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admin.py
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"""Admin routes"""
import sys
import traceback
from askomics.api.auth import api_auth, admin_required
from askomics.libaskomics.DatasetsHandler import DatasetsHandler
from askomics.libaskomics.FilesHandler import FilesHandler
from askomics.libaskomics.LocalAuth import LocalAuth
from askomics.libaskomics.Mailer import Mailer
from askomics.libaskomics.PrefixManager import PrefixManager
from askomics.libaskomics.OntologyManager import OntologyManager
from askomics.libaskomics.Result import Result
from askomics.libaskomics.ResultsHandler import ResultsHandler
from flask import (Blueprint, current_app, jsonify, request, session)
admin_bp = Blueprint('admin', __name__, url_prefix='/')
@admin_bp.route('/api/admin/getusers', methods=['GET'])
@api_auth
@admin_required
def get_users():
"""Get all users
Returns
-------
json
users: list of all users info
error: True if error, else False
errorMessage: the error message of error, else an empty string
"""
try:
local_auth = LocalAuth(current_app, session)
all_users = local_auth.get_all_users()
except Exception as e:
traceback.print_exc(file=sys.stdout)
return jsonify({
'users': [],
'error': True,
'errorMessage': str(e)
}), 500
return jsonify({
'users': all_users,
'error': False,
'errorMessage': ''
})
@admin_bp.route('/api/admin/getdatasets', methods=['GET'])
@api_auth
@admin_required
def get_datasets():
"""Get all datasets
Returns
-------
json
users: list of all datasets
error: True if error, else False
errorMessage: the error message of error, else an empty string
"""
try:
datasets_handler = DatasetsHandler(current_app, session)
datasets = datasets_handler.get_all_datasets()
except Exception as e:
traceback.print_exc(file=sys.stdout)
return jsonify({
'datasets': [],
'error': True,
'errorMessage': str(e)
}), 500
return jsonify({
'datasets': datasets,
'error': False,
'errorMessage': ''
})
@admin_bp.route('/api/admin/getfiles', methods=['GET'])
@api_auth
@admin_required
def get_files():
"""Get all files info
Returns
-------
json
files: list of all files
error: True if error, else False
errorMessage: the error message of error, else an empty string
"""
try:
files_handler = FilesHandler(current_app, session)
files = files_handler.get_all_files_infos()
except Exception as e:
traceback.print_exc(file=sys.stdout)
return jsonify({
'files': [],
'error': True,
'errorMessage': str(e)
}), 500
return jsonify({
'files': files,
'error': False,
'errorMessage': ''
})
@admin_bp.route('/api/admin/getqueries', methods=['GET'])
@api_auth
@admin_required
def get_queries():
"""Get all public queries
Returns
-------
json
startpoint: list of public queries
error: True if error, else False
errorMessage: the error message of error, else an empty string
"""
try:
results_handler = ResultsHandler(current_app, session)
public_queries = results_handler.get_admin_public_queries()
except Exception as e:
traceback.print_exc(file=sys.stdout)
return jsonify({
"queries": [],
'error': True,
'errorMessage': str(e)
}), 500
return jsonify({
"queries": public_queries,
'error': False,
'errorMessage': ''
})
@admin_bp.route('/api/admin/setadmin', methods=['POST'])
@api_auth
@admin_required
def set_admin():
"""change admin status of a user
Returns
-------
json
error: True if error, else False
errorMessage: the error message of error, else an empty string
"""
data = request.get_json()
try:
local_auth = LocalAuth(current_app, session)
local_auth.set_admin(data['newAdmin'], data['username'])
except Exception as e:
traceback.print_exc(file=sys.stdout)
return jsonify({
'error': True,
'errorMessage': str(e)
}), 500
return jsonify({
'error': False,
'errorMessage': ''
})
@admin_bp.route('/api/admin/setquota', methods=["POST"])
@api_auth
@admin_required
def set_quota():
"""Change quota of a user
Returns
-------
json
users: updated users
error: True if error, else False
errorMessage: the error message of error, else an empty string
"""
data = request.get_json()
try:
local_auth = LocalAuth(current_app, session)
local_auth.set_quota(data['quota'], data['username'])
all_users = local_auth.get_all_users()
except Exception as e:
traceback.print_exc(file=sys.stdout)
return jsonify({
'users': [],
'error': True,
'errorMessage': str(e)
}), 500
return jsonify({
'users': all_users,
'error': False,
'errorMessage': ''
})
@admin_bp.route('/api/admin/setblocked', methods=['POST'])
@api_auth
@admin_required
def set_blocked():
"""Change blocked status of a user
Returns
-------
json
error: True if error, else False
errorMessage: the error message of error, else an empty string
"""
data = request.get_json()
try:
local_auth = LocalAuth(current_app, session)
local_auth.set_blocked(data['newBlocked'], data['username'])
except Exception as e:
traceback.print_exc(file=sys.stdout)
return jsonify({
'error': True,
'errorMessage': str(e)
}), 500
return jsonify({
'error': False,
'errorMessage': ''
})
@admin_bp.route('/api/admin/publicize_dataset', methods=['POST'])
@api_auth
@admin_required
def toogle_public_dataset():
"""Toggle public status of a dataset
Returns
-------
json
error: True if error, else False
errorMessage: the error message of error, else an empty string
"""
data = request.get_json()
datasets_info = [{'id': data["datasetId"]}]
try:
# Change status to queued for all datasets
datasets_handler = DatasetsHandler(current_app, session, datasets_info=datasets_info)
datasets_handler.handle_datasets(admin=True)
for dataset in datasets_handler.datasets:
if (not data.get("newStatus", False) and dataset.ontology):
return jsonify({
'datasets': [],
'error': True,
'errorMessage': "Cannot unpublicize a dataset linked to an ontology"
}), 400
current_app.logger.debug(data["newStatus"])
dataset.toggle_public(data["newStatus"], admin=True)
datasets = datasets_handler.get_all_datasets()
except Exception as e:
traceback.print_exc(file=sys.stdout)
return jsonify({
'datasets': [],
'error': True,
'errorMessage': str(e)
}), 500
return jsonify({
'datasets': datasets,
'error': False,
'errorMessage': ''
})
@admin_bp.route('/api/admin/publicize_query', methods=['POST'])
@api_auth
@admin_required
def togle_public_query():
"""Publish a query template from a result
Returns
-------
json
error: True if error, else False
errorMessage: the error message of error, else an empty string
"""
try:
json = request.get_json()
result_info = {"id": json["queryId"]}
result = Result(current_app, session, result_info)
result.publish_query(json["newStatus"], admin=True)
results_handler = ResultsHandler(current_app, session)
public_queries = results_handler.get_admin_public_queries()
except Exception as e:
traceback.print_exc(file=sys.stdout)
return jsonify({
'queries': [],
'error': True,
'errorMessage': 'Failed to publish query: \n{}'.format(str(e))
}), 500
return jsonify({
'queries': public_queries,
'error': False,
'errorMessage': ''
})
@admin_bp.route("/api/admin/adduser", methods=["POST"])
@api_auth
@admin_required
def add_user():
"""Change blocked status of a user
Returns
-------
json
instanceUrl: The instance URL
user: the new created user
displayPassword: Display password on the interface ?
error: True if error, else False
errorMessage: the error message of error, else an empty string
"""
data = request.get_json()
user = {}
display_password = True
try:
local_auth = LocalAuth(current_app, session)
local_auth.check_inputs(data, admin_add=True)
if not local_auth.get_error():
# Create a user
user = local_auth.persist_user_admin(data)
local_auth.create_user_directories(user['id'], user['username'])
# Send a email to this user (if askomics can send emails)
mailer = Mailer(current_app, session)
if mailer.check_mailer():
display_password = False
current_app.celery.send_task('send_mail_new_user', ({'user': session['user']}, user))
# Don't send password user to frontend
user.pop("password")
except Exception as e:
traceback.print_exc(file=sys.stdout)
return jsonify({
'instanceUrl': "",
'user': user,
'displayPassword': False,
'error': True,
'errorMessage': str(e)
}), 500
return jsonify({
'instanceUrl': current_app.iniconfig.get("askomics", "instance_url"),
'user': user,
'displayPassword': display_password,
'error': local_auth.get_error(),
'errorMessage': local_auth.get_error_message()
})
@admin_bp.route("/api/admin/delete_users", methods=["POST"])
@api_auth
@admin_required
def delete_users():
"""Delete users data
Returns
-------
json
users: remaining users
error: True if error, else False
errorMessage: the error message of error, else an empty string
"""
data = request.get_json()
try:
usernames = data["usersToDelete"]
users = []
# Remove current user from the list
if session["user"]["username"] in usernames:
usernames.remove(session["user"]["username"])
# Remove users from database
local_auth = LocalAuth(current_app, session)
for username in usernames:
# Get user info
users.append(local_auth.get_user(username))
local_auth.delete_user_database(username)
# Celery task to delete users' data from filesystem and rdf triplestore
session_dict = {'user': session['user']}
current_app.celery.send_task('delete_users_data', (session_dict, users, True))
# Get remaining users
users = local_auth.get_all_users()
except Exception as e:
traceback.print_exc(file=sys.stdout)
return jsonify({
'users': [],
'error': True,
'errorMessage': str(e)
}), 500
return jsonify({
'users': users,
'error': local_auth.get_error(),
'errorMessage': local_auth.get_error_message()
})
@admin_bp.route("/api/admin/delete_files", methods=["POST"])
@api_auth
@admin_required
def delete_files():
"""Delete files
Returns
-------
json
files: list of all files of current user
error: True if error, else False
errorMessage: the error message of error, else an empty string
"""
data = request.get_json()
try:
files = FilesHandler(current_app, session)
remaining_files = files.delete_files(data['filesIdToDelete'], admin=True)
except Exception as e:
traceback.print_exc(file=sys.stdout)
return jsonify({
'files': [],
'error': True,
'errorMessage': str(e)
}), 500
return jsonify({
'files': remaining_files,
'error': False,
'errorMessage': ''
})
@admin_bp.route("/api/admin/delete_datasets", methods=["POST"])
@api_auth
@admin_required
def delete_datasets():
"""Delete some datasets (db and triplestore) with a celery task
Returns
-------
json
error: True if error, else False
errorMessage: the error message of error, else an empty string
"""
data = request.get_json()
datasets_info = []
for dataset_id in data['datasetsIdToDelete']:
datasets_info.append({'id': dataset_id})
session_dict = {'user': session['user']}
try:
# Change status to queued for all datasets
datasets_handler = DatasetsHandler(current_app, session, datasets_info=datasets_info)
datasets_handler.handle_datasets(admin=True)
datasets_handler.update_status_in_db('queued', admin=True)
# Launch a celery task for each datasets to delete
for dataset in datasets_handler.datasets:
dataset_info = [{
"id": dataset.id
}, ]
current_app.logger.debug(dataset_info)
# kill integration celery task
current_app.celery.control.revoke(dataset.celery_id, terminate=True)
# Trigger the celery task to delete the dataset
task = current_app.celery.send_task('delete_datasets', (session_dict, dataset_info, True))
# replace the task id with the new
dataset.update_celery(task.id, admin=True)
datasets = datasets_handler.get_all_datasets()
except Exception as e:
traceback.print_exc(file=sys.stdout)
return jsonify({
'datasets': [],
'error': True,
'errorMessage': str(e)
}), 500
return jsonify({
'datasets': datasets,
'error': False,
'errorMessage': ''
})
@admin_bp.route("/api/admin/getprefixes", methods=["GET"])
@api_auth
@admin_required
def get_prefixes():
"""Get all custom prefixes
Returns
-------
json
prefixes: list of all custom prefixes
error: True if error, else False
errorMessage: the error message of error, else an empty string
"""
try:
pm = PrefixManager(current_app, session)
prefixes = pm.get_custom_prefixes()
except Exception as e:
traceback.print_exc(file=sys.stdout)
return jsonify({
'prefixes': [],
'error': True,
'errorMessage': str(e)
}), 500
return jsonify({
'prefixes': prefixes,
'error': False,
'errorMessage': ''
})
@admin_bp.route("/api/admin/addprefix", methods=["POST"])
@api_auth
@admin_required
def add_prefix():
"""Create a new prefix
Returns
-------
json
prefixes: list of all custom prefixes
error: True if error, else False
errorMessage: the error message of error, else an empty string
"""
data = request.get_json()
if not data or not (data.get("prefix") and data.get("namespace")):
return jsonify({
'prefixes': [],
'error': True,
'errorMessage': "Missing parameter"
}), 400
pm = PrefixManager(current_app, session)
prefixes = pm.get_custom_prefixes()
prefix = data.get("prefix")
namespace = data.get("namespace")
if any([prefix == custom['prefix'] for custom in prefixes]):
return jsonify({
'prefixes': [],
'error': True,
'errorMessage': "Prefix {} is already in use".format(prefix)
}), 400
try:
pm.add_custom_prefix(prefix, namespace)
prefixes = pm.get_custom_prefixes()
except Exception as e:
traceback.print_exc(file=sys.stdout)
return jsonify({
'prefixes': [],
'error': True,
'errorMessage': str(e)
}), 500
return jsonify({
'prefixes': prefixes,
'error': False,
'errorMessage': ''
})
@admin_bp.route("/api/admin/delete_prefixes", methods=["POST"])
@api_auth
@admin_required
def delete_prefix():
"""Delete a prefix
Returns
-------
json
prefixes: list of all custom prefixes
error: True if error, else False
errorMessage: the error message of error, else an empty string
"""
data = request.get_json()
if not data or not data.get("prefixesIdToDelete"):
return jsonify({
'prefixes': [],
'error': True,
'errorMessage': "Missing prefixesIdToDelete parameter"
}), 400
pm = PrefixManager(current_app, session)
try:
pm.remove_custom_prefixes(data.get("prefixesIdToDelete"))
prefixes = pm.get_custom_prefixes()
except Exception as e:
traceback.print_exc(file=sys.stdout)
return jsonify({
'prefixes': [],
'error': True,
'errorMessage': str(e)
}), 500
return jsonify({
'prefixes': prefixes,
'error': False,
'errorMessage': ''
})
@admin_bp.route("/api/admin/getontologies", methods=["GET"])
@api_auth
@admin_required
def get_ontologies():
"""Get all ontologies
Returns
-------
json
prefixes: list of all custom prefixes
error: True if error, else False
errorMessage: the error message of error, else an empty string
"""
try:
om = OntologyManager(current_app, session)
ontologies = om.list_full_ontologies()
except Exception as e:
traceback.print_exc(file=sys.stdout)
return jsonify({
'ontologies': [],
'error': True,
'errorMessage': str(e)
}), 500
return jsonify({
'ontologies': ontologies,
'error': False,
'errorMessage': ''
})
@admin_bp.route("/api/admin/addontology", methods=["POST"])
@api_auth
@admin_required
def add_ontology():
"""Create a new ontology
Returns
-------
json
ontologies: list of all ontologies
error: True if error, else False
errorMessage: the error message of error, else an empty string
"""
data = request.get_json()
if not data or not (data.get("name") and data.get("uri") and data.get("shortName") and data.get("type") and data.get("datasetId") and data.get("labelUri")):
return jsonify({
'ontologies': [],
'error': True,
'errorMessage': "Missing parameter"
}), 400
name = data.get("name")
uri = data.get("uri")
short_name = data.get("shortName")
type = data.get("type")
dataset_id = data.get("datasetId")
label_uri = data.get("labelUri")
om = OntologyManager(current_app, session)
if type == "ols" and not om.test_ols_ontology(short_name):
return jsonify({
'ontologies': [],
'error': True,
'errorMessage': "{} ontology not found in OLS".format(short_name)
}), 400
om = OntologyManager(current_app, session)
ontologies = om.list_full_ontologies()
if type not in ["none", "local", "ols"]:
return jsonify({
'ontologies': [],
'error': True,
'errorMessage': "Invalid type"
}), 400
datasets_info = [{'id': dataset_id}]
try:
datasets_handler = DatasetsHandler(current_app, session, datasets_info=datasets_info)
datasets_handler.handle_datasets()
except IndexError:
return jsonify({
'ontologies': [],
'error': True,
'errorMessage': "Dataset {} not found".format(dataset_id)
}), 400
if not len(datasets_handler.datasets) == 1 or not datasets_handler.datasets[0].public:
return jsonify({
'ontologies': [],
'error': True,
'errorMessage': "Invalid dataset id"
}), 400
dataset = datasets_handler.datasets[0]
if any([name == onto['name'] or short_name == onto['short_name'] for onto in ontologies]):
return jsonify({
'ontologies': [],
'error': True,
'errorMessage': "Name and short name must be unique"
}), 400
if any([dataset_id == onto['dataset_id'] for onto in ontologies]):
return jsonify({
'ontologies': [],
'error': True,
'errorMessage': "Dataset is already linked to another ontology"
}), 400
try:
om.add_ontology(name, uri, short_name, dataset.id, dataset.graph_name, dataset.endpoint, type, label_uri)
ontologies = om.list_full_ontologies()
except Exception as e:
traceback.print_exc(file=sys.stdout)
return jsonify({
'ontologies': [],
'error': True,
'errorMessage': str(e)
}), 500
return jsonify({
'ontologies': ontologies,
'error': False,
'errorMessage': ''
})
@admin_bp.route("/api/admin/delete_ontologies", methods=["POST"])
@api_auth
@admin_required
def delete_ontologies():
"""Delete one or more ontologies
Returns
-------
json
ontologies: list of all ontologies
error: True if error, else False
errorMessage: the error message of error, else an empty string
"""
data = request.get_json()
if not data or not data.get("ontologiesIdToDelete"):
return jsonify({
'ontologies': [],
'error': True,
'errorMessage': "Missing ontologiesIdToDelete parameter"
}), 400
om = OntologyManager(current_app, session)
ontologies = om.list_full_ontologies()
onto_to_delete = [{"id": ontology['id'], "dataset_id": ontology['dataset_id']} for ontology in ontologies if ontology['id'] in data.get("ontologiesIdToDelete")]
try:
om.remove_ontologies(onto_to_delete)
ontologies = om.list_full_ontologies()
except Exception as e:
traceback.print_exc(file=sys.stdout)
return jsonify({
'ontologies': [],
'error': True,
'errorMessage': str(e)
}), 500
return jsonify({
'ontologies': ontologies,
'error': False,
'errorMessage': ''
})