diff options
Diffstat (limited to 'wqflask/utility')
| -rw-r--r-- | wqflask/utility/authentication_tools.py | 96 | ||||
| -rw-r--r-- | wqflask/utility/helper_functions.py | 11 | ||||
| -rw-r--r-- | wqflask/utility/hmac.py | 2 | ||||
| -rw-r--r-- | wqflask/utility/redis_tools.py | 240 | ||||
| -rw-r--r-- | wqflask/utility/tools.py | 2 |
5 files changed, 340 insertions, 11 deletions
diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py new file mode 100644 index 00000000..f9028f32 --- /dev/null +++ b/wqflask/utility/authentication_tools.py @@ -0,0 +1,96 @@ +from __future__ import absolute_import, print_function, division + +import json +import requests + +from base import data_set, webqtlConfig + +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 + +import logging +logger = logging.getLogger(__name__ ) + +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 webqtlConfig.SUPER_PRIVILEGES + + response = None + + #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 + + resource_id = get_resource_id(dataset, trait_id) + + if resource_id: + resource_info = get_resource_info(resource_id) + if not resource_info: + return webqtlConfig.DEFAULT_PRIVILEGES + else: + return response #ZS: Need to substitute in something that creates the resource in Redis later + + 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'] + + if response: + return response + else: #ZS: No idea how this would happen, but just in case + return False + +def check_admin(resource_id=None): + 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: + 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 not resource_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 "owner" + + resource_info = get_resource_info(resource_id) + if resource_info: + if g.user_session.user_id == resource_info['owner_id']: + return "owner" + else: + return check_admin(resource_id) + + return "not-admin" \ No newline at end of file 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/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..6c912a23 100644 --- a/wqflask/utility/redis_tools.py +++ b/wqflask/utility/redis_tools.py @@ -1,17 +1,26 @@ from __future__ import print_function, division, absolute_import +import uuid import simplejson as json +import datetime 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=6379) + return Redis + +Redis = get_redis_conn() + def is_redis_available(): try: Redis.ping() @@ -21,6 +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: @@ -42,6 +52,30 @@ 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 "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) + 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 @@ -70,11 +104,209 @@ 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: + try: + group_ob = json.loads(groups_list[key]) + group_admins = set(group_ob['admins']) + group_members = set(group_ob['members']) + if user_id in group_admins: + admin_group_ids.append(group_ob['id']) + elif user_id in group_members: + user_group_ids.append(group_ob['id']) + else: + continue + except: + continue + + 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) + group_info = None + if group_json: + group_info = json.loads(group_json) + + 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 """ + + matched_groups = [] + + 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 + if column_value in group_info[column_name]: + matched_groups.append(group_info) + else: + if group_info[column_name] == column_value: + matched_groups.append(group_info) + + 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()) + new_group = { + "id" : group_id, + "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, json.dumps(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["members"]) + + 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["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)) + 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 + 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 -= 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)) + +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 + +def get_resources(): + resource_list = Redis.hgetall("resources") + return resource_list + +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) + if resource_info: + return json.loads(resource_info) else: return None - flash("Invalid code: Password reset code does not exist or might have expired!", "error") + +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']))) + + if 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 + + 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/utility/tools.py b/wqflask/utility/tools.py index 2914d354..89d88516 100644 --- a/wqflask/utility/tools.py +++ b/wqflask/utility/tools.py @@ -292,7 +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")) |