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-rw-r--r--wqflask/utility/authentication_tools.py41
-rw-r--r--wqflask/utility/hmac.py9
-rw-r--r--wqflask/utility/redis_tools.py120
3 files changed, 114 insertions, 56 deletions
diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py
index 3553b92b..239b08e3 100644
--- a/wqflask/utility/authentication_tools.py
+++ b/wqflask/utility/authentication_tools.py
@@ -1,4 +1,6 @@
from __future__ import absolute_import, print_function, division
+import logging
+from flask import Flask, g, redirect, url_for
import json
import requests
@@ -9,33 +11,31 @@ from utility import hmac
from utility.redis_tools import get_redis_conn, get_resource_info, get_resource_id, add_resource
Redis = get_redis_conn()
-from flask import Flask, g, redirect, url_for
-import logging
-logger = logging.getLogger(__name__ )
+logger = logging.getLogger(__name__)
+
def check_resource_availability(dataset, trait_id=None):
- #At least for now assume temporary entered traits are accessible
- if type(dataset) == str:
- return webqtlConfig.DEFAULT_PRIVILEGES
- if dataset.type == "Temp":
+ # At least for now assume temporary entered traits are accessible
+ if type(dataset) == str or dataset.type == "Temp":
return webqtlConfig.DEFAULT_PRIVILEGES
resource_id = get_resource_id(dataset, trait_id)
- if resource_id: #ZS: This should never be false, but it's technically possible if a non-Temp dataset somehow had a type other than Publish/ProbeSet/Geno
+ if resource_id: # ZS: This should never be false, but it's technically possible if a non-Temp dataset somehow had a type other than Publish/ProbeSet/Geno
resource_info = get_resource_info(resource_id)
- if not resource_info: #ZS: If resource isn't already in redis, add it with default privileges
+ if not resource_info: # ZS: If resource isn't already in redis, add it with default privileges
resource_info = add_new_resource(dataset, trait_id)
- #ZS: Check if super-user - we should probably come up with some way to integrate this into the proxy
+ # ZS: Check if super-user - we should probably come up with some way to integrate this into the proxy
if g.user_session.user_id in Redis.smembers("super_users"):
- return webqtlConfig.SUPER_PRIVILEGES
+ return webqtlConfig.SUPER_PRIVILEGES
response = None
- the_url = "http://localhost:8080/available?resource={}&user={}".format(resource_id, g.user_session.user_id)
+ the_url = "http://localhost:8080/available?resource={}&user={}".format(
+ resource_id, g.user_session.user_id)
try:
response = json.loads(requests.get(the_url).content)
except:
@@ -43,18 +43,19 @@ def check_resource_availability(dataset, trait_id=None):
return response
+
def add_new_resource(dataset, trait_id=None):
resource_ob = {
- 'owner_id' : "none", # webqtlConfig.DEFAULT_OWNER_ID,
+ 'owner_id': "none", # webqtlConfig.DEFAULT_OWNER_ID,
'default_mask': webqtlConfig.DEFAULT_PRIVILEGES,
- 'group_masks' : {}
+ 'group_masks': {}
}
if dataset.type == "Publish":
resource_ob['name'] = get_group_code(dataset) + "_" + str(trait_id)
resource_ob['data'] = {
'dataset': dataset.id,
- 'trait' : trait_id
+ 'trait': trait_id
}
resource_ob['type'] = 'dataset-publish'
elif dataset.type == "Geno":
@@ -74,15 +75,19 @@ def add_new_resource(dataset, trait_id=None):
return resource_info
+
def get_group_code(dataset):
- results = g.db.execute("SELECT InbredSetCode from InbredSet where Name='{}'".format(dataset.group.name)).fetchone()
+ results = g.db.execute("SELECT InbredSetCode from InbredSet where Name='{}'".format(
+ dataset.group.name)).fetchone()
if results[0]:
return results[0]
else:
return ""
+
def check_admin(resource_id=None):
- the_url = "http://localhost:8080/available?resource={}&user={}".format(resource_id, g.user_session.user_id)
+ the_url = "http://localhost:8080/available?resource={}&user={}".format(
+ resource_id, g.user_session.user_id)
try:
response = json.loads(requests.get(the_url).content)['admin']
except:
@@ -96,6 +101,7 @@ def check_admin(resource_id=None):
else:
return "not-admin"
+
def check_owner(dataset=None, trait_id=None, resource_id=None):
if resource_id:
resource_info = get_resource_info(resource_id)
@@ -110,6 +116,7 @@ def check_owner(dataset=None, trait_id=None, resource_id=None):
return False
+
def check_owner_or_admin(dataset=None, trait_id=None, resource_id=None):
if not resource_id:
if dataset.type == "Temp":
diff --git a/wqflask/utility/hmac.py b/wqflask/utility/hmac.py
index b08be97e..fd75803e 100644
--- a/wqflask/utility/hmac.py
+++ b/wqflask/utility/hmac.py
@@ -7,11 +7,11 @@ from flask import url_for
from wqflask import app
+
def hmac_creation(stringy):
"""Helper function to create the actual hmac"""
secret = app.config['SECRET_HMAC_CODE']
-
hmaced = hmac.new(secret, stringy, hashlib.sha1)
hm = hmaced.hexdigest()
# ZS: Leaving the below comment here to ask Pjotr about
@@ -20,10 +20,12 @@ def hmac_creation(stringy):
hm = hm[:20]
return hm
+
def data_hmac(stringy):
- """Takes arbitray data string and appends :hmac so we know data hasn't been tampered with"""
+ """Takes arbitrary data string and appends :hmac so we know data hasn't been tampered with"""
return stringy + ":" + hmac_creation(stringy)
+
def url_for_hmac(endpoint, **values):
"""Like url_for but adds an hmac at the end to insure the url hasn't been tampered with"""
@@ -36,5 +38,6 @@ def url_for_hmac(endpoint, **values):
combiner = "?"
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 81ba04ea..ef02268e 100644
--- a/wqflask/utility/redis_tools.py
+++ b/wqflask/utility/redis_tools.py
@@ -4,23 +4,21 @@ import uuid
import simplejson as json
import datetime
-import redis # used for collections
-
-import logging
-
-from flask import (render_template, flash)
-
-from utility import hmac
+import redis # used for collections
+from utility.hmac import hmac_creation
from utility.logger import getLogger
logger = getLogger(__name__)
+
def get_redis_conn():
Redis = redis.StrictRedis(port=6379)
return Redis
+
Redis = get_redis_conn()
+
def is_redis_available():
try:
Redis.ping()
@@ -28,6 +26,7 @@ def is_redis_available():
return False
return True
+
def get_user_id(column_name, column_value):
user_list = Redis.hgetall("users")
key_list = []
@@ -38,6 +37,7 @@ def get_user_id(column_name, column_value):
return None
+
def get_user_by_unique_column(column_name, column_value):
item_details = None
@@ -52,9 +52,11 @@ 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
+ """Like previous function, but this only checks if the input is a
+ subset of a field and can return multiple results
+
"""
matched_users = []
@@ -74,7 +76,6 @@ def get_users_like_unique_column(column_name, 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))
@@ -82,6 +83,7 @@ def set_user_attribute(user_id, column_name, column_value):
Redis.hset("users", user_id, json.dumps(user_info))
+
def get_user_collections(user_id):
collections = None
collections = Redis.hget("collections", user_id)
@@ -91,22 +93,27 @@ def get_user_collections(user_id):
else:
return []
+
def save_user(user, user_id):
Redis.hset("users", user_id, json.dumps(user))
+
def save_collections(user_id, collections_ob):
Redis.hset("collections", user_id, collections_ob)
+
def save_verification_code(user_email, code):
Redis.hset("verification_codes", code, user_email)
+
def check_verification_code(code):
email_address = None
user_details = None
email_address = Redis.hget("verification_codes", code)
if email_address:
- user_details = get_user_by_unique_column('email_address', email_address)
+ user_details = get_user_by_unique_column(
+ 'email_address', email_address)
if user_details:
return user_details
else:
@@ -114,10 +121,12 @@ def check_verification_code(code):
else:
return None
+
def get_user_groups(user_id):
- #ZS: Get the groups where a user is an admin or a member and return lists corresponding to those two sets of groups
- admin_group_ids = [] #ZS: Group IDs where user is an admin
- user_group_ids = [] #ZS: Group IDs where user is a regular user
+ # ZS: Get the groups where a user is an admin or a member and
+ # return lists corresponding to those two sets of groups
+ admin_group_ids = [] # ZS: Group IDs where user is an admin
+ user_group_ids = [] # ZS: Group IDs where user is a regular user
groups_list = Redis.hgetall("groups")
for key in groups_list:
try:
@@ -142,6 +151,7 @@ def get_user_groups(user_id):
return admin_groups, user_groups
+
def get_group_info(group_id):
group_json = Redis.hget("groups", group_id)
group_info = None
@@ -150,6 +160,7 @@ def get_group_info(group_id):
return group_info
+
def get_group_by_unique_column(column_name, column_value):
""" Get group by column; not sure if there's a faster way to do this """
@@ -158,7 +169,8 @@ def get_group_by_unique_column(column_name, column_value):
all_group_list = Redis.hgetall("groups")
for key in all_group_list:
group_info = json.loads(all_group_list[key])
- if column_name == "admins" or column_name == "members": #ZS: Since these fields are lists, search in the list
+ # ZS: Since these fields are lists, search in the list
+ if column_name == "admins" or column_name == "members":
if column_value in group_info[column_name]:
matched_groups.append(group_info)
else:
@@ -167,9 +179,11 @@ 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
+ """Like previous function, but this only checks if the input is a
+ subset of a field and can return multiple results
+
"""
matched_groups = []
@@ -178,7 +192,8 @@ def get_groups_like_unique_column(column_name, column_value):
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
+ # ZS: Since these fields are lists, search in the list
+ if column_name == "admins" or column_name == "members":
if column_value in group_info[column_name]:
matched_groups.append(group_info)
else:
@@ -190,13 +205,15 @@ def get_groups_like_unique_column(column_name, column_value):
return matched_groups
-def create_group(admin_user_ids, member_user_ids = [], group_name = "Default 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,
+ "id": group_id,
"admins": admin_user_ids,
- "members" : member_user_ids,
- "name" : group_name,
+ "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')
}
@@ -205,8 +222,9 @@ def create_group(admin_user_ids, member_user_ids = [], group_name = "Default Gro
return new_group
+
def delete_group(user_id, group_id):
- #ZS: If user is an admin of a group, remove it from the groups hash
+ # ZS: If user is an admin of a group, remove it from the groups hash
group_info = get_group_info(group_id)
if user_id in group_info["admins"]:
Redis.hdel("groups", group_id)
@@ -214,9 +232,15 @@ def delete_group(user_id, group_id):
else:
None
-def add_users_to_group(user_id, group_id, user_emails = [], admins = False): #ZS "admins" is just to indicate whether the users should be added to the groups admins or regular users set
+
+# ZS "admins" is just to indicate whether the users should be added to
+# the groups admins or regular users set
+def add_users_to_group(user_id, group_id, user_emails=[], admins=False):
group_info = get_group_info(group_id)
- if user_id in group_info["admins"]: #ZS: Just to make sure that the user is an admin for the group, even though they shouldn't be able to reach this point unless they are
+ # ZS: Just to make sure that the user is an admin for the group,
+ # even though they shouldn't be able to reach this point unless
+ # they are
+ if user_id in group_info["admins"]:
if admins:
group_users = set(group_info["admins"])
else:
@@ -231,25 +255,36 @@ def add_users_to_group(user_id, group_id, user_emails = [], admins = False): #ZS
else:
group_info["members"] = list(group_users)
- group_info["changed_timestamp"] = datetime.datetime.utcnow().strftime('%b %d %Y %I:%M%p')
+ group_info["changed_timestamp"] = datetime.datetime.utcnow().strftime(
+ '%b %d %Y %I:%M%p')
Redis.hset("groups", group_id, json.dumps(group_info))
return group_info
else:
return None
-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
+
+# 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"):
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
+ # 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
+ if user_type == "admins" and user_id in users_to_remove_set:
users_to_remove_set.remove(user_id)
group_users = set(group_info[user_type])
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')
+ group_info["changed_timestamp"] = datetime.datetime.utcnow().strftime(
+ '%b %d %Y %I:%M%p')
Redis.hset("groups", group_id, json.dumps(group_info))
+
def change_group_name(user_id, group_id, new_name):
group_info = get_group_info(group_id)
if user_id in group_info["admins"]:
@@ -259,22 +294,28 @@ def change_group_name(user_id, group_id, new_name):
else:
return None
+
def get_resources():
resource_list = Redis.hgetall("resources")
return resource_list
+
def get_resource_id(dataset, trait_id=None):
resource_id = False
if dataset.type == "Publish":
if trait_id:
- resource_id = hmac.hmac_creation("{}:{}:{}".format('dataset-publish', dataset.id, trait_id))
+ resource_id = hmac_creation("{}:{}:{}".format(
+ 'dataset-publish', dataset.id, trait_id))
elif dataset.type == "ProbeSet":
- resource_id = hmac.hmac_creation("{}:{}".format('dataset-probeset', dataset.id))
+ resource_id = hmac_creation(
+ "{}:{}".format('dataset-probeset', dataset.id))
elif dataset.type == "Geno":
- resource_id = hmac.hmac_creation("{}:{}".format('dataset-geno', dataset.id))
+ resource_id = hmac_creation(
+ "{}:{}".format('dataset-geno', dataset.id))
return resource_id
+
def get_resource_info(resource_id):
resource_info = Redis.hget("resources", resource_id)
if resource_info:
@@ -282,17 +323,23 @@ def get_resource_info(resource_id):
else:
return None
+
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'])))
+ resource_id = 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'])))
+ resource_id = hmac_creation('{}:{}'.format(
+ str(resource_info['type']), str(resource_info['data']['dataset'])))
if update or not Redis.hexists("resources", resource_id):
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
@@ -301,9 +348,10 @@ def add_access_mask(resource_id, group_id, access_mask):
return the_resource
+
def change_resource_owner(resource_id, new_owner_id):
- the_resource= get_resource_info(resource_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
+ Redis.hset("resources", resource_id, json.dumps(the_resource))
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-22 22:19:51 +0000