diff options
Diffstat (limited to 'wqflask')
| -rw-r--r-- | wqflask/base/trait.py | 17 | ||||
| -rw-r--r-- | wqflask/base/webqtlConfig.py | 4 | ||||
| -rw-r--r-- | wqflask/maintenance/set_resource_defaults.py | 20 | ||||
| -rw-r--r-- | wqflask/utility/authentication_tools.py | 79 | ||||
| -rw-r--r-- | wqflask/wqflask/resource_manager.py | 6 | ||||
| -rw-r--r-- | wqflask/wqflask/views.py | 20 |
6 files changed, 90 insertions, 56 deletions
diff --git a/wqflask/base/trait.py b/wqflask/base/trait.py index 7700ecd5..c2b8b910 100644 --- a/wqflask/base/trait.py +++ b/wqflask/base/trait.py @@ -42,11 +42,11 @@ def create_trait(**kw): if kw.get('dataset_name') != "Temp": if dataset.type == 'Publish': - permitted = check_resource_availability(dataset, kw.get('name')) + permissions = check_resource_availability(dataset, kw.get('name')) else: - permitted = check_resource_availability(dataset) + permissions = check_resource_availability(dataset) - if permitted != "no-access": + if "view" in permissions['data']: the_trait = GeneralTrait(**kw) if the_trait.dataset.type != "Temp": @@ -382,9 +382,16 @@ def retrieve_trait_info(trait, dataset, get_qtl_info=False): resource_id = get_resource_id(dataset, trait.name) if dataset.type == 'Publish': - the_url = "http://localhost:8080/run-action?resource={}&user={}&branch=data&action=view".format(resource_id, g.user_session.user_id) + the_url = "http://localhost:8081/run-action?resource={}&user={}&branch=data&action=view".format(resource_id, g.user_session.user_id) else: - the_url = "http://localhost:8080/run-action?resource={}&user={}&branch=data&action=view&trait={}".format(resource_id, g.user_session.user_id, trait.name) + the_url = "http://localhost:8081/run-action?resource={}&user={}&branch=data&action=view&trait={}".format(resource_id, g.user_session.user_id, trait.name) + + response = requests.get(the_url).content + if response.strip() == "no-access": + trait.view = False + return trait + else: + trait_info = json.loads(response) try: response = requests.get(the_url).content diff --git a/wqflask/base/webqtlConfig.py b/wqflask/base/webqtlConfig.py index 55407123..3d86bc22 100644 --- a/wqflask/base/webqtlConfig.py +++ b/wqflask/base/webqtlConfig.py @@ -17,6 +17,10 @@ DEBUG = 1 #USER privilege USERDICT = {'guest':1,'user':2, 'admin':3, 'root':4} +#Set privileges +SUPER_PRIVILEGES = {'data': ['no-access', 'view', 'edit'], 'metadata': ['no-access', 'view', 'edit'], 'admin': ['not-admin', 'edit-access', 'edit-admins']} +DEFAULT_PRIVILEGES = {'data': ['no-access', 'view'], 'metadata': ['no-access', 'view'], 'admin': ['not-admin']} + #minimum number of informative strains KMININFORMATIVE = 5 diff --git a/wqflask/maintenance/set_resource_defaults.py b/wqflask/maintenance/set_resource_defaults.py index 0c221bbf..ddb3b17b 100644 --- a/wqflask/maintenance/set_resource_defaults.py +++ b/wqflask/maintenance/set_resource_defaults.py @@ -68,9 +68,13 @@ def insert_probeset_resources(default_owner_id): resource_ob['data'] = { "dataset" : str(resource[0])} resource_ob['type'] = "dataset-probeset" if resource[2] < 1 and resource[3] > 0: - resource_ob['default_mask'] = { "data": "view" } + resource_ob['default_mask'] = { "data": "view", + "metadata": "view", + "admin": "not-admin"} else: - resource_ob['default_mask'] = { "data": "no-access" } + resource_ob['default_mask'] = { "data": "no-access", + "metadata": "no-access", + "admin": "not-admin"} resource_ob['group_masks'] = {} add_resource(resource_ob) @@ -98,7 +102,9 @@ def insert_publish_resources(default_owner_id): resource_ob['data'] = { "dataset" : str(resource[1]) , "trait" : str(resource[0])} resource_ob['type'] = "dataset-publish" - resource_ob['default_mask'] = { "data": "view" } + resource_ob['default_mask'] = { "data": "view", + "metadata": "view", + "admin": "not-admin"} resource_ob['group_masks'] = {} @@ -124,9 +130,13 @@ def insert_geno_resources(default_owner_id): resource_ob['data'] = { "dataset" : str(resource[0]) } resource_ob['type'] = "dataset-geno" if resource[2] < 1: - resource_ob['default_mask'] = { "data": "view" } + resource_ob['default_mask'] = { "data": "view", + "metadata": "view", + "admin": "not-admin"} else: - resource_ob['default_mask'] = { "data": "no-access" } + resource_ob['default_mask'] = { "data": "no-access", + "metadata": "no-access", + "admin": "not-admin"} resource_ob['group_masks'] = {} add_resource(resource_ob) diff --git a/wqflask/utility/authentication_tools.py b/wqflask/utility/authentication_tools.py index dfa0e2d9..6c88949b 100644 --- a/wqflask/utility/authentication_tools.py +++ b/wqflask/utility/authentication_tools.py @@ -3,7 +3,7 @@ from __future__ import absolute_import, print_function, division import json import requests -from base import data_set +from base import data_set, webqtlConfig from utility import hmac from utility.redis_tools import get_redis_conn, get_resource_info, get_resource_id @@ -18,45 +18,47 @@ 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 "edit" + return webqtlConfig.SUPER_PRIVILEGES - resource_id = get_resource_id(dataset, trait_id) response = None - if resource_id: - resource_info = get_resource_info(resource_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)['data'] - except: - response = resource_info['default_mask']['data'] - if 'edit' in response: - return "edit" - elif 'view' in response: - return "view" - else: - return "no-access" + #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 - return False + resource_id = get_resource_id(dataset, trait_id) -def check_admin(resource_id=None): + if resource_id: + resource_info = get_resource_info(resource_id) + else: + return response #ZS: Need to substitute in something that creates the resource in Redis later - return "not-admin" + the_url = "http://localhost:8081/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'] - # ZS: commented out until proxy can return this - # 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']['admin'] + if response: + return response + else: #ZS: No idea how this would happen, but just in case + return False - # if 'edit-admins' in response: - # return "edit-admins" - # elif 'edit-access' in response: - # return "edit-access" - # else: - # return "not-admin" +def check_admin(resource_id=None): + the_url = "http://localhost:8081/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: @@ -74,15 +76,18 @@ def check_owner(dataset=None, trait_id=None, resource_id=None): def check_owner_or_admin(dataset=None, trait_id=None, resource_id=None): if not resource_id: - resource_id = get_resource_id(dataset, trait_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 [resource_id, "owner"] + return "owner" resource_info = get_resource_info(resource_id) if g.user_session.user_id == resource_info['owner_id']: - return [resource_id, "owner"] + return "owner" else: - return [resource_id, check_admin(resource_id)] + return check_admin(resource_id) - return [resource_id, "not-admin"]
\ No newline at end of file + return "not-admin"
\ No newline at end of file diff --git a/wqflask/wqflask/resource_manager.py b/wqflask/wqflask/resource_manager.py index 0f9f5c9d..39a07310 100644 --- a/wqflask/wqflask/resource_manager.py +++ b/wqflask/wqflask/resource_manager.py @@ -18,7 +18,7 @@ def manage_resource(): params = request.form if request.form else request.args if 'resource_id' in request.args: resource_id = request.args['resource_id'] - admin_status = check_owner_or_admin(resource_id=resource_id)[1] + admin_status = check_owner_or_admin(resource_id=resource_id) resource_info = get_resource_info(resource_id) group_masks = resource_info['group_masks'] @@ -67,7 +67,7 @@ def search_for_groups(): def change_owner(): resource_id = request.form['resource_id'] if 'new_owner' in request.form: - admin_status = check_owner_or_admin(resource_id=resource_id)[1] + admin_status = check_owner_or_admin(resource_id=resource_id) if admin_status == "owner": new_owner_id = request.form['new_owner'] change_resource_owner(resource_id, new_owner_id) @@ -100,7 +100,7 @@ def change_default_privileges(): @app.route("/resources/add_group", methods=('POST',)) def add_group_to_resource(): resource_id = request.form['resource_id'] - admin_status = check_owner_or_admin(resource_id=resource_id)[1] + admin_status = check_owner_or_admin(resource_id=resource_id) if admin_status == "owner" or admin_status == "edit-admins" or admin_status == "edit-access": if 'selected_group' in request.form: group_id = request.form['selected_group'] diff --git a/wqflask/wqflask/views.py b/wqflask/wqflask/views.py index dc431aa9..bc01839b 100644 --- a/wqflask/wqflask/views.py +++ b/wqflask/wqflask/views.py @@ -96,13 +96,21 @@ def check_access_permissions(): pass else: if 'dataset' in request.args: - dataset = create_dataset(request.args['dataset']) - if 'trait_id' in request.args: - available = check_resource_availability(dataset, request.args['trait_id']) + if request.args['dataset'] == "Temp": + permissions = check_resource_availability("Temp") else: - available = check_resource_availability(dataset) - - if available == "no-access": + dataset = create_dataset(request.args['dataset']) + + if dataset.type == "Temp": + permissions = False + if 'trait_id' in request.args: + permissions = check_resource_availability(dataset, request.args['trait_id']) + elif dataset.type != "Publish": + permissions = check_resource_availability(dataset) + else: + return None + + if 'view' not in permissions['data']: return redirect(url_for("no_access_page")) @app.teardown_appcontext |