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-rw-r--r--wqflask/utility/hmac.py2
-rw-r--r--wqflask/utility/redis_tools.py142
-rw-r--r--wqflask/utility/startup_config.py4
-rw-r--r--wqflask/utility/tools.py13
4 files changed, 150 insertions, 11 deletions
diff --git a/wqflask/utility/hmac.py b/wqflask/utility/hmac.py
index d8a0eace..b08be97e 100644
--- a/wqflask/utility/hmac.py
+++ b/wqflask/utility/hmac.py
@@ -3,6 +3,8 @@ from __future__ import print_function, division, absolute_import
import hmac
import hashlib
+from flask import url_for
+
from wqflask import app
def hmac_creation(stringy):
diff --git a/wqflask/utility/redis_tools.py b/wqflask/utility/redis_tools.py
index 0754e16f..15841032 100644
--- a/wqflask/utility/redis_tools.py
+++ b/wqflask/utility/redis_tools.py
@@ -1,17 +1,25 @@
from __future__ import print_function, division, absolute_import
+import uuid
import simplejson as json
import redis # used for collections
-Redis = redis.StrictRedis()
import logging
from flask import (render_template, flash)
+from utility import hmac
+
from utility.logger import getLogger
logger = getLogger(__name__)
+def get_redis_conn():
+ Redis = redis.StrictRedis(port=6380)
+ return Redis
+
+Redis = get_redis_conn()
+
def is_redis_available():
try:
Redis.ping()
@@ -70,11 +78,137 @@ def check_verification_code(code):
email_address = None
user_details = None
email_address = Redis.hget("verification_codes", code)
- return email_address
if email_address:
user_details = get_user_by_unique_column('email_address', email_address)
- return user_details
+ if user_details:
+ return user_details
+ else:
+ return None
+ 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
+ groups_list = Redis.hgetall("groups")
+ for key in groups_list:
+ group_ob = json.loads(groups_list[key])
+ group_admins = set(group_ob['admins'])
+ group_users = set(group_ob['users'])
+ if user_id in group_admins:
+ admin_group_ids.append(group_ob['id'])
+ elif user_id in group_users:
+ user_group_ids.append(group_ob['id'])
+ else:
+ continue
+
+ return admin_group_ids, user_group_ids
+
+def get_group_info(group_id):
+ group_json = Redis.hget("groups", group_id)
+ group_info = None
+ if group_json:
+ group_info = json.loads(group_json)
+
+ return group_info
+
+def create_group(admin_member_ids, user_member_ids = [], group_name = ""):
+ group_id = str(uuid.uuid4())
+ new_group = {
+ "id" : group_id,
+ "admins": admin_member_ids,
+ "users" : user_member_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)
+
+ 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
+ group_info = get_group_info(group_id)
+ if user_id in group_info["admins"]:
+ Redis.hdel("groups", group_id)
+ return get_user_groups(user_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
+ 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
+ if admins:
+ group_users = set(group_info["admins"])
+ else:
+ group_users = set(group_info["users"])
+
+ for email in user_emails:
+ user_id = get_user_id("email_address", email)
+ group_users.add(user_id)
+
+ if admins:
+ group_info["admins"] = list(group_users)
+ else:
+ group_info["users"] = 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))
+ return group_info
+ 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
+ group_info = get_group_info(group_id)
+ if user_id in group_info["admins"]:
+ group_users = set(group_info[user_type])
+ group_users -= set(users_to_remove_ids)
+ 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))
+
+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
+ return group_info
else:
return None
- flash("Invalid code: Password reset code does not exist or might have expired!", "error")
+
+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]
+ else:
+ return False
+
+def get_resource_info(resource_id):
+ resource_info = Redis.hget("resources", resource_id)
+ return json.loads(resource_info)
+
+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'])))
+ else:
+ resource_id = hmac.data_hmac('{}'.format(str(resource_info['data']['dataset'])))
+
+ Redis.hset("resources", resource_id, json.dumps(resource_info))
+
+ return resource_info
diff --git a/wqflask/utility/startup_config.py b/wqflask/utility/startup_config.py
index 5a62cc50..817284dd 100644
--- a/wqflask/utility/startup_config.py
+++ b/wqflask/utility/startup_config.py
@@ -33,7 +33,7 @@ def app_config():
if page.status_code != 200:
raise Exception("API server not found!")
- import utility.elasticsearch_tools as es
- es.test_elasticsearch_connection()
+ # 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")))
diff --git a/wqflask/utility/tools.py b/wqflask/utility/tools.py
index 75bddb24..89d88516 100644
--- a/wqflask/utility/tools.py
+++ b/wqflask/utility/tools.py
@@ -233,7 +233,10 @@ def show_settings():
# Cached values
GN_VERSION = get_setting('GN_VERSION')
HOME = get_setting('HOME')
+SERVER_PORT = get_setting('SERVER_PORT')
WEBSERVER_MODE = get_setting('WEBSERVER_MODE')
+GN2_BASE_URL = get_setting('GN2_BASE_URL')
+GN2_BRANCH_URL = get_setting('GN2_BRANCH_URL')
GN_SERVER_URL = get_setting('GN_SERVER_URL')
SERVER_PORT = get_setting_int('SERVER_PORT')
SQL_URI = get_setting('SQL_URI')
@@ -267,10 +270,10 @@ if ORCID_CLIENT_ID != 'UNKNOWN' and ORCID_CLIENT_SECRET:
ORCID_CLIENT_ID+"&client_secret="+ORCID_CLIENT_SECRET
ORCID_TOKEN_URL = get_setting('ORCID_TOKEN_URL')
-ELASTICSEARCH_HOST = get_setting('ELASTICSEARCH_HOST')
-ELASTICSEARCH_PORT = get_setting('ELASTICSEARCH_PORT')
-import utility.elasticsearch_tools as es
-es.test_elasticsearch_connection()
+# ELASTICSEARCH_HOST = get_setting('ELASTICSEARCH_HOST')
+# ELASTICSEARCH_PORT = get_setting('ELASTICSEARCH_PORT')
+# import utility.elasticsearch_tools as es
+# es.test_elasticsearch_connection()
SMTP_CONNECT = get_setting('SMTP_CONNECT')
SMTP_USERNAME = get_setting('SMTP_USERNAME')
@@ -289,7 +292,7 @@ JS_GUIX_PATH = get_setting("JS_GUIX_PATH")
assert_dir(JS_GUIX_PATH)
assert_dir(JS_GUIX_PATH+'/cytoscape-panzoom')
-CSS_PATH = "UNKNOWN"
+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"))
generated by cgit v1.2.3 (git 2.44.0) at 2024-11-23 04:47:35 +0000