Really should have split this into many more commits:

- Now use proxy to pull trait data and hide traits/results that the user
doesn't have view permission for

- Created a factory method for creating trait ob so it can return None
when user doesn't have view permissions (this is why such a large number
of files are changed)

- Added metadata to permutation export

- Added current group management code

- Added fixed password verification e-mail code

2 files changed, 38 insertions, 31 deletions

diff --git a/wqflask/utility/helper_functions.py b/wqflask/utility/helper_functions.py
index e7c04fef..9ce809b6 100644
--- a/wqflask/utility/helper_functions.py
+++ b/wqflask/utility/helper_functions.py
@@ -1,7 +1,7 @@
 from __future__ import absolute_import, print_function, division
 
-from base.trait import GeneralTrait
 from base import data_set
+from base.trait import create_trait
 from base.species import TheSpecies
 
 from utility import hmac
@@ -11,7 +11,6 @@ from flask import Flask, g
 import logging
 logger = logging.getLogger(__name__ )
 
-
 def get_species_dataset_trait(self, start_vars):
     #assert type(read_genotype) == type(bool()), "Expecting boolean value for read_genotype"
     if "temp_trait" in start_vars.keys():
@@ -24,7 +23,7 @@ def get_species_dataset_trait(self, start_vars):
     logger.debug("After creating dataset")
     self.species = TheSpecies(dataset=self.dataset)
     logger.debug("After creating species")
-    self.this_trait = GeneralTrait(dataset=self.dataset,
+    self.this_trait = create_trait(dataset=self.dataset,
                                    name=start_vars['trait_id'],
                                    cellid=None,
                                    get_qtl_info=True)
@@ -34,7 +33,6 @@ def get_species_dataset_trait(self, start_vars):
     #self.dataset.group.read_genotype_file()
     #self.genotype = self.dataset.group.genotype
 
-
 def get_trait_db_obs(self, trait_db_list):
     if isinstance(trait_db_list, basestring):
         trait_db_list = trait_db_list.split(",")
@@ -49,10 +47,11 @@ def get_trait_db_obs(self, trait_db_list):
             dataset_ob = data_set.create_dataset(dataset_name=dataset_name, dataset_type="Temp", group_name=trait_name.split("_")[2])
         else:
             dataset_ob = data_set.create_dataset(dataset_name)
-        trait_ob = GeneralTrait(dataset=dataset_ob,
+        trait_ob = create_trait(dataset=dataset_ob,
                                name=trait_name,
                                cellid=None)
-        self.trait_list.append((trait_ob, dataset_ob))
+        if trait_ob:
+            self.trait_list.append((trait_ob, dataset_ob))
 
 def get_species_groups():
 
diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py
index 15841032..0ad96879 100644
--- a/wqflask/utility/redis_tools.py
+++ b/wqflask/utility/redis_tools.py
@@ -2,6 +2,7 @@ from __future__ import print_function, division, absolute_import
 
 import uuid
 import simplejson as json
+import datetime
 
 import redis # used for collections
 
@@ -96,15 +97,22 @@ def get_user_groups(user_id):
     for key in groups_list:
         group_ob = json.loads(groups_list[key])
         group_admins = set(group_ob['admins'])
-        group_users = set(group_ob['users'])
+        group_members = set(group_ob['members'])
         if user_id in group_admins:
             admin_group_ids.append(group_ob['id'])
-        elif user_id in group_users:
+        elif user_id in group_members:
             user_group_ids.append(group_ob['id'])
         else:
             continue
 
-    return admin_group_ids, user_group_ids
+    admin_groups = []
+    user_groups = []
+    for the_id in admin_group_ids:
+        admin_groups.append(get_group_info(the_id))
+    for the_id in user_group_ids:
+        user_groups.append(get_group_info(the_id))
+
+    return admin_groups, user_groups
 
 def get_group_info(group_id):
     group_json = Redis.hget("groups", group_id)
@@ -114,18 +122,18 @@ def get_group_info(group_id):
 
     return group_info
 
-def create_group(admin_member_ids, user_member_ids = [], group_name = ""):
+def create_group(admin_user_ids, member_user_ids = [], group_name = "Default Group Name"):
     group_id = str(uuid.uuid4())
     new_group = {
         "id"    : group_id,
-        "admins": admin_member_ids,
-        "users" : user_member_ids,
+        "admins": admin_user_ids,
+        "members" : member_user_ids,
         "name"  : group_name,
         "created_timestamp": datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p'),
         "changed_timestamp": datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p')
     }
 
-    Redis.hset("groups", group_id, new_group)
+    Redis.hset("groups", group_id, json.dumps(new_group))
 
     return new_group
 
@@ -144,7 +152,7 @@ def add_users_to_group(user_id, group_id, user_emails = [], admins = False): #ZS
         if admins:
             group_users = set(group_info["admins"])
         else:
-            group_users = set(group_info["users"])
+            group_users = set(group_info["members"])
 
         for email in user_emails:
             user_id = get_user_id("email_address", email)
@@ -153,7 +161,7 @@ def add_users_to_group(user_id, group_id, user_emails = [], admins = False): #ZS
         if admins:
             group_info["admins"] = list(group_users)
         else:
-            group_info["users"] = list(group_users)
+            group_info["members"] = 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))
@@ -161,7 +169,7 @@ def add_users_to_group(user_id, group_id, user_emails = [], admins = False): #ZS
     else:
         return None
 
-def remove_users_from_group(user_id, users_to_remove_ids, group_id, user_type = "users"): #ZS: User type is because I assume admins can remove other admins
+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"]:
         group_users = set(group_info[user_type])
@@ -174,6 +182,7 @@ def change_group_name(user_id, group_id, new_name):
     group_info = get_group_info(group_id)
     if user_id in group_info["admins"]:
         group_info["name"] = new_name
+        Redis.hset("groups", group_id, json.dumps(group_info))
         return group_info
     else:
         return None
@@ -182,22 +191,21 @@ def get_resources():
     resource_list = Redis.hgetall("resources")
     return resource_list
 
-def get_resource_id(dataset_type, dataset_id, trait_id = None, all_resources = None):
-    if not all_resources:
-        all_resources = get_resources()
-
-    resource_list = [[key, json.loads(value)] for key, value in all_resources.items()]
-
-    if not trait_id:
-        matched_resources = [resource[0] for resource in resource_list if resource[1]['data']['dataset'] == dataset_id]
-    else:
-        matched_resources = [resource[0] for resource in resource_list if resource[1]['data']['dataset'] == dataset_id and resource[1]['data']['trait'] == trait_id]
-
-    if len(matched_resources):
-        return matched_resources[0]
+def get_resource_id(dataset, trait_id=None):
+    if dataset.type == "Publish":
+        if trait_id:
+            resource_id = hmac.hmac_creation("{}:{}:{}".format('dataset-publish', dataset.id, trait_id))
+        else:
+            return False
+    elif dataset.type == "ProbeSet":
+        resource_id = hmac.hmac_creation("{}:{}".format('dataset-probeset', dataset.id))
+    elif dataset.type == "Geno":
+        resource_id = hmac.hmac_creation("{}:{}".format('dataset-geno', dataset.id))
     else:
         return False
 
+    return resource_id
+
 def get_resource_info(resource_id):
     resource_info = Redis.hget("resources", resource_id)
     return json.loads(resource_info)
@@ -205,9 +213,9 @@ def get_resource_info(resource_id):
 def add_resource(resource_info):
 
     if 'trait' in resource_info['data']:
-        resource_id = hmac.data_hmac('{}:{}'.format(str(resource_info['data']['dataset']), str(resource_info['data']['trait'])))
+        resource_id = hmac.hmac_creation('{}:{}:{}'.format(str(resource_info['type']), str(resource_info['data']['dataset']), str(resource_info['data']['trait'])))
     else:
-        resource_id = hmac.data_hmac('{}'.format(str(resource_info['data']['dataset'])))
+        resource_id = hmac.hmac_creation('{}:{}'.format(str(resource_info['type']), str(resource_info['data']['dataset'])))
 
     Redis.hset("resources", resource_id, json.dumps(resource_info))