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/maintenance/set_resource_defaults.py | 155 +++++++++++++++++++++++++++
 1 file changed, 155 insertions(+)
 create mode 100644 wqflask/maintenance/set_resource_defaults.py

(limited to 'wqflask/maintenance/set_resource_defaults.py')

diff --git a/wqflask/maintenance/set_resource_defaults.py b/wqflask/maintenance/set_resource_defaults.py
new file mode 100644
index 00000000..ba102d9c
--- /dev/null
+++ b/wqflask/maintenance/set_resource_defaults.py
@@ -0,0 +1,155 @@
+"""
+
+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()
+    main()
\ 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/maintenance/set_resource_defaults.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/maintenance/set_resource_defaults.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/maintenance/set_resource_defaults.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 0a0d733af4b6c61c381a1c4ec9fa162182a057e9 Mon Sep 17 00:00:00 2001
From: zsloan
Date: Mon, 6 Jul 2020 14:47:04 -0500
Subject: Fixed some of the logic with how traits are authenticated to avoid
 situation where a trait is authenticated twice

---
 wqflask/base/trait.py                        | 30 ++++++++--------------------
 wqflask/maintenance/set_resource_defaults.py |  6 +++---
 wqflask/utility/redis_tools.py               |  5 +++--
 3 files changed, 14 insertions(+), 27 deletions(-)

(limited to 'wqflask/maintenance/set_resource_defaults.py')

diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 7fc016f3..4c3e790c 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -49,7 +49,6 @@ def create_trait(**kw):
     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'))
         return the_trait
     else:
@@ -144,6 +143,7 @@ class GeneralTrait(object):
                 formatted = self.post_publication_description
         else:
             formatted = "Not available"
+
         return formatted
 
     @property
@@ -388,27 +388,14 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
 
     try:
         response = requests.get(the_url).content
-        if response.strip() == "no-access":
-            trait.view = False
-            return trait
-        else:
-            trait_info = json.loads(response)
-    except:
-        resource_info = get_resource_info(resource_id)
-        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
-
+        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
         if dataset.type == 'Publish':
             query = """
                     SELECT
-                            PublishXRef.Id, Publication.PubMed_ID,
+                            PublishXRef.Id, InbredSet.InbredSetCode, Publication.PubMed_ID,
                             Phenotype.Pre_publication_description, Phenotype.Post_publication_description, Phenotype.Original_description,
-                            Phenotype.Pre_publication_abbreviation, Phenotype.Post_publication_abbreviation,
+                            Phenotype.Pre_publication_abbreviation, Phenotype.Post_publication_abbreviation, PublishXRef.mean,
                             Phenotype.Lab_code, Phenotype.Submitter, Phenotype.Owner, Phenotype.Authorized_Users,
                             Publication.Authors, Publication.Title, Publication.Abstract,
                             Publication.Journal, Publication.Volume, Publication.Pages,
@@ -472,11 +459,10 @@ 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]
-            #if isinstance(trait_info[i], basestring):
-            #    holder = holder.encode('latin1')
+            holder =  trait_info[i]
+            # if isinstance(trait_info[i], basestring):
+            #     holder = unicode(holder.strip(codecs.BOM_UTF8), 'utf-8', "ignore")
             setattr(trait, field, holder)
 
         if dataset.type == 'Publish':
diff --git a/wqflask/maintenance/set_resource_defaults.py b/wqflask/maintenance/set_resource_defaults.py
index ddb3b17b..54fd8e7e 100644
--- a/wqflask/maintenance/set_resource_defaults.py
+++ b/wqflask/maintenance/set_resource_defaults.py
@@ -77,7 +77,7 @@ def insert_probeset_resources(default_owner_id):
                                             "admin": "not-admin"}
         resource_ob['group_masks'] = {}
 
-        add_resource(resource_ob)
+        add_resource(resource_ob, update=False)
 
 def insert_publish_resources(default_owner_id):
     current_resources = Redis.hgetall("resources")
@@ -108,7 +108,7 @@ def insert_publish_resources(default_owner_id):
 
             resource_ob['group_masks'] = {}
 
-            add_resource(resource_ob)
+            add_resource(resource_ob, update=False)
         else:
             continue
 
@@ -139,7 +139,7 @@ def insert_geno_resources(default_owner_id):
                                             "admin": "not-admin"}
         resource_ob['group_masks'] = {}
 
-        add_resource(resource_ob)
+        add_resource(resource_ob, update=False)
 
 def insert_resources(default_owner_id):
     current_resources = get_resources()
diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py
index 8a5f95ee..6c912a23 100644
--- a/wqflask/utility/redis_tools.py
+++ b/wqflask/utility/redis_tools.py
@@ -285,13 +285,14 @@ def get_resource_info(resource_id):
     else:
         return None
 
-def add_resource(resource_info):
+def add_resource(resource_info, update=True):
     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:
         resource_id = hmac.hmac_creation('{}:{}'.format(str(resource_info['type']), str(resource_info['data']['dataset'])))
 
-    Redis.hset("resources", resource_id, json.dumps(resource_info))
+    if not Redis.hexists("resources", resource_id):
+        Redis.hset("resources", resource_id, json.dumps(resource_info))
 
     return resource_info
 
-- 
cgit v1.2.3


From db41cd49b6d8ccd2c3318209118ffe098bc9293e Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Wed, 19 Aug 2020 03:57:05 +0300
Subject: Remove extra whitespace(or add it) from comma separated items

See: <https://docs.python.org/2/library/2to3.html#2to3fixer-urllib>
---
 etc/default_settings.py                            |   2 +-
 scripts/maintenance/QTL_Reaper_v6.py               |   4 +-
 scripts/maintenance/readProbeSetMean_v7.py         |  28 ++--
 setup.py                                           |   2 +-
 wqflask/base/trait.py                              |   6 +-
 wqflask/db/call.py                                 |  10 +-
 wqflask/db/webqtlDatabaseFunction.py               |   8 +-
 wqflask/maintenance/gen_select_dataset.py          |   2 +-
 wqflask/maintenance/quantile_normalize.py          |   2 +-
 wqflask/maintenance/set_resource_defaults.py       |   2 +-
 wqflask/utility/Plot.py                            |  48 +++---
 wqflask/utility/elasticsearch_tools.py             |   2 +-
 wqflask/utility/logger.py                          |  26 +--
 wqflask/utility/pillow_utils.py                    |   4 +-
 wqflask/utility/startup_config.py                  |   2 +-
 wqflask/utility/svg.py                             | 130 +++++++-------
 wqflask/utility/tools.py                           |  32 ++--
 wqflask/utility/webqtlUtil.py                      |  16 +-
 wqflask/wqflask/api/router.py                      |   8 +-
 wqflask/wqflask/correlation/show_corr_results.py   |  12 +-
 .../wqflask/correlation_matrix/show_corr_matrix.py |   8 +-
 wqflask/wqflask/do_search.py                       |   4 +-
 .../wqflask/external_tools/send_to_geneweaver.py   |   8 +-
 .../marker_regression/display_mapping_results.py   | 186 ++++++++++-----------
 wqflask/wqflask/marker_regression/plink_mapping.py |   6 +-
 wqflask/wqflask/marker_regression/run_mapping.py   |   2 +-
 wqflask/wqflask/search_results.py                  |   2 +-
 wqflask/wqflask/show_trait/SampleList.py           |   2 +-
 wqflask/wqflask/user_manager.py                    |   2 +-
 wqflask/wqflask/views.py                           |   8 +-
 30 files changed, 287 insertions(+), 287 deletions(-)

(limited to 'wqflask/maintenance/set_resource_defaults.py')

diff --git a/etc/default_settings.py b/etc/default_settings.py
index f368237b..82c605da 100644
--- a/etc/default_settings.py
+++ b/etc/default_settings.py
@@ -24,7 +24,7 @@
 import os
 import sys
 
-GN_VERSION = open("../etc/VERSION","r").read()
+GN_VERSION = open("../etc/VERSION", "r").read()
 GN_SERVER_URL = "http://localhost:8880/" # REST API server
 
 # ---- MySQL
diff --git a/scripts/maintenance/QTL_Reaper_v6.py b/scripts/maintenance/QTL_Reaper_v6.py
index 2fbeb53b..35f2d1a1 100755
--- a/scripts/maintenance/QTL_Reaper_v6.py
+++ b/scripts/maintenance/QTL_Reaper_v6.py
@@ -7,7 +7,7 @@ import reaper
 import MySQLdb
 import time
 
-con = MySQLdb.Connect(db='db_webqtl',user='username',passwd='', host="localhost")
+con = MySQLdb.Connect(db='db_webqtl', user='username', passwd='', host="localhost")
 cursor = con.cursor()
 
 genotypeDir = '/gnshare/gn/web/genotypes/'
@@ -102,7 +102,7 @@ for ProbeSetFreezeId in ProbeSetFreezeIds:
 
 		kj += 1
 		if kj%1000==0:
-			print((ProbeSetFreezeId, InbredSets[InbredSetId],kj))
+			print((ProbeSetFreezeId, InbredSets[InbredSetId], kj))
 
 
 	print(ProbeSetFreezeIds)
diff --git a/scripts/maintenance/readProbeSetMean_v7.py b/scripts/maintenance/readProbeSetMean_v7.py
index 864b4e08..59a51cf9 100755
--- a/scripts/maintenance/readProbeSetMean_v7.py
+++ b/scripts/maintenance/readProbeSetMean_v7.py
@@ -39,7 +39,7 @@ fp = open("%s" % input_file_name, 'rb')
 
 try:
         passwd = getpass.getpass('Please enter mysql password here : ') 
-        con = MySQLdb.Connect(db='db_webqtl',host='localhost', user='username',passwd=passwd)
+        con = MySQLdb.Connect(db='db_webqtl', host='localhost', user='username', passwd=passwd)
 
         db = con.cursor()
         print("You have successfully connected to mysql.\n")
@@ -60,14 +60,14 @@ print('Checking if each line have same number of members')
 GeneList = []
 isCont = 1
 header = fp.readline()
-header = string.split(string.strip(header),'\t')
+header = string.split(string.strip(header), '\t')
 header = list(map(string.strip, header))
 nfield = len(header)
 line = fp.readline()
 
 kj=0
 while line:
-	line2 = string.split(string.strip(line),'\t')
+	line2 = string.split(string.strip(line), '\t')
 	line2 = list(map(string.strip, line2))
 	if len(line2) != nfield:
 		print(("Error : " + line))
@@ -78,7 +78,7 @@ while line:
 
 	kj+=1
 	if kj%100000 == 0:
-		print(('checked ',kj,' lines'))
+		print(('checked ', kj, ' lines'))
 
 GeneList = sorted(map(string.lower, GeneList))
 	
@@ -86,7 +86,7 @@ if isCont==0:
 	sys.exit(0)
 
 
-print(('used ',time.time()-time0,' seconds'))
+print(('used ', time.time()-time0, ' seconds'))
 #########################################################################
 #
 #  Check if each strain exist in database
@@ -98,7 +98,7 @@ print('Checking if each strain exist in database')
 isCont = 1
 fp.seek(0)
 header = fp.readline()
-header = string.split(string.strip(header),'\t')
+header = string.split(string.strip(header), '\t')
 header = list(map(string.strip, header))
 header = list(map(translateAlias, header))
 header = header[dataStart:]
@@ -108,14 +108,14 @@ for item in header:
 		db.execute('select Id from Strain where Name = "%s"' % item)
 		Ids.append(db.fetchall()[0][0])
 	except:
-		print((item,'does not exist, check the if the strain name is correct'))
+		print((item, 'does not exist, check the if the strain name is correct'))
 		isCont=0
 
 if isCont==0:
 	sys.exit(0)
 
 
-print(('used ',time.time()-time0,' seconds'))
+print(('used ', time.time()-time0, ' seconds'))
 ########################################################################
 #
 # Check if each ProbeSet exist in database
@@ -126,7 +126,7 @@ print('Check if each ProbeSet exist in database')
 ##---- find PID is name or target ----##
 line = fp.readline()
 line = fp.readline()
-line2 = string.split(string.strip(line),'\t')
+line2 = string.split(string.strip(line), '\t')
 line2 = list(map(string.strip, line2))
 PId = line2[0]
 
@@ -185,7 +185,7 @@ if isCont==0:
 	sys.exit(0)
 
 
-print(('used ',time.time()-time0,' seconds'))
+print(('used ', time.time()-time0, ' seconds'))
 #########################################################################
 #
 # Insert data into database
@@ -200,7 +200,7 @@ results = db.fetchall()
 NameIds = {}
 for item in results:
 	NameIds[item[0]] = item[1]
-print(('used ',time.time()-time0,' seconds'))
+print(('used ', time.time()-time0, ' seconds'))
 
 
 print('inserting data')
@@ -220,7 +220,7 @@ kj = 0
 values1 = []
 values2 = []
 while line:
-	line2 = string.split(string.strip(line),'\t')
+	line2 = string.split(string.strip(line), '\t')
 	line2 = list(map(string.strip, line2))
 	PId = line2[0]
 	recordId = NameIds[PId]
@@ -253,8 +253,8 @@ while line:
 
 		values1=[]
 		values2=[]
-		print(('Inserted ', kj,' lines'))
-		print(('used ',time.time()-time0,' seconds'))
+		print(('Inserted ', kj, ' lines'))
+		print(('used ', time.time()-time0, ' seconds'))
 	
 	line = fp.readline()
 
diff --git a/setup.py b/setup.py
index a9b71fab..8436dcd3 100644
--- a/setup.py
+++ b/setup.py
@@ -9,7 +9,7 @@ setup(name='genenetwork2',
       url = "https://github.com/genenetwork/genenetwork2/blob/master/README.md",
       description = 'Website and tools for genetics.',
       include_package_data=True,
-      packages=['wqflask','etc'],
+      packages=['wqflask', 'etc'],
       scripts=['bin/genenetwork2'],
       # package_data = {
       #   'etc': ['*.py']
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py
index 2b8f2e72..05b272c3 100644
--- a/wqflask/base/trait.py
+++ b/wqflask/base/trait.py
@@ -193,7 +193,7 @@ class GeneralTrait(object):
         '''
 
         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:
@@ -440,7 +440,7 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
         #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 = string.join(dataset.display_fields,',Geno.')
+            display_fields_string = string.join(dataset.display_fields, ',Geno.')
             display_fields_string = 'Geno.' + display_fields_string
             query = """
                     SELECT %s
@@ -459,7 +459,7 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False):
             query = """SELECT %s FROM %s WHERE Name = %s"""
             logger.sql(query)
             trait_info = g.db.execute(query,
-                                    (string.join(dataset.display_fields,','),
+                                    (string.join(dataset.display_fields, ','),
                                                 dataset.type, trait.name)).fetchone()
 
     if trait_info:
diff --git a/wqflask/db/call.py b/wqflask/db/call.py
index 82cfebb4..3b8f782e 100644
--- a/wqflask/db/call.py
+++ b/wqflask/db/call.py
@@ -26,8 +26,8 @@ GN_SERVER result when set (which should return a Tuple)
         else:
             res2 = result,
         if LOG_SQL:
-            logger.debug("Replaced SQL call",query)
-        logger.debug(path,res2)
+            logger.debug("Replaced SQL call", query)
+        logger.debug(path, res2)
         return res2
     else:
         return fetchone(query)
@@ -37,7 +37,7 @@ def fetchone(query):
 original fetchone, but with logging)
 
     """
-    with Bench("SQL",LOG_SQL):
+    with Bench("SQL", LOG_SQL):
         def helper(query):
             res = g.db.execute(query)
             return res.fetchone()
@@ -48,7 +48,7 @@ def fetchall(query):
 original fetchall, but with logging)
 
     """
-    with Bench("SQL",LOG_SQL):
+    with Bench("SQL", LOG_SQL):
         def helper(query):
             res = g.db.execute(query)
             return res.fetchall()
@@ -58,7 +58,7 @@ def gn_server(path):
     """Return JSON record by calling GN_SERVER
 
     """
-    with Bench("GN_SERVER",LOG_SQL):
+    with Bench("GN_SERVER", LOG_SQL):
         res = urllib.request.urlopen(GN_SERVER_URL+path)
         rest = res.read()
         res2 = json.loads(rest)
diff --git a/wqflask/db/webqtlDatabaseFunction.py b/wqflask/db/webqtlDatabaseFunction.py
index 8a9dc79d..2805febd 100644
--- a/wqflask/db/webqtlDatabaseFunction.py
+++ b/wqflask/db/webqtlDatabaseFunction.py
@@ -35,13 +35,13 @@ def retrieve_species(group):
     """Get the species of a group (e.g. returns string "mouse" on "BXD"
 
     """
-    result = fetch1("select Species.Name from Species, InbredSet where InbredSet.Name = '%s' and InbredSet.SpeciesId = Species.Id" % (group),"/cross/"+group+".json",lambda r: (r["species"],))[0]
-    logger.debug("retrieve_species result:",result)
+    result = fetch1("select Species.Name from Species, InbredSet where InbredSet.Name = '%s' and InbredSet.SpeciesId = Species.Id" % (group), "/cross/"+group+".json", lambda r: (r["species"],))[0]
+    logger.debug("retrieve_species result:", result)
     return result
 
 
 def retrieve_species_id(group):
 
-    result = fetch1("select SpeciesId from InbredSet where Name = '%s'" % (group),"/cross/"+group+".json",lambda r: (r["species_id"],))[0]
-    logger.debug("retrieve_species_id result:",result)
+    result = fetch1("select SpeciesId from InbredSet where Name = '%s'" % (group), "/cross/"+group+".json", lambda r: (r["species_id"],))[0]
+    logger.debug("retrieve_species_id result:", result)
     return result
diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py
index 78217587..d12b328f 100644
--- a/wqflask/maintenance/gen_select_dataset.py
+++ b/wqflask/maintenance/gen_select_dataset.py
@@ -41,7 +41,7 @@ from __future__ import print_function, division
 import sys
 
 # NEW: Note we prepend the current path - otherwise a guix instance of GN2 may be used instead
-sys.path.insert(0,'./')
+sys.path.insert(0, './')
 # NEW: import app to avoid a circular dependency on utility.tools
 from wqflask import app
 
diff --git a/wqflask/maintenance/quantile_normalize.py b/wqflask/maintenance/quantile_normalize.py
index 82b695f4..43edfd13 100644
--- a/wqflask/maintenance/quantile_normalize.py
+++ b/wqflask/maintenance/quantile_normalize.py
@@ -1,7 +1,7 @@
 from __future__ import absolute_import, print_function, division
 
 import sys
-sys.path.insert(0,'./')
+sys.path.insert(0, './')
 
 
 
diff --git a/wqflask/maintenance/set_resource_defaults.py b/wqflask/maintenance/set_resource_defaults.py
index 54fd8e7e..d53a255b 100644
--- a/wqflask/maintenance/set_resource_defaults.py
+++ b/wqflask/maintenance/set_resource_defaults.py
@@ -22,7 +22,7 @@ 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,'./')
+sys.path.insert(0, './')
 
 # NEW: import app to avoid a circular dependency on utility.tools
 from wqflask import app
diff --git a/wqflask/utility/Plot.py b/wqflask/utility/Plot.py
index c9053dde..4f6e694e 100644
--- a/wqflask/utility/Plot.py
+++ b/wqflask/utility/Plot.py
@@ -58,7 +58,7 @@ def cformat(d, rank=0):
     strD = "%2.6f" % d
 
     if rank == 0:
-        while strD[-1] in ('0','.'):
+        while strD[-1] in ('0', '.'):
             if strD[-1] == '0' and strD[-2] == '.' and len(strD) <= 4:
                 break
             elif strD[-1] == '.':
@@ -162,7 +162,7 @@ def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLab
        j = int((item-xLow)/step)
        Count[j] += 1
 
-    yLow, yTop, stepY=detScale(0,max(Count))
+    yLow, yTop, stepY=detScale(0, max(Count))
 
     #draw data
     xScale = plotWidth/(xTop-xLow)
@@ -174,7 +174,7 @@ def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLab
            xc = (dataXY[i]-xLow)*xScale+xLeftOffset
            yc =-(count-yLow)*yScale+yTopOffset+plotHeight
            im_drawer.rectangle(
-               xy=((xc+2,yc),(xc+barWidth-2,yTopOffset+plotHeight)),
+               xy=((xc+2, yc), (xc+barWidth-2, yTopOffset+plotHeight)),
                outline=barColor, fill=barColor)
 
     #draw drawing region
@@ -183,81 +183,81 @@ def plotBar(canvas, data, barColor=BLUE, axesColor=BLACK, labelColor=BLACK, XLab
     )
 
     #draw scale
-    scaleFont=ImageFont.truetype(font=COUR_FILE,size=11)
+    scaleFont=ImageFont.truetype(font=COUR_FILE, size=11)
     x=xLow
     for i in range(int(stepX)+1):
        xc=xLeftOffset+(x-xLow)*xScale
        im_drawer.line(
-           xy=((xc,yTopOffset+plotHeight),(xc,yTopOffset+plotHeight+5)),
+           xy=((xc, yTopOffset+plotHeight), (xc, yTopOffset+plotHeight+5)),
            fill=axesColor)
        strX = cformat(d=x, rank=0)
        im_drawer.text(
            text=strX,
-           xy=(xc-im_drawer.textsize(strX,font=scaleFont)[0]/2,
-               yTopOffset+plotHeight+14),font=scaleFont)
+           xy=(xc-im_drawer.textsize(strX, font=scaleFont)[0]/2,
+               yTopOffset+plotHeight+14), font=scaleFont)
        x+= (xTop - xLow)/stepX
 
     y=yLow
     for i in range(int(stepY)+1):
        yc=yTopOffset+plotHeight-(y-yLow)*yScale
-       im_drawer.line(xy=((xLeftOffset,yc),(xLeftOffset-5,yc)), fill=axesColor)
+       im_drawer.line(xy=((xLeftOffset, yc), (xLeftOffset-5, yc)), fill=axesColor)
        strY = "%d" %y
        im_drawer.text(
            text=strY,
-           xy=(xLeftOffset-im_drawer.textsize(strY,font=scaleFont)[0]-6,yc+5),
+           xy=(xLeftOffset-im_drawer.textsize(strY, font=scaleFont)[0]-6, yc+5),
            font=scaleFont)
        y+= (yTop - yLow)/stepY
 
     #draw label
-    labelFont=ImageFont.truetype(font=TAHOMA_FILE,size=17)
+    labelFont=ImageFont.truetype(font=TAHOMA_FILE, size=17)
     if XLabel:
        im_drawer.text(
            text=XLabel,
            xy=(xLeftOffset+(
-               plotWidth-im_drawer.textsize(XLabel,font=labelFont)[0])/2.0,
+               plotWidth-im_drawer.textsize(XLabel, font=labelFont)[0])/2.0,
                yTopOffset+plotHeight+yBottomOffset-10),
-           font=labelFont,fill=labelColor)
+           font=labelFont, fill=labelColor)
 
     if YLabel:
         draw_rotated_text(canvas, text=YLabel,
                           xy=(19,
                               yTopOffset+plotHeight-(
                                   plotHeight-im_drawer.textsize(
-                                      YLabel,font=labelFont)[0])/2.0),
+                                      YLabel, font=labelFont)[0])/2.0),
                           font=labelFont, fill=labelColor, angle=90)
 
-    labelFont=ImageFont.truetype(font=VERDANA_FILE,size=16)
+    labelFont=ImageFont.truetype(font=VERDANA_FILE, size=16)
     if title:
        im_drawer.text(
            text=title,
            xy=(xLeftOffset+(plotWidth-im_drawer.textsize(
-               title,font=labelFont)[0])/2.0,
+               title, font=labelFont)[0])/2.0,
                20),
-           font=labelFont,fill=labelColor)
+           font=labelFont, fill=labelColor)
 
 # This function determines the scale of the plot
-def detScaleOld(min,max):
+def detScaleOld(min, max):
     if min>=max:
         return None
     elif min == -1.0 and max == 1.0:
-        return [-1.2,1.2,12]
+        return [-1.2, 1.2, 12]
     else:
         a=max-min
         b=floor(log10(a))
-        c=pow(10.0,b)
+        c=pow(10.0, b)
         if a < c*5.0:
             c/=2.0
         #print a,b,c
         low=c*floor(min/c)
         high=c*ceil(max/c)
-        return [low,high,round((high-low)/c)]
+        return [low, high, round((high-low)/c)]
 
 def detScale(min=0,max=0):
 
     if min>=max:
         return None
     elif min == -1.0 and max == 1.0:
-        return [-1.2,1.2,12]
+        return [-1.2, 1.2, 12]
     else:
         a=max-min
         if max != 0:
@@ -269,7 +269,7 @@ def detScale(min=0,max=0):
                 min -= 0.1*a
         a=max-min
         b=floor(log10(a))
-        c=pow(10.0,b)
+        c=pow(10.0, b)
         low=c*floor(min/c)
         high=c*ceil(max/c)
         n = round((high-low)/c)
@@ -287,7 +287,7 @@ def detScale(min=0,max=0):
             high=c*ceil(max/c)
             n = round((high-low)/c)
 
-        return [low,high,n]
+        return [low, high, n]
 
 def bluefunc(x):
     return 1.0 / (1.0 + exp(-10*(x-0.6)))
@@ -296,7 +296,7 @@ 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)
+    return 1 - pow(redfunc(x+0.2), 2) - bluefunc(x-0.3)
 
 def colorSpectrum(n=100):
     multiple = 10
diff --git a/wqflask/utility/elasticsearch_tools.py b/wqflask/utility/elasticsearch_tools.py
index 15cdd0bc..a5580811 100644
--- a/wqflask/utility/elasticsearch_tools.py
+++ b/wqflask/utility/elasticsearch_tools.py
@@ -59,7 +59,7 @@ def get_elasticsearch_connection(for_user=True):
     try:
         assert(ELASTICSEARCH_HOST)
         assert(ELASTICSEARCH_PORT)
-        logger.info("ES HOST",ELASTICSEARCH_HOST)
+        logger.info("ES HOST", ELASTICSEARCH_HOST)
 
         es = Elasticsearch([{
             "host": ELASTICSEARCH_HOST, "port": ELASTICSEARCH_PORT
diff --git a/wqflask/utility/logger.py b/wqflask/utility/logger.py
index 510b1041..e904eb94 100644
--- a/wqflask/utility/logger.py
+++ b/wqflask/utility/logger.py
@@ -42,10 +42,10 @@ class GNLogger:
 
     """
 
-    def __init__(self,name):
+    def __init__(self, name):
         self.logger = logging.getLogger(name)
 
-    def setLevel(self,value):
+    def setLevel(self, value):
         """Set the undelying log level"""
         self.logger.setLevel(value)
 
@@ -54,7 +54,7 @@ class GNLogger:
 level=num to filter on LOG_LEVEL_DEBUG.
 
         """
-        self.collect(self.logger.debug,*args)
+        self.collect(self.logger.debug, *args)
 
     def debug20(self,*args):
         """Call logging.debug for multiple args. Use level=num to filter on
@@ -63,15 +63,15 @@ LOG_LEVEL_DEBUG (NYI).
         """
         if level <= LOG_LEVEL_DEBUG:
             if self.logger.getEffectiveLevel() < 20:
-                self.collect(self.logger.debug,*args)
+                self.collect(self.logger.debug, *args)
 
     def info(self,*args):
         """Call logging.info for multiple args"""
-        self.collect(self.logger.info,*args)
+        self.collect(self.logger.info, *args)
 
     def warning(self,*args):
         """Call logging.warning for multiple args"""
-        self.collect(self.logger.warning,*args)
+        self.collect(self.logger.warning, *args)
         # self.logger.warning(self.collect(*args))
 
     def error(self,*args):
@@ -79,13 +79,13 @@ LOG_LEVEL_DEBUG (NYI).
         now = datetime.datetime.utcnow()
         time_str = now.strftime('%H:%M:%S UTC %Y%m%d')
         l = [time_str]+list(args)
-        self.collect(self.logger.error,*l)
+        self.collect(self.logger.error, *l)
 
     def infof(self,*args):
         """Call logging.info for multiple args lazily"""
         # only evaluate function when logging
         if self.logger.getEffectiveLevel() < 30:
-            self.collectf(self.logger.debug,*args)
+            self.collectf(self.logger.debug, *args)
 
     def debugf(self,level=0,*args):
         """Call logging.debug for multiple args lazily and handle
@@ -95,15 +95,15 @@ LOG_LEVEL_DEBUG (NYI).
         # only evaluate function when logging
         if level <= LOG_LEVEL_DEBUG:
             if self.logger.getEffectiveLevel() < 20:
-                self.collectf(self.logger.debug,*args)
+                self.collectf(self.logger.debug, *args)
 
     def sql(self, sqlcommand, fun = None):
         """Log SQL command, optionally invoking a timed fun"""
         if LOG_SQL:
             caller = stack()[1][3]
-            if caller in ['fetchone','fetch1','fetchall']:
+            if caller in ['fetchone', 'fetch1', 'fetchall']:
                 caller = stack()[2][3]
-            self.info(caller,sqlcommand)
+            self.info(caller, sqlcommand)
         if fun:
             result = fun(sqlcommand)
             if LOG_SQL:
@@ -119,7 +119,7 @@ LOG_LEVEL_DEBUG (NYI).
             if isinstance(a, str):
                 out = out + a
             else:
-                out = out + pf(a,width=160)
+                out = out + pf(a, width=160)
         fun(out)
 
     def collectf(self,fun,*args):
@@ -134,7 +134,7 @@ LOG_LEVEL_DEBUG (NYI).
                     if isinstance(a, str):
                         out = out + a
                     else:
-                        out = out + pf(a,width=160)
+                        out = out + pf(a, width=160)
         fun(out)
 
 # Get the module logger. You can override log levels at the
diff --git a/wqflask/utility/pillow_utils.py b/wqflask/utility/pillow_utils.py
index dfbf3e19..1e2ed075 100644
--- a/wqflask/utility/pillow_utils.py
+++ b/wqflask/utility/pillow_utils.py
@@ -10,9 +10,9 @@ WHITE = ImageColor.getrgb("white")
 def draw_rotated_text(canvas, text, font, xy, fill=BLACK, angle=-90):
     # type: (Image, str, ImageFont, tuple, ImageColor, int)
     """Utility function draw rotated text"""
-    tmp_img = Image.new("RGBA", font.getsize(text), color=(0,0,0,0))
+    tmp_img = Image.new("RGBA", font.getsize(text), color=(0, 0, 0, 0))
     draw_text = ImageDraw.Draw(tmp_img)
-    draw_text.text(text=text, xy=(0,0), font=font, fill=fill)
+    draw_text.text(text=text, xy=(0, 0), font=font, fill=fill)
     tmp_img2 = tmp_img.rotate(angle, expand=1)
     tmp_img2.save("/tmp/{}.png".format(text), format="png")
     canvas.paste(im=tmp_img2, box=tuple([int(i) for i in xy]))
diff --git a/wqflask/utility/startup_config.py b/wqflask/utility/startup_config.py
index 42ead709..f1aaebb6 100644
--- a/wqflask/utility/startup_config.py
+++ b/wqflask/utility/startup_config.py
@@ -36,4 +36,4 @@ def app_config():
     # import utility.elasticsearch_tools as es
     # es.test_elasticsearch_connection()
 
-    print(("GN2 is running. Visit %s[http://localhost:%s/%s](%s)" % (BLUE,str(port),ENDC,get_setting("WEBSERVER_URL"))))
+    print(("GN2 is running. Visit %s[http://localhost:%s/%s](%s)" % (BLUE, str(port), ENDC, get_setting("WEBSERVER_URL"))))
diff --git a/wqflask/utility/svg.py b/wqflask/utility/svg.py
index 874ada9d..19eda0ce 100644
--- a/wqflask/utility/svg.py
+++ b/wqflask/utility/svg.py
@@ -447,7 +447,7 @@ class rect(SVGelement):
         if width == None or height == None:
             raise ValueError('both height and width are required')
 
-        SVGelement.__init__(self,'rect',{'width':width,'height':height},**args)
+        SVGelement.__init__(self, 'rect', {'width':width,'height':height}, **args)
         if x!=None:
             self.attributes['x']=x
         if y!=None:
@@ -468,7 +468,7 @@ class ellipse(SVGelement):
         if rx==None or ry== None:
             raise ValueError('both rx and ry are required')
 
-        SVGelement.__init__(self,'ellipse',{'rx':rx,'ry':ry},**args)
+        SVGelement.__init__(self, 'ellipse', {'rx':rx,'ry':ry}, **args)
         if cx!=None:
             self.attributes['cx']=cx
         if cy!=None:
@@ -489,7 +489,7 @@ class circle(SVGelement):
     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')
-        SVGelement.__init__(self,'circle',{'r':r},**args)
+        SVGelement.__init__(self, 'circle', {'r':r}, **args)
         if cx!=None:
             self.attributes['cx']=cx
         if cy!=None:
@@ -508,7 +508,7 @@ class point(circle):
     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)
+        circle.__init__(self, x, y, 1, fill, **args)
 
 class line(SVGelement):
     """l=line(x1,y1,x2,y2,stroke,stroke_width,**args)
@@ -516,7 +516,7 @@ class line(SVGelement):
     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)
+        SVGelement.__init__(self, 'line', **args)
         if x1!=None:
             self.attributes['x1']=x1
         if y1!=None:
@@ -536,7 +536,7 @@ class polyline(SVGelement):
     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)
+        SVGelement.__init__(self, 'polyline', {'points':_xypointlist(points)}, **args)
         if fill!=None:
             self.attributes['fill']=fill
         if stroke_width!=None:
@@ -550,7 +550,7 @@ class polygon(SVGelement):
     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)
+        SVGelement.__init__(self, 'polygon', {'points':_xypointlist(points)}, **args)
         if fill!=None:
             self.attributes['fill']=fill
         if stroke_width!=None:
@@ -564,7 +564,7 @@ class path(SVGelement):
     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)
+        SVGelement.__init__(self, 'path', {'d':str(pathdata)}, **args)
         if stroke!=None:
             self.attributes['stroke']=stroke
         if fill!=None:
@@ -581,7 +581,7 @@ 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)
+        SVGelement.__init__(self, 'text', **args)
         if x!=None:
             self.attributes['x']=x
         if y!=None:
@@ -602,7 +602,7 @@ 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)
+        SVGelement.__init__(self, 'textPath', {'xlink:href':link}, **args)
         if text!=None:
             self.text=text
 
@@ -614,7 +614,7 @@ class pattern(SVGelement):
     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)
+        SVGelement.__init__(self, 'pattern', **args)
         if x!=None:
             self.attributes['x']=x
         if y!=None:
@@ -633,7 +633,7 @@ class title(SVGelement):
     add at least one to the root svg element
     """
     def __init__(self,text=None,**args):
-        SVGelement.__init__(self,'title',**args)
+        SVGelement.__init__(self, 'title', **args)
         if text!=None:
             self.text=text
 
@@ -644,7 +644,7 @@ class description(SVGelement):
     Add this element before adding other elements.
     """
     def __init__(self,text=None,**args):
-        SVGelement.__init__(self,'desc',**args)
+        SVGelement.__init__(self, 'desc', **args)
         if text!=None:
             self.text=text
 
@@ -655,7 +655,7 @@ class lineargradient(SVGelement):
     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)
+        SVGelement.__init__(self, 'linearGradient', **args)
         if x1!=None:
             self.attributes['x1']=x1
         if y1!=None:
@@ -674,7 +674,7 @@ class radialgradient(SVGelement):
     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)
+        SVGelement.__init__(self, 'radialGradient', **args)
         if cx!=None:
             self.attributes['cx']=cx
         if cy!=None:
@@ -694,7 +694,7 @@ class stop(SVGelement):
     Puts a stop color at the specified radius
     """
     def __init__(self,offset,stop_color=None,**args):
-        SVGelement.__init__(self,'stop',{'offset':offset},**args)
+        SVGelement.__init__(self, 'stop', {'offset':offset}, **args)
         if stop_color!=None:
             self.attributes['stop-color']=stop_color
 
@@ -704,7 +704,7 @@ class style(SVGelement):
     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)
+        SVGelement.__init__(self, 'style', {'type':type}, cdata=cdata, **args)
 
 
 class image(SVGelement):
@@ -715,7 +715,7 @@ class image(SVGelement):
     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')
-        SVGelement.__init__(self,'image',{'xlink:href':url,'width':width,'height':height},**args)
+        SVGelement.__init__(self, 'image', {'xlink:href':url,'width':width,'height':height}, **args)
         if x!=None:
             self.attributes['x']=x
         if y!=None:
@@ -727,7 +727,7 @@ class cursor(SVGelement):
     defines a custom cursor for a element or a drawing
     """
     def __init__(self,url,**args):
-        SVGelement.__init__(self,'cursor',{'xlink:href':url},**args)
+        SVGelement.__init__(self, 'cursor', {'xlink:href':url}, **args)
 
 
 class marker(SVGelement):
@@ -737,7 +737,7 @@ class marker(SVGelement):
     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)
+        SVGelement.__init__(self, 'marker', **args)
         if id!=None:
             self.attributes['id']=id
         if viewBox!=None:
@@ -758,7 +758,7 @@ class group(SVGelement):
     g.addElement(SVGelement)
     """
     def __init__(self,id=None,**args):
-        SVGelement.__init__(self,'g',**args)
+        SVGelement.__init__(self, 'g', **args)
         if id!=None:
             self.attributes['id']=id
 
@@ -772,7 +772,7 @@ class symbol(SVGelement):
     """
 
     def __init__(self,id=None,viewBox=None,**args):
-        SVGelement.__init__(self,'symbol',**args)
+        SVGelement.__init__(self, 'symbol', **args)
         if id!=None:
             self.attributes['id']=id
         if viewBox!=None:
@@ -784,7 +784,7 @@ class defs(SVGelement):
     container for defining elements
     """
     def __init__(self,**args):
-        SVGelement.__init__(self,'defs',**args)
+        SVGelement.__init__(self, 'defs', **args)
 
 class switch(SVGelement):
     """sw=switch(**args)
@@ -794,7 +794,7 @@ class switch(SVGelement):
     Refer to the SVG specification for details.
     """
     def __init__(self,**args):
-        SVGelement.__init__(self,'switch',**args)
+        SVGelement.__init__(self, 'switch', **args)
 
 
 class use(SVGelement):
@@ -803,7 +803,7 @@ 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)
+        SVGelement.__init__(self, 'use', {'xlink:href':link}, **args)
         if x!=None:
             self.attributes['x']=x
         if y!=None:
@@ -822,14 +822,14 @@ class link(SVGelement):
     a.addElement(SVGelement)
     """
     def __init__(self,link='',**args):
-        SVGelement.__init__(self,'a',{'xlink:href':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)
+        SVGelement.__init__(self, 'view', **args)
         if id!=None:
             self.attributes['id']=id
 
@@ -840,7 +840,7 @@ class script(SVGelement):
 
     """
     def __init__(self,type,cdata=None,**args):
-        SVGelement.__init__(self,'script',{'type':type},cdata=cdata,**args)
+        SVGelement.__init__(self, 'script', {'type':type}, cdata=cdata, **args)
 
 class animate(SVGelement):
     """an=animate(attribute,from,to,during,**args)
@@ -848,7 +848,7 @@ class animate(SVGelement):
     animates an attribute.
     """
     def __init__(self,attribute,fr=None,to=None,dur=None,**args):
-        SVGelement.__init__(self,'animate',{'attributeName':attribute},**args)
+        SVGelement.__init__(self, 'animate', {'attributeName':attribute}, **args)
         if fr!=None:
             self.attributes['from']=fr
         if to!=None:
@@ -862,7 +862,7 @@ class animateMotion(SVGelement):
     animates a SVGelement over the given path in dur seconds
     """
     def __init__(self,pathdata,dur,**args):
-        SVGelement.__init__(self,'animateMotion',**args)
+        SVGelement.__init__(self, 'animateMotion', **args)
         if pathdata!=None:
             self.attributes['path']=str(pathdata)
         if dur!=None:
@@ -874,7 +874,7 @@ class animateTransform(SVGelement):
     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)
+        SVGelement.__init__(self, 'animateTransform', {'attributeName':'transform'}, **args)
         # As far as I know the attributeName is always transform
         if type!=None:
             self.attributes['type']=type
@@ -890,7 +890,7 @@ class animateColor(SVGelement):
     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)
+        SVGelement.__init__(self, 'animateColor', {'attributeName':attribute}, **args)
         if type!=None:
             self.attributes['type']=type
         if fr!=None:
@@ -905,7 +905,7 @@ class set(SVGelement):
     sets an attribute to a value for a
     """
     def __init__(self,attribute,to=None,dur=None,**args):
-        SVGelement.__init__(self,'set',{'attributeName':attribute},**args)
+        SVGelement.__init__(self, 'set', {'attributeName':attribute}, **args)
         if to!=None:
             self.attributes['to']=to
         if dur!=None:
@@ -929,7 +929,7 @@ class svg(SVGelement):
     d.toXml()
     """
     def __init__(self,viewBox=None, width=None, height=None,**args):
-        SVGelement.__init__(self,'svg',**args)
+        SVGelement.__init__(self, 'svg', **args)
         if viewBox!=None:
             self.attributes['viewBox']=_viewboxlist(viewBox)
         if width!=None:
@@ -952,7 +952,7 @@ class drawing:
     def __init__(self, entity={}):
         self.svg=None
         self.entity = entity
-    def setSVG(self,svg):
+    def setSVG(self, svg):
         self.svg=svg
         # Voeg een element toe aan de grafiek toe.
     if use_dom_implementation==0:
@@ -967,12 +967,12 @@ class drawing:
                     xml.write("<!ENTITY %s \"%s\">\n" % (item, self.entity[item]))
                 xml.write("]")
             xml.write(">\n")
-            self.svg.toXml(0,xml)
+            self.svg.toXml(0, xml)
             if not filename:
                 if compress:
                     import gzip
                     f=cStringIO.StringIO()
-                    zf=gzip.GzipFile(fileobj=f,mode='wb')
+                    zf=gzip.GzipFile(fileobj=f, mode='wb')
                     zf.write(xml.getvalue())
                     zf.close()
                     f.seek(0)
@@ -982,11 +982,11 @@ class drawing:
             else:
                 if filename[-4:]=='svgz':
                     import gzip
-                    f=gzip.GzipFile(filename=filename,mode="wb", compresslevel=9)
+                    f=gzip.GzipFile(filename=filename, mode="wb", compresslevel=9)
                     f.write(xml.getvalue())
                     f.close()
                 else:
-                    f=file(filename,'w')
+                    f=file(filename, 'w')
                     f.write(xml.getvalue())
                     f.close()
 
@@ -997,40 +997,40 @@ class drawing:
             writes a svg drawing to the screen or to a file
             compresses if filename ends with svgz or if compress is true
             """
-            doctype = implementation.createDocumentType('svg',"-//W3C//DTD SVG 1.0//EN""",'http://www.w3.org/TR/2001/REC-SVG-20010904/DTD/svg10.dtd ')
+            doctype = implementation.createDocumentType('svg', "-//W3C//DTD SVG 1.0//EN""", 'http://www.w3.org/TR/2001/REC-SVG-20010904/DTD/svg10.dtd ')
 
             global root
             # root is defined global so it can be used by the appender. Its also possible to use it as an arugument but
             # that is a bit messy.
-            root=implementation.createDocument(None,None,doctype)
+            root=implementation.createDocument(None, None, doctype)
             # Create the xml document.
             global appender
-            def appender(element,elementroot):
+            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"""
                 if element.namespace:
-                    e=root.createElementNS(element.namespace,element.type)
+                    e=root.createElementNS(element.namespace, element.type)
                 else:
                     e=root.createElement(element.type)
                 if element.text:
                     textnode=root.createTextNode(element.text)
                     e.appendChild(textnode)
                 for attribute in list(element.attributes.keys()):   #in element.attributes is supported from python 2.2
-                    e.setAttribute(attribute,str(element.attributes[attribute]))
+                    e.setAttribute(attribute, str(element.attributes[attribute]))
                 if element.elements:
                     for el in element.elements:
-                        e=appender(el,e)
+                        e=appender(el, e)
                 elementroot.appendChild(e)
                 return elementroot
-            root=appender(self.svg,root)
+            root=appender(self.svg, root)
             if not filename:
                 import cStringIO
                 xml=cStringIO.StringIO()
-                PrettyPrint(root,xml)
+                PrettyPrint(root, xml)
                 if compress:
                     import gzip
                     f=cStringIO.StringIO()
-                    zf=gzip.GzipFile(fileobj=f,mode='wb')
+                    zf=gzip.GzipFile(fileobj=f, mode='wb')
                     zf.write(xml.getvalue())
                     zf.close()
                     f.seek(0)
@@ -1043,13 +1043,13 @@ class drawing:
                         import gzip
                         import cStringIO
                         xml=cStringIO.StringIO()
-                        PrettyPrint(root,xml)
-                        f=gzip.GzipFile(filename=filename,mode='wb',compresslevel=9)
+                        PrettyPrint(root, xml)
+                        f=gzip.GzipFile(filename=filename, mode='wb', compresslevel=9)
                         f.write(xml.getvalue())
                         f.close()
                     else:
-                        f=open(filename,'w')
-                        PrettyPrint(root,f)
+                        f=open(filename, 'w')
+                        PrettyPrint(root, f)
                         f.close()
                 except:
                     print(("Cannot write SVG file: " + filename))
@@ -1070,32 +1070,32 @@ if __name__=='__main__':
 
 
     d=drawing()
-    s=svg((0,0,100,100))
-    r=rect(-100,-100,300,300,'cyan')
+    s=svg((0, 0, 100, 100))
+    r=rect(-100, -100, 300, 300, 'cyan')
     s.addElement(r)
 
     t=title('SVGdraw Demo')
     s.addElement(t)
     g=group('animations')
-    e=ellipse(0,0,5,2)
+    e=ellipse(0, 0, 5, 2)
     g.addElement(e)
-    c=circle(0,0,1,'red')
+    c=circle(0, 0, 1, 'red')
     g.addElement(c)
-    pd=pathdata(0,-10)
+    pd=pathdata(0, -10)
     for i in range(6):
-        pd.relsmbezier(10,5,0,10)
-        pd.relsmbezier(-10,5,0,10)
-    an=animateMotion(pd,10)
+        pd.relsmbezier(10, 5, 0, 10)
+        pd.relsmbezier(-10, 5, 0, 10)
+    an=animateMotion(pd, 10)
     an.attributes['rotate']='auto-reverse'
     an.attributes['repeatCount']="indefinite"
     g.addElement(an)
     s.addElement(g)
-    for i in range(20,120,20):
-        u=use('#animations',i,0)
+    for i in range(20, 120, 20):
+        u=use('#animations', i, 0)
         s.addElement(u)
-    for i in range(0,120,20):
-        for j in range(5,105,10):
-            c=circle(i,j,1,'red','black',.5)
+    for i in range(0, 120, 20):
+        for j in range(5, 105, 10):
+            c=circle(i, j, 1, 'red', 'black', .5)
             s.addElement(c)
     d.setSVG(s)
 
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 51a87fe1..68ef0f04 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -15,7 +15,7 @@ OVERRIDES = {}
 
 def app_set(command_id, value):
     """Set application wide value"""
-    app.config.setdefault(command_id,value)
+    app.config.setdefault(command_id, value)
     return value
 
 def get_setting(command_id,guess=None):
@@ -45,7 +45,7 @@ def get_setting(command_id,guess=None):
     def value(command):
         if command:
             # sys.stderr.write("Found "+command+"\n")
-            app_set(command_id,command)
+            app_set(command_id, command)
             return command
         else:
             return None
@@ -68,7 +68,7 @@ def get_setting(command_id,guess=None):
 
 def get_setting_bool(id):
     v = get_setting(id)
-    if v not in [0,False,'False','FALSE',None]:
+    if v not in [0, False, 'False', 'FALSE', None]:
       return True
     return False
 
@@ -108,16 +108,16 @@ def js_path(module=None):
     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)
+    return get_setting("REAPER_COMMAND", guess)
 
 def gemma_command(guess=None):
-    return assert_bin(get_setting("GEMMA_COMMAND",guess))
+    return assert_bin(get_setting("GEMMA_COMMAND", guess))
 
 def gemma_wrapper_command(guess=None):
-    return assert_bin(get_setting("GEMMA_WRAPPER_COMMAND",guess))
+    return assert_bin(get_setting("GEMMA_WRAPPER_COMMAND", guess))
 
 def plink_command(guess=None):
-    return assert_bin(get_setting("PLINK_COMMAND",guess))
+    return assert_bin(get_setting("PLINK_COMMAND", guess))
 
 def flat_file_exists(subdir):
     base = get_setting("GENENETWORK_FILES")
@@ -180,7 +180,7 @@ def locate(name, subdir=None):
     raise Exception("Can not locate "+name+" in "+base)
 
 def locate_phewas(name, subdir=None):
-    return locate(name,'/phewas/'+subdir)
+    return locate(name, '/phewas/'+subdir)
 
 def locate_ignore_error(name, subdir=None):
     """
@@ -204,7 +204,7 @@ def tempdir():
     """
     Get UNIX TMPDIR by default
     """
-    return valid_path(get_setting("TMPDIR","/tmp"))
+    return valid_path(get_setting("TMPDIR", "/tmp"))
 
 BLUE  = '\033[94m'
 GREEN = '\033[92m'
@@ -225,9 +225,9 @@ def show_settings():
     keylist.sort()
     for k in keylist:
         try:
-            print(("%s: %s%s%s%s" % (k,BLUE,BOLD,get_setting(k),ENDC)))
+            print(("%s: %s%s%s%s" % (k, BLUE, BOLD, get_setting(k), ENDC)))
         except:
-            print(("%s: %s%s%s%s" % (k,GREEN,BOLD,app.config[k],ENDC)))
+            print(("%s: %s%s%s%s" % (k, GREEN, BOLD, app.config[k], ENDC)))
 
 
 # Cached values
@@ -279,10 +279,10 @@ SMTP_CONNECT = get_setting('SMTP_CONNECT')
 SMTP_USERNAME = get_setting('SMTP_USERNAME')
 SMTP_PASSWORD = get_setting('SMTP_PASSWORD')
 
-REAPER_COMMAND     = app_set("REAPER_COMMAND",reaper_command())
-GEMMA_COMMAND      = app_set("GEMMA_COMMAND",gemma_command())
+REAPER_COMMAND     = app_set("REAPER_COMMAND", reaper_command())
+GEMMA_COMMAND      = app_set("GEMMA_COMMAND", gemma_command())
 assert(GEMMA_COMMAND is not None)
-PLINK_COMMAND      = app_set("PLINK_COMMAND",plink_command())
+PLINK_COMMAND      = app_set("PLINK_COMMAND", plink_command())
 GEMMA_WRAPPER_COMMAND = gemma_wrapper_command()
 TEMPDIR            = tempdir() # defaults to UNIX TMPDIR
 assert_dir(TEMPDIR)
@@ -295,11 +295,11 @@ assert_dir(JS_GUIX_PATH+'/cytoscape-panzoom')
 CSS_PATH = JS_GUIX_PATH  # The CSS is bundled together with the JS
 # assert_dir(JS_PATH)
 
-JS_TWITTER_POST_FETCHER_PATH = get_setting("JS_TWITTER_POST_FETCHER_PATH",js_path("javascript-twitter-post-fetcher"))
+JS_TWITTER_POST_FETCHER_PATH = get_setting("JS_TWITTER_POST_FETCHER_PATH", js_path("javascript-twitter-post-fetcher"))
 assert_dir(JS_TWITTER_POST_FETCHER_PATH)
 assert_file(JS_TWITTER_POST_FETCHER_PATH+"/js/twitterFetcher_min.js")
 
-JS_CYTOSCAPE_PATH = get_setting("JS_CYTOSCAPE_PATH",js_path("cytoscape"))
+JS_CYTOSCAPE_PATH = get_setting("JS_CYTOSCAPE_PATH", js_path("cytoscape"))
 assert_dir(JS_CYTOSCAPE_PATH)
 assert_file(JS_CYTOSCAPE_PATH+'/cytoscape.min.js')
 
diff --git a/wqflask/utility/webqtlUtil.py b/wqflask/utility/webqtlUtil.py
index 79991149..77cc3416 100644
--- a/wqflask/utility/webqtlUtil.py
+++ b/wqflask/utility/webqtlUtil.py
@@ -41,22 +41,22 @@ ParInfo ={
 'C57BL-6JxC57BL-6NJF2':['', '', 'C57BL/6J', 'C57BL/6NJ'],
 'BXD300':['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'],
 'B6BTBRF2':['B6BTBRF1', 'BTBRB6F1', 'C57BL/6J', 'BTBRT<+>tf/J'],
-'BHHBF2':['B6HF2','HB6F2','C57BL/6J','C3H/HeJ'],
-'BHF2':['B6HF2','HB6F2','C57BL/6J','C3H/HeJ'],
+'BHHBF2':['B6HF2', 'HB6F2', 'C57BL/6J', 'C3H/HeJ'],
+'BHF2':['B6HF2', 'HB6F2', 'C57BL/6J', 'C3H/HeJ'],
 'B6D2F2':['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'],
 'BDF2-1999':['B6D2F2', 'D2B6F2', 'C57BL/6J', 'DBA/2J'],
 'BDF2-2005':['B6D2F1', 'D2B6F1', 'C57BL/6J', 'DBA/2J'],
-'CTB6F2':['CTB6F2','B6CTF2','C57BL/6J','Castaneous'],
+'CTB6F2':['CTB6F2', 'B6CTF2', 'C57BL/6J', 'Castaneous'],
 'CXB':['CBF1', 'BCF1', 'C57BL/6ByJ', 'BALB/cByJ'],
 'AXBXA':['ABF1', 'BAF1', 'C57BL/6J', 'A/J'],
 'AXB':['ABF1', 'BAF1', 'C57BL/6J', 'A/J'],
 'BXA':['BAF1', 'ABF1', 'C57BL/6J', 'A/J'],
 'LXS':['LSF1', 'SLF1', 'ISS', 'ILS'],
 'HXBBXH':['SHR_BNF1', 'BN_SHRF1', 'BN-Lx/Cub', 'SHR/OlaIpcv'],
-'BayXSha':['BayXShaF1', 'ShaXBayF1', 'Bay-0','Shahdara'],
-'ColXBur':['ColXBurF1', 'BurXColF1', 'Col-0','Bur-0'],
-'ColXCvi':['ColXCviF1', 'CviXColF1', 'Col-0','Cvi'],
-'SXM':['SMF1', 'MSF1', 'Steptoe','Morex'],
+'BayXSha':['BayXShaF1', 'ShaXBayF1', 'Bay-0', 'Shahdara'],
+'ColXBur':['ColXBurF1', 'BurXColF1', 'Col-0', 'Bur-0'],
+'ColXCvi':['ColXCviF1', 'CviXColF1', 'Col-0', 'Cvi'],
+'SXM':['SMF1', 'MSF1', 'Steptoe', 'Morex'],
 'HRDP':['SHR_BNF1', 'BN_SHRF1', 'BN-Lx/Cub', 'SHR/OlaIpcv']
 }
 
@@ -91,7 +91,7 @@ def readLineCSV(line): ### dcrowell July 2008
     returnList[0]=returnList[0][1:]
     return returnList
 
-def cmpEigenValue(A,B):
+def cmpEigenValue(A, B):
     try:
         if A[0] > B[0]:
             return -1
diff --git a/wqflask/wqflask/api/router.py b/wqflask/wqflask/api/router.py
index 3fa1d5ba..b81da0dc 100644
--- a/wqflask/wqflask/api/router.py
+++ b/wqflask/wqflask/api/router.py
@@ -558,10 +558,10 @@ def trait_sample_data(dataset_name, trait_name, file_format = "json"):
         sample_list = []
         for sample in sample_data:
             sample_dict = {
-              "sample_name"   : sample[0],
-              "sample_name_2" : sample[1],
-              "value"         : sample[2],
-              "data_id"       : sample[3],
+              "sample_name": sample[0],
+              "sample_name_2": sample[1],
+              "value": sample[2],
+              "data_id": sample[3],
             }
             if sample[4]:
                 sample_dict["se"] = sample[4]
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index 15a21ee6..4116e2df 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -108,17 +108,17 @@ class CorrelationResults(object):
             self.sample_data = {}
             self.corr_type = start_vars['corr_type']
             self.corr_method = start_vars['corr_sample_method']
-            self.min_expr = get_float(start_vars,'min_expr')
-            self.p_range_lower = get_float(start_vars,'p_range_lower',-1.0)
-            self.p_range_upper = get_float(start_vars,'p_range_upper',1.0)
+            self.min_expr = get_float(start_vars, 'min_expr')
+            self.p_range_lower = get_float(start_vars, 'p_range_lower', -1.0)
+            self.p_range_upper = get_float(start_vars, 'p_range_upper', 1.0)
 
             if ('loc_chr' in start_vars and
                 'min_loc_mb' in start_vars and
                 'max_loc_mb' in start_vars):
 
-                self.location_chr = get_string(start_vars,'loc_chr')
-                self.min_location_mb = get_int(start_vars,'min_loc_mb')
-                self.max_location_mb = get_int(start_vars,'max_loc_mb')
+                self.location_chr = get_string(start_vars, 'loc_chr')
+                self.min_location_mb = get_int(start_vars, 'min_loc_mb')
+                self.max_location_mb = get_int(start_vars, 'max_loc_mb')
             else:
                 self.location_chr = self.min_location_mb = self.max_location_mb = None
 
diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
index 832746bb..b582cd23 100644
--- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
+++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
@@ -275,8 +275,8 @@ def zScore(trait_data_array):
         i = 0
         for data in trait_data_array:
             N = len(data)
-            S = reduce(lambda x,y: x+y, data, 0.)
-            SS = reduce(lambda x,y: x+y*y, data, 0.)
+            S = reduce(lambda x, y: x+y, data, 0.)
+            SS = reduce(lambda x, y: x+y*y, data, 0.)
             mean = S/N
             var = SS - S*S/N
             stdev = math.sqrt(var/(N-1))
@@ -294,7 +294,7 @@ def sortEigenVectors(vector):
         combines = []
         i = 0
         for item in eigenValues:
-            combines.append([eigenValues[i],eigenVectors[i]])
+            combines.append([eigenValues[i], eigenVectors[i]])
             i += 1
         combines.sort(webqtlUtil.cmpEigenValue)
         A = []
@@ -302,7 +302,7 @@ def sortEigenVectors(vector):
         for item in combines:
             A.append(item[0])
             B.append(item[1])
-        sum = reduce(lambda x,y: x+y, A, 0.0)
+        sum = reduce(lambda x, y: x+y, A, 0.0)
         A = [x*100.0/sum for x in A] 
         return [A, B]
     except:
diff --git a/wqflask/wqflask/do_search.py b/wqflask/wqflask/do_search.py
index 1e15d28f..cc9c1860 100644
--- a/wqflask/wqflask/do_search.py
+++ b/wqflask/wqflask/do_search.py
@@ -46,8 +46,8 @@ class DoSearch(object):
 
     def handle_wildcard(self, str):
         keyword = str.strip()
-        keyword = keyword.replace("*",".*")
-        keyword = keyword.replace("?",".")
+        keyword = keyword.replace("*", ".*")
+        keyword = keyword.replace("?", ".")
 
         return keyword
 
diff --git a/wqflask/wqflask/external_tools/send_to_geneweaver.py b/wqflask/wqflask/external_tools/send_to_geneweaver.py
index 7a5dba73..9844bab4 100644
--- a/wqflask/wqflask/external_tools/send_to_geneweaver.py
+++ b/wqflask/wqflask/external_tools/send_to_geneweaver.py
@@ -54,10 +54,10 @@ class SendToGeneWeaver(object):
             trait_name_list = get_trait_name_list(self.trait_list)
 
             self.hidden_vars = {
-                                 'client'                     : "genenetwork",
-                                 'species'                    : species_name,
-                                 'idtype'                     : self.chip_name,
-                                 'list'                       : string.join(trait_name_list, ","),
+                                 'client': "genenetwork",
+                                 'species': species_name,
+                                 'idtype': self.chip_name,
+                                 'list': string.join(trait_name_list, ","),
                                }
 
 def get_trait_name_list(trait_list):
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index c8b9c405..f282b010 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -27,8 +27,8 @@
 import datetime
 import string
 from math import *
-from PIL import (Image,ImageDraw,ImageFont,ImageColor)
-import sys,os
+from PIL import (Image, ImageDraw, ImageFont, ImageColor)
+import sys, os
 import cPickle
 import httplib
 import json
@@ -426,7 +426,7 @@ class DisplayMappingResults(object):
                 else:
                     continue
             samplelist = list(self.genotype.prgy)
-            for j,_geno in enumerate (self.genotype[0][1].genotype):
+            for j, _geno in enumerate (self.genotype[0][1].genotype):
                 for item in smd:
                     if item.name == samplelist[j]:
                         self.NR_INDIVIDUALS = self.NR_INDIVIDUALS + 1
@@ -518,7 +518,7 @@ class DisplayMappingResults(object):
 
         #Scales plot differently for high resolution
         if self.draw2X:
-            intCanvasX2 = Image.new("RGBA", size=(self.graphWidth*2,self.graphHeight*2))
+            intCanvasX2 = Image.new("RGBA", size=(self.graphWidth*2, self.graphHeight*2))
             gifmapX2 = self.plotIntMapping(intCanvasX2, startMb = self.startMb, endMb = self.endMb, showLocusForm= showLocusForm, zoom=2)
             intCanvasX2.save(
                 "{}.png".format(
@@ -745,17 +745,17 @@ class DisplayMappingResults(object):
         bootScale = bootScale[:-1] + [highestPercent]
 
         bootOffset = 50*fontZoom
-        bootScaleFont=ImageFont.truetype(font=VERDANA_FILE,size=13*fontZoom)
+        bootScaleFont=ImageFont.truetype(font=VERDANA_FILE, size=13*fontZoom)
         im_drawer.rectangle(
             xy=((canvas.size[0]-bootOffset, yZero-bootHeightThresh),
-                (canvas.size[0]-bootOffset-15*zoom,yZero)),
+                (canvas.size[0]-bootOffset-15*zoom, yZero)),
             fill = YELLOW, outline=BLACK)
         im_drawer.line(
             xy=((canvas.size[0]-bootOffset+4, yZero),
                 (canvas.size[0]-bootOffset, yZero)),
             fill=BLACK)
         TEXT_Y_DISPLACEMENT = -8
-        im_drawer.text(xy=(canvas.size[0]-bootOffset+10,yZero+TEXT_Y_DISPLACEMENT), text='0%',
+        im_drawer.text(xy=(canvas.size[0]-bootOffset+10, yZero+TEXT_Y_DISPLACEMENT), text='0%',
                        font=bootScaleFont, fill=BLACK)
 
         for item in bootScale:
@@ -763,10 +763,10 @@ class DisplayMappingResults(object):
                 continue
             bootY = yZero-bootHeightThresh*item/highestPercent
             im_drawer.line(
-                xy=((canvas.size[0]-bootOffset+4,bootY),
-                 (canvas.size[0]-bootOffset,bootY)),
+                xy=((canvas.size[0]-bootOffset+4, bootY),
+                 (canvas.size[0]-bootOffset, bootY)),
                 fill=BLACK)
-            im_drawer.text(xy=(canvas.size[0]-bootOffset+10,bootY+TEXT_Y_DISPLACEMENT),
+            im_drawer.text(xy=(canvas.size[0]-bootOffset+10, bootY+TEXT_Y_DISPLACEMENT),
                            text='%2.1f'%item, font=bootScaleFont, fill=BLACK)
 
         if self.legendChecked:
@@ -775,7 +775,7 @@ class DisplayMappingResults(object):
             smallLabelFont = ImageFont.truetype(font=TREBUC_FILE, size=12*fontZoom)
             leftOffset = xLeftOffset+(nCol-1)*200
             im_drawer.rectangle(
-                xy=((leftOffset,startPosY-6), (leftOffset+12,startPosY+6)),
+                xy=((leftOffset, startPosY-6), (leftOffset+12, startPosY+6)),
                 fill=YELLOW, outline=BLACK)
             im_drawer.text(xy=(leftOffset+ 20, startPosY+TEXT_Y_DISPLACEMENT),
                            text='Frequency of the Peak LRS',
@@ -872,7 +872,7 @@ class DisplayMappingResults(object):
             TEXT_Y_DISPLACEMENT = -8
             im_drawer.text(
                 text="Sequence Site",
-                xy=(leftOffset+15,startPosY+TEXT_Y_DISPLACEMENT), font=smallLabelFont,
+                xy=(leftOffset+15, startPosY+TEXT_Y_DISPLACEMENT), font=smallLabelFont,
                 fill=self.TOP_RIGHT_INFO_COLOR)
 
     def drawSNPTrackNew(self, canvas, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
@@ -922,7 +922,7 @@ class DisplayMappingResults(object):
     def drawMultiTraitName(self, fd, canvas, gifmap, showLocusForm, offset= (40, 120, 80, 10), zoom = 1):
         nameWidths = []
         yPaddingTop = 10
-        colorFont=ImageFont.truetype(font=TREBUC_FILE,size=12)
+        colorFont=ImageFont.truetype(font=TREBUC_FILE, size=12)
         if len(self.qtlresults) >20 and self.selectedChr > -1:
             rightShift = 20
             rightShiftStep = 60
@@ -941,20 +941,20 @@ class DisplayMappingResults(object):
                 rightShift += rightShiftStep
 
             name = thisTrait.displayName()
-            nameWidth, nameHeight = im_drawer.textsize(name,font=colorFont)
+            nameWidth, nameHeight = im_drawer.textsize(name, font=colorFont)
             nameWidths.append(nameWidth)
 
             im_drawer.rectangle(
-                xy=((rightShift,yPaddingTop+kstep*15),
-                    (rectWidth+rightShift,yPaddingTop+10+kstep*15)),
+                xy=((rightShift, yPaddingTop+kstep*15),
+                    (rectWidth+rightShift, yPaddingTop+10+kstep*15)),
                 fill=thisLRSColor, outline=BLACK)
             im_drawer.text(
-                text=name,xy=(rectWidth+2+rightShift,yPaddingTop+10+kstep*15),
-                font=colorFont,fill=BLACK)
+                text=name, xy=(rectWidth+2+rightShift, yPaddingTop+10+kstep*15),
+                font=colorFont, fill=BLACK)
             if thisTrait.db:
-                COORDS = "%d,%d,%d,%d" %(rectWidth+2+rightShift,yPaddingTop+kstep*15,rectWidth+2+rightShift+nameWidth,yPaddingTop+10+kstep*15,)
+                COORDS = "%d,%d,%d,%d" %(rectWidth+2+rightShift, yPaddingTop+kstep*15, rectWidth+2+rightShift+nameWidth, yPaddingTop+10+kstep*15,)
                 HREF= "javascript:showDatabase3('%s','%s','%s','');" % (showLocusForm, thisTrait.db.name, thisTrait.name)
-                Areas = HT.Area(shape='rect',coords=COORDS,href=HREF)
+                Areas = HT.Area(shape='rect', coords=COORDS, href=HREF)
                 gifmap.areas.append(Areas)
 
     def drawLegendPanel(self, canvas, offset= (40, 120, 80, 10), zoom = 1):
@@ -968,80 +968,80 @@ class DisplayMappingResults(object):
         if zoom == 2:
             fontZoom = 1.5
 
-        labelFont=ImageFont.truetype(font=TREBUC_FILE,size=12*fontZoom)
+        labelFont=ImageFont.truetype(font=TREBUC_FILE, size=12*fontZoom)
         startPosY = 15
         stepPosY = 12*fontZoom
         if self.manhattan_plot != True:
             im_drawer.line(
-                xy=((xLeftOffset,startPosY),(xLeftOffset+32,startPosY)),
+                xy=((xLeftOffset, startPosY), (xLeftOffset+32, startPosY)),
                 fill=self.LRS_COLOR, width=2)
             im_drawer.text(
-                text=self.LRS_LOD, xy=(xLeftOffset+40,startPosY+TEXT_Y_DISPLACEMENT),
-                font=labelFont,fill=BLACK)
+                text=self.LRS_LOD, xy=(xLeftOffset+40, startPosY+TEXT_Y_DISPLACEMENT),
+                font=labelFont, fill=BLACK)
             startPosY += stepPosY
 
         if self.additiveChecked:
             startPosX = xLeftOffset
             im_drawer.line(
-                xy=((startPosX,startPosY),(startPosX+17,startPosY)),
+                xy=((startPosX, startPosY), (startPosX+17, startPosY)),
                 fill=self.ADDITIVE_COLOR_POSITIVE, width=2)
             im_drawer.line(
-                xy=((startPosX+18,startPosY),(startPosX+32,startPosY)),
+                xy=((startPosX+18, startPosY), (startPosX+32, startPosY)),
                 fill=self.ADDITIVE_COLOR_NEGATIVE, width=2)
             im_drawer.text(
-                text='Additive Effect',xy=(startPosX+40,startPosY+TEXT_Y_DISPLACEMENT),
-                font=labelFont,fill=BLACK)
+                text='Additive Effect', xy=(startPosX+40, startPosY+TEXT_Y_DISPLACEMENT),
+                font=labelFont, fill=BLACK)
 
         if self.genotype.type == 'intercross' and self.dominanceChecked:
             startPosX = xLeftOffset
             startPosY += stepPosY
             im_drawer.line(
-                xy=((startPosX,startPosY),(startPosX+17,startPosY)),
+                xy=((startPosX, startPosY), (startPosX+17, startPosY)),
                 fill=self.DOMINANCE_COLOR_POSITIVE, width=4)
             im_drawer.line(
-                xy=((startPosX+18,startPosY),(startPosX+35,startPosY)),
+                xy=((startPosX+18, startPosY), (startPosX+35, startPosY)),
                 fill=self.DOMINANCE_COLOR_NEGATIVE, width=4)
             im_drawer.text(
-                text='Dominance Effect', xy=(startPosX+42,startPosY+5),
-                font=labelFont,fill=BLACK)
+                text='Dominance Effect', xy=(startPosX+42, startPosY+5),
+                font=labelFont, fill=BLACK)
 
         if self.haplotypeAnalystChecked:
             startPosY += stepPosY
             startPosX = xLeftOffset
             im_drawer.line(
-                xy=((startPosX,startPosY),(startPosX+17,startPosY)),
+                xy=((startPosX, startPosY), (startPosX+17, startPosY)),
                 fill=self.HAPLOTYPE_POSITIVE, width=4)
             im_drawer.line(
-                xy=((startPosX+18,startPosY),(startPosX+35,startPosY)),
+                xy=((startPosX+18, startPosY), (startPosX+35, startPosY)),
                 fill=self.HAPLOTYPE_NEGATIVE, width=4)
             im_drawer.line(
-                xy=((startPosX+36,startPosY),(startPosX+53,startPosY)),
+                xy=((startPosX+36, startPosY), (startPosX+53, startPosY)),
                 fill=self.HAPLOTYPE_HETEROZYGOUS, width=4)
             im_drawer.line(
-                xy=((startPosX+54,startPosY),(startPosX+67,startPosY)),
+                xy=((startPosX+54, startPosY), (startPosX+67, startPosY)),
                 fill=self.HAPLOTYPE_RECOMBINATION, width=4)
             im_drawer.text(
                 text='Haplotypes (Pat, Mat, Het, Unk)',
-                xy=(startPosX+76,startPosY+5),font=labelFont,fill=BLACK)
+                xy=(startPosX+76, startPosY+5), font=labelFont, fill=BLACK)
 
         if self.permChecked and self.nperm > 0:
             startPosY += stepPosY
             startPosX = xLeftOffset
             im_drawer.line(
-                xy=((startPosX, startPosY),( startPosX + 32, startPosY)),
+                xy=((startPosX, startPosY), ( startPosX + 32, startPosY)),
                 fill=self.SIGNIFICANT_COLOR, width=self.SIGNIFICANT_WIDTH)
             im_drawer.line(
-                xy=((startPosX, startPosY + stepPosY),( startPosX + 32, startPosY + stepPosY)),
+                xy=((startPosX, startPosY + stepPosY), ( startPosX + 32, startPosY + stepPosY)),
                 fill=self.SUGGESTIVE_COLOR, width=self.SUGGESTIVE_WIDTH)
             im_drawer.text(
-                text='Significant %s = %2.2f' % (self.LRS_LOD,self.significant),
-                xy=(xLeftOffset+42,startPosY+TEXT_Y_DISPLACEMENT),font=labelFont,fill=BLACK)
+                text='Significant %s = %2.2f' % (self.LRS_LOD, self.significant),
+                xy=(xLeftOffset+42, startPosY+TEXT_Y_DISPLACEMENT), font=labelFont, fill=BLACK)
             im_drawer.text(
                 text='Suggestive %s = %2.2f' % (self.LRS_LOD, self.suggestive),
-                xy=(xLeftOffset+42,startPosY + TEXT_Y_DISPLACEMENT +stepPosY),font=labelFont,
+                xy=(xLeftOffset+42, startPosY + TEXT_Y_DISPLACEMENT +stepPosY), font=labelFont,
                 fill=BLACK)
 
-        labelFont = ImageFont.truetype(font=VERDANA_FILE,size=12*fontZoom)
+        labelFont = ImageFont.truetype(font=VERDANA_FILE, size=12*fontZoom)
         labelColor = BLACK
         if self.dataset.type == "Publish" or self.dataset.type == "Geno":
             dataset_label = self.dataset.fullname
@@ -1109,22 +1109,22 @@ class DisplayMappingResults(object):
                 im_drawer.textsize(string2, font=labelFont)[0])
             im_drawer.text(
                 text=identification,
-                xy=(canvas.size[0] - xRightOffset-d,20*fontZoom),font=labelFont,
+                xy=(canvas.size[0] - xRightOffset-d, 20*fontZoom), font=labelFont,
                 fill=labelColor)
         else:
             d = 4+ max(
                 im_drawer.textsize(string1, font=labelFont)[0],
                 im_drawer.textsize(string2, font=labelFont)[0])
         im_drawer.text(
-            text=string1,xy=(canvas.size[0] - xRightOffset-d,35*fontZoom),
-            font=labelFont,fill=labelColor)
+            text=string1, xy=(canvas.size[0] - xRightOffset-d, 35*fontZoom),
+            font=labelFont, fill=labelColor)
         im_drawer.text(
-            text=string2,xy=(canvas.size[0] - xRightOffset-d,50*fontZoom),
-            font=labelFont,fill=labelColor)
+            text=string2, xy=(canvas.size[0] - xRightOffset-d, 50*fontZoom),
+            font=labelFont, fill=labelColor)
         if string3 != '':
             im_drawer.text(
-                text=string3,xy=(canvas.size[0] - xRightOffset-d,65*fontZoom),
-                font=labelFont,fill=labelColor)
+                text=string3, xy=(canvas.size[0] - xRightOffset-d, 65*fontZoom),
+                font=labelFont, fill=labelColor)
 
 
     def drawGeneBand(self, canvas, gifmap, plotXScale, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
@@ -1345,7 +1345,7 @@ class DisplayMappingResults(object):
                             labelText = "3'"
                             im_drawer.text(
                                 text=labelText,
-                                xy=(utrEndPix+2,geneYLocation+self.EACH_GENE_HEIGHT),
+                                xy=(utrEndPix+2, geneYLocation+self.EACH_GENE_HEIGHT),
                                 font=ImageFont.truetype(font=ARIAL_FILE, size=2))
 
             #draw the genes as rectangles
@@ -1357,7 +1357,7 @@ class DisplayMappingResults(object):
 
             COORDS = "%d, %d, %d, %d" %(geneStartPix, geneYLocation, geneEndPix, (geneYLocation + self.EACH_GENE_HEIGHT))
             # NL: 06-02-2011 Rob required to display NCBI info in a new window
-            gifmap.areas.append(HT.Area(shape='rect',coords=COORDS,href=HREF, title=TITLE,target="_blank"))
+            gifmap.areas.append(HT.Area(shape='rect', coords=COORDS, href=HREF, title=TITLE, target="_blank"))
 
 ## BEGIN HaplotypeAnalyst
     def drawHaplotypeBand(self, canvas, gifmap, plotXScale, offset= (40, 120, 80, 10), zoom = 1, startMb = None, endMb = None):
@@ -1490,7 +1490,7 @@ class DisplayMappingResults(object):
                                         counter = counter + 1
                                         if item.name == samplelist[k]:
                                             ind = counter
-                                    maxind=max(ind,maxind)
+                                    maxind=max(ind, maxind)
 
                                     # lines
                                     if (oldgeno[k] == -1 and _geno == -1):
@@ -1523,7 +1523,7 @@ class DisplayMappingResults(object):
                                     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 = ''
-                                    gifmap.areas.append(HT.Area(shape='rect',coords=COORDS,href=HREF, title=TITLE))
+                                    gifmap.areas.append(HT.Area(shape='rect', coords=COORDS, href=HREF, title=TITLE))
 
                                     # if there are no more markers in a chromosome, the plotRight value calculated above will be before the plotWidth
                                     # resulting in some empty space on the right side of the plot area. This draws an "unknown" bar from plotRight to the edge.
@@ -1642,14 +1642,14 @@ class DisplayMappingResults(object):
                 WEBQTL_HREF = "javascript:rangeView('%s', %f, %f)" % (self.selectedChr - 1, max(0, (calBase-webqtlZoomWidth))/1000000.0, (calBase+webqtlZoomWidth)/1000000.0)
 
                 WEBQTL_TITLE = "Click to view this section of the genome in WebQTL"
-                gifmap.areas.append(HT.Area(shape='rect',coords=WEBQTL_COORDS,href=WEBQTL_HREF, title=WEBQTL_TITLE))
+                gifmap.areas.append(HT.Area(shape='rect', coords=WEBQTL_COORDS, href=WEBQTL_HREF, title=WEBQTL_TITLE))
                 im_drawer.rectangle(
                     xy=((xBrowse1, paddingTop),
                         (xBrowse2, (paddingTop + self.BAND_HEIGHT))),
                     outline=self.CLICKABLE_WEBQTL_REGION_COLOR,
                     fill=self.CLICKABLE_WEBQTL_REGION_COLOR)
                 im_drawer.line(
-                    xy=((xBrowse1, paddingTop),( xBrowse1, (paddingTop + self.BAND_HEIGHT))),
+                    xy=((xBrowse1, paddingTop), ( xBrowse1, (paddingTop + self.BAND_HEIGHT))),
                     fill=self.CLICKABLE_WEBQTL_REGION_OUTLINE_COLOR)
 
                 if self.dataset.group.species == "mouse" or self.dataset.group.species == "rat":
@@ -1659,14 +1659,14 @@ class DisplayMappingResults(object):
                     else:
                         PHENOGEN_HREF = "https://phenogen.org/gene.jsp?speciesCB=Mm&auto=Y&geneTxt=chr%s:%d-%d&genomeVer=mm10" % (self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases)
                     PHENOGEN_TITLE = "Click to view this section of the genome in PhenoGen"
-                    gifmap.areas.append(HT.Area(shape='rect',coords=PHENOGEN_COORDS,href=PHENOGEN_HREF, title=PHENOGEN_TITLE))
+                    gifmap.areas.append(HT.Area(shape='rect', coords=PHENOGEN_COORDS, href=PHENOGEN_HREF, title=PHENOGEN_TITLE))
                     im_drawer.rectangle(
                         xy=((xBrowse1, phenogenPaddingTop),
                             (xBrowse2, (phenogenPaddingTop+self.BAND_HEIGHT))),
                         outline=self.CLICKABLE_PHENOGEN_REGION_COLOR,
                         fill=self.CLICKABLE_PHENOGEN_REGION_COLOR)
                     im_drawer.line(
-                        xy=((xBrowse1, phenogenPaddingTop),( xBrowse1, (phenogenPaddingTop+self.BAND_HEIGHT))),
+                        xy=((xBrowse1, phenogenPaddingTop), ( xBrowse1, (phenogenPaddingTop+self.BAND_HEIGHT))),
                         fill=self.CLICKABLE_PHENOGEN_REGION_OUTLINE_COLOR)
 
                 UCSC_COORDS = "%d, %d, %d, %d" %(xBrowse1, ucscPaddingTop, xBrowse2, (ucscPaddingTop+self.BAND_HEIGHT))
@@ -1675,7 +1675,7 @@ class DisplayMappingResults(object):
                 else:
                     UCSC_HREF = "http://genome.ucsc.edu/cgi-bin/hgTracks?db=%s&position=chr%s:%d-%d" % (self._ucscDb, self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases)
                 UCSC_TITLE = "Click to view this section of the genome in the UCSC Genome Browser"
-                gifmap.areas.append(HT.Area(shape='rect',coords=UCSC_COORDS,href=UCSC_HREF, title=UCSC_TITLE))
+                gifmap.areas.append(HT.Area(shape='rect', coords=UCSC_COORDS, href=UCSC_HREF, title=UCSC_TITLE))
                 im_drawer.rectangle(
                     xy=((xBrowse1, ucscPaddingTop),
                         (xBrowse2, (ucscPaddingTop+self.BAND_HEIGHT))),
@@ -1692,7 +1692,7 @@ class DisplayMappingResults(object):
                 else:
                     ENSEMBL_HREF = "http://www.ensembl.org/Rattus_norvegicus/contigview?chr=%s&start=%d&end=%d" % (self.selectedChr, max(0, calBase-flankingWidthInBases), calBase+flankingWidthInBases)
                 ENSEMBL_TITLE = "Click to view this section of the genome in the Ensembl Genome Browser"
-                gifmap.areas.append(HT.Area(shape='rect',coords=ENSEMBL_COORDS,href=ENSEMBL_HREF, title=ENSEMBL_TITLE))
+                gifmap.areas.append(HT.Area(shape='rect', coords=ENSEMBL_COORDS, href=ENSEMBL_HREF, title=ENSEMBL_TITLE))
                 im_drawer.rectangle(
                     xy=((xBrowse1, ensemblPaddingTop),
                         (xBrowse2, (ensemblPaddingTop+self.BAND_HEIGHT))),
@@ -1789,8 +1789,8 @@ class DisplayMappingResults(object):
                         continue
                     Xc = xLeftOffset + plotXScale*(_Mb - startMb)
                     if counter % NUM_MINOR_TICKS == 0: # Draw a MAJOR mark, not just a minor tick mark
-                        im_drawer.line(xy=((Xc,yZero),
-                                           (Xc,yZero+xMajorTickHeight)),
+                        im_drawer.line(xy=((Xc, yZero),
+                                           (Xc, yZero+xMajorTickHeight)),
                                        fill=xAxisTickMarkColor,
                                        width=X_MAJOR_TICK_THICKNESS) # Draw the MAJOR tick mark
                         labelStr = str(formatStr % _Mb) # What Mbase location to put on the label
@@ -1800,8 +1800,8 @@ class DisplayMappingResults(object):
                                        text=labelStr, font=MBLabelFont,
                                        fill=xAxisLabelColor)
                     else:
-                        im_drawer.line(xy=((Xc,yZero),
-                                          (Xc,yZero+xMinorTickHeight)),
+                        im_drawer.line(xy=((Xc, yZero),
+                                          (Xc, yZero+xMinorTickHeight)),
                                        fill=xAxisTickMarkColor,
                                        width=X_MINOR_TICK_THICKNESS) # Draw the MINOR tick mark
 
@@ -1834,7 +1834,7 @@ class DisplayMappingResults(object):
                 text="Megabases",
                 xy=(
                     xLeftOffset+(plotWidth-im_drawer.textsize(
-                        "Megabases",font=megabaseLabelFont)[0])/2,
+                        "Megabases", font=megabaseLabelFont)[0])/2,
                     strYLoc+MBLabelFont.font.height+10*(zoom%2)),
                 font=megabaseLabelFont, fill=BLACK)
             pass
@@ -1889,7 +1889,7 @@ class DisplayMappingResults(object):
             for j, ChrInfo in enumerate(ChrAInfo):
                 preLpos = -1
                 for i, item in enumerate(ChrInfo):
-                    Lname,Lpos = item
+                    Lname, Lpos = item
                     if Lpos != preLpos:
                         offsetA += stepA
                         differ = 1
@@ -1903,17 +1903,17 @@ class DisplayMappingResults(object):
                         Zorder = 0
                     if differ:
                         im_drawer.line(
-                            xy=((startPosX+Lpos,yZero),(xLeftOffset+offsetA,\
+                            xy=((startPosX+Lpos, yZero), (xLeftOffset+offsetA,\
                         yZero+25)),
                             fill=lineColor)
                         im_drawer.line(
-                            xy=((xLeftOffset+offsetA,yZero+25),(xLeftOffset+offsetA,\
+                            xy=((xLeftOffset+offsetA, yZero+25), (xLeftOffset+offsetA,\
                         yZero+40+Zorder*(LRectWidth+3))),
                             fill=lineColor)
                         rectColor = ORANGE
                     else:
                         im_drawer.line(
-                            xy=((xLeftOffset+offsetA, yZero+40+Zorder*(LRectWidth+3)-3),(\
+                            xy=((xLeftOffset+offsetA, yZero+40+Zorder*(LRectWidth+3)-3), (\
                         xLeftOffset+offsetA, yZero+40+Zorder*(LRectWidth+3))),
                             fill=lineColor)
                         rectColor = DEEPPINK
@@ -1921,9 +1921,9 @@ class DisplayMappingResults(object):
                         xy=((xLeftOffset+offsetA, yZero+40+Zorder*(LRectWidth+3)),
                             (xLeftOffset+offsetA-LRectHeight,
                              yZero+40+Zorder*(LRectWidth+3)+LRectWidth)),
-                        outline=rectColor,fill=rectColor,width = 0)
+                        outline=rectColor, fill=rectColor, width = 0)
                     COORDS="%d,%d,%d,%d"%(xLeftOffset+offsetA-LRectHeight, yZero+40+Zorder*(LRectWidth+3),\
-                            xLeftOffset+offsetA,yZero+40+Zorder*(LRectWidth+3)+LRectWidth)
+                            xLeftOffset+offsetA, yZero+40+Zorder*(LRectWidth+3)+LRectWidth)
                     HREF="/show_trait?trait_id=%s&dataset=%s" % (Lname, self.dataset.group.name+"Geno")
                     #HREF="javascript:showDatabase3('%s','%s','%s','');" % (showLocusForm,fd.RISet+"Geno", Lname)
                     Areas=HT.Area(shape='rect', coords=COORDS, href=HREF, target="_blank", title="Locus : " + Lname)
@@ -1931,7 +1931,7 @@ class DisplayMappingResults(object):
                 ##piddle bug
                 if j == 0:
                     im_drawer.line(
-                        xy=((startPosX,yZero),(startPosX,yZero+40)),
+                        xy=((startPosX, yZero), (startPosX, yZero+40)),
                         fill=lineColor)
                 startPosX += (self.ChrLengthDistList[j]+self.GraphInterval)*plotXScale
 
@@ -1943,7 +1943,7 @@ class DisplayMappingResults(object):
                     strYLoc + MBLabelFont.font.height+ 10*(zoom%2)),
                 font=centimorganLabelFont, fill=BLACK)
 
-        im_drawer.line(xy=((xLeftOffset,yZero), (xLeftOffset+plotWidth,yZero)),
+        im_drawer.line(xy=((xLeftOffset, yZero), (xLeftOffset+plotWidth, yZero)),
                        fill=BLACK, width=X_AXIS_THICKNESS) # Draw the X axis itself
 
 
@@ -2079,7 +2079,7 @@ class DisplayMappingResults(object):
                 LRS_LOD_Max = 0.000001
             yTopOffset + 30*(zoom - 1)
             yLRS = yZero - (item/LRS_LOD_Max) * LRSHeightThresh
-            im_drawer.line(xy=((xLeftOffset,yLRS), (xLeftOffset-4,yLRS)),
+            im_drawer.line(xy=((xLeftOffset, yLRS), (xLeftOffset-4, yLRS)),
                            fill=self.LRS_COLOR, width=1*zoom)
             if all_int:
                 scaleStr = "%d" % item
@@ -2127,8 +2127,8 @@ class DisplayMappingResults(object):
                 else:
                     sugg_title = "Suggestive LOD = %0.2f" % (self.suggestive/4.61)
                     sig_title = "Significant LOD = %0.2f" % (self.significant/4.61)
-                Areas1 = HT.Area(shape='rect',coords=sugg_coords,title=sugg_title)
-                Areas2 = HT.Area(shape='rect',coords=sig_coords,title=sig_title)
+                Areas1 = HT.Area(shape='rect', coords=sugg_coords, title=sugg_title)
+                Areas2 = HT.Area(shape='rect', coords=sig_coords, title=sig_title)
                 gifmap.areas.append(Areas1)
                 gifmap.areas.append(Areas2)
 
@@ -2316,7 +2316,7 @@ class DisplayMappingResults(object):
                     im_drawer.text(
                         text="5",
                         xy=(
-                            Xc-im_drawer.textsize("5",font=symbolFont)[0]/2+1,
+                            Xc-im_drawer.textsize("5", font=symbolFont)[0]/2+1,
                             Yc-4),
                         fill=point_color, font=symbolFont)
                 else:
@@ -2383,8 +2383,8 @@ class DisplayMappingResults(object):
                             )
                         else:
                             im_drawer.line(
-                                xy=((Xc0,yZero-(Yc0-yZero)),
-                                    (Xc,yZero-(Yc-yZero))),
+                                xy=((Xc0, yZero-(Yc0-yZero)),
+                                    (Xc, yZero-(Yc-yZero))),
                                 fill=minusColor, width=lineWidth
                                 #, clipX=(xLeftOffset, xLeftOffset + plotWidth)
                             )
@@ -2471,8 +2471,8 @@ class DisplayMappingResults(object):
 
         ###draw additive scale
         if not self.multipleInterval and self.additiveChecked:
-            additiveScaleFont=ImageFont.truetype(font=VERDANA_FILE,size=16*zoom)
-            additiveScale = Plot.detScaleOld(0,additiveMax)
+            additiveScaleFont=ImageFont.truetype(font=VERDANA_FILE, size=16*zoom)
+            additiveScale = Plot.detScaleOld(0, additiveMax)
             additiveStep = (additiveScale[1]-additiveScale[0])/additiveScale[2]
             additiveAxisList = Plot.frange(0, additiveScale[1], additiveStep)
             addPlotScale = AdditiveHeightThresh/additiveMax
@@ -2482,18 +2482,18 @@ class DisplayMappingResults(object):
             for item in additiveAxisList:
                 additiveY = yZero - item*addPlotScale
                 im_drawer.line(
-                    xy=((xLeftOffset + plotWidth,additiveY),
-                        (xLeftOffset+4+ plotWidth,additiveY)),
+                    xy=((xLeftOffset + plotWidth, additiveY),
+                        (xLeftOffset+4+ plotWidth, additiveY)),
                     fill=self.ADDITIVE_COLOR_POSITIVE, width=1*zoom)
                 scaleStr = "%2.3f" % item
                 im_drawer.text(
                     text=scaleStr,
-                    xy=(xLeftOffset + plotWidth +6,additiveY+TEXT_Y_DISPLACEMENT),
-                    font=additiveScaleFont,fill=self.ADDITIVE_COLOR_POSITIVE)
+                    xy=(xLeftOffset + plotWidth +6, additiveY+TEXT_Y_DISPLACEMENT),
+                    font=additiveScaleFont, fill=self.ADDITIVE_COLOR_POSITIVE)
 
             im_drawer.line(
-                xy=((xLeftOffset+plotWidth,additiveY),
-                    (xLeftOffset+plotWidth,yZero)),
+                xy=((xLeftOffset+plotWidth, additiveY),
+                    (xLeftOffset+plotWidth, yZero)),
                 fill=self.ADDITIVE_COLOR_POSITIVE, width=1*zoom)
 
         im_drawer.line(
@@ -2553,7 +2553,7 @@ class DisplayMappingResults(object):
                 chrFontZoom = 2
             else:
                 chrFontZoom = 1
-            chrLabelFont=ImageFont.truetype(font=VERDANA_FILE,size=24*chrFontZoom)
+            chrLabelFont=ImageFont.truetype(font=VERDANA_FILE, size=24*chrFontZoom)
 
             for i, _chr in enumerate(self.genotype):
                 if (i % 2 == 0):
@@ -2575,10 +2575,10 @@ class DisplayMappingResults(object):
                 TEXT_Y_DISPLACEMENT = 0
                 im_drawer.text(xy=(chrStartPix, yTopOffset + TEXT_Y_DISPLACEMENT),
                                text=_chr.name, font=chrLabelFont, fill=BLACK)
-                COORDS = "%d,%d,%d,%d" %(chrStartPix, yTopOffset, chrEndPix,yTopOffset +20)
+                COORDS = "%d,%d,%d,%d" %(chrStartPix, yTopOffset, chrEndPix, yTopOffset +20)
 
                 #add by NL 09-03-2010
-                HREF = "javascript:chrView(%d,%s);" % (i,self.ChrLengthMbList)
+                HREF = "javascript:chrView(%d,%s);" % (i, self.ChrLengthMbList)
                 #HREF = "javascript:changeView(%d,%s);" % (i,self.ChrLengthMbList)
                 Areas = HT.Area(shape='rect', coords=COORDS, href=HREF)
                 gifmap.areas.append(Areas)
@@ -2720,7 +2720,7 @@ class DisplayMappingResults(object):
                     else:
                         chr_as_int = int(theGO["Chromosome"]) - 1
                     if refGene:
-                        literatureCorrelationString = str(self.getLiteratureCorrelation(self.cursor,refGene,theGO['GeneID']) or "N/A")
+                        literatureCorrelationString = str(self.getLiteratureCorrelation(self.cursor, refGene, theGO['GeneID']) or "N/A")
 
                         this_row = [selectCheck.__str__(),
                                     str(tableIterationsCnt),
@@ -2820,8 +2820,8 @@ class DisplayMappingResults(object):
         lCorr = None
         try:
             query = 'SELECT Value FROM LCorrRamin3 WHERE GeneId1 = %s and GeneId2 = %s'
-            for x,y in [(geneId1,geneId2),(geneId2,geneId1)]:
-                cursor.execute(query,(x,y))
+            for x, y in [(geneId1, geneId2), (geneId2, geneId1)]:
+                cursor.execute(query, (x, y))
                 lCorr =  cursor.fetchone()
                 if lCorr:
                     lCorr = lCorr[0]
diff --git a/wqflask/wqflask/marker_regression/plink_mapping.py b/wqflask/wqflask/marker_regression/plink_mapping.py
index d4ee6fe6..2f282adc 100644
--- a/wqflask/wqflask/marker_regression/plink_mapping.py
+++ b/wqflask/wqflask/marker_regression/plink_mapping.py
@@ -54,7 +54,7 @@ def gen_pheno_txt_file_plink(this_trait, dataset, vals, pheno_filename = ''):
     for i, sample in enumerate(ped_sample_list):
         try:
             value = vals[i]
-            value = str(value).replace('value=','')
+            value = str(value).replace('value=', '')
             value = value.strip()
         except:
             value = -9999
@@ -78,7 +78,7 @@ def gen_pheno_txt_file_plink(this_trait, dataset, vals, pheno_filename = ''):
 
 # get strain name from ped file in order
 def get_samples_from_ped_file(dataset):
-    ped_file= open("{}{}.ped".format(flat_files('mapping'), dataset.group.name),"r")
+    ped_file= open("{}{}.ped".format(flat_files('mapping'), dataset.group.name), "r")
     line = ped_file.readline()
     sample_list=[]
 
@@ -155,7 +155,7 @@ def parse_plink_output(output_filename, species):
 # output: lineList list
 #######################################################
 def build_line_list(line=None):
-    line_list = string.split(string.strip(line),' ')# irregular number of whitespaces between columns
+    line_list = string.split(string.strip(line), ' ')# irregular number of whitespaces between columns
     line_list = [item for item in line_list if item !='']
     line_list = list(map(string.strip, line_list))
 
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index 145dbc77..1e6dff57 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -707,7 +707,7 @@ def get_perm_strata(this_trait, sample_list, categorical_vars, used_samples):
 
         perm_strata_strings.append(combined_string)
 
-    d = dict([(y,x+1) for x,y in enumerate(sorted(set(perm_strata_strings)))])
+    d = dict([(y, x+1) for x, y in enumerate(sorted(set(perm_strata_strings)))])
     list_to_numbers = [d[x] for x in perm_strata_strings]
     perm_strata = list_to_numbers
 
diff --git a/wqflask/wqflask/search_results.py b/wqflask/wqflask/search_results.py
index 5b3946e3..c07a7670 100644
--- a/wqflask/wqflask/search_results.py
+++ b/wqflask/wqflask/search_results.py
@@ -53,7 +53,7 @@ views.py).
         search = self.search_terms
         self.original_search_string = self.search_terms
         # check for dodgy search terms
-        rx = re.compile(r'.*\W(href|http|sql|select|update)\W.*',re.IGNORECASE)
+        rx = re.compile(r'.*\W(href|http|sql|select|update)\W.*', re.IGNORECASE)
         if rx.match(search):
             logger.info("Regex failed search")
             self.search_term_exists = False
diff --git a/wqflask/wqflask/show_trait/SampleList.py b/wqflask/wqflask/show_trait/SampleList.py
index 21ba7f63..f17e825e 100644
--- a/wqflask/wqflask/show_trait/SampleList.py
+++ b/wqflask/wqflask/show_trait/SampleList.py
@@ -57,7 +57,7 @@ class SampleList(object):
                     sample = webqtlCaseData.webqtlCaseData(name=sample_name)
 
             sample.extra_info = {}
-            if self.dataset.group.name == 'AXBXA' and sample_name in ('AXB18/19/20','AXB13/14','BXA8/17'):
+            if self.dataset.group.name == 'AXBXA' and sample_name in ('AXB18/19/20', 'AXB13/14', 'BXA8/17'):
                 sample.extra_info['url'] = "/mouseCross.html#AXB/BXA"
                 sample.extra_info['css_class'] = "fs12"
 
diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py
index a871e91a..232cb8da 100644
--- a/wqflask/wqflask/user_manager.py
+++ b/wqflask/wqflask/user_manager.py
@@ -867,7 +867,7 @@ def forgot_password_submit():
     email_address = params['email_address']
     next_page = None
     if email_address != "":
-        logger.debug("Wants to send password E-mail to ",email_address)
+        logger.debug("Wants to send password E-mail to ", email_address)
         user_details = get_user_by_unique_column("email_address", email_address)
         if user_details:
             ForgotPasswordEmail(user_details["email_address"])
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 394a9e28..92c20fc7 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -55,7 +55,7 @@ from wqflask.ctl import ctl_analysis
 from wqflask.snp_browser import snp_browser
 
 from utility import temp_data
-from utility.tools import SQL_URI,TEMPDIR,USE_REDIS,USE_GN_SERVER,GN_SERVER_URL,GN_VERSION,JS_TWITTER_POST_FETCHER_PATH,JS_GUIX_PATH, CSS_PATH
+from utility.tools import SQL_URI, TEMPDIR, USE_REDIS, USE_GN_SERVER, GN_SERVER_URL, GN_VERSION, JS_TWITTER_POST_FETCHER_PATH, JS_GUIX_PATH, CSS_PATH
 from utility.helper_functions import get_species_groups
 from utility.authentication_tools import check_resource_availability
 from utility.redis_tools import get_redis_conn
@@ -133,10 +133,10 @@ def handle_bad_request(e):
         list = [fn for fn in os.listdir("./wqflask/static/gif/error") if fn.endswith(".gif") ]
         animation = random.choice(list)
 
-    resp = make_response(render_template("error.html",message=err_msg,stack=formatted_lines,error_image=animation,version=GN_VERSION))
+    resp = make_response(render_template("error.html", message=err_msg, stack=formatted_lines, error_image=animation, version=GN_VERSION))
 
     # logger.error("Set cookie %s with %s" % (err_msg, animation))
-    resp.set_cookie(err_msg[:32],animation)
+    resp.set_cookie(err_msg[:32], animation)
     return resp
 
 @app.route("/authentication_needed")
@@ -257,7 +257,7 @@ def docedit():
 @app.route('/generated/<filename>')
 def generated_file(filename):
     logger.info(request.url)
-    return send_from_directory(GENERATED_IMAGE_DIR,filename)
+    return send_from_directory(GENERATED_IMAGE_DIR, filename)
 
 @app.route("/help")
 def help():
-- 
cgit v1.2.3


From 1f4fb6b24f3508d80be1f07cd62e38ac9385ef41 Mon Sep 17 00:00:00 2001
From: BonfaceKilz
Date: Thu, 20 Aug 2020 16:35:17 +0300
Subject: Handle module renames in the standard library

Run:
```
2to3-3.8 -f imports -w . && \
2to3-3.8 -f imports2 -w .
```

See: <https://docs.python.org/2/library/2to3.html#2to3fixer-imports> and
<https://docs.python.org/2/library/2to3.html#2to3fixer-imports2>
---
 wqflask/base/data_set.py                                 |  2 +-
 wqflask/maintenance/gen_select_dataset.py                |  4 ++--
 wqflask/maintenance/quantile_normalize.py                |  4 ++--
 wqflask/maintenance/set_resource_defaults.py             |  4 ++--
 wqflask/utility/svg.py                                   | 16 ++++++++--------
 wqflask/wqflask/api/router.py                            | 14 +++++++-------
 wqflask/wqflask/collect.py                               |  2 +-
 .../wqflask/comparison_bar_chart/comparison_bar_chart.py |  2 +-
 wqflask/wqflask/correlation/show_corr_results.py         |  2 +-
 wqflask/wqflask/correlation_matrix/show_corr_matrix.py   |  2 +-
 wqflask/wqflask/export_traits.py                         |  4 ++--
 wqflask/wqflask/heatmap/heatmap.py                       |  4 ++--
 .../wqflask/marker_regression/display_mapping_results.py |  4 ++--
 wqflask/wqflask/marker_regression/run_mapping.py         |  2 +-
 wqflask/wqflask/network_graph/network_graph.py           |  2 +-
 wqflask/wqflask/show_trait/show_trait.py                 |  2 +-
 wqflask/wqflask/user_manager.py                          |  2 +-
 wqflask/wqflask/views.py                                 | 12 ++++++------
 18 files changed, 42 insertions(+), 42 deletions(-)

(limited to 'wqflask/maintenance/set_resource_defaults.py')

diff --git a/wqflask/base/data_set.py b/wqflask/base/data_set.py
index 43beec26..8151a29d 100644
--- a/wqflask/base/data_set.py
+++ b/wqflask/base/data_set.py
@@ -44,7 +44,7 @@ import codecs
 import json
 import requests
 import gzip
-import cPickle as pickle
+import pickle as pickle
 import itertools
 
 from redis import Redis
diff --git a/wqflask/maintenance/gen_select_dataset.py b/wqflask/maintenance/gen_select_dataset.py
index d12b328f..fd65a52a 100644
--- a/wqflask/maintenance/gen_select_dataset.py
+++ b/wqflask/maintenance/gen_select_dataset.py
@@ -50,7 +50,7 @@ from utility.tools import locate, locate_ignore_error, TEMPDIR, SQL_URI
 import MySQLdb
 
 import simplejson as json
-import urlparse
+import urllib.parse
 
 
 #import sqlalchemy as sa
@@ -66,7 +66,7 @@ from pprint import pformat as pf
 def parse_db_uri():
     """Converts a database URI to the db name, host name, user name, and password"""
 
-    parsed_uri = urlparse.urlparse(SQL_URI)
+    parsed_uri = urllib.parse.urlparse(SQL_URI)
 
     db_conn_info = dict(
                         db = parsed_uri.path[1:],
diff --git a/wqflask/maintenance/quantile_normalize.py b/wqflask/maintenance/quantile_normalize.py
index 43edfd13..4d6e03bf 100644
--- a/wqflask/maintenance/quantile_normalize.py
+++ b/wqflask/maintenance/quantile_normalize.py
@@ -6,7 +6,7 @@ sys.path.insert(0, './')
 
 
 import MySQLdb
-import urlparse
+import urllib.parse
 
 import numpy as np
 import pandas as pd
@@ -22,7 +22,7 @@ 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"""
 
-    parsed_uri = urlparse.urlparse(SQL_URI)
+    parsed_uri = urllib.parse.urlparse(SQL_URI)
 
     db_conn_info = dict(
                         db = parsed_uri.path[1:],
diff --git a/wqflask/maintenance/set_resource_defaults.py b/wqflask/maintenance/set_resource_defaults.py
index d53a255b..abd5416c 100644
--- a/wqflask/maintenance/set_resource_defaults.py
+++ b/wqflask/maintenance/set_resource_defaults.py
@@ -34,7 +34,7 @@ Redis = get_redis_conn()
 
 import MySQLdb
 
-import urlparse
+import urllib.parse
 
 from utility.logger import getLogger
 logger = getLogger(__name__)
@@ -42,7 +42,7 @@ 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)
+    parsed_uri = urllib.parse.urlparse(SQL_URI)
 
     db_conn_info = dict(
                         db = parsed_uri.path[1:],
diff --git a/wqflask/utility/svg.py b/wqflask/utility/svg.py
index 19eda0ce..b92cc2d1 100644
--- a/wqflask/utility/svg.py
+++ b/wqflask/utility/svg.py
@@ -957,8 +957,8 @@ class drawing:
         # Voeg een element toe aan de grafiek toe.
     if use_dom_implementation==0:
         def toXml(self, filename='',compress=False):
-            import cStringIO
-            xml=cStringIO.StringIO()
+            import io
+            xml=io.StringIO()
             xml.write("<?xml version='1.0' encoding='UTF-8'?>\n")
             xml.write("<!DOCTYPE svg PUBLIC \"-//W3C//DTD SVG 1.0//EN\" \"http://www.w3.org/TR/2001/REC-SVG-20010904/DTD/svg10.dtd\"")
             if self.entity:
@@ -971,7 +971,7 @@ class drawing:
             if not filename:
                 if compress:
                     import gzip
-                    f=cStringIO.StringIO()
+                    f=io.StringIO()
                     zf=gzip.GzipFile(fileobj=f, mode='wb')
                     zf.write(xml.getvalue())
                     zf.close()
@@ -1024,12 +1024,12 @@ class drawing:
                 return elementroot
             root=appender(self.svg, root)
             if not filename:
-                import cStringIO
-                xml=cStringIO.StringIO()
+                import io
+                xml=io.StringIO()
                 PrettyPrint(root, xml)
                 if compress:
                     import gzip
-                    f=cStringIO.StringIO()
+                    f=io.StringIO()
                     zf=gzip.GzipFile(fileobj=f, mode='wb')
                     zf.write(xml.getvalue())
                     zf.close()
@@ -1041,8 +1041,8 @@ class drawing:
                 try:
                     if filename[-4:]=='svgz':
                         import gzip
-                        import cStringIO
-                        xml=cStringIO.StringIO()
+                        import io
+                        xml=io.StringIO()
                         PrettyPrint(root, xml)
                         f=gzip.GzipFile(filename=filename, mode='wb', compresslevel=9)
                         f.write(xml.getvalue())
diff --git a/wqflask/wqflask/api/router.py b/wqflask/wqflask/api/router.py
index b81da0dc..5f9b81b8 100644
--- a/wqflask/wqflask/api/router.py
+++ b/wqflask/wqflask/api/router.py
@@ -6,7 +6,7 @@ import os, io, csv, json, datetime, requests, yaml
 import zlib
 from zipfile import ZipFile, ZIP_DEFLATED
 
-import StringIO
+import io
 
 import flask
 from flask import g, Response, request, make_response, render_template, send_from_directory, jsonify, redirect, send_file
@@ -308,7 +308,7 @@ def fetch_traits(dataset_name, file_format = "json"):
         else:
             filename = dataset_name + "_trait_ids.csv"
 
-            si = StringIO.StringIO()
+            si = io.StringIO()
             csv_writer = csv.writer(si)
             csv_writer.writerows([[trait_id] for trait_id in trait_ids])
             output = make_response(si.getvalue())
@@ -322,7 +322,7 @@ def fetch_traits(dataset_name, file_format = "json"):
         else:
             filename = dataset_name + "_trait_names.csv"
 
-            si = StringIO.StringIO()
+            si = io.StringIO()
             csv_writer = csv.writer(si)
             csv_writer.writerows([[trait_name] for trait_name in trait_names])
             output = make_response(si.getvalue())
@@ -413,7 +413,7 @@ def fetch_traits(dataset_name, file_format = "json"):
                 for result in g.db.execute(final_query).fetchall():
                     results_list.append(result)
 
-                si = StringIO.StringIO()
+                si = io.StringIO()
                 csv_writer = csv.writer(si)
                 csv_writer.writerows(results_list)
                 output = make_response(si.getvalue())
@@ -519,7 +519,7 @@ def all_sample_data(dataset_name, file_format = "csv"):
 
             results_list = list(map(list, zip(*results_list)))
 
-            si = StringIO.StringIO()
+            si = io.StringIO()
             csv_writer = csv.writer(si)
             csv_writer.writerows(results_list)
             output = make_response(si.getvalue())
@@ -706,7 +706,7 @@ def get_mapping_results():
         if format == "csv":
             filename = "mapping_" + datetime.datetime.utcnow().strftime("%b_%d_%Y_%I:%M%p") + ".csv"
 
-            si = StringIO.StringIO()
+            si = io.StringIO()
             csv_writer = csv.writer(si)
             csv_writer.writerows(results)
             output = make_response(si.getvalue())
@@ -732,7 +732,7 @@ def get_genotypes(group_name, file_format="csv", dataset_name=None):
         if request.args['limit_to'].isdigit():
             limit_num = int(request.args['limit_to'])
 
-    si = StringIO.StringIO()
+    si = io.StringIO()
     if file_format == "csv" or file_format == "geno":
         filename = group_name + ".geno"
 
diff --git a/wqflask/wqflask/collect.py b/wqflask/wqflask/collect.py
index 4c6e38e6..d77567f8 100644
--- a/wqflask/wqflask/collect.py
+++ b/wqflask/wqflask/collect.py
@@ -10,7 +10,7 @@ import uuid
 import hashlib
 import base64
 
-import urlparse
+import urllib.parse
 
 import simplejson as json
 
diff --git a/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py b/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py
index 09d6b9cc..3e5daa50 100644
--- a/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py
+++ b/wqflask/wqflask/comparison_bar_chart/comparison_bar_chart.py
@@ -24,7 +24,7 @@ import sys
 # sys.path.append(".")   Never do this in a webserver!
 
 import string
-import cPickle
+import pickle
 import os
 import time
 import pp
diff --git a/wqflask/wqflask/correlation/show_corr_results.py b/wqflask/wqflask/correlation/show_corr_results.py
index 4116e2df..65360040 100644
--- a/wqflask/wqflask/correlation/show_corr_results.py
+++ b/wqflask/wqflask/correlation/show_corr_results.py
@@ -23,7 +23,7 @@ from __future__ import absolute_import, print_function, division
 import sys
 
 import string
-import cPickle
+import pickle
 import os
 import time
 import pp
diff --git a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
index b582cd23..ea786289 100644
--- a/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
+++ b/wqflask/wqflask/correlation_matrix/show_corr_matrix.py
@@ -24,7 +24,7 @@ import sys
 # sys.path.append(".")   Never do this in a webserver!
 
 import string
-import cPickle
+import pickle
 import os
 import datetime
 import time
diff --git a/wqflask/wqflask/export_traits.py b/wqflask/wqflask/export_traits.py
index a8b49829..2f4e9aac 100644
--- a/wqflask/wqflask/export_traits.py
+++ b/wqflask/wqflask/export_traits.py
@@ -2,7 +2,7 @@ from __future__ import print_function, division
 
 import csv
 import xlsxwriter
-import StringIO 
+import io 
 import datetime
 import itertools
 
@@ -63,7 +63,7 @@ def export_search_results_csv(targs):
     file_list = []
     for group in list(traits_by_group.keys()):
         group_traits = traits_by_group[group]
-        buff = StringIO.StringIO()
+        buff = io.StringIO()
         writer = csv.writer(buff)
         csv_rows = []
 
diff --git a/wqflask/wqflask/heatmap/heatmap.py b/wqflask/wqflask/heatmap/heatmap.py
index 577426b0..4fdc1f13 100644
--- a/wqflask/wqflask/heatmap/heatmap.py
+++ b/wqflask/wqflask/heatmap/heatmap.py
@@ -4,7 +4,7 @@ import sys
 # sys.path.append(".") Never in a running webserver
 
 import string
-import cPickle
+import pickle
 import os
 import datetime
 import time
@@ -30,7 +30,7 @@ from utility.tools import flat_files, REAPER_COMMAND, TEMPDIR
 
 from MySQLdb import escape_string as escape
 
-import cPickle as pickle
+import pickle as pickle
 import simplejson as json
 
 from pprint import pformat as pf
diff --git a/wqflask/wqflask/marker_regression/display_mapping_results.py b/wqflask/wqflask/marker_regression/display_mapping_results.py
index f282b010..f06db5d5 100644
--- a/wqflask/wqflask/marker_regression/display_mapping_results.py
+++ b/wqflask/wqflask/marker_regression/display_mapping_results.py
@@ -29,8 +29,8 @@ import string
 from math import *
 from PIL import (Image, ImageDraw, ImageFont, ImageColor)
 import sys, os
-import cPickle
-import httplib
+import pickle
+import http.client
 import json
 
 from flask import Flask, g
diff --git a/wqflask/wqflask/marker_regression/run_mapping.py b/wqflask/wqflask/marker_regression/run_mapping.py
index 1e6dff57..67512bc6 100644
--- a/wqflask/wqflask/marker_regression/run_mapping.py
+++ b/wqflask/wqflask/marker_regression/run_mapping.py
@@ -18,7 +18,7 @@ import uuid
 import rpy2.robjects as ro
 import numpy as np
 
-import cPickle as pickle
+import pickle as pickle
 import itertools
 
 import simplejson as json
diff --git a/wqflask/wqflask/network_graph/network_graph.py b/wqflask/wqflask/network_graph/network_graph.py
index ac2ff017..7916651f 100644
--- a/wqflask/wqflask/network_graph/network_graph.py
+++ b/wqflask/wqflask/network_graph/network_graph.py
@@ -23,7 +23,7 @@ from __future__ import absolute_import, print_function, division
 import sys
 
 import string
-import cPickle
+import pickle
 import os
 import time
 import pp
diff --git a/wqflask/wqflask/show_trait/show_trait.py b/wqflask/wqflask/show_trait/show_trait.py
index 65899ab2..738aa28a 100644
--- a/wqflask/wqflask/show_trait/show_trait.py
+++ b/wqflask/wqflask/show_trait/show_trait.py
@@ -3,7 +3,7 @@ from __future__ import absolute_import, print_function, division
 import string
 import os
 import datetime
-import cPickle
+import pickle
 import uuid
 import requests
 import json as json
diff --git a/wqflask/wqflask/user_manager.py b/wqflask/wqflask/user_manager.py
index 232cb8da..56d1c084 100644
--- a/wqflask/wqflask/user_manager.py
+++ b/wqflask/wqflask/user_manager.py
@@ -9,7 +9,7 @@ import uuid
 import hashlib
 import hmac
 import base64
-import urlparse
+import urllib.parse
 
 import simplejson as json
 
diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py
index 92c20fc7..83d5202e 100644
--- a/wqflask/wqflask/views.py
+++ b/wqflask/wqflask/views.py
@@ -14,13 +14,13 @@ import csv
 import simplejson as json
 import yaml
 import xlsxwriter
-import StringIO  # Todo: Use cStringIO?
+import io  # Todo: Use cStringIO?
 
 from zipfile import ZipFile, ZIP_DEFLATED
 
 import gc
 import numpy as np
-import cPickle as pickle
+import pickle as pickle
 import uuid
 
 import flask
@@ -373,7 +373,7 @@ def export_trait_excel():
 
     logger.info("sample_data - type: %s -- size: %s" % (type(sample_data), len(sample_data)))
 
-    buff = StringIO.StringIO()
+    buff = io.StringIO()
     workbook = xlsxwriter.Workbook(buff, {'in_memory': True})
     worksheet = workbook.add_worksheet()
     for i, row in enumerate(sample_data):
@@ -397,7 +397,7 @@ def export_trait_csv():
 
     logger.info("sample_data - type: %s -- size: %s" % (type(sample_data), len(sample_data)))
 
-    buff = StringIO.StringIO()
+    buff = io.StringIO()
     writer = csv.writer(buff)
     for row in sample_data:
         writer.writerow(row)
@@ -417,7 +417,7 @@ def export_traits_csv():
     file_list = export_traits.export_search_results_csv(request.form)
 
     if len(file_list) > 1:
-        memory_file = StringIO.StringIO()
+        memory_file = io.StringIO()
         with ZipFile(memory_file, mode='w', compression=ZIP_DEFLATED) as zf:
             for the_file in file_list:
                 zf.writestr(the_file[0], the_file[1])
@@ -460,7 +460,7 @@ def export_perm_data():
         ["#Comment: Results sorted from low to high peak linkage"]
     ]
 
-    buff = StringIO.StringIO()
+    buff = io.StringIO()
     writer = csv.writer(buff)
     writer.writerows(the_rows)
     for item in perm_info['perm_data']:
-- 
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/maintenance/set_resource_defaults.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
-- 
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