aboutsummaryrefslogtreecommitdiff
path: root/wqflask/utility
diff options
context:
space:
mode:
Diffstat (limited to 'wqflask/utility')
-rw-r--r--wqflask/utility/helper_functions.py11
-rw-r--r--wqflask/utility/redis_tools.py58
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))