintenance/convert_dryad_to_bimbam.py
@@ -55,15 +55,18 @@ def read_dryad_file(filename):
     #            
     # return geno_rows
 
+
 def write_bimbam_files(geno_rows):
     with open('/home/zas1024/cfw_data/CFW_geno.txt', 'w') as geno_fh:
         for row in geno_rows:
             geno_fh.write(", ".join(row) + "\n")
 
+
 def convert_dryad_to_bimbam(filename):
     geno_file_rows = read_dryad_file(filename)
     write_bimbam_files(geno_file_rows)
 
+
 if __name__ == "__main__":
     input_filename = "/home/zas1024/cfw_data/" + sys.argv[1] + ".txt"
     convert_dryad_to_bimbam(input_filename)
diff --git a/wqflask/maintenance/convert_geno_to_bimbam.py b/wqflask/maintenance/convert_geno_to_bimbam.py
index dc01cbb3..5b2369c9 100644
--- a/wqflask/maintenance/convert_geno_to_bimbam.py
+++ b/wqflask/maintenance/convert_geno_to_bimbam.py
@@ -20,8 +20,10 @@ import simplejson as json
 
 from pprint import pformat as pf
 
+
 class EmptyConfigurations(Exception): pass
 
+
 class Marker:
     def __init__(self):
         self.name = None
@@ -30,6 +32,7 @@ class Marker:
         self.Mb = None
         self.genotypes = []
 
+
 class ConvertGenoFile:
 
     def __init__(self, input_file, output_files):
@@ -178,6 +181,7 @@ class ConvertGenoFile:
                 print("    Row is:", convertob.latest_row_value)
                 break
 
+
 if __name__ == "__main__":
     Old_Geno_Directory = """/export/local/home/zas1024/gn2-zach/genotype_files/genotype"""
     New_Geno_Directory = """/export/local/home/zas1024/gn2-zach/genotype_files/genotype/bimbam"""
diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py
index f480d63f..583a06e1 100644
--- a/wqflask/maintenance/gen_select_dataset.py
+++ b/wqflask/maintenance/gen_select_dataset.py
@@ -55,6 +55,7 @@ from pprint import pformat as pf
 
 #conn = Engine.connect()
 
+
 def parse_db_uri():
     """Converts a database URI to the db name, host name, user name, and password"""
 
@@ -143,6 +144,7 @@ def phenotypes_exist(group_name):
     else:
         return False
 
+
 def genotypes_exist(group_name):
     #print("group_name:", group_name)
     Cursor.execute("""select Name from GenoFreeze
@@ -156,6 +158,7 @@ def genotypes_exist(group_name):
     else:
         return False
 
+
 def build_types(species, group):
     """Fetches tissues
 
@@ -184,6 +187,7 @@ def build_types(species, group):
 
     return results
 
+
 def get_datasets(types):
     """Build datasets list"""
     datasets = {}
@@ -308,6 +312,7 @@ def _test_it():
     datasets = build_datasets("Mouse", "BXD", "Hippocampus")
     #print("build_datasets:", pf(datasets))
 
+
 if __name__ == '__main__':
     Conn = MySQLdb.Connect(**parse_db_uri())
     Cursor = Conn.cursor()
diff --git a/wqflask/maintenance/generate_kinship_from_bimbam.py b/wqflask/maintenance/generate_kinship_from_bimbam.py
index 664e9e48..7cc60c9e 100644
--- a/wqflask/maintenance/generate_kinship_from_bimbam.py
+++ b/wqflask/maintenance/generate_kinship_from_bimbam.py
@@ -13,6 +13,7 @@ sys.path.append("..")
 import os
 import glob
 
+
 class GenerateKinshipMatrices:
     def __init__(self, group_name, geno_file, pheno_file):
         self.group_name = group_name
diff --git a/wqflask/maintenance/generate_probesetfreeze_file.py b/wqflask/maintenance/generate_probesetfreeze_file.py
index b1e41e9a..bd9c2ab4 100644
--- a/wqflask/maintenance/generate_probesetfreeze_file.py
+++ b/wqflask/maintenance/generate_probesetfreeze_file.py
@@ -23,10 +23,12 @@ def get_cursor():
     cursor = con.cursor()
     return cursor
 
+
 def show_progress(process, counter):
     if counter % 1000 == 0:
         print("{}: {}".format(process, counter))
 
+
 def get_strains(cursor):
     cursor.execute("""select Strain.Name
                       from Strain, StrainXRef, InbredSet
@@ -42,6 +44,7 @@ def get_strains(cursor):
 
     return strains
 
+
 def get_probeset_vals(cursor, dataset_name):
     cursor.execute(""" select ProbeSet.Id, ProbeSet.Name
                 from ProbeSetXRef,
@@ -77,6 +80,7 @@ def get_probeset_vals(cursor, dataset_name):
 
     return probeset_vals
 
+
 def trim_strains(strains, probeset_vals):
     trimmed_strains = []
     #print("probeset_vals is:", pf(probeset_vals))
@@ -89,6 +93,7 @@ def trim_strains(strains, probeset_vals):
     print("trimmed_strains:", pf(trimmed_strains))
     return trimmed_strains
 
+
 def write_data_matrix_file(strains, probeset_vals, filename):
     with open(filename, "wb") as fh:
         csv_writer = csv.writer(fh, delimiter=",", quoting=csv.QUOTE_ALL)
@@ -103,6 +108,7 @@ def write_data_matrix_file(strains, probeset_vals, filename):
             csv_writer.writerow(row_data)
             show_progress("Writing", counter)
 
+
 def main():
     filename = os.path.expanduser("~/gene/wqflask/maintenance/" +
                 "ProbeSetFreezeId_210_FullName_Eye_AXBXA_Illumina_V6.2" +
@@ -117,5 +123,6 @@ def main():
     trimmed_strains = trim_strains(strains, probeset_vals)
     write_data_matrix_file(trimmed_strains, probeset_vals, filename)
 
+
 if __name__ == '__main__':
     main()
diff --git a/wqflask/maintenance/geno_to_json.py b/wqflask/maintenance/geno_to_json.py
index fa0dcebd..ad3f2b72 100644
--- a/wqflask/maintenance/geno_to_json.py
+++ b/wqflask/maintenance/geno_to_json.py
@@ -25,10 +25,10 @@ from pprint import pformat as pf
 
 #from utility.tools import flat_files
 
+
 class EmptyConfigurations(Exception): pass
 
         
-
 class Marker:
     def __init__(self):
         self.name = None
@@ -37,6 +37,7 @@ class Marker:
         self.Mb = None
         self.genotypes = []
 
+
 class ConvertGenoFile:
 
     def __init__(self, input_file, output_file):
@@ -78,7 +79,6 @@ class ConvertGenoFile:
             # elif self.file_type == "snps":
             #    self.process_snps_file()
 
-
     def process_csv(self):
         for row_count, row in enumerate(self.process_rows()):
             row_items = row.split("\t")
@@ -121,7 +121,6 @@ class ConvertGenoFile:
                     
             # self.output_fh.write("\n")
 
-
     def process_rows(self):
         for self.latest_row_pos, row in enumerate(self.input_fh):
             # if self.input_file.endswith(".geno.gz"):
@@ -182,7 +181,6 @@ class ConvertGenoFile:
     #    convertob = ConvertGenoFile(input_file, output_file)
         
 
-
 if __name__ == "__main__":
     Old_Geno_Directory = """/export/local/home/zas1024/gn2-zach/genotype_files/genotype"""
     New_Geno_Directory = """/export/local/home/zas1024/gn2-zach/genotype_files/genotype/json"""
diff --git a/wqflask/maintenance/get_group_samplelists.py b/wqflask/maintenance/get_group_samplelists.py
index 3f9d0278..0a450d3f 100644
--- a/wqflask/maintenance/get_group_samplelists.py
+++ b/wqflask/maintenance/get_group_samplelists.py
@@ -4,12 +4,14 @@ import gzip
 
 from base import webqtlConfig
 
+
 def get_samplelist(file_type, geno_file):
     if file_type == "geno":
         return get_samplelist_from_geno(geno_file)
     elif file_type == "plink":
         return get_samplelist_from_plink(geno_file)
 
+
 def get_samplelist_from_geno(genofilename):
     if os.path.isfile(genofilename + '.gz'):
         genofilename += '.gz'
@@ -33,6 +35,7 @@ def get_samplelist_from_geno(genofilename):
         samplelist = headers[3:]
     return samplelist
 
+
 def get_samplelist_from_plink(genofilename):
     genofile = open(genofilename)
 
diff --git a/wqflask/maintenance/print_benchmark.py b/wqflask/maintenance/print_benchmark.py
index a1046c86..9d12da8a 100644
--- a/wqflask/maintenance/print_benchmark.py
+++ b/wqflask/maintenance/print_benchmark.py
@@ -15,15 +15,18 @@ class TheCounter:
         self.time_took = time.time() - start_time
         TheCounter.Counters[self.__class__.__name__] = self.time_took
 
+
 class PrintAll(TheCounter):
     def print_it(self, counter):
         print(counter)
 
+
 class PrintSome(TheCounter):
     def print_it(self, counter):
         if counter % 1000 == 0:
             print(counter)
 
+
 class PrintNone(TheCounter):
     def print_it(self, counter):
         pass
@@ -37,5 +40,6 @@ def new_main():
 
     print(pf(TheCounter.Counters))
 
+
 if __name__ == '__main__':
     new_main()
diff --git a/wqflask/maintenance/quantile_normalize.py b/wqflask/maintenance/quantile_normalize.py
index 6751a8e5..1896bc52 100644
--- a/wqflask/maintenance/quantile_normalize.py
+++ b/wqflask/maintenance/quantile_normalize.py
@@ -14,6 +14,7 @@ from wqflask import app
 from utility.elasticsearch_tools import get_elasticsearch_connection
 from utility.tools import ELASTICSEARCH_HOST, ELASTICSEARCH_PORT, SQL_URI
 
+
 def parse_db_uri():
     """Converts a database URI to the db name, host name, user name, and password"""
 
@@ -28,6 +29,7 @@ def parse_db_uri():
     print(db_conn_info)
     return db_conn_info
 
+
 def create_dataframe(input_file):
     with open(input_file) as f:
         ncols = len(f.readline().split("\t"))
@@ -36,6 +38,8 @@ def create_dataframe(input_file):
     return pd.DataFrame(input_array)
 
 # This function taken from https://github.com/ShawnLYU/Quantile_Normalize
+
+
 def quantileNormalize(df_input):
     df = df_input.copy()
     # compute rank
@@ -50,6 +54,7 @@ def quantileNormalize(df_input):
         df[col] = [rank[i] for i in t]
     return df
 
+
 def set_data(dataset_name):
     orig_file = "/home/zas1024/cfw_data/" + dataset_name + ".txt"
 
@@ -95,6 +100,7 @@ def set_data(dataset_name):
                     }
                 }
 
+
 if __name__ == '__main__':
     Conn = MySQLdb.Connect(**parse_db_uri())
     Cursor = Conn.cursor()
diff --git a/wqflask/maintenance/set_resource_defaults.py b/wqflask/maintenance/set_resource_defaults.py
index 286094dd..c6c4f44c 100644
--- a/wqflask/maintenance/set_resource_defaults.py
+++ b/wqflask/maintenance/set_resource_defaults.py
@@ -37,6 +37,7 @@ 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"""
 
@@ -51,6 +52,7 @@ def parse_db_uri():
     print(db_conn_info)
     return db_conn_info
 
+
 def insert_probeset_resources(default_owner_id):
     current_resources = Redis.hgetall("resources")
     Cursor.execute("""  SELECT
@@ -77,6 +79,7 @@ def insert_probeset_resources(default_owner_id):
 
         add_resource(resource_ob, update=False)
 
+
 def insert_publish_resources(default_owner_id):
     current_resources = Redis.hgetall("resources")
     Cursor.execute("""  SELECT 
@@ -110,6 +113,7 @@ def insert_publish_resources(default_owner_id):
         else:
             continue
 
+
 def insert_geno_resources(default_owner_id):
     current_resources = Redis.hgetall("resources")
     Cursor.execute("""  SELECT
@@ -139,6 +143,7 @@ def insert_geno_resources(default_owner_id):
 
         add_resource(resource_ob, update=False)
 
+
 def insert_resources(default_owner_id):
     current_resources = get_resources()
     print("START")
@@ -149,6 +154,7 @@ def insert_resources(default_owner_id):
     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"""
 
@@ -158,6 +164,7 @@ def main():
 
     insert_resources(owner_id)
 
+
 if __name__ == '__main__':
     Conn = MySQLdb.Connect(**parse_db_uri())
     Cursor = Conn.cursor()
diff --git a/wqflask/run_gunicorn.py b/wqflask/run_gunicorn.py
index 58108e03..03f310eb 100644
--- a/wqflask/run_gunicorn.py
+++ b/wqflask/run_gunicorn.py
@@ -14,9 +14,11 @@ from utility.startup_config import app_config
 
 app_config()
 
+
 @app.route("/gunicorn")
 def hello():
     return "<h1 style='color:blue'>Hello There!</h1>"
 
+
 if __name__ == "__main__":
     app.run(host='0.0.0.0')
diff --git a/wqflask/tests/unit/base/test_webqtl_case_data.py b/wqflask/tests/unit/base/test_webqtl_case_data.py
index 8e8ba482..cebd41ce 100644
--- a/wqflask/tests/unit/base/test_webqtl_case_data.py
+++ b/wqflask/tests/unit/base/test_webqtl_case_data.py
@@ -4,6 +4,7 @@ import unittest
 from wqflask import app  # Required because of utility.tools in webqtlCaseData.py
 from base.webqtlCaseData import webqtlCaseData
 
+
 class TestWebqtlCaseData(unittest.TestCase):
     """Tests for WebqtlCaseData class"""
 
diff --git a/wqflask/tests/unit/utility/test_authentication_tools.py b/wqflask/tests/unit/utility/test_authentication_tools.py
index 42dcae88..024ab43f 100644
--- a/wqflask/tests/unit/utility/test_authentication_tools.py
+++ b/wqflask/tests/unit/utility/test_authentication_tools.py
@@ -5,6 +5,7 @@ from unittest import mock
 from utility.authentication_tools import check_resource_availability
 from utility.authentication_tools import add_new_resource
 
+
 class TestResponse:
     """Mock Test Response after a request"""
     @property
diff --git a/wqflask/tests/unit/utility/test_chunks.py b/wqflask/tests/unit/utility/test_chunks.py
index 8d90a1ec..1d349193 100644
--- a/wqflask/tests/unit/utility/test_chunks.py
+++ b/wqflask/tests/unit/utility/test_chunks.py
@@ -7,6 +7,7 @@ from utility.chunks import divide_into_chunks
 
 class TestChunks(unittest.TestCase):
     "Test Utility method for chunking"
+
     def test_divide_into_chunks(self):
         "Check that a list is chunked correctly"
         self.assertEqual(divide_into_chunks([1, 2, 7, 3, 22, 8, 5, 22, 333], 3),
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_display_mapping_results.py b/wqflask/tests/unit/wqflask/marker_regression/test_display_mapping_results.py
index 8ae0f09f..219a6a29 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_display_mapping_results.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_display_mapping_results.py
@@ -9,6 +9,7 @@ from wqflask.marker_regression.display_mapping_results import (
 
 class TestDisplayMappingResults(unittest.TestCase):
     """Basic Methods to test Mapping Results"""
+
     def test_pil_colors(self):
         """Test that colors use PILLOW color format"""
         self.assertEqual(DisplayMappingResults.CLICKABLE_WEBQTL_REGION_COLOR,
@@ -17,6 +18,7 @@ class TestDisplayMappingResults(unittest.TestCase):
 
 class TestHtmlGenWrapper(unittest.TestCase):
     """Test Wrapper around HTMLGen"""
+
     def test_create_image(self):
         """Test HT.Image method"""
         self.assertEqual(
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_plink_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_plink_mapping.py
index 5eec93f1..fd21a825 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_plink_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_plink_mapping.py
@@ -12,9 +12,10 @@ class AttributeSetter:
     def __init__(self, obj):
         for key, val in obj.items():
             setattr(self, key, val)
-class TestPlinkMapping(unittest.TestCase):
 
 
+class TestPlinkMapping(unittest.TestCase):
+
     def test_build_line_list(self):
         """test for building line list"""
         line_1 = "this is line one test"
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py
index bbb79f98..5cc8fd0f 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_qtlreaper_mapping.py
@@ -4,6 +4,8 @@ from wqflask.marker_regression.qtlreaper_mapping import gen_pheno_txt_file
 
 # issues some methods in genofile object are not defined
 # modify samples should equal to vals
+
+
 class TestQtlReaperMapping(unittest.TestCase):
 	@mock.patch("wqflask.marker_regression.qtlreaper_mapping.TEMPDIR", "/home/user/data")
 	def test_gen_pheno_txt_file(self):                   
diff --git a/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py b/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py
index 0e617e93..6267ce9a 100644
--- a/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py
+++ b/wqflask/tests/unit/wqflask/marker_regression/test_rqtl_mapping.py
@@ -5,6 +5,7 @@ from wqflask.marker_regression.rqtl_mapping import get_trait_data_type
 from wqflask.marker_regression.rqtl_mapping import sanitize_rqtl_phenotype
 from wqflask.marker_regression.rqtl_mapping import sanitize_rqtl_names
 
+
 class TestRqtlMapping(unittest.TestCase):
 
 	def setUp(self):
@@ -14,7 +15,6 @@ class TestRqtlMapping(unittest.TestCase):
 	def tearDown(self):
 		self.app_context.pop()
 
-
 	@mock.patch("wqflask.marker_regression.rqtl_mapping.g")
 	@mock.patch("wqflask.marker_regression.rqtl_mapping.logger")
 	def test_get_trait_data(self, mock_logger, mock_db):
diff --git a/wqflask/tests/unit/wqflask/test_collect.py b/wqflask/tests/unit/wqflask/test_collect.py
index 9a36132d..2a914fb2 100644
--- a/wqflask/tests/unit/wqflask/test_collect.py
+++ b/wqflask/tests/unit/wqflask/test_collect.py
@@ -11,6 +11,7 @@ app = Flask(__name__)
 
 class MockSession:
     """Helper class for mocking wqflask.collect.g.user_session.logged_in"""
+
     def __init__(self, is_logged_in=False):
         self.is_logged_in = is_logged_in
 
@@ -21,6 +22,7 @@ class MockSession:
 
 class MockFlaskG:
     """Helper class for mocking wqflask.collect.g.user_session"""
+
     def __init__(self, is_logged_in=False):
         self.is_logged_in = is_logged_in
 
diff --git a/wqflask/tests/wqflask/show_trait/test_show_trait.py b/wqflask/tests/wqflask/show_trait/test_show_trait.py
index 8c866874..24c3923e 100644
--- a/wqflask/tests/wqflask/show_trait/test_show_trait.py
+++ b/wqflask/tests/wqflask/show_trait/test_show_trait.py
@@ -242,7 +242,6 @@ class TestTraits(unittest.TestCase):
         self.assertEqual(get_genotype_scales(file_location), expected_results)
         mock_get_scales.assert_called_once_with(file_location)
 
-
     @mock.patch("wqflask.show_trait.show_trait.locate_ignore_error")
     def test_get_scales_from_genofile_found(self, mock_ignore_location):
         """"add test for get scales from genofile where file is found"""
diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py
index 68c2cb72..d35b2089 100644
--- a/wqflask/utility/Plot.py
+++ b/wqflask/utility/Plot.py
@@ -47,6 +47,7 @@ COUR_FILE = "./wqflask/static/fonts/courbd.ttf"
 TAHOMA_FILE = "./wqflask/static/fonts/tahoma.ttf"
 # ---- END: FONT FILES ---- #
 
+
 def cformat(d, rank=0):
     'custom string format'
     strD = "%2.6f" % d
@@ -68,6 +69,7 @@ def cformat(d, rank=0):
         strD = '0.0'
     return strD
 
+
 def frange(start, end=None, inc=1.0):
     "A faster range-like function that does accept float increments..."
     if end == None:
@@ -84,6 +86,7 @@ def frange(start, end=None, inc=1.0):
         L[i] = start + i * inc
     return L
 
+
 def find_outliers(vals):
     """Calculates the upper and lower bounds of a set of sample/case values
 
@@ -119,6 +122,8 @@ def find_outliers(vals):
 
 # parameter: data is either object returned by reaper permutation function (called by MarkerRegressionPage.py)
 # or the first object returned by direct (pair-scan) permu function (called by DirectPlotPage.py)
+
+
 def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLabel=None, YLabel=None, title=None, offset=(60, 20, 40, 40), zoom=1):
     im_drawer = ImageDraw.Draw(canvas)
     xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
@@ -230,6 +235,8 @@ def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLab
            font=labelFont, fill=labelColor)
 
 # This function determines the scale of the plot
+
+
 def detScaleOld(min, max):
     if min >= max:
         return None
@@ -246,6 +253,7 @@ def detScaleOld(min, max):
         high = c * ceil(max / c)
         return [low, high, round((high - low) / c)]
 
+
 def detScale(min=0, max=0):
 
     if min >= max:
@@ -283,15 +291,19 @@ def detScale(min=0, max=0):
 
         return [low, high, n]
 
+
 def bluefunc(x):
     return 1.0 / (1.0 + exp(-10 * (x - 0.6)))
 
+
 def redfunc(x):
     return 1.0 / (1.0 + exp(10 * (x - 0.5)))
 
+
 def greenfunc(x):
     return 1 - pow(redfunc(x + 0.2), 2) - bluefunc(x - 0.3)
 
+
 def colorSpectrum(n=100):
     multiple = 10
     if n == 1:
@@ -319,6 +331,7 @@ def colorSpectrum(n=100):
     out2.append(out[-1])
     return out2
 
+
 def _test():
     import doctest
     doctest.testmod()
diff --git a/wqflask/utility/__init__.py b/wqflask/utility/__init__.py
index ec7e72d0..d540c96e 100644
--- a/wqflask/utility/__init__.py
+++ b/wqflask/utility/__init__.py
@@ -2,8 +2,10 @@ from pprint import pformat as pf
 
 # Todo: Move these out of __init__
 
+
 class Bunch:
     """Like a dictionary but using object notation"""
+
     def __init__(self, **kw):
             self.__dict__ = kw
 
diff --git a/wqflask/utility/after.py b/wqflask/utility/after.py
index 06091ecb..2b560e48 100644
--- a/wqflask/utility/after.py
+++ b/wqflask/utility/after.py
@@ -7,6 +7,7 @@ from flask import g
 
 from wqflask import app
 
+
 def after_this_request(f):
     if not hasattr(g, 'after_request_callbacks'):
         g.after_request_callbacks = []
diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py
index 672b36d5..57dbf8ba 100644
--- a/wqflask/utility/authentication_tools.py
+++ b/wqflask/utility/authentication_tools.py
@@ -11,6 +11,7 @@ from utility.redis_tools import (get_redis_conn,
                                  add_resource)
 Redis = get_redis_conn()
 
+
 def check_resource_availability(dataset, trait_id=None):
     # At least for now assume temporary entered traits are accessible
     if type(dataset) == str or dataset.type == "Temp":
diff --git a/wqflask/utility/benchmark.py b/wqflask/utility/benchmark.py
index 3d40a3b8..48ab1dc0 100644
--- a/wqflask/utility/benchmark.py
+++ b/wqflask/utility/benchmark.py
@@ -6,6 +6,7 @@ from utility.tools import LOG_BENCH
 from utility.logger import getLogger
 logger = getLogger(__name__)
 
+
 class Bench:
     entries = collections.OrderedDict()
 
diff --git a/wqflask/utility/corestats.py b/wqflask/utility/corestats.py
index 15d1cb8d..523280a1 100644
--- a/wqflask/utility/corestats.py
+++ b/wqflask/utility/corestats.py
@@ -16,6 +16,8 @@
 import sys
 
 # ZS: Should switch to using some third party library for this; maybe scipy has an equivalent
+
+
 class Stats:
 
     def __init__(self, sequence):
diff --git a/wqflask/utility/elasticsearch_tools.py b/wqflask/utility/elasticsearch_tools.py
index ae1181e4..9415cef0 100644
--- a/wqflask/utility/elasticsearch_tools.py
+++ b/wqflask/utility/elasticsearch_tools.py
@@ -47,11 +47,13 @@ logger = getLogger(__name__)
 
 from utility.tools import ELASTICSEARCH_HOST, ELASTICSEARCH_PORT
 
+
 def test_elasticsearch_connection():
     es = Elasticsearch(['http://' + ELASTICSEARCH_HOST + ":" + str(ELASTICSEARCH_PORT) + '/'], verify_certs=True)
     if not es.ping():
         logger.warning("Elasticsearch is DOWN")
 
+
 def get_elasticsearch_connection(for_user=True):
     """Return a connection to ES. Returns None on failure"""
     logger.info("get_elasticsearch_connection")
@@ -77,6 +79,7 @@ def get_elasticsearch_connection(for_user=True):
 
     return es
 
+
 def setup_users_index(es_connection):
     if es_connection:
         index_settings = {
@@ -87,12 +90,15 @@ def setup_users_index(es_connection):
         es_connection.indices.create(index='users', ignore=400)
         es_connection.indices.put_mapping(body=index_settings, index="users", doc_type="local")
 
+
 def get_user_by_unique_column(es, column_name, column_value, index="users", doc_type="local"):
     return get_item_by_unique_column(es, column_name, column_value, index=index, doc_type=doc_type)
 
+
 def save_user(es, user, user_id):
     es_save_data(es, "users", "local", user, user_id)
 
+
 def get_item_by_unique_column(es, column_name, column_value, index, doc_type):
     item_details = None
     try:
@@ -106,6 +112,7 @@ def get_item_by_unique_column(es, column_name, column_value, index, doc_type):
         pass
     return item_details
 
+
 def es_save_data(es, index, doc_type, data_item, data_id,):
     from time import sleep
     es.create(index, doc_type, body=data_item, id=data_id)
diff --git a/wqflask/utility/external.py b/wqflask/utility/external.py
index c1bf4043..805d2ffe 100644
--- a/wqflask/utility/external.py
+++ b/wqflask/utility/external.py
@@ -4,6 +4,7 @@ import os
 import sys
 import subprocess
 
+
 def shell(command):
     if subprocess.call(command, shell=True) != 0:
         raise Exception("ERROR: failed on " + command)
diff --git a/wqflask/utility/gen_geno_ob.py b/wqflask/utility/gen_geno_ob.py
index 9cfa39f9..24604e58 100644
--- a/wqflask/utility/gen_geno_ob.py
+++ b/wqflask/utility/gen_geno_ob.py
@@ -1,6 +1,7 @@
 import utility.logger
 logger = utility.logger.getLogger(__name__)
 
+
 class genotype:
     """
     Replacement for reaper.Dataset so we can remove qtlreaper use while still generating mapping output figure
@@ -119,6 +120,7 @@ class genotype:
 
             self.chromosomes.append(chr_ob)
 
+
 class Chr:
     def __init__(self, name, geno_ob):
         self.name = name
@@ -140,6 +142,7 @@ class Chr:
     def add_marker(self, marker_row):
         self.loci.append(Locus(self.geno_ob, marker_row))
 
+
 class Locus:
     def __init__(self, geno_ob, marker_row=None):
         self.chr = None
diff --git a/wqflask/utility/genofile_parser.py b/wqflask/utility/genofile_parser.py
index f8e96d19..94a08c17 100644
--- a/wqflask/utility/genofile_parser.py
+++ b/wqflask/utility/genofile_parser.py
@@ -12,6 +12,7 @@ import simplejson as json
 
 from pprint import pformat as pf
 
+
 class Marker:
   def __init__(self):
     self.name = None
diff --git a/wqflask/utility/logger.py b/wqflask/utility/logger.py
index 16912e58..47079818 100644
--- a/wqflask/utility/logger.py
+++ b/wqflask/utility/logger.py
@@ -35,6 +35,7 @@ import datetime
 
 from utility.tools import LOG_LEVEL, LOG_LEVEL_DEBUG, LOG_SQL
 
+
 class GNLogger:
     """A logger class with some additional functionality, such as
     multiple parameter logging, SQL logging, timing, colors, and lazy
@@ -139,6 +140,8 @@ LOG_LEVEL_DEBUG (NYI).
 
 # Get the module logger. You can override log levels at the
 # module level
+
+
 def getLogger(name, level=None):
     gnlogger = GNLogger(name)
     logger = gnlogger.logger
diff --git a/wqflask/utility/pillow_utils.py b/wqflask/utility/pillow_utils.py
index 6e95beb0..5713e155 100644
--- a/wqflask/utility/pillow_utils.py
+++ b/wqflask/utility/pillow_utils.py
@@ -9,6 +9,8 @@ BLACK = ImageColor.getrgb("black")
 WHITE = ImageColor.getrgb("white")
 
 # def draw_rotated_text(canvas: Image, text: str, font: ImageFont, xy: tuple, fill: ImageColor=BLACK, angle: int=-90):
+
+
 def draw_rotated_text(canvas, text, font, xy, fill=BLACK, angle=-90):
     # type: (Image, str, ImageFont, tuple, ImageColor, int)
     """Utility function draw rotated text"""
@@ -20,6 +22,8 @@ def draw_rotated_text(canvas, text, font, xy, fill=BLACK, angle=-90):
     canvas.paste(im=tmp_img2, box=tuple([int(i) for i in xy]))
 
 # def draw_open_polygon(canvas: Image, xy: tuple, fill: ImageColor=WHITE, outline: ImageColor=BLACK):
+
+
 def draw_open_polygon(canvas, xy, fill=None, outline=BLACK, width=0):
     # type: (Image, tuple, ImageColor, ImageColor)
     draw_ctx = ImageDraw.Draw(canvas)
diff --git a/wqflask/utility/startup_config.py b/wqflask/utility/startup_config.py
index f22f4b14..92f944bc 100644
--- a/wqflask/utility/startup_config.py
+++ b/wqflask/utility/startup_config.py
@@ -10,6 +10,7 @@ GREEN = '\033[92m'
 BOLD = '\033[1m'
 ENDC = '\033[0m'
 
+
 def app_config():
     app.config['SESSION_TYPE'] = 'filesystem'
     if not app.config.get('SECRET_KEY'):
diff --git a/wqflask/utility/svg.py b/wqflask/utility/svg.py
index 4c478c36..f5ef81e1 100644
--- a/wqflask/utility/svg.py
+++ b/wqflask/utility/svg.py
@@ -459,11 +459,13 @@ class rect(SVGelement):
         if stroke_width != None:
             self.attributes['stroke-width'] = stroke_width
 
+
 class ellipse(SVGelement):
     """e=ellipse(rx,ry,x,y,fill,stroke,stroke_width,**args)
 
     an ellipse is defined as a center and a x and y radius.
     """
+
     def __init__(self, cx=None, cy=None, rx=None, ry=None,fill=None,stroke=None,stroke_width=None,**args):
         if rx == None or ry == None:
             raise ValueError('both rx and ry are required')
@@ -486,6 +488,7 @@ class circle(SVGelement):
 
     The circle creates an element using a x, y and radius values eg
     """
+
     def __init__(self, cx=None, cy=None, r=None, fill=None,stroke=None,stroke_width=None,**args):
         if r == None:
             raise ValueError('r is required')
@@ -501,20 +504,24 @@ class circle(SVGelement):
         if stroke_width != None:
             self.attributes['stroke-width'] = stroke_width
 
+
 class point(circle):
     """p=point(x,y,color)
 
     A point is defined as a circle with a size 1 radius. It may be more efficient to use a
     very small rectangle if you use many points because a circle is difficult to render.
     """
+
     def __init__(self, x, y, fill='black', **args):
         circle.__init__(self, x, y, 1, fill, **args)
 
+
 class line(SVGelement):
     """l=line(x1,y1,x2,y2,stroke,stroke_width,**args)
 
     A line is defined by a begin x,y pair and an end x,y pair
     """
+
     def __init__(self, x1=None, y1=None, x2=None, y2=None,stroke=None,stroke_width=None,**args):
         SVGelement.__init__(self, 'line', **args)
         if x1 != None:
@@ -530,11 +537,13 @@ class line(SVGelement):
         if stroke != None:
             self.attributes['stroke'] = stroke
 
+
 class polyline(SVGelement):
     """pl=polyline([[x1,y1],[x2,y2],...],fill,stroke,stroke_width,**args)
 
     a polyline is defined by a list of xy pairs
     """
+
     def __init__(self, points, fill=None, stroke=None, stroke_width=None,**args):
         SVGelement.__init__(self, 'polyline', {'points': _xypointlist(points)}, **args)
         if fill != None:
@@ -544,11 +553,13 @@ class polyline(SVGelement):
         if stroke != None:
             self.attributes['stroke'] = stroke
 
+
 class polygon(SVGelement):
     """pl=polyline([[x1,y1],[x2,y2],...],fill,stroke,stroke_width,**args)
 
     a polygon is defined by a list of xy pairs
     """
+
     def __init__(self, points, fill=None, stroke=None, stroke_width=None,**args):
         SVGelement.__init__(self, 'polygon', {'points': _xypointlist(points)}, **args)
         if fill != None:
@@ -558,11 +569,13 @@ class polygon(SVGelement):
         if stroke != None:
             self.attributes['stroke'] = stroke
 
+
 class path(SVGelement):
     """p=path(path,fill,stroke,stroke_width,**args)
 
     a path is defined by a path object and optional width, stroke and fillcolor
     """
+
     def __init__(self, pathdata, fill=None, stroke=None, stroke_width=None,id=None,**args):
         SVGelement.__init__(self, 'path', {'d': str(pathdata)}, **args)
         if stroke != None:
@@ -580,6 +593,7 @@ class text(SVGelement):
 
     a text element can bge used for displaying text on the screen
     """
+
     def __init__(self, x=None, y=None, text=None, font_size=None,font_family=None,text_anchor=None,**args):
         SVGelement.__init__(self, 'text', **args)
         if x != None:
@@ -601,11 +615,13 @@ class textpath(SVGelement):
 
     a textpath places a text on a path which is referenced by a link.
     """
+
     def __init__(self, link, text=None, **args):
         SVGelement.__init__(self, 'textPath', {'xlink:href': link}, **args)
         if text != None:
             self.text = text
 
+
 class pattern(SVGelement):
     """p=pattern(x,y,width,height,patternUnits,**args)
 
@@ -613,6 +629,7 @@ class pattern(SVGelement):
     graphic object which can be replicated ("tiled") at fixed intervals
     in x and y to cover the areas to be painted.
     """
+
     def __init__(self, x=None, y=None, width=None, height=None,patternUnits=None,**args):
         SVGelement.__init__(self, 'pattern', **args)
         if x != None:
@@ -626,34 +643,40 @@ class pattern(SVGelement):
         if patternUnits != None:
             self.attributes['patternUnits'] = patternUnits
 
+
 class title(SVGelement):
     """t=title(text,**args)
 
     a title is a text element. The text is displayed in the title bar
     add at least one to the root svg element
     """
+
     def __init__(self, text=None, **args):
         SVGelement.__init__(self, 'title', **args)
         if text != None:
             self.text = text
 
+
 class description(SVGelement):
     """d=description(text,**args)
 
     a description can be added to any element and is used for a tooltip
     Add this element before adding other elements.
     """
+
     def __init__(self, text=None, **args):
         SVGelement.__init__(self, 'desc', **args)
         if text != None:
             self.text = text
 
+
 class lineargradient(SVGelement):
     """lg=lineargradient(x1,y1,x2,y2,id,**args)
 
     defines a lineargradient using two xy pairs.
     stop elements van be added to define the gradient colors.
     """
+
     def __init__(self, x1=None, y1=None, x2=None, y2=None,id=None,**args):
         SVGelement.__init__(self, 'linearGradient', **args)
         if x1 != None:
@@ -667,12 +690,14 @@ class lineargradient(SVGelement):
         if id != None:
             self.attributes['id'] = id
 
+
 class radialgradient(SVGelement):
     """rg=radialgradient(cx,cy,r,fx,fy,id,**args)
 
     defines a radial gradient using a outer circle which are defined by a cx,cy and r and by using a focalpoint.
     stop elements van be added to define the gradient colors.
     """
+
     def __init__(self, cx=None, cy=None, r=None, fx=None,fy=None,id=None,**args):
         SVGelement.__init__(self, 'radialGradient', **args)
         if cx != None:
@@ -688,21 +713,25 @@ class radialgradient(SVGelement):
         if id != None:
             self.attributes['id'] = id
 
+
 class stop(SVGelement):
     """st=stop(offset,stop_color,**args)
 
     Puts a stop color at the specified radius
     """
+
     def __init__(self, offset, stop_color=None, **args):
         SVGelement.__init__(self, 'stop', {'offset': offset}, **args)
         if stop_color != None:
             self.attributes['stop-color'] = stop_color
 
+
 class style(SVGelement):
     """st=style(type,cdata=None,**args)
 
     Add a CDATA element to this element for defing in line stylesheets etc..
     """
+
     def __init__(self, type, cdata=None, **args):
         SVGelement.__init__(self, 'style', {'type': type}, cdata=cdata, **args)
 
@@ -712,6 +741,7 @@ class image(SVGelement):
 
     adds an image to the drawing. Supported formats are .png, .jpg and .svg.
     """
+
     def __init__(self, url, x=None, y=None, width=None,height=None,**args):
         if width == None or height == None:
             raise ValueError('both height and width are required')
@@ -721,11 +751,13 @@ class image(SVGelement):
         if y != None:
             self.attributes['y'] = y
 
+
 class cursor(SVGelement):
     """c=cursor(url,**args)
 
     defines a custom cursor for a element or a drawing
     """
+
     def __init__(self, url, **args):
         SVGelement.__init__(self, 'cursor', {'xlink:href': url}, **args)
 
@@ -736,6 +768,7 @@ class marker(SVGelement):
     defines a marker which can be used as an endpoint for a line or other pathtypes
     add an element to it which should be used as a marker.
     """
+
     def __init__(self, id=None, viewBox=None, refx=None, refy=None,markerWidth=None,markerHeight=None,**args):
         SVGelement.__init__(self, 'marker', **args)
         if id != None:
@@ -751,17 +784,20 @@ class marker(SVGelement):
         if markerHeight != None:
             self.attributes['markerHeight'] = markerHeight
 
+
 class group(SVGelement):
     """g=group(id,**args)
 
     a group is defined by an id and is used to contain elements
     g.addElement(SVGelement)
     """
+
     def __init__(self, id=None, **args):
         SVGelement.__init__(self, 'g', **args)
         if id != None:
             self.attributes['id'] = id
 
+
 class symbol(SVGelement):
     """sy=symbol(id,viewbox,**args)
 
@@ -778,14 +814,17 @@ class symbol(SVGelement):
         if viewBox != None:
             self.attributes['viewBox'] = _viewboxlist(viewBox)
 
+
 class defs(SVGelement):
     """d=defs(**args)
 
     container for defining elements
     """
+
     def __init__(self, **args):
         SVGelement.__init__(self, 'defs', **args)
 
+
 class switch(SVGelement):
     """sw=switch(**args)
 
@@ -793,6 +832,7 @@ class switch(SVGelement):
     requiredFeatures, requiredExtensions and systemLanguage.
     Refer to the SVG specification for details.
     """
+
     def __init__(self, **args):
         SVGelement.__init__(self, 'switch', **args)
 
@@ -802,6 +842,7 @@ class use(SVGelement):
 
     references a symbol by linking to its id and its position, height and width
     """
+
     def __init__(self, link, x=None, y=None, width=None,height=None,**args):
         SVGelement.__init__(self, 'use', {'xlink:href': link}, **args)
         if x != None:
@@ -821,32 +862,39 @@ class link(SVGelement):
     a link  is defined by a hyperlink. add elements which have to be linked
     a.addElement(SVGelement)
     """
+
     def __init__(self, link='', **args):
         SVGelement.__init__(self, 'a', {'xlink:href': link}, **args)
 
+
 class view(SVGelement):
     """v=view(id,**args)
 
     a view can be used to create a view with different attributes"""
+
     def __init__(self, id=None, **args):
         SVGelement.__init__(self, 'view', **args)
         if id != None:
             self.attributes['id'] = id
 
+
 class script(SVGelement):
     """sc=script(type,type,cdata,**args)
 
     adds a script element which contains CDATA to the SVG drawing
 
     """
+
     def __init__(self, type, cdata=None, **args):
         SVGelement.__init__(self, 'script', {'type': type}, cdata=cdata, **args)
 
+
 class animate(SVGelement):
     """an=animate(attribute,from,to,during,**args)
 
     animates an attribute.
     """
+
     def __init__(self, attribute, fr=None, to=None, dur=None,**args):
         SVGelement.__init__(self, 'animate', {'attributeName': attribute}, **args)
         if fr != None:
@@ -856,11 +904,13 @@ class animate(SVGelement):
         if dur != None:
             self.attributes['dur'] = dur
 
+
 class animateMotion(SVGelement):
     """an=animateMotion(pathdata,dur,**args)
 
     animates a SVGelement over the given path in dur seconds
     """
+
     def __init__(self, pathdata, dur, **args):
         SVGelement.__init__(self, 'animateMotion', **args)
         if pathdata != None:
@@ -868,11 +918,13 @@ class animateMotion(SVGelement):
         if dur != None:
             self.attributes['dur'] = dur
 
+
 class animateTransform(SVGelement):
     """antr=animateTransform(type,from,to,dur,**args)
 
     transform an element from and to a value.
     """
+
     def __init__(self, type=None, fr=None, to=None, dur=None,**args):
         SVGelement.__init__(self, 'animateTransform', {'attributeName': 'transform'}, **args)
         # As far as I know the attributeName is always transform
@@ -884,11 +936,14 @@ class animateTransform(SVGelement):
             self.attributes['to'] = to
         if dur != None:
             self.attributes['dur'] = dur
+
+
 class animateColor(SVGelement):
     """ac=animateColor(attribute,type,from,to,dur,**args)
 
     Animates the color of a element
     """
+
     def __init__(self, attribute, type=None, fr=None, to=None,dur=None,**args):
         SVGelement.__init__(self, 'animateColor', {'attributeName': attribute}, **args)
         if type != None:
@@ -899,11 +954,14 @@ class animateColor(SVGelement):
             self.attributes['to'] = to
         if dur != None:
             self.attributes['dur'] = dur
+
+
 class set(SVGelement):
     """st=set(attribute,to,during,**args)
 
     sets an attribute to a value for a
     """
+
     def __init__(self, attribute, to=None, dur=None, **args):
         SVGelement.__init__(self, 'set', {'attributeName': attribute}, **args)
         if to != None:
@@ -912,7 +970,6 @@ class set(SVGelement):
             self.attributes['dur'] = dur
 
 
-
 class svg(SVGelement):
     """s=svg(viewbox,width,height,**args)
 
@@ -928,6 +985,7 @@ class svg(SVGelement):
     d.setSVG(s)
     d.toXml()
     """
+
     def __init__(self, viewBox=None, width=None, height=None, **args):
         SVGelement.__init__(self, 'svg', **args)
         if viewBox != None:
@@ -938,6 +996,7 @@ class svg(SVGelement):
             self.attributes['height'] = height
         self.namespace = "http://www.w3.org/2000/svg"
 
+
 class drawing:
     """d=drawing()
 
@@ -952,6 +1011,7 @@ class drawing:
     def __init__(self, entity={}):
         self.svg = None
         self.entity = entity
+
     def setSVG(self, svg):
         self.svg = svg
         # Voeg een element toe aan de grafiek toe.
@@ -1005,6 +1065,7 @@ class drawing:
             root = implementation.createDocument(None, None, doctype)
             # Create the xml document.
             global appender
+
             def appender(element, elementroot):
                 """This recursive function appends elements to an element and sets the attributes
                 and type. It stops when alle elements have been appended"""
@@ -1053,6 +1114,7 @@ class drawing:
                         f.close()
                 except:
                     print(("Cannot write SVG file: " + filename))
+
     def validate(self):
         try:
             import xml.parsers.xmlproc.xmlval
@@ -1066,9 +1128,10 @@ class drawing:
             raise Exception("SVG is not well formed, see messages above")
         else:
             print("SVG well formed")
-if __name__ == '__main__':
 
 
+if __name__ == '__main__':
+
     d = drawing()
     s = svg((0, 0, 100, 100))
     r = rect(-100, -100, 300, 300, 'cyan')
diff --git a/wqflask/utility/temp_data.py b/wqflask/utility/temp_data.py
index 2088ba9a..07c5a318 100644
--- a/wqflask/utility/temp_data.py
+++ b/wqflask/utility/temp_data.py
@@ -2,6 +2,7 @@ from redis import Redis
 
 import simplejson as json
 
+
 class TempData:
 
     def __init__(self, temp_uuid):
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 9b751344..4fe4db08 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -13,11 +13,13 @@ logger = logging.getLogger(__name__)
 
 OVERRIDES = {}
 
+
 def app_set(command_id, value):
     """Set application wide value"""
     app.config.setdefault(command_id, value)
     return value
 
+
 def get_setting(command_id, guess=None):
     """Resolve a setting from the environment or the global settings in
     app.config, with valid_path is a function checking whether the
@@ -66,12 +68,14 @@ def get_setting(command_id, guess=None):
     # print("Set "+command_id+"="+str(command))
     return command
 
+
 def get_setting_bool(id):
     v = get_setting(id)
     if v not in [0, False, 'False', 'FALSE', None]:
       return True
     return False
 
+
 def get_setting_int(id):
     v = get_setting(id)
     if isinstance(v, str):
@@ -80,21 +84,25 @@ def get_setting_int(id):
         return 0
     return v
 
+
 def valid_bin(bin):
     if os.path.islink(bin) or valid_file(bin):
         return bin
     return None
 
+
 def valid_file(fn):
     if os.path.isfile(fn):
         return fn
     return None
 
+
 def valid_path(dir):
     if os.path.isdir(dir):
         return dir
     return None
 
+
 def js_path(module=None):
     """
     Find the JS module in the two paths
@@ -107,38 +115,47 @@ def js_path(module=None):
         return try_guix
     raise "No JS path found for " + module + " (if not in Guix check JS_GN_PATH)"
 
+
 def reaper_command(guess=None):
     return get_setting("REAPER_COMMAND", guess)
 
+
 def gemma_command(guess=None):
     return assert_bin(get_setting("GEMMA_COMMAND", guess))
 
+
 def gemma_wrapper_command(guess=None):
     return assert_bin(get_setting("GEMMA_WRAPPER_COMMAND", guess))
 
+
 def plink_command(guess=None):
     return assert_bin(get_setting("PLINK_COMMAND", guess))
 
+
 def flat_file_exists(subdir):
     base = get_setting("GENENETWORK_FILES")
     return valid_path(base + "/" + subdir)
 
+
 def flat_files(subdir=None):
     base = get_setting("GENENETWORK_FILES")
     if subdir:
         return assert_dir(base + "/" + subdir)
     return assert_dir(base)
 
+
 def assert_bin(fn):
     if not valid_bin(fn):
         raise Exception("ERROR: can not find binary " + fn)
     return fn
 
+
 def assert_dir(dir):
     if not valid_path(dir):
         raise Exception("ERROR: can not find directory " + dir)
     return dir
 
+
 def assert_writable_dir(dir):
     try:
         fn = dir + "/test.txt"
@@ -150,16 +167,19 @@ def assert_writable_dir(dir):
         raise Exception('Unable to write test.txt to directory ' + dir)
     return dir
 
+
 def assert_file(fn):
     if not valid_file(fn):
         raise Exception('Unable to find file ' + fn)
     return fn
 
+
 def mk_dir(dir):
     if not valid_path(dir):
         os.makedirs(dir)
     return assert_dir(dir)
 
+
 def locate(name, subdir=None):
     """
     Locate a static flat file in the GENENETWORK_FILES environment.
@@ -179,9 +199,11 @@ def locate(name, subdir=None):
     if subdir: sys.stderr.write(subdir)
     raise Exception("Can not locate " + name + " in " + base)
 
+
 def locate_phewas(name, subdir=None):
     return locate(name, '/phewas/' + subdir)
 
+
 def locate_ignore_error(name, subdir=None):
     """
     Locate a static flat file in the GENENETWORK_FILES environment.
@@ -200,17 +222,20 @@ def locate_ignore_error(name, subdir=None):
     logger.info("WARNING: file " + name + " not found\n")
     return None
 
+
 def tempdir():
     """
     Get UNIX TMPDIR by default
     """
     return valid_path(get_setting("TMPDIR", "/tmp"))
 
+
 BLUE = '\033[94m'
 GREEN = '\033[92m'
 BOLD = '\033[1m'
 ENDC = '\033[0m'
 
+
 def show_settings():
     from utility.tools import LOG_LEVEL
 
diff --git a/wqflask/utility/type_checking.py b/wqflask/utility/type_checking.py
index 662bf794..00f14ba9 100644
--- a/wqflask/utility/type_checking.py
+++ b/wqflask/utility/type_checking.py
@@ -7,6 +7,7 @@ def is_float(value):
     except:
         return False
 
+
 def is_int(value):
     try:
         int(value)
@@ -14,6 +15,7 @@ def is_int(value):
     except:
         return False
 
+
 def is_str(value):
     if value is None:
         return False
@@ -23,18 +25,21 @@ def is_str(value):
     except:
         return False
 
+
 def get_float(vars_obj, name, default=None):
     if name in vars_obj:
         if is_float(vars_obj[name]):
             return float(vars_obj[name])
     return default
 
+
 def get_int(vars_obj, name, default=None):
     if name in vars_obj:
         if is_int(vars_obj[name]):
             return float(vars_obj[name])
     return default
 
+
 def get_string(vars_obj, name, default=None):
     if name in vars_obj:
         if not vars_obj[name] is None:
diff --git a/wqflask/utility/webqtlUtil.py b/wqflask/utility/webqtlUtil.py
index ed59b0eb..f355a865 100644
--- a/wqflask/utility/webqtlUtil.py
+++ b/wqflask/utility/webqtlUtil.py
@@ -64,6 +64,7 @@ ParInfo = {
 #      Accessory Functions
 #########################################
 
+
 def genRandStr(prefix="", length=8, chars=string.ascii_letters + string.digits):
     from random import choice
     _str = prefix[:]
@@ -71,6 +72,7 @@ def genRandStr(prefix="", length=8, chars=string.ascii_letters + string.digits):
         _str += choice(chars)
     return _str
 
+
 def ListNotNull(lst):
     '''Obsolete - Use built in function any (or all or whatever)
 
@@ -83,6 +85,7 @@ def ListNotNull(lst):
             return 1
     return None
 
+
 def readLineCSV(line):  # dcrowell July 2008
     """Parses a CSV string of text and returns a list containing each element as a string.
     Used by correlationPage"""
@@ -91,6 +94,7 @@ def readLineCSV(line):  # dcrowell July 2008
     returnList[0] = returnList[0][1:]
     return returnList
 
+
 def cmpEigenValue(A, B):
     try:
         if A[0] > B[0]:
@@ -102,6 +106,7 @@ def cmpEigenValue(A, B):
     except:
         return 0
 
+
 def hasAccessToConfidentialPhenotypeTrait(privilege, userName, authorized_users):
     access_to_confidential_phenotype_trait = 0
     if webqtlConfig.USERDICT[privilege] > webqtlConfig.USERDICT['user']:
diff --git a/wqflask/wqflask/__init__.py b/wqflask/wqflask/__init__.py
index bab87115..712517a3 100644
--- a/wqflask/wqflask/__init__.py
+++ b/wqflask/wqflask/__init__.py
@@ -30,6 +30,7 @@ app.register_blueprint(policies_blueprint, url_prefix="/policies")
 app.register_blueprint(environments_blueprint, url_prefix="/environments")
 app.register_blueprint(facilities_blueprint, url_prefix="/facilities")
 
+
 @app.before_request
 def before_request():
     g.request_start_time = time.time()
diff --git a/wqflask/wqflask/api/correlation.py b/wqflask/wqflask/api/correlation.py
index e0b7fea0..f1dd148f 100644
--- a/wqflask/wqflask/api/correlation.py
+++ b/wqflask/wqflask/api/correlation.py
@@ -18,6 +18,7 @@ from utility.benchmark import Bench
 import utility.logger
 logger = utility.logger.getLogger(__name__)
 
+
 def do_correlation(start_vars):
     assert('db' in start_vars)
     assert('target_db' in start_vars)
@@ -66,6 +67,7 @@ def do_correlation(start_vars):
 
     return final_results
 
+
 def calculate_results(this_trait, this_dataset, target_dataset, corr_params):
     corr_results = {}
 
@@ -91,6 +93,7 @@ def calculate_results(this_trait, this_dataset, target_dataset, corr_params):
 
     return sorted_results
 
+
 def do_tissue_correlation_for_all_traits(this_trait, trait_symbol_dict, corr_params, tissue_dataset_id=1):
     # Gets tissue expression values for the primary trait
     primary_trait_tissue_vals_dict = correlation_functions.get_trait_symbol_and_tissue_values(symbol_list=[this_trait.symbol])
@@ -113,6 +116,7 @@ def do_tissue_correlation_for_all_traits(this_trait, trait_symbol_dict, corr_par
 
         return tissue_corr_data
 
+
 def do_literature_correlation_for_all_traits(this_trait, target_dataset, trait_geneid_dict, corr_params):
     input_trait_mouse_gene_id = convert_to_mouse_gene_id(target_dataset.group.species.lower(), this_trait.geneid)
 
@@ -145,6 +149,7 @@ def do_literature_correlation_for_all_traits(this_trait, target_dataset, trait_g
 
     return lit_corr_data
 
+
 def get_sample_r_and_p_values(this_trait, this_dataset, target_vals, target_dataset, type):
     """
     Calculates the sample r (or rho) and p-value
@@ -176,6 +181,7 @@ def get_sample_r_and_p_values(this_trait, this_dataset, target_vals, target_data
         else:
             return [sample_r, sample_p, num_overlap]
 
+
 def convert_to_mouse_gene_id(species=None, gene_id=None):
     """If the species is rat or human, translate the gene_id to the mouse geneid
 
@@ -212,6 +218,7 @@ def convert_to_mouse_gene_id(species=None, gene_id=None):
 
     return mouse_gene_id
 
+
 def init_corr_params(start_vars):
     method = "pearson"
     if 'method' in start_vars:
diff --git a/wqflask/wqflask/api/mapping.py b/wqflask/wqflask/api/mapping.py
index fbfbc879..662090d5 100644
--- a/wqflask/wqflask/api/mapping.py
+++ b/wqflask/wqflask/api/mapping.py
@@ -10,6 +10,7 @@ from wqflask.marker_regression import gemma_mapping, rqtl_mapping, qtlreaper_map
 import utility.logger
 logger = utility.logger.getLogger(__name__)
 
+
 def do_mapping_for_api(start_vars):
     assert('db' in start_vars)
     assert('trait_id' in start_vars)
@@ -74,7 +75,6 @@ def do_mapping_for_api(start_vars):
         return result_markers, None
 
 
-
 def initialize_parameters(start_vars, dataset, this_trait):
     mapping_params = {}
 
diff --git a/wqflask/wqflask/api/router.py b/wqflask/wqflask/api/router.py
index b0559a07..4f9cc6e5 100644
--- a/wqflask/wqflask/api/router.py
+++ b/wqflask/wqflask/api/router.py
@@ -27,10 +27,12 @@ logger = utility.logger.getLogger(__name__)
 
 version = "pre1"
 
+
 @app.route("/api/v_{}/".format(version))
 def hello_world():
     return flask.jsonify({"hello": "world"})
 
+
 @app.route("/api/v_{}/species".format(version))
 def get_species_list():
     results = g.db.execute("SELECT SpeciesId, Name, FullName, TaxonomyId FROM Species;")
@@ -47,6 +49,7 @@ def get_species_list():
 
     return flask.jsonify(species_list)
 
+
 @app.route("/api/v_{}/species/<path:species_name>".format(version))
 @app.route("/api/v_{}/species/<path:species_name>.<path:file_format>".format(version))
 def get_species_info(species_name, file_format="json"):
@@ -64,6 +67,7 @@ def get_species_info(species_name, file_format="json"):
     
     return flask.jsonify(species_dict)
 
+
 @app.route("/api/v_{}/groups".format(version))
 @app.route("/api/v_{}/groups/<path:species_name>".format(version))
 def get_groups_list(species_name=None):
@@ -102,6 +106,7 @@ def get_groups_list(species_name=None):
     else:
         return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
 
+
 @app.route("/api/v_{}/group/<path:group_name>".format(version))
 @app.route("/api/v_{}/group/<path:group_name>.<path:file_format>".format(version))
 @app.route("/api/v_{}/group/<path:species_name>/<path:group_name>".format(version))
@@ -145,6 +150,7 @@ def get_group_info(group_name, species_name=None, file_format="json"):
     else:
         return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
 
+
 @app.route("/api/v_{}/datasets/<path:group_name>".format(version))
 @app.route("/api/v_{}/datasets/<path:species_name>/<path:group_name>".format(version))
 def get_datasets_for_group(group_name, species_name=None):
@@ -197,6 +203,7 @@ def get_datasets_for_group(group_name, species_name=None):
     else:
         return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
 
+
 @app.route("/api/v_{}/dataset/<path:dataset_name>".format(version))
 @app.route("/api/v_{}/dataset/<path:dataset_name>.<path:file_format>".format(version))
 @app.route("/api/v_{}/dataset/<path:group_name>/<path:dataset_name>".format(version))
@@ -302,6 +309,7 @@ def get_dataset_info(dataset_name, group_name=None, file_format="json"):
     else:
         return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
 
+
 @app.route("/api/v_{}/traits/<path:dataset_name>".format(version), methods=("GET",))
 @app.route("/api/v_{}/traits/<path:dataset_name>.<path:file_format>".format(version), methods=("GET",))
 def fetch_traits(dataset_name, file_format="json"):
@@ -430,6 +438,7 @@ def fetch_traits(dataset_name, file_format="json"):
         else:
             return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
 
+
 @app.route("/api/v_{}/sample_data/<path:dataset_name>".format(version))
 @app.route("/api/v_{}/sample_data/<path:dataset_name>.<path:file_format>".format(version))
 def all_sample_data(dataset_name, file_format="csv"):
@@ -536,6 +545,7 @@ def all_sample_data(dataset_name, file_format="csv"):
     else:
         return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
 
+
 @app.route("/api/v_{}/sample_data/<path:dataset_name>/<path:trait_name>".format(version))
 @app.route("/api/v_{}/sample_data/<path:dataset_name>/<path:trait_name>.<path:file_format>".format(version))
 def trait_sample_data(dataset_name, trait_name, file_format="json"):
@@ -625,6 +635,7 @@ def trait_sample_data(dataset_name, trait_name, file_format="json"):
         else:
             return return_error(code=204, source=request.url_rule.rule, title="No Results", details="") 
 
+
 @app.route("/api/v_{}/trait/<path:dataset_name>/<path:trait_name>".format(version))
 @app.route("/api/v_{}/trait/<path:dataset_name>/<path:trait_name>.<path:file_format>".format(version))
 @app.route("/api/v_{}/trait_info/<path:dataset_name>/<path:trait_name>".format(version))
@@ -694,6 +705,7 @@ def get_trait_info(dataset_name, trait_name, file_format="json"):
         else:
             return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
 
+
 @app.route("/api/v_{}/correlation".format(version), methods=("GET",))
 def get_corr_results():
     results = correlation.do_correlation(request.args)
@@ -703,6 +715,7 @@ def get_corr_results():
     else:
         return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
 
+
 @app.route("/api/v_{}/mapping".format(version), methods=("GET",))
 def get_mapping_results():
     results, format = mapping.do_mapping_for_api(request.args)
@@ -726,6 +739,7 @@ def get_mapping_results():
     else:
         return return_error(code=204, source=request.url_rule.rule, title="No Results", details="")
 
+
 @app.route("/api/v_{}/genotypes/<string:file_format>/<string:group_name>/<string:dataset_name>.zip".format(version))
 @app.route("/api/v_{}/genotypes/<string:file_format>/<string:group_name>/<string:dataset_name>".format(version))
 @app.route("/api/v_{}/genotypes/<string:file_format>/<string:group_name>.zip".format(version))
@@ -813,6 +827,7 @@ def get_genotypes(group_name, file_format="csv", dataset_name=None):
 
     return output
 
+
 @app.route("/api/v_{}/gen_dropdown".format(version), methods=("GET",))
 def gen_dropdown_menu():
     results = gen_menu.gen_dropdown_json()
@@ -822,6 +837,7 @@ def gen_dropdown_menu():
     else:
         return return_error(code=500, source=request.url_rule.rule, title="Some error occurred", details="")
 
+
 def return_error(code, source, title, details):
     json_ob = {"errors": [
         {
@@ -834,6 +850,7 @@ def return_error(code, source, title, details):
 
     return flask.jsonify(json_ob)
 
+
 def get_dataset_trait_ids(dataset_name, start_vars):
 
     if 'limit_to' in start_vars:
@@ -906,6 +923,7 @@ def get_dataset_trait_ids(dataset_name, start_vars):
         dataset_id = results[0][2]
         return trait_ids, trait_names, data_type, dataset_id
 
+
 def get_samplelist(dataset_name):
     group_id = get_group_id_from_dataset(dataset_name)
 
@@ -922,6 +940,7 @@ def get_samplelist(dataset_name):
 
     return samplelist
 
+
 def get_group_id_from_dataset(dataset_name):
     if "Publish" in dataset_name:
         query = """
@@ -962,6 +981,7 @@ def get_group_id_from_dataset(dataset_name):
     else:
         return None
 
+
 def get_group_id(group_name):
     query = """
                SELECT InbredSet.Id
diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py
index 6a1b88ca..61f73106 100644
--- a/wqflask/wqflask/collect.py
+++ b/wqflask/wqflask/collect.py
@@ -40,6 +40,7 @@ def process_traits(unprocessed_traits):
 
     return traits
 
+
 def report_change(len_before, len_now):
     new_length = len_now - len_before
     if new_length:
@@ -48,6 +49,7 @@ def report_change(len_before, len_now):
     else:
         logger.debug("No new traits were added.")
 
+
 @app.route("/collections/store_trait_list", methods=('POST',))
 def store_traits_list():
    params = request.form
@@ -59,6 +61,7 @@ def store_traits_list():
 
    return hash
 
+
 @app.route("/collections/add")
 def collections_add():
 
@@ -82,6 +85,7 @@ def collections_add():
                                 collections=collections,
                               )
 
+
 @app.route("/collections/new")
 def collections_new():
     params = request.args
@@ -118,6 +122,7 @@ def collections_new():
         # CauseAnError
         pass
 
+
 def create_new(collection_name):
     params = request.args
 
@@ -133,6 +138,7 @@ def create_new(collection_name):
 
     return redirect(url_for('view_collection', uc_id=uc_id))
 
+
 @app.route("/collections/list")
 def list_collections():
     params = request.args
@@ -143,6 +149,7 @@ def list_collections():
                             collections=user_collections,
                             )
 
+
 @app.route("/collections/remove", methods=('POST',))
 def remove_traits():
     params = request.form
@@ -216,6 +223,7 @@ def view_collection():
                            **collection_info
                            )
 
+
 @app.route("/collections/change_name", methods=('POST',))
 def change_collection_name():
     params = request.form
diff --git a/wqflask/wqflask/correlation/corr_scatter_plot.py b/wqflask/wqflask/correlation/corr_scatter_plot.py
index 22941ad5..6afea715 100644
--- a/wqflask/wqflask/correlation/corr_scatter_plot.py
+++ b/wqflask/wqflask/correlation/corr_scatter_plot.py
@@ -11,6 +11,7 @@ import numpy as np
 import utility.logger
 logger = utility.logger.getLogger(__name__)
 
+
 class CorrScatterPlot:
     """Page that displays a correlation scatterplot with a line fitted to it"""
 
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index 051ac1cb..e2fe1ff4 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -172,7 +172,6 @@ class CorrelationResults:
             self.correlation_data = collections.OrderedDict(sorted(list(self.correlation_data.items()),
                                                                    key=lambda t: -abs(t[1][0])))
 
-
             # ZS: Convert min/max chromosome to an int for the location range option
             range_chr_as_int = None
             for order_id, chr_info in list(self.dataset.species.chromosomes.chromosomes.items()):
@@ -348,7 +347,6 @@ class CorrelationResults:
             else:
                 trait.lit_corr = 0
 
-
     def do_lit_correlation_for_all_traits(self):
         input_trait_mouse_gene_id = self.convert_to_mouse_gene_id(self.dataset.group.species.lower(), self.this_trait.geneid)
 
@@ -484,6 +482,7 @@ def do_bicor(this_trait_vals, target_trait_vals):
 
     return the_r, the_p
 
+
 def generate_corr_json(corr_results, this_trait, dataset, target_dataset, for_api=False):
     results_list = []
     for i, trait in enumerate(corr_results):
@@ -574,6 +573,7 @@ def generate_corr_json(corr_results, this_trait, dataset, target_dataset, for_ap
 
     return json.dumps(results_list)
 
+
 def get_header_fields(data_type, corr_method):
     if data_type == "ProbeSet":
         if corr_method == "spearman":
diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
index 94c8931f..331cb1dc 100644
--- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
+++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
@@ -233,6 +233,7 @@ class CorrelationMatrix:
             loadings_array.append(loadings_row)
         return loadings_array
 
+
 def export_corr_matrix(corr_results):
     corr_matrix_filename = "corr_matrix_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6))
     matrix_export_path = "{}{}.csv".format(GENERATED_TEXT_DIR, corr_matrix_filename)
@@ -263,6 +264,7 @@ def export_corr_matrix(corr_results):
 
     return corr_matrix_filename, matrix_export_path
 
+
 def zScore(trait_data_array):
     NN = len(trait_data_array[0])
     if NN < 10:
@@ -283,6 +285,7 @@ def zScore(trait_data_array):
             i += 1
         return trait_data_array
 
+
 def sortEigenVectors(vector):
     try:
         eigenValues = vector[0].tolist()
diff --git a/wqflask/wqflask/ctl/ctl_analysis.py b/wqflask/wqflask/ctl/ctl_analysis.py
index 2fa90a93..ec66e59f 100644
--- a/wqflask/wqflask/ctl/ctl_analysis.py
+++ b/wqflask/wqflask/ctl/ctl_analysis.py
@@ -39,6 +39,7 @@ r_write_table = ro.r["write.table"]         # Map the write.table function
 r_data_frame = ro.r["data.frame"]         # Map the write.table function
 r_as_numeric = ro.r["as.numeric"]         # Map the write.table function
 
+
 class CTL:
     def __init__(self):
         logger.info("Initialization of CTL")
diff --git a/wqflask/wqflask/database.py b/wqflask/wqflask/database.py
index b6e85494..e743c4b3 100644
--- a/wqflask/wqflask/database.py
+++ b/wqflask/wqflask/database.py
@@ -17,6 +17,7 @@ db_session = scoped_session(sessionmaker(autocommit=False,
 Base = declarative_base()
 Base.query = db_session.query_property()
 
+
 def init_db():
     # import all modules here that might define models so that
     # they will be registered properly on the metadata.  Otherwise
@@ -27,4 +28,5 @@ def init_db():
     Base.metadata.create_all(bind=engine)
     logger.info("Done creating all model metadata")
 
+
 init_db()
diff --git a/wqflask/wqflask/db_info.py b/wqflask/wqflask/db_info.py
index 25e624ef..c7558ed8 100644
--- a/wqflask/wqflask/db_info.py
+++ b/wqflask/wqflask/db_info.py
@@ -90,6 +90,7 @@ class InfoPage:
         except Exception as e:
             pass
 
+
 def process_query_results(results):
     info_ob = {
         'info_page_name': results[0],
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index 115182e4..7442dc72 100644
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -73,6 +73,7 @@ class DoSearch:
         else:
             return None
 
+
 class MrnaAssaySearch(DoSearch):
     """A search within an expression dataset, including mRNA, protein, SNP, but not phenotype or metabolites"""
 
@@ -296,6 +297,7 @@ class PhenotypeSearch(DoSearch):
 
         return self.execute(query)
 
+
 class GenotypeSearch(DoSearch):
     """A search within a genotype dataset"""
 
@@ -339,7 +341,6 @@ class GenotypeSearch(DoSearch):
 
         from_clause = self.normalize_spaces(from_clause)
 
-
         if self.search_term[0] == "*":
             query = (self.base_query +
                     """WHERE Geno.Id = GenoXRef.GenoId
@@ -367,6 +368,7 @@ class GenotypeSearch(DoSearch):
 
         return self.execute(self.query)
 
+
 class RifSearch(MrnaAssaySearch):
     """Searches for traits with a Gene RIF entry including the search term."""
 
@@ -390,6 +392,7 @@ class RifSearch(MrnaAssaySearch):
 
         return self.execute(query)
 
+
 class WikiSearch(MrnaAssaySearch):
     """Searches GeneWiki for traits other people have annotated"""
 
@@ -415,6 +418,7 @@ class WikiSearch(MrnaAssaySearch):
 
         return self.execute(query)
 
+
 class GoSearch(MrnaAssaySearch):
     """Searches for synapse-associated genes listed in the Gene Ontology."""
 
@@ -449,6 +453,8 @@ class GoSearch(MrnaAssaySearch):
         return self.execute(query)
 
 # ZS: Not sure what the best way to deal with LRS searches is
+
+
 class LrsSearch(DoSearch):
     """Searches for genes with a QTL within the given LRS values
 
@@ -526,7 +532,6 @@ class LrsSearch(DoSearch):
 
         return where_clause
 
-
     def run(self):
 
         self.from_clause = self.get_from_clause()
@@ -550,6 +555,7 @@ class MrnaLrsSearch(LrsSearch, MrnaAssaySearch):
 
         return self.execute(self.query)
 
+
 class PhenotypeLrsSearch(LrsSearch, PhenotypeSearch):
 
     for search_key in ('LRS', 'LOD'):
@@ -649,6 +655,7 @@ class CisTransLrsSearch(DoSearch):
 
         return where_clause
 
+
 class CisLrsSearch(CisTransLrsSearch, MrnaAssaySearch):
     """
     Searches for genes on a particular chromosome with a cis-eQTL within the given LRS values
@@ -680,6 +687,7 @@ class CisLrsSearch(CisTransLrsSearch, MrnaAssaySearch):
 
         return self.execute(self.query)
 
+
 class TransLrsSearch(CisTransLrsSearch, MrnaAssaySearch):
     """Searches for genes on a particular chromosome with a cis-eQTL within the given LRS values
 
@@ -744,6 +752,7 @@ class MeanSearch(MrnaAssaySearch):
 
         return self.execute(self.query)
 
+
 class RangeSearch(MrnaAssaySearch):
     """Searches for genes with a range of expression varying between two values"""
 
@@ -779,6 +788,7 @@ class RangeSearch(MrnaAssaySearch):
 
         return self.execute(self.query)
 
+
 class PositionSearch(DoSearch):
     """Searches for genes/markers located within a specified range on a specified chromosome"""
 
@@ -800,7 +810,6 @@ class PositionSearch(DoSearch):
                                                               self.dataset.type,
                                                               max(self.mb_min, self.mb_max))
 
-
         return where_clause
 
     def get_chr(self):
@@ -819,6 +828,7 @@ class PositionSearch(DoSearch):
 
         return self.execute(self.query)
 
+
 class MrnaPositionSearch(PositionSearch, MrnaAssaySearch):
     """Searches for genes located within a specified range on a specified chromosome"""
 
@@ -832,6 +842,7 @@ class MrnaPositionSearch(PositionSearch, MrnaAssaySearch):
 
         return self.execute(self.query)
 
+
 class GenotypePositionSearch(PositionSearch, GenotypeSearch):
     """Searches for genes located within a specified range on a specified chromosome"""
 
@@ -845,6 +856,7 @@ class GenotypePositionSearch(PositionSearch, GenotypeSearch):
 
         return self.execute(self.query)
 
+
 class PvalueSearch(MrnaAssaySearch):
     """Searches for traits with a permutationed p-value between low and high"""
 
@@ -878,6 +890,7 @@ class PvalueSearch(MrnaAssaySearch):
         logger.sql(self.query)
         return self.execute(self.query)
 
+
 class AuthorSearch(PhenotypeSearch):
     """Searches for phenotype traits with specified author(s)"""
 
@@ -900,6 +913,7 @@ def is_number(s):
     except ValueError:
         return False
 
+
 def get_aliases(symbol, species):
     if species == "mouse":
         symbol_string = symbol.capitalize()
@@ -923,6 +937,7 @@ def get_aliases(symbol, species):
 
     return filtered_aliases
 
+
 if __name__ == "__main__":
     # Usually this will be used as a library, but call it from the command line for testing
     # And it runs the code below
diff --git a/wqflask/wqflask/docs.py b/wqflask/wqflask/docs.py
index 207767c4..81424b9c 100644
--- a/wqflask/wqflask/docs.py
+++ b/wqflask/wqflask/docs.py
@@ -5,6 +5,7 @@ from flask import g
 from utility.logger import getLogger
 logger = getLogger(__name__)
 
+
 class Docs:
 
     def __init__(self, entry, start_vars={}):
@@ -23,7 +24,6 @@ class Docs:
             self.title = result[0]
             self.content = result[1].decode("utf-8")
 
-
         self.editable = "false"
         # ZS: Removing option to edit to see if text still gets vandalized
         try:
diff --git a/wqflask/wqflask/export_traits.py b/wqflask/wqflask/export_traits.py
index 95c20673..d0745ef7 100644
--- a/wqflask/wqflask/export_traits.py
+++ b/wqflask/wqflask/export_traits.py
@@ -15,6 +15,7 @@ from pprint import pformat as pf
 from utility.logger import getLogger
 logger = getLogger(__name__)
 
+
 def export_search_results_csv(targs):
 
     table_data = json.loads(targs['export_data'])
@@ -132,6 +133,7 @@ def export_search_results_csv(targs):
 
     return file_list
 
+
 def sort_traits_by_group(trait_list=[]):
     traits_by_group = {}
     for trait in trait_list:
diff --git a/wqflask/wqflask/external_tools/send_to_bnw.py b/wqflask/wqflask/external_tools/send_to_bnw.py
index 9836eb9c..1556c6a0 100644
--- a/wqflask/wqflask/external_tools/send_to_bnw.py
+++ b/wqflask/wqflask/external_tools/send_to_bnw.py
@@ -24,6 +24,7 @@ from utility import helper_functions, corr_result_helpers
 import utility.logger
 logger = utility.logger.getLogger(__name__)
 
+
 class SendToBNW:
     def __init__(self, start_vars):
         trait_db_list = [trait.strip() for trait in start_vars['trait_list'].split(',')]
diff --git a/wqflask/wqflask/external_tools/send_to_geneweaver.py b/wqflask/wqflask/external_tools/send_to_geneweaver.py
index 36f1b8e5..c55c43e6 100644
--- a/wqflask/wqflask/external_tools/send_to_geneweaver.py
+++ b/wqflask/wqflask/external_tools/send_to_geneweaver.py
@@ -29,6 +29,7 @@ from utility import helper_functions, corr_result_helpers
 import utility.logger
 logger = utility.logger.getLogger(__name__)
 
+
 class SendToGeneWeaver:
     def __init__(self, start_vars):
         trait_db_list = [trait.strip() for trait in start_vars['trait_list'].split(',')]
@@ -58,6 +59,7 @@ class SendToGeneWeaver:
                                  'list': ",".join(trait_name_list),
                                }
 
+
 def get_trait_name_list(trait_list):
     name_list = []
     for trait_db in trait_list:
@@ -65,6 +67,7 @@ def get_trait_name_list(trait_list):
 
     return name_list
 
+
 def test_chip(trait_list):
     final_chip_name = ""
 
diff --git a/wqflask/wqflask/external_tools/send_to_webgestalt.py b/wqflask/wqflask/external_tools/send_to_webgestalt.py
index f50eeb8b..6b78725c 100644
--- a/wqflask/wqflask/external_tools/send_to_webgestalt.py
+++ b/wqflask/wqflask/external_tools/send_to_webgestalt.py
@@ -29,6 +29,7 @@ from utility import helper_functions, corr_result_helpers
 import utility.logger
 logger = utility.logger.getLogger(__name__)
 
+
 class SendToWebGestalt:
     def __init__(self, start_vars):
         trait_db_list = [trait.strip() for trait in start_vars['trait_list'].split(',')]
@@ -69,6 +70,7 @@ class SendToWebGestalt:
             else:
                 self.hidden_vars['organism'] = "others"
 
+
 def test_chip(trait_list):
     final_chip_name = ""
 
@@ -113,6 +115,7 @@ def test_chip(trait_list):
 
     return chip_name
 
+
 def gen_gene_id_list(trait_list):
     trait_name_list = []
     gene_id_list = []
diff --git a/wqflask/wqflask/group_manager.py b/wqflask/wqflask/group_manager.py
index f29c0e4d..92a65112 100644
--- a/wqflask/wqflask/group_manager.py
+++ b/wqflask/wqflask/group_manager.py
@@ -12,6 +12,7 @@ from utility.redis_tools import get_user_groups, get_group_info, save_user, crea
 from utility.logger import getLogger
 logger = getLogger(__name__)
 
+
 @app.route("/groups/manage", methods=('GET', 'POST'))
 def manage_groups():
    params = request.form if request.form else request.args
@@ -21,6 +22,7 @@ def manage_groups():
       admin_groups, member_groups = get_user_groups(g.user_session.user_id)
       return render_template("admin/group_manager.html", admin_groups=admin_groups, member_groups=member_groups)
 
+
 @app.route("/groups/view", methods=('GET', 'POST'))
 def view_group():
    params = request.form if request.form else request.args
@@ -58,6 +60,7 @@ def view_group():
 
    return render_template("admin/view_group.html", group_info=group_info, admins=admins_info, members=members_info, user_is_admin=user_is_admin, resources=resources_info)
 
+
 @app.route("/groups/remove", methods=('POST',))
 def remove_groups():
    group_ids_to_remove = request.form['selected_group_ids']
@@ -66,6 +69,7 @@ def remove_groups():
 
    return redirect(url_for('manage_groups'))
 
+
 @app.route("/groups/remove_users", methods=('POST',))
 def remove_users():
    group_id = request.form['group_id']
@@ -77,6 +81,7 @@ def remove_users():
 
    return redirect(url_for('view_group', id=group_id))
 
+
 @app.route("/groups/add_<path:user_type>", methods=('POST',))
 def add_users(user_type='members'):
    group_id = request.form['group_id']
@@ -89,6 +94,7 @@ def add_users(user_type='members'):
 
    return redirect(url_for('view_group', id=group_id))
 
+
 @app.route("/groups/change_name", methods=('POST',))
 def change_name():
    group_id = request.form['group_id']
@@ -97,6 +103,7 @@ def change_name():
 
    return new_name
 
+
 @app.route("/groups/create", methods=('GET', 'POST'))
 def add_or_edit_group():
    params = request.form if request.form else request.args
@@ -125,6 +132,8 @@ def add_or_edit_group():
       return render_template("admin/create_group.html")
 
 # ZS: Will integrate this later, for now just letting users be added directly
+
+
 def send_group_invites(group_id, user_email_list=[], user_type="members"):
    for user_email in user_email_list:
       user_details = get_user_by_unique_column("email_address", user_email)
diff --git a/wqflask/wqflask/gsearch.py b/wqflask/wqflask/gsearch.py
index 8cb81dcc..a21dae84 100644
--- a/wqflask/wqflask/gsearch.py
+++ b/wqflask/wqflask/gsearch.py
@@ -18,6 +18,7 @@ from utility.type_checking import is_float, is_int, is_str, get_float, get_int,
 from utility.logger import getLogger
 logger = getLogger(__name__)
 
+
 class GSearch:
 
     def __init__(self, kw):
diff --git a/wqflask/wqflask/heatmap/heatmap.py b/wqflask/wqflask/heatmap/heatmap.py
index f8ef7028..0b477446 100644
--- a/wqflask/wqflask/heatmap/heatmap.py
+++ b/wqflask/wqflask/heatmap/heatmap.py
@@ -14,6 +14,7 @@ Redis = Redis()
 
 logger = getLogger(__name__)
 
+
 class Heatmap:
 
     def __init__(self, start_vars, temp_uuid):
@@ -132,6 +133,7 @@ class Heatmap:
                 else:
                     self.trait_results[this_trait.name].append(float(qtl['lrs_value']))
 
+
 def gen_pheno_txt_file(samples, vals, filename):
     """Generates phenotype file for GEMMA"""
 
@@ -151,6 +153,7 @@ def gen_pheno_txt_file(samples, vals, filename):
         values_string = "\t".join(filtered_vals_list)
         outfile.write(values_string)
 
+
 def parse_reaper_output(gwa_filename):
     included_markers = []
     p_values = []
diff --git a/wqflask/wqflask/interval_analyst/GeneUtil.py b/wqflask/wqflask/interval_analyst/GeneUtil.py
index 9779878e..8dd1c7c0 100644
--- a/wqflask/wqflask/interval_analyst/GeneUtil.py
+++ b/wqflask/wqflask/interval_analyst/GeneUtil.py
@@ -4,6 +4,8 @@ from flask import Flask, g
 
 # Just return a list of dictionaries
 # each dictionary contains sub-dictionary
+
+
 def loadGenes(chrName, diffCol, startMb, endMb, species='mouse'):
 	fetchFields = ['SpeciesId', 'Id', 'GeneSymbol', 'GeneDescription', 'Chromosome', 'TxStart', 'TxEnd',
 	'Strand', 'GeneID', 'NM_ID', 'kgID', 'GenBankID', 'UnigenID', 'ProteinID', 'AlignID',
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index 3753d1ce..5c7b81dd 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -509,9 +509,6 @@ class DisplayMappingResults:
             self.graphHeight = self.graphHeight + 2 * (self.NR_INDIVIDUALS + 10) * self.EACH_GENE_HEIGHT
 # END HaplotypeAnalyst
 
-
-
-
         #########################
         # Get the sorting column
         #########################
@@ -1640,7 +1637,6 @@ class DisplayMappingResults:
                                                  geneYLocation + 2 *ind*self.EACH_GENE_HEIGHT + 2*self.EACH_GENE_HEIGHT*zoom)),
                                             outline=outlineColor, fill=fillColor)
 
-
                                     COORDS = "%d, %d, %d, %d" % (geneStartPix, geneYLocation + ind * self.EACH_GENE_HEIGHT, geneEndPix + 1, (geneYLocation + ind * self.EACH_GENE_HEIGHT))
                                     TITLE = "Strain: %s, marker (%s) \n Position  %2.3f Mb." % (samplelist[k], _chr[j].name, float(txStart))
                                     HREF = ''
@@ -1663,7 +1659,6 @@ class DisplayMappingResults:
                                             geneYLocation + 7 + 2*ind*self.EACH_GENE_HEIGHT*zoom)),
                                         fill= mylineColor, width=zoom * (self.EACH_GENE_HEIGHT + 2))
 
-
                             if lastGene == 0:
                                 draw_rotated_text(
                                     canvas, text="%s" % (_chr[j].name),
@@ -2085,7 +2080,6 @@ class DisplayMappingResults:
         im_drawer.line(xy=((xLeftOffset, yZero), (xLeftOffset + plotWidth, yZero)),
                        fill=BLACK, width=X_AXIS_THICKNESS)  # Draw the X axis itself
 
-
     def drawQTL(self, canvas, drawAreaHeight, gifmap, plotXScale, offset=(40, 120, 80, 10), zoom=1, startMb= None, endMb = None):
         im_drawer = ImageDraw.Draw(canvas)
         xLeftOffset, xRightOffset, yTopOffset, yBottomOffset = offset
@@ -2427,7 +2421,6 @@ class DisplayMappingResults:
 
                 yLRS = yZero - (item / LRS_LOD_Max) * LRSHeightThresh
 
-
                 if 'lrs_value' in qtlresult:
                     if self.LRS_LOD == "LOD" or self.LRS_LOD == "-logP":
                         if qtlresult['lrs_value'] > 460 or qtlresult['lrs_value'] == 'inf':
@@ -2621,7 +2614,6 @@ class DisplayMappingResults:
                                 # , clipX=(xLeftOffset, xLeftOffset + plotWidth)
                             )
 
-
         # draw additive scale
         if not self.multipleInterval and self.additiveChecked:
             additiveScaleFont = ImageFont.truetype(font=VERDANA_FILE, size=16 * zoom)
@@ -2653,7 +2645,6 @@ class DisplayMappingResults:
             xy=((xLeftOffset, yZero), (xLeftOffset, yTopOffset + 30 * (zoom - 1))),
             fill=self.LRS_COLOR, width=1 * zoom)  # the blue line running up the y axis
 
-
     def drawGraphBackground(self, canvas, gifmap, offset=(80, 120, 80, 50), zoom=1, startMb= None, endMb = None):
         # conditions
         # multiple Chromosome view
diff --git a/wqflask/wqflask/marker_regression/plink_mapping.py b/wqflask/wqflask/marker_regression/plink_mapping.py
index e6c78536..22a50bb8 100644
--- a/wqflask/wqflask/marker_regression/plink_mapping.py
+++ b/wqflask/wqflask/marker_regression/plink_mapping.py
@@ -8,11 +8,11 @@ from utility.tools import flat_files, PLINK_COMMAND
 import utility.logger
 logger = utility.logger.getLogger(__name__)
 
+
 def run_plink(this_trait, dataset, species, vals, maf):
     plink_output_filename = webqtlUtil.genRandStr(f"{dataset.group.name}_{this_trait.name}_")
     gen_pheno_txt_file(dataset, vals)
 
-    
     plink_command = f"{PLINK_COMMAND}  --noweb --bfile {flat_files('mapping')}/{dataset.group.name} --no-pheno --no-fid --no-parents --no-sex --maf {maf} --out { TMPDIR}{plink_output_filename} --assoc "
     logger.debug("plink_command:", plink_command)
 
@@ -25,6 +25,7 @@ def run_plink(this_trait, dataset, species, vals, maf):
 
     return dataset.group.markers.markers
 
+
 def gen_pheno_txt_file(this_dataset, vals):
     """Generates phenotype file for GEMMA/PLINK"""
 
@@ -42,6 +43,7 @@ def gen_pheno_txt_file(this_dataset, vals):
                 this_val = vals[i]
             outfile.write("0 " + line[1] + " " + line[2] + " " + line[3] + " " + line[4] + " " + str(this_val) + "\n")
 
+
 def gen_pheno_txt_file_plink(this_trait, dataset, vals, pheno_filename=''):
     ped_sample_list = get_samples_from_ped_file(dataset)
     output_file = open(f"{TMPDIR}{pheno_filename}.txt", "wb")
@@ -77,6 +79,8 @@ def gen_pheno_txt_file_plink(this_trait, dataset, vals, pheno_filename=''):
     output_file.close()
 
 # get strain name from ped file in order
+
+
 def get_samples_from_ped_file(dataset):
     ped_file = open(f"{flat_files('mapping')}{dataset.group.name}.ped", "r")
     line = ped_file.readline()
@@ -93,6 +97,7 @@ def get_samples_from_ped_file(dataset):
 
     return sample_list
 
+
 def parse_plink_output(output_filename, species):
     plink_results = {}
 
@@ -154,6 +159,8 @@ def parse_plink_output(output_filename, species):
 # function: convert line from str to list;
 # output: lineList list
 #######################################################
+
+
 def build_line_list(line=""):
     line_list = line.strip().split(' ')  # irregular number of whitespaces between columns
     line_list = [item for item in line_list if item != '']
diff --git a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
index dd044cb0..313c40ca 100644
--- a/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
+++ b/wqflask/wqflask/marker_regression/qtlreaper_mapping.py
@@ -8,6 +8,7 @@ from utility.tools import flat_files, REAPER_COMMAND, TEMPDIR
 import utility.logger
 logger = utility.logger.getLogger(__name__)
 
+
 def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boot_check, num_bootstrap, do_control, control_marker, manhattan_plot, first_run=True, output_files=None):
     """Generates p-values for each marker using qtlreaper"""
 
@@ -73,6 +74,7 @@ def run_reaper(this_trait, this_dataset, samples, vals, json_data, num_perm, boo
     return (marker_obs, permu_vals, suggestive, significant, bootstrap_vals, 
         [output_filename, permu_filename, bootstrap_filename])
 
+
 def gen_pheno_txt_file(samples, vals, trait_filename):
     """Generates phenotype file for GEMMA"""
 
@@ -92,6 +94,7 @@ def gen_pheno_txt_file(samples, vals, trait_filename):
         values_string = "\t".join(filtered_vals_list)
         outfile.write(values_string)
 
+
 def parse_reaper_output(gwa_filename, permu_filename, bootstrap_filename):
     included_markers = []
     p_values = []
@@ -163,6 +166,7 @@ def parse_reaper_output(gwa_filename, permu_filename, bootstrap_filename):
 
     return marker_obs, permu_vals, bootstrap_vals
 
+
 def run_original_reaper(this_trait, dataset, samples_before, trait_vals, json_data, num_perm, bootCheck, num_bootstrap, do_control, control_marker, manhattan_plot):
     genotype = dataset.group.read_genotype_file(use_reaper=True)
 
@@ -255,6 +259,7 @@ def run_original_reaper(this_trait, dataset, samples_before, trait_vals, json_da
         qtl_results.append(qtl)
     return qtl_results, json_data, perm_output, suggestive, significant, bootstrap_results
 
+
 def natural_sort(marker_list):
     """
     Function to naturally sort numbers + strings, adopted from user Mark Byers here: https://stackoverflow.com/questions/4836710/does-python-have-a-built-in-function-for-string-natural-sort
diff --git a/wqflask/wqflask/marker_regression/rqtl_mapping.py b/wqflask/wqflask/marker_regression/rqtl_mapping.py
index 2bd94512..588600f5 100644
--- a/wqflask/wqflask/marker_regression/rqtl_mapping.py
+++ b/wqflask/wqflask/marker_regression/rqtl_mapping.py
@@ -16,6 +16,8 @@ import utility.logger
 logger = utility.logger.getLogger(__name__)
 
 # Get a trait's type (numeric, categorical, etc) from the DB
+
+
 def get_trait_data_type(trait_db_string):
     logger.info("get_trait_data_type");
     the_query = "SELECT value FROM TraitMetadata WHERE type='trait_data_type'"
@@ -133,6 +135,7 @@ def run_rqtl_geno(vals, samples, dataset, mapping_scale, method, model, permChec
         else:
             return process_rqtl_results(result_data_frame, dataset.group.species)
 
+
 def generate_cross_from_rdata(dataset):
     rdata_location = locate(dataset.group.name + ".RData", "genotype/rdata")
     ro.r("""
@@ -143,6 +146,7 @@ def generate_cross_from_rdata(dataset):
        }
     """ % (rdata_location))
 
+
 def generate_cross_from_geno(dataset, scale_units):        # TODO: Need to figure out why some genofiles have the wrong format and don't convert properly
 
     ro.r("""
@@ -187,6 +191,7 @@ def generate_cross_from_geno(dataset, scale_units):        # TODO: Need to figur
       }
     """ % (dataset.group.genofile, scale_units))
 
+
 def add_perm_strata(cross, perm_strata):
     col_string = 'c("the_strata")'
     perm_strata_string = "c("
@@ -201,6 +206,7 @@ def add_perm_strata(cross, perm_strata):
 
     return cross, strata_ob
 
+
 def sanitize_rqtl_phenotype(vals):
     pheno_as_string = "c("
     for i, val in enumerate(vals):
@@ -218,6 +224,7 @@ def sanitize_rqtl_phenotype(vals):
 
     return pheno_as_string
 
+
 def sanitize_rqtl_names(vals):
     pheno_as_string = "c("
     for i, val in enumerate(vals):
@@ -235,12 +242,14 @@ def sanitize_rqtl_names(vals):
 
     return pheno_as_string
 
+
 def add_phenotype(cross, pheno_as_string, col_name):
     ro.globalenv["the_cross"] = cross
     ro.r('pheno <- data.frame(pull.pheno(the_cross))')
     ro.r('the_cross$pheno <- cbind(pheno, ' + col_name + ' = as.numeric(' + pheno_as_string + '))')
     return ro.r["the_cross"]
 
+
 def add_categorical_covar(cross, covar_as_string, i):
     ro.globalenv["the_cross"] = cross
     logger.info("cross set"); 
@@ -275,12 +284,14 @@ def add_names(cross, names_as_string, col_name):
     ro.r('the_cross$pheno <- cbind(pheno, ' + col_name + ' = ' + names_as_string + ')')
     return ro.r["the_cross"]
 
+
 def pull_var(var_name, cross, var_string):
     ro.globalenv["the_cross"] = cross
     ro.r(var_name + ' <- pull.pheno(the_cross, ' + var_string + ')')
 
     return ro.r[var_name]
 
+
 def add_cofactors(cross, this_dataset, covariates, samples):
     ro.numpy2ri.activate()
 
@@ -341,6 +352,7 @@ def add_cofactors(cross, this_dataset, covariates, samples):
     covars_ob = pull_var("trait_covars", cross, covar_name_string)
     return cross, covars_ob
 
+
 def create_marker_covariates(control_marker, cross):
     ro.globalenv["the_cross"] = cross
     ro.r('genotypes <- pull.geno(the_cross)')                             # Get the genotype matrix
@@ -358,6 +370,7 @@ def create_marker_covariates(control_marker, cross):
     # TODO: Create a design matrix from the marker covars for the markers in case of an F2, 4way, etc
     return ro.r["marker_covars"]
 
+
 def process_pair_scan_results(result):
     pair_scan_results = []
 
@@ -374,6 +387,7 @@ def process_pair_scan_results(result):
 
     return pair_scan_results
 
+
 def process_rqtl_perm_results(num_perm, results):
     perm_vals = []
     for line in str(results).split("\n")[1:(num_perm + 1)]:
@@ -386,6 +400,7 @@ def process_rqtl_perm_results(num_perm, results):
 
     return perm_output, suggestive, significant
 
+
 def process_rqtl_results(result, species_name):        # TODO: how to make this a one liner and not copy the stuff in a loop
     qtl_results = []
     output = [tuple([result[j][i] for j in range(result.ncol)]) for i in range(result.nrow)]
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index f1665570..31c58083 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -45,6 +45,7 @@ from base.webqtlConfig import TMPDIR, GENERATED_TEXT_DIR
 import utility.logger
 logger = utility.logger.getLogger(__name__)
 
+
 class RunMapping:
 
     def __init__(self, start_vars, temp_uuid):
@@ -504,6 +505,7 @@ class RunMapping:
             trimmed_genotype_data.append(new_genotypes)
         return trimmed_genotype_data
 
+
 def export_mapping_results(dataset, trait, markers, results_path, mapping_scale, score_type, transform, covariates, n_samples):
     with open(results_path, "w+") as output_file:
         output_file.write("Time/Date: " + datetime.datetime.now().strftime("%x / %X") + "\n")
@@ -564,6 +566,7 @@ def export_mapping_results(dataset, trait, markers, results_path, mapping_scale,
             if i < (len(markers) - 1):
                 output_file.write("\n")
 
+
 def trim_markers_for_figure(markers):
     if 'p_wald' in list(markers[0].keys()):
         score_type = 'p_wald'
@@ -624,6 +627,7 @@ def trim_markers_for_figure(markers):
                 filtered_markers.append(marker)
     return filtered_markers
 
+
 def trim_markers_for_table(markers):
     if 'lod_score' in list(markers[0].keys()):
         sorted_markers = sorted(markers, key=lambda k: k['lod_score'], reverse=True)
@@ -637,6 +641,7 @@ def trim_markers_for_table(markers):
     else:
         return sorted_markers
 
+
 def write_input_for_browser(this_dataset, gwas_results, annotations):
     file_base = this_dataset.group.name + "_" + ''.join(random.choice(string.ascii_uppercase + string.digits) for _ in range(6))
     gwas_filename = file_base + "_GWAS"
@@ -650,6 +655,7 @@ def write_input_for_browser(this_dataset, gwas_results, annotations):
 
     return [gwas_filename, annot_filename]
 
+
 def geno_db_exists(this_dataset):
     geno_db_name = this_dataset.group.name + "Geno"
     try:
@@ -658,6 +664,7 @@ def geno_db_exists(this_dataset):
     except:
         return "False"
 
+
 def get_chr_lengths(mapping_scale, mapping_method, dataset, qtl_results):
     chr_lengths = []
     if mapping_scale == "physic":
@@ -696,6 +703,7 @@ def get_chr_lengths(mapping_scale, mapping_method, dataset, qtl_results):
 
     return chr_lengths
 
+
 def get_genofile_samplelist(dataset):
     genofile_samplelist = []
 
@@ -706,6 +714,7 @@ def get_genofile_samplelist(dataset):
 
     return genofile_samplelist
 
+
 def get_perm_strata(this_trait, sample_list, categorical_vars, used_samples):
     perm_strata_strings = []
     for sample in used_samples:
diff --git a/wqflask/wqflask/model.py b/wqflask/wqflask/model.py
index 8abd6516..d7c9ef95 100644
--- a/wqflask/wqflask/model.py
+++ b/wqflask/wqflask/model.py
@@ -14,6 +14,7 @@ from sqlalchemy.orm import relationship
 
 from wqflask.database import Base, init_db
 
+
 class User(Base):
     __tablename__ = "user"
     id = Column(Unicode(36), primary_key=True, default=lambda: str(uuid.uuid4()))
@@ -63,7 +64,6 @@ class User(Base):
             print("Couldn't display_num_collections:", why)
             return ""
 
-
     def get_collection_by_name(self, collection_name):
         try:
             collect = self.user_collections.filter_by(name=collection_name).first()
@@ -83,7 +83,6 @@ class User(Base):
     def login_count(self):
         return self.logins.filter_by(successful=True).count()
 
-
     @property
     def confirmed_at(self):
         if self.confirmed:
@@ -116,6 +115,7 @@ class User(Base):
         except IndexError:
             return None
 
+
 class Login(Base):
     __tablename__ = "login"
     id = Column(Unicode(36), primary_key=True, default=lambda: str(uuid.uuid4()))
@@ -134,6 +134,7 @@ class Login(Base):
 
 ##################################################################################################
 
+
 class UserCollection(Base):
     __tablename__ = "user_collection"
     id = Column(Unicode(36), primary_key=True, default=lambda: str(uuid.uuid4()))
@@ -158,12 +159,14 @@ class UserCollection(Base):
     def members_as_set(self):
         return set(json.loads(self.members))
 
+
 def display_collapsible(number):
     if number:
         return number
     else:
         return ""
 
+
 def user_uuid():
     """Unique cookie for a user"""
     user_uuid = request.cookies.get('user_uuid')
diff --git a/wqflask/wqflask/network_graph/network_graph.py b/wqflask/wqflask/network_graph/network_graph.py
index 93785a3a..e089643e 100644
--- a/wqflask/wqflask/network_graph/network_graph.py
+++ b/wqflask/wqflask/network_graph/network_graph.py
@@ -27,6 +27,7 @@ from utility import helper_functions
 from utility import corr_result_helpers
 from utility.tools import GN2_BRANCH_URL
 
+
 class NetworkGraph:
 
     def __init__(self, start_vars):
diff --git a/wqflask/wqflask/news.py b/wqflask/wqflask/news.py
index 861a93f2..e262dd51 100644
--- a/wqflask/wqflask/news.py
+++ b/wqflask/wqflask/news.py
@@ -1,5 +1,6 @@
 from flask import g
 
+
 class News:
 
     def __init__(self):
diff --git a/wqflask/wqflask/parser.py b/wqflask/wqflask/parser.py
index dfd374e2..6b836e20 100644
--- a/wqflask/wqflask/parser.py
+++ b/wqflask/wqflask/parser.py
@@ -24,6 +24,7 @@ from pprint import pformat as pf
 from utility.logger import getLogger
 logger = getLogger(__name__)
 
+
 def parse(pstring):
     """
 
diff --git a/wqflask/wqflask/pbkdf2.py b/wqflask/wqflask/pbkdf2.py
index 6346df03..1a965fc5 100644
--- a/wqflask/wqflask/pbkdf2.py
+++ b/wqflask/wqflask/pbkdf2.py
@@ -4,6 +4,8 @@ from werkzeug.security import safe_str_cmp as ssc
 
 # Replace this because it just wraps around Python3's internal
 # functions. Added this during migration.
+
+
 def pbkdf2_hex(data, salt, iterations=1000, keylen=24, hashfunc="sha1"):
     """Wrapper function of python's hashlib.pbkdf2_hmac.
     """
diff --git a/wqflask/wqflask/resource_manager.py b/wqflask/wqflask/resource_manager.py
index a1fe0f8f..4591710c 100644
--- a/wqflask/wqflask/resource_manager.py
+++ b/wqflask/wqflask/resource_manager.py
@@ -11,6 +11,7 @@ from utility.redis_tools import get_resource_info, get_group_info, get_groups_li
 from utility.logger import getLogger
 logger = getLogger(__name__)
 
+
 @app.route("/resources/manage", methods=('GET', 'POST'))
 def manage_resource():
     params = request.form if request.form else request.args
@@ -40,6 +41,7 @@ def manage_resource():
 
         return render_template("admin/manage_resource.html", owner_name=owner_display_name, resource_id=resource_id, resource_info=resource_info, default_mask=default_mask, group_masks=group_masks_with_names, admin_status=admin_status)
 
+
 @app.route("/search_for_users", methods=('POST',))
 def search_for_user():
     params = request.form
@@ -49,6 +51,7 @@ def search_for_user():
 
     return json.dumps(user_list)
 
+
 @app.route("/search_for_groups", methods=('POST',))
 def search_for_groups():
     params = request.form
@@ -65,6 +68,7 @@ def search_for_groups():
 
     return json.dumps(group_list)
 
+
 @app.route("/resources/change_owner", methods=('POST',))
 def change_owner():
     resource_id = request.form['resource_id']
@@ -81,6 +85,7 @@ def change_owner():
     else:
         return render_template("admin/change_resource_owner.html", resource_id=resource_id)
 
+
 @app.route("/resources/change_default_privileges", methods=('POST',))
 def change_default_privileges():
     resource_id = request.form['resource_id']
@@ -99,6 +104,7 @@ def change_default_privileges():
     else:
         return redirect(url_for("no_access_page"))
 
+
 @app.route("/resources/add_group", methods=('POST',))
 def add_group_to_resource():
     resource_id = request.form['resource_id']
@@ -125,6 +131,7 @@ def add_group_to_resource():
     else:
         return redirect(url_for("no_access_page"))
 
+
 def get_group_names(group_masks):
     group_masks_with_names = {}
     for group_id, group_mask in list(group_masks.items()):
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index 16eb1864..ed5f9bad 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -24,6 +24,7 @@ from utility.type_checking import is_str
 from utility.logger import getLogger
 logger = getLogger(__name__)
 
+
 class SearchResultPage:
     #maxReturn = 3000
 
@@ -270,6 +271,7 @@ class SearchResultPage:
         else:
             return None
 
+
 def get_GO_symbols(a_search):
     query = """SELECT genes
                FROM GORef
@@ -287,6 +289,7 @@ def get_GO_symbols(a_search):
 
     return new_terms
 
+
 def insert_newlines(string, every=64):
     """ This is because it is seemingly impossible to change the width of the description column, so I'm just manually adding line breaks """
     lines = []
@@ -294,6 +297,7 @@ def insert_newlines(string, every=64):
         lines.append(string[i:i + every])
     return '\n'.join(lines)
 
+
 def get_aliases(symbol_list, species):
 
     updated_symbols = []
diff --git a/wqflask/wqflask/send_mail.py b/wqflask/wqflask/send_mail.py
index 86e8a558..299c866a 100644
--- a/wqflask/wqflask/send_mail.py
+++ b/wqflask/wqflask/send_mail.py
@@ -8,10 +8,12 @@ Redis = StrictRedis()
 
 import mailer
 
+
 def timestamp():
     ts = datetime.datetime.utcnow()
     return ts.isoformat()
 
+
 def main():
     while True:
         print("I'm alive!")
@@ -31,7 +33,6 @@ def main():
             process_message(msg)
 
 
-
 def process_message(msg):
     msg = json.loads(msg)
 
diff --git a/wqflask/wqflask/server_side.py b/wqflask/wqflask/server_side.py
index 48761fa0..8b3a4faa 100644
--- a/wqflask/wqflask/server_side.py
+++ b/wqflask/wqflask/server_side.py
@@ -1,7 +1,6 @@
 # handles server side table processing
 
 
-
 class ServerSideTable:
     """
         This class is used to do server-side processing
diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py
index 388f831f..496dee57 100644
--- a/wqflask/wqflask/show_trait/SampleList.py
+++ b/wqflask/wqflask/show_trait/SampleList.py
@@ -8,6 +8,7 @@ from pprint import pformat as pf
 from utility import Plot
 from utility import Bunch
 
+
 class SampleList:
     def __init__(self,
                  dataset,
diff --git a/wqflask/wqflask/show_trait/export_trait_data.py b/wqflask/wqflask/show_trait/export_trait_data.py
index 379b746c..f0fcd27d 100644
--- a/wqflask/wqflask/show_trait/export_trait_data.py
+++ b/wqflask/wqflask/show_trait/export_trait_data.py
@@ -5,6 +5,7 @@ from functools import cmp_to_key
 from base.trait import create_trait
 from base import data_set
 
+
 def export_sample_table(targs):
 
     sample_data = json.loads(targs['export_data'])
@@ -28,6 +29,7 @@ def export_sample_table(targs):
 
     return trait_name, final_sample_data
 
+
 def get_export_metadata(trait_id, dataset_name):
     dataset = data_set.create_dataset(dataset_name)
     this_trait = create_trait(dataset=dataset,
@@ -64,6 +66,7 @@ def dict_to_sorted_list(dictionary):
     sorted_values = [item[1] for item in sorted_list]
     return sorted_values
 
+
 def cmp_samples(a, b):
     if b[0] == 'name':
         return 1
diff --git a/wqflask/wqflask/snp_browser/snp_browser.py b/wqflask/wqflask/snp_browser/snp_browser.py
index 7a0df94b..e5c67165 100644
--- a/wqflask/wqflask/snp_browser/snp_browser.py
+++ b/wqflask/wqflask/snp_browser/snp_browser.py
@@ -9,6 +9,7 @@ logger = getLogger(__name__)
 from base import species
 from base import webqtlConfig
 
+
 class SnpBrowser:
 
     def __init__(self, start_vars):
@@ -472,7 +473,6 @@ class SnpBrowser:
                 base_color_dict = {"A": "#C33232", "C": "#1569C7", "T": "#CFCF32", "G": "#32C332", 
                                    "t": "#FF6", "c": "#5CB3FF", "a": "#F66", "g": "#CF9", ":": "#FFFFFF", "-": "#FFFFFF", "?": "#FFFFFF"}
 
-
                 the_bases = []
                 for j, item in enumerate(allele_value_list):
                     if item and isinstance(item, str):
@@ -641,6 +641,7 @@ class SnpBrowser:
         # for i in range(n_click):
         #    href = url_for('snp_browser', first_run="false", chosen_strains_mouse=self.chosen_strains_mouse, chosen_strains_rat=self.chosen_strains_rat, variant=self.variant_type, species=self.species_name, gene_name=self.gene_name, chr=self.chr, start_mb=self.start_mb, end_mb=self.end_mb, limit_strains=self.limit_strains, domain=self.domain, function=self.function, criteria=self.criteria, score=self.score, diff_alleles=self.diff_alleles)
 
+
 def get_browser_sample_lists(species_id=1):
     strain_lists = {}
     mouse_strain_list = []
@@ -660,6 +661,7 @@ def get_browser_sample_lists(species_id=1):
 
     return strain_lists
 
+
 def get_header_list(variant_type, strains, species=None, empty_columns=None):
     if species == "Mouse":
         strain_list = strains['mouse']
@@ -715,6 +717,7 @@ def get_header_list(variant_type, strains, species=None, empty_columns=None):
 
     return header_fields, empty_field_count, header_data_names
 
+
 def get_effect_details_by_category(effect_name=None, effect_value=None):
     gene_list = []
     transcript_list = []
@@ -764,6 +767,7 @@ def get_effect_details_by_category(effect_name=None, effect_value=None):
 
     return [gene_list, transcript_list, exon_list, function_list, function_detail_list]
 
+
 def get_effect_info(effect_list):
     domain = ""
     effect_detail_list = []
@@ -836,6 +840,7 @@ def get_effect_info(effect_list):
 
     return effect_info_dict
 
+
 def get_gene_id(species_id, gene_name):
     query = """
                 SELECT
@@ -853,6 +858,7 @@ def get_gene_id(species_id, gene_name):
     else:
         return ""
 
+
 def get_gene_id_name_dict(species_id, gene_name_list):
     gene_id_name_dict = {}
     if len(gene_name_list) == 0:
@@ -877,6 +883,7 @@ def get_gene_id_name_dict(species_id, gene_name_list):
 
     return gene_id_name_dict
 
+
 def check_if_in_gene(species_id, chr, mb):
     if species_id != 0:  # ZS: Check if this is necessary
         query = """SELECT geneId, geneSymbol
diff --git a/wqflask/wqflask/submit_bnw.py b/wqflask/wqflask/submit_bnw.py
index 4ad6f9e3..b21a88cc 100644
--- a/wqflask/wqflask/submit_bnw.py
+++ b/wqflask/wqflask/submit_bnw.py
@@ -5,5 +5,6 @@ from utility import helper_functions
 import utility.logger
 logger = utility.logger.getLogger(__name__)
 
+
 def get_bnw_input(start_vars):
     logger.debug("BNW VARS:", start_vars)
diff --git a/wqflask/wqflask/update_search_results.py b/wqflask/wqflask/update_search_results.py
index 08b4f9f5..07073d6a 100644
--- a/wqflask/wqflask/update_search_results.py
+++ b/wqflask/wqflask/update_search_results.py
@@ -10,6 +10,7 @@ from utility.benchmark import Bench
 from utility.logger import getLogger
 logger = getLogger(__name__)
 
+
 class GSearch:
 
     def __init__(self, kw):
diff --git a/wqflask/wqflask/user_login.py b/wqflask/wqflask/user_login.py
index 3f5b43ee..2a2f8484 100644
--- a/wqflask/wqflask/user_login.py
+++ b/wqflask/wqflask/user_login.py
@@ -29,9 +29,11 @@ from utility.tools import SMTP_CONNECT, SMTP_USERNAME, SMTP_PASSWORD, LOG_SQL_AL
 
 THREE_DAYS = 60 * 60 * 24 * 3
 
+
 def timestamp():
     return datetime.datetime.utcnow().isoformat()
 
+
 def basic_info():
     return dict(timestamp=timestamp(),
                 ip_address=request.remote_addr,
@@ -54,6 +56,7 @@ def encode_password(pass_gen_fields, unencrypted_password):
 
     return pass_gen_fields
 
+
 def set_password(password):
     pass_gen_fields = {
       "unencrypted_password": password,
@@ -71,6 +74,7 @@ def set_password(password):
 
     return encoded_password
 
+
 def get_signed_session_id(user):
     session_id = str(uuid.uuid4())
 
@@ -109,6 +113,7 @@ def get_signed_session_id(user):
     
     return session_id_signed
 
+
 def send_email(toaddr, msg, fromaddr="no-reply@genenetwork.org"):
     """Send an E-mail through SMTP_CONNECT host. If SMTP_USERNAME is not
     'UNKNOWN' TLS is used
@@ -125,6 +130,7 @@ def send_email(toaddr, msg, fromaddr="no-reply@genenetwork.org"):
         server.quit()
     logger.info("Successfully sent email to " + toaddr)
 
+
 def send_verification_email(user_details, template_name="email/user_verification.txt", key_prefix="verification_code", subject = "GeneNetwork e-mail verification"):
     verification_code = str(uuid.uuid4())
     key = key_prefix + ":" + verification_code
@@ -139,12 +145,14 @@ def send_verification_email(user_details, template_name="email/user_verification
     send_email(recipient, subject, body)
     return {"recipient": recipient, "subject": subject, "body": body}
 
+
 def send_invitation_email(user_email, temp_password, template_name="email/user_invitation.txt", subject= "You've been added to a GeneNetwork user group"):
     recipient = user_email
     body = render_template(template_name, temp_password)
     send_email(recipient, subject, body)
     return {"recipient": recipient, "subject": subject, "body": body}
 
+
 @app.route("/manage/verify_email")
 def verify_email():
     if 'code' in request.args:
@@ -160,6 +168,7 @@ def verify_email():
         else:
             flash("Invalid code: Password reset code does not exist or might have expired!", "error")
 
+
 @app.route("/n/login", methods=('GET', 'POST'))
 def login():
     params = request.form if request.form else request.args
@@ -232,6 +241,7 @@ def login():
 
                 return response
 
+
 @app.route("/n/login/github_oauth2", methods=('GET', 'POST'))
 def github_oauth2():
     from utility.tools import GITHUB_CLIENT_ID, GITHUB_CLIENT_SECRET, GITHUB_AUTH_URL
@@ -264,12 +274,14 @@ def github_oauth2():
     url = "/n/login?type=github&uid=" + user_details["user_id"]
     return redirect(url)
 
+
 def get_github_user_details(access_token):
     from utility.tools import GITHUB_API_URL
     result = requests.get(GITHUB_API_URL, headers={'Authorization': 'token ' + access_token}).content
 
     return json.loads(result)
 
+
 @app.route("/n/login/orcid_oauth2", methods=('GET', 'POST'))
 def orcid_oauth2():
     from uuid import uuid4
@@ -308,6 +320,7 @@ def orcid_oauth2():
         flash("There was an error getting code from ORCID")
     return redirect(url)
 
+
 def get_github_user_details(access_token):
     from utility.tools import GITHUB_API_URL
     result = requests.get(GITHUB_API_URL, headers={'Authorization': 'token ' + access_token}).content
@@ -325,6 +338,7 @@ def logout():
     response.set_cookie(UserSession.user_cookie_name, '', expires=0)
     return response
 
+
 @app.route("/n/forgot_password", methods=['GET'])
 def forgot_password():
     """Entry point for forgotten password"""
@@ -333,6 +347,7 @@ def forgot_password():
     print("ERRORS: ", errors)
     return render_template("new_security/forgot_password.html", errors=errors)
 
+
 def send_forgot_password_email(verification_email):
     from email.mime.multipart import MIMEMultipart
     from email.mime.text import MIMEText
@@ -365,6 +380,7 @@ def send_forgot_password_email(verification_email):
 
     return subject
 
+
 @app.route("/n/forgot_password_submit", methods=('POST',))
 def forgot_password_submit():
     """When a forgotten password form is submitted we get here"""
@@ -386,6 +402,7 @@ def forgot_password_submit():
         flash("You MUST provide an email", "alert-danger")
         return redirect(url_for("forgot_password"))
 
+
 @app.route("/n/password_reset", methods=['GET'])
 def password_reset():
     """Entry point after user clicks link in E-mail"""
@@ -405,6 +422,7 @@ def password_reset():
     else:
         return redirect(url_for("login"))
 
+
 @app.route("/n/password_reset_step2", methods=('POST',))
 def password_reset_step2():
     """Handle confirmation E-mail for password reset"""
@@ -422,6 +440,7 @@ def password_reset_step2():
     flash("Password changed successfully. You can now sign in.", "alert-info")
     return redirect(url_for('login'))
 
+
 def register_user(params):
         thank_you_mode = False
         errors = []
@@ -461,6 +480,7 @@ def register_user(params):
 
         return errors
 
+
 @app.route("/n/register", methods=('GET', 'POST'))
 def register():
     errors = []
@@ -478,6 +498,7 @@ def register():
 
     return render_template("new_security/register_user.html", values=params, errors=errors)
 
+
 @app.errorhandler(401)
 def unauthorized(error):
     return redirect(url_for('login'))
diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py
index 013920f9..a9bd65e6 100644
--- a/wqflask/wqflask/user_manager.py
+++ b/wqflask/wqflask/user_manager.py
@@ -151,6 +151,7 @@ def verify_cookie(cookie):
     assert the_signature == actual_hmac_creation(the_uuid), "Uh-oh, someone tampering with the cookie?"
     return the_uuid
 
+
 def create_signed_cookie():
     the_uuid = str(uuid.uuid4())
     signature = actual_hmac_creation(the_uuid)
@@ -158,6 +159,7 @@ def create_signed_cookie():
     logger.debug("uuid_signed:", uuid_signed)
     return the_uuid, uuid_signed
 
+
 class UserSession:
     """Logged in user handling"""
 
@@ -341,6 +343,7 @@ class UserSession:
         Redis.delete(self.cookie_name)
         logger.debug("At end of delete_session")
 
+
 @app.before_request
 def get_cookie():
     logger.info("@app.before_request get cookie")
@@ -348,16 +351,20 @@ def get_cookie():
     g.cookie_session = AnonUser()
 
 # @app.after_request
+
+
 def set_cookie(response):
     if not request.cookies.get(g.cookie_session.cookie_name):
         response.set_cookie(g.cookie_session.cookie_name, g.cookie_session.cookie)
     return response
 
+
 class UsersManager:
     def __init__(self):
         self.users = model.User.query.all()
         logger.debug("Users are:", self.users)
 
+
 class UserManager:
     def __init__(self, kw):
         self.user_id = kw['user_id']
@@ -419,6 +426,7 @@ class RegisterUser:
         self.user.registration_info = json.dumps(basic_info(), sort_keys=True)
         save_user(self.user.__dict__, self.user.user_id)
 
+
 def set_password(password, user):
     pwfields = Bunch()
 
@@ -476,6 +484,7 @@ class VerificationEmail:
                                verification_code=verification_code)
         send_email(to, subject, body)
 
+
 class ForgotPasswordEmail(VerificationEmail):
     template_name = "email/forgot_password.txt"
     key_prefix = "forgot_password_code"
@@ -496,7 +505,6 @@ class ForgotPasswordEmail(VerificationEmail):
 
         save_verification_code(toaddr, verification_code)
 
-
         subject = self.subject
         body = render_template(
             self.template_name,
@@ -530,6 +538,8 @@ def basic_info():
                 user_agent=request.headers.get('User-Agent'))
 
 # @app.route("/manage/verify_email")
+
+
 def verify_email():
     user = DecodeUser(VerificationEmail.key_prefix).user
     user.confirmed = json.dumps(basic_info(), sort_keys=True)
@@ -544,6 +554,8 @@ def verify_email():
     return response
 
 # @app.route("/n/password_reset", methods=['GET'])
+
+
 def password_reset():
     """Entry point after user clicks link in E-mail"""
     logger.debug("in password_reset request.url is:", request.url)
@@ -568,6 +580,8 @@ def password_reset():
         return redirect(url_for("login"))
 
 # @app.route("/n/password_reset_step2", methods=('POST',))
+
+
 def password_reset_step2():
     """Handle confirmation E-mail for password reset"""
     logger.debug("in password_reset request.url is:", request.url)
@@ -577,7 +591,6 @@ def password_reset_step2():
 
     logger.debug("locals are:", locals())
 
-
     user = Bunch()
     password = request.form['password']
     set_password(password, user)
@@ -589,6 +602,7 @@ def password_reset_step2():
 
     return response
 
+
 class DecodeUser:
 
     def __init__(self, code_prefix):
@@ -612,6 +626,8 @@ class DecodeUser:
         return model.User.query.get(data['id'])
 
 # @app.route("/n/login", methods=('GET', 'POST'))
+
+
 def login():
     lu = LoginUser()
     login_type = request.args.get("type")
@@ -622,6 +638,8 @@ def login():
         return lu.standard_login()
 
 # @app.route("/n/login/github_oauth2", methods=('GET', 'POST'))
+
+
 def github_oauth2():
     from utility.tools import GITHUB_CLIENT_ID, GITHUB_CLIENT_SECRET
     code = request.args.get("code")
@@ -646,6 +664,8 @@ def github_oauth2():
     return redirect(url)
 
 # @app.route("/n/login/orcid_oauth2", methods=('GET', 'POST'))
+
+
 def orcid_oauth2():
     from uuid import uuid4
     from utility.tools import ORCID_CLIENT_ID, ORCID_CLIENT_SECRET, ORCID_TOKEN_URL, ORCID_AUTH_URL
@@ -673,11 +693,13 @@ def orcid_oauth2():
         flash("There was an error getting code from ORCID")
     return redirect(url)
 
+
 def get_github_user_details(access_token):
     from utility.tools import GITHUB_API_URL
     result = requests.get(GITHUB_API_URL, params={"access_token": access_token})
     return result.json()
 
+
 class LoginUser:
     remember_time = 60 * 60 * 24 * 30  # One month in seconds
 
@@ -814,6 +836,8 @@ class LoginUser:
         db_session.commit()
 
 # @app.route("/n/logout")
+
+
 def logout():
     logger.debug("Logging out...")
     UserSession().delete_session()
@@ -833,6 +857,8 @@ def forgot_password():
     return render_template("new_security/forgot_password.html", errors=errors)
 
 # @app.route("/n/forgot_password_submit", methods=('POST',))
+
+
 def forgot_password_submit():
     """When a forgotten password form is submitted we get here"""
     params = request.form
@@ -853,10 +879,12 @@ def forgot_password_submit():
         flash("You MUST provide an email", "alert-danger")
         return redirect(url_for("forgot_password"))
 
+
 @app.errorhandler(401)
 def unauthorized(error):
     return redirect(url_for('login'))
 
+
 def is_redis_available():
     try:
         Redis.ping()
@@ -922,7 +950,6 @@ def register():
     params = None
     errors = None
 
-
     params = request.form if request.form else request.args
     params = params.to_dict(flat=True)
 
@@ -952,6 +979,7 @@ def url_for_hmac(endpoint, **values):
         combiner = "?"
     return url + combiner + "hm=" + hm
 
+
 def data_hmac(stringy):
     """Takes arbitray data string and appends :hmac so we know data hasn't been tampered with"""
     return stringy + ":" + actual_hmac_creation(stringy)
@@ -974,6 +1002,7 @@ def verify_url_hmac(url):
 
     assert hm == hmac, "Unexpected url (stage 3)"
 
+
 def actual_hmac_creation(stringy):
     """Helper function to create the actual hmac"""
 
@@ -986,6 +1015,7 @@ def actual_hmac_creation(stringy):
     hm = hm[:20]
     return hm
 
+
 app.jinja_env.globals.update(url_for_hmac=url_for_hmac,
                              data_hmac=data_hmac)
 
@@ -998,6 +1028,7 @@ app.jinja_env.globals.update(url_for_hmac=url_for_hmac,
 #                      Body=body))
 #     Redis.rpush("mail_queue", msg)
 
+
 def send_email(toaddr, msg, fromaddr="no-reply@genenetwork.org"):
     """Send an E-mail through SMTP_CONNECT host. If SMTP_USERNAME is not
     'UNKNOWN' TLS is used
@@ -1020,6 +1051,7 @@ def send_email(toaddr, msg, fromaddr="no-reply@genenetwork.org"):
         server.quit()
     logger.info("Successfully sent email to " + toaddr)
 
+
 class GroupsManager:
     def __init__(self, kw):
         self.datasets = create_datasets_list()
diff --git a/wqflask/wqflask/user_session.py b/wqflask/wqflask/user_session.py
index 78db7bd2..f0f0d60c 100644
--- a/wqflask/wqflask/user_session.py
+++ b/wqflask/wqflask/user_session.py
@@ -20,6 +20,7 @@ logger = getLogger(__name__)
 THREE_DAYS = 60 * 60 * 24 * 3
 THIRTY_DAYS = 60 * 60 * 24 * 30
 
+
 @app.before_request
 def get_user_session():
     logger.info("@app.before_request get_session")
@@ -30,6 +31,7 @@ def get_user_session():
         response.set_cookie('session_id_v2', '', expires=0)
         return response
 
+
 @app.after_request
 def set_user_session(response):
     if hasattr(g, 'user_session'):
@@ -37,6 +39,7 @@ def set_user_session(response):
             response.set_cookie(g.user_session.cookie_name, g.user_session.cookie)
     return response
 
+
 def verify_cookie(cookie):
     the_uuid, separator, the_signature = cookie.partition(':')
     assert len(the_uuid) == 36, "Is session_id a uuid?"
@@ -44,6 +47,7 @@ def verify_cookie(cookie):
     assert the_signature == hmac.hmac_creation(the_uuid), "Uh-oh, someone tampering with the cookie?"
     return the_uuid
 
+
 def create_signed_cookie():
     the_uuid = str(uuid.uuid4())
     signature = hmac.hmac_creation(the_uuid)
@@ -51,6 +55,7 @@ def create_signed_cookie():
     logger.debug("uuid_signed:", uuid_signed)
     return the_uuid, uuid_signed
 
+
 @app.route("/user/manage", methods=('GET', 'POST'))
 def manage_user():
     params = request.form if request.form else request.args
@@ -63,6 +68,7 @@ def manage_user():
 
     return render_template("admin/manage_user.html", user_details=user_details)
 
+
 class UserSession:
     """Logged in user handling"""
 
-- 
cgit v1.2.3


From 48ac21fda375b8255bec86e83496d730bb57ffff Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 12 Jul 2021 17:49:09 +0000
Subject: Encode user_id as bytestring if not already bytestring to account for
 some user_ids being stored as different encoding

---
 wqflask/utility/authentication_tools.py | 10 +++++++---
 1 file changed, 7 insertions(+), 3 deletions(-)

(limited to 'wqflask/utility/authentication_tools.py')

diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py
index 57dbf8ba..6802d689 100644
--- a/wqflask/utility/authentication_tools.py
+++ b/wqflask/utility/authentication_tools.py
@@ -11,7 +11,6 @@ from utility.redis_tools import (get_redis_conn,
                                  add_resource)
 Redis = get_redis_conn()
 
-
 def check_resource_availability(dataset, trait_id=None):
     # At least for now assume temporary entered traits are accessible
     if type(dataset) == str or dataset.type == "Temp":
@@ -133,12 +132,17 @@ def check_owner_or_admin(dataset=None, trait_id=None, resource_id=None):
         else:
             resource_id = get_resource_id(dataset, trait_id)
 
-    if g.user_session.user_id in Redis.smembers("super_users"):
+    try:
+        user_id = g.user_session.user_id.encode('utf-8')
+    except:
+        user_id = g.user_session.user_id
+
+    if user_id in Redis.smembers("super_users"):
         return "owner"
 
     resource_info = get_resource_info(resource_id)
     if resource_info:
-        if g.user_session.user_id == resource_info['owner_id']:
+        if user_id == resource_info['owner_id']:
             return "owner"
         else:
             return check_admin(resource_id)
-- 
cgit v1.2.3


From a05d0e4eb9412d9495a0f96980df27acb1526a03 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Fri, 22 Oct 2021 18:45:10 +0000
Subject: Replace hardcoded GN proxy URLs with one pulled from settings

---
 wqflask/utility/authentication_tools.py | 11 ++++++-----
 1 file changed, 6 insertions(+), 5 deletions(-)

(limited to 'wqflask/utility/authentication_tools.py')

diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py
index 6802d689..afea69e1 100644
--- a/wqflask/utility/authentication_tools.py
+++ b/wqflask/utility/authentication_tools.py
@@ -4,11 +4,12 @@ import requests
 from flask import g
 from base import webqtlConfig
 
-
 from utility.redis_tools import (get_redis_conn,
                                  get_resource_info,
                                  get_resource_id,
                                  add_resource)
+from utility.tools import GN_PROXY_URL
+
 Redis = get_redis_conn()
 
 def check_resource_availability(dataset, trait_id=None):
@@ -24,19 +25,19 @@ def check_resource_availability(dataset, trait_id=None):
     if resource_id:
         resource_info = get_resource_info(resource_id)
 
-        # ZS: If resource isn't already in redis, add it with default
+        # If resource isn't already in redis, add it with default
         # privileges
         if not resource_info:
             resource_info = add_new_resource(dataset, trait_id)
 
-    # ZS: Check if super-user - we should probably come up with some
+    # Check if super-user - we should probably come up with some
     # way to integrate this into the proxy
     if g.user_session.user_id in Redis.smembers("super_users"):
         return webqtlConfig.SUPER_PRIVILEGES
 
     response = None
 
-    the_url = "http://localhost:8080/available?resource={}&user={}".format(
+    the_url = GN_PROXY_URL + "available?resource={}&user={}".format(
         resource_id, g.user_session.user_id)
 
     try:
@@ -93,7 +94,7 @@ def get_group_code(dataset):
 
 
 def check_admin(resource_id=None):
-    the_url = "http://localhost:8080/available?resource={}&user={}".format(
+    the_url = GN_PROXY_URL + "available?resource={}&user={}".format(
         resource_id, g.user_session.user_id)
     try:
         response = json.loads(requests.get(the_url).content)['admin']
-- 
cgit v1.2.3


From 8ba81937fec81c7e9790db422a52d99f4234a194 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Mon, 18 Oct 2021 12:02:51 +0300
Subject: authentication_tools: Mark `check_owner_or_admin` as deprecated

Use the new auth proxy tools instead.
---
 wqflask/utility/authentication_tools.py | 2 ++
 1 file changed, 2 insertions(+)

(limited to 'wqflask/utility/authentication_tools.py')

diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py
index afea69e1..c4801c8c 100644
--- a/wqflask/utility/authentication_tools.py
+++ b/wqflask/utility/authentication_tools.py
@@ -1,6 +1,7 @@
 import json
 import requests
 
+from deprecated import deprecated
 from flask import g
 from base import webqtlConfig
 
@@ -126,6 +127,7 @@ def check_owner(dataset=None, trait_id=None, resource_id=None):
     return False
 
 
+@deprecated
 def check_owner_or_admin(dataset=None, trait_id=None, resource_id=None):
     if not resource_id:
         if dataset.type == "Temp":
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