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commit 52b77bd5a2f1b1e0ad94612b680051080adec3e4 Author: Olivier Sallou <[email protected]> Date: Thu Aug 17 08:04:21 2017 +0000 New upstream version 3.0.5 --- .gitignore | 72 ++++ .travis.yml | 33 ++ CHANGES.txt | 12 + LICENSE | 662 +++++++++++++++++++++++++++++++++++++ MANIFEST.in | 2 + README.md | 20 ++ bin/biomaj-users.py | 101 ++++++ biomaj_user/__init__.py | 0 biomaj_user/biomaj_user_service.py | 132 ++++++++ biomaj_user/user.py | 187 +++++++++++ biomaj_user/wsgi.py | 4 + config.yml | 44 +++ requirements.txt | 10 + setup.cfg | 2 + setup.py | 64 ++++ tests/biomaj_tests.py | 207 ++++++++++++ tests/global.properties | 123 +++++++ 17 files changed, 1675 insertions(+) diff --git a/.gitignore b/.gitignore new file mode 100644 index 0000000..754c2a7 --- /dev/null +++ b/.gitignore @@ -0,0 +1,72 @@ +# Byte-compiled / optimized / DLL files +__pycache__/ +*.py[cod] + +# Coveralls +.coveralls.yml + +# C extensions +*.so + +# Distribution / packaging +.Python +env/ +build/ +develop-eggs/ +dist/ +downloads/ +eggs/ +lib/ +lib64/ +parts/ +sdist/ +var/ +*.egg-info/ +.installed.cfg +*.egg + +# PyInstaller +# Usually these files are written by a python script from a template +# before PyInstaller builds the exe, so as to inject date/other infos into it. +*.manifest +*.spec + +# Installer logs +pip-log.txt +pip-delete-this-directory.txt + +# Unit test / coverage reports +htmlcov/ +.tox/ +.coverage +.cache +nosetests.xml +coverage.xml + +# Translations +*.mo +*.pot + +# Django stuff: +*.log + +# Sphinx documentation +docs/_build/ + +# PyBuilder +target/ + +# PyCharm +.idea + +# Vim +.viminfo +# Less history +.lesshst + +.dbshell +.emacs* +.ipython +.mongo* +#*.properties + diff --git a/.travis.yml b/.travis.yml new file mode 100644 index 0000000..def52a6 --- /dev/null +++ b/.travis.yml @@ -0,0 +1,33 @@ +language: python +sudo: false +python: + - "2.7" + - "3.4" + - "3.5" +services: + - mongodb +# Apply only on main branches +branches: + except: + - /^feature.*$/ +# command to install dependencies +#before_install: +# - "sudo apt-get update -qq" +# - "sudo apt-get install -qq libldap2-dev libsasl2-dev" +install: + - "pip install flake8" + - "pip install -r requirements.txt" + - "pip install coverage" + - "pip install python-coveralls" + - "python setup.py -q install" +# - "echo data_file=$TRAVIS_BUILD_DIR/.coverage >> .coveragerc" +before_script: + - sleep 10 + +# command to run tests +script: + - python setup.py test + - flake8 --ignore E501 biomaj_user/*.py +#after_success: +# - coveralls + diff --git a/CHANGES.txt b/CHANGES.txt new file mode 100644 index 0000000..70ce365 --- /dev/null +++ b/CHANGES.txt @@ -0,0 +1,12 @@ +3.0.5: + fix ldap authentication +3.0.4: + fix api key checks via API +3.0.3: + move biomaj_create_user and biomaj_delete_user to biomaj_users script with cmd line options +3.0.2: + add scripts to add/remove a user +3.0.1: + move biomaj_user_service.py to package +3.0.0: + separation of biomaj and biomaj_user diff --git a/LICENSE b/LICENSE new file mode 100644 index 0000000..cebe035 --- /dev/null +++ b/LICENSE @@ -0,0 +1,662 @@ +GNU AFFERO GENERAL PUBLIC LICENSE + Version 3, 19 November 2007 + + Copyright (C) 2007 Free Software Foundation, Inc. <http://fsf.org/> + Everyone is permitted to copy and distribute verbatim copies + of this license document, but changing it is not allowed. + + Preamble + + The GNU Affero General Public License is a free, copyleft license for +software and other kinds of works, specifically designed to ensure +cooperation with the community in the case of network server software. + + The licenses for most software and other practical works are designed +to take away your freedom to share and change the works. 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It is safest +to attach them to the start of each source file to most effectively +state the exclusion of warranty; and each file should have at least +the "copyright" line and a pointer to where the full notice is found. + + <one line to give the program's name and a brief idea of what it does.> + Copyright (C) <year> <name of author> + + This program is free software: you can redistribute it and/or modify + it under the terms of the GNU Affero General Public License as published + by the Free Software Foundation, either version 3 of the License, or + (at your option) any later version. + + This program is distributed in the hope that it will be useful, + but WITHOUT ANY WARRANTY; without even the implied warranty of + MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the + GNU Affero General Public License for more details. + + You should have received a copy of the GNU Affero General Public License + along with this program. If not, see <http://www.gnu.org/licenses/>. + +Also add information on how to contact you by electronic and paper mail. + + If your software can interact with users remotely through a computer +network, you should also make sure that it provides a way for users to +get its source. For example, if your program is a web application, its +interface could display a "Source" link that leads users to an archive +of the code. There are many ways you could offer source, and different +solutions will be better for different programs; see section 13 for the +specific requirements. + + You should also get your employer (if you work as a programmer) or school, +if any, to sign a "copyright disclaimer" for the program, if necessary. +For more information on this, and how to apply and follow the GNU AGPL, see +<http://www.gnu.org/licenses/>. + diff --git a/MANIFEST.in b/MANIFEST.in new file mode 100644 index 0000000..2cf39f3 --- /dev/null +++ b/MANIFEST.in @@ -0,0 +1,2 @@ +include *.txt *.md +recursive-include biomaj_user *.txt diff --git a/README.md b/README.md new file mode 100644 index 0000000..9566867 --- /dev/null +++ b/README.md @@ -0,0 +1,20 @@ +# Biomaj user + +Biomaj user management library + +Creation/deletion/... scripts should not be accessible to end user, only to admin. +End users can have access to their API Key via the biomaj-watcher interface. + + +# Web server + + export BIOMAJ_CONFIG=path_to_config.yml + gunicorn biomaj_user.biomaj_user_service:app + +Web processes should be behind a proxy/load balancer, API base url /api/user + +# Managing users + + usage: biomaj-users.py [-h] -A ACTION [-C </path/to/config.yml>] [-E EMAIL] -U <username> [-P <password>] + +Availables actions: create, delete, update, view, renew (apikey) diff --git a/bin/biomaj-users.py b/bin/biomaj-users.py new file mode 100644 index 0000000..4362fcf --- /dev/null +++ b/bin/biomaj-users.py @@ -0,0 +1,101 @@ +import argparse +from argparse import Namespace as options +import os +import random +import yaml +import string +import sys +import bcrypt +from tabulate import tabulate +from biomaj_user.user import BmajUser +from biomaj_core.utils import Utils +SUPPORTED_ACTIONS = ['add', 'create', 'delete', 'remove', 'rm', 'renew', 'update', 'view'] + + +def main(): + """This is the main function treating arguments passed on the command line.""" + description = "BioMAJ user: Manager users." + parser = argparse.ArgumentParser(description=description) + # Options without value + parser.add_argument('-A', '--action', dest="action", default=None, + help="Action to perform for user " + str(SUPPORTED_ACTIONS) + + "'renew': Create new api key", + required=True) + parser.add_argument('-C', '--config', dest="config", metavar='</path/to/config.yml>', type=str, + help="Path to config.yml. By default read from env variable BIOMAJ_CONFIG") + parser.add_argument('-E', '--email', dest="email", type=str, + help="User email, optional") + parser.add_argument('-U', '--user', dest="user", metavar='<username>', type=str, + required=True, help="User name to manage") + parser.add_argument('-P', '--password', dest="passwd", metavar="<password>", type=str, + help="User password to use when creating new user. If not given, automatically generated, accepts env variable BIOMAJ_USER_PASSWORD env variable") + parser.parse_args(namespace=options) + if not len(sys.argv) > 1: + parser.print_help() + sys.exit(1) + if options.action not in SUPPORTED_ACTIONS: + print("Unsupported action '%s'" % str(options.action)) + sys.exit(1) + + if options.config: + config = options.config + elif 'BIOMAJ_CONFIG' in os.environ: + config = os.environ['BIOMAJ_CONFIG'] + else: + config = 'config.yml' + with open(config, 'r') as ymlfile: + config = yaml.load(ymlfile) + Utils.service_config_override(config) + + BmajUser.set_config(config) + user = BmajUser(options.user) + if options.action in ['add', 'create']: + if user.user is None: + if options.passwd is None: + if 'BIOMAJ_USER_PASSWORD' in os.environ: + options.passwd = os.environ['BIOMAJ_USER_PASSWORD'] + else: + options.passwd = ''.join(random.SystemRandom().choice(string.ascii_uppercase + string.digits) + for _ in range(10)) + user.create(options.passwd, email=options.email) + print("User successfully created") + print(tabulate([["User", "Password", "API Key"], + [user.user['id'], str(options.passwd), str(user.user['apikey'])]], + headers="firstrow", tablefmt="psql")) + sys.exit(0) + else: + print("User %s already exist" % user.user['id']) + sys.exit(1) + + if user.user is None: + print("[%s] User %s does not exist" % (str(options.action), str(options.user))) + sys.exit(1) + + if options.action in ['delete', 'remove', 'rm']: + user.remove() + print("User %s successfully deleted" % user.user['id']) + if options.action == 'update': + update = {} + if options.passwd: + update['hashed_password'] = bcrypt.hashpw(options.passwd, user.user['hashed_password']) + if options.email: + update['email'] = options.email + if update.items(): + BmajUser.users.update({'id': user.user['id']}, {'$set': update}) + print("User %s successfully updated" % str(user.user['id'])) + else: + print("[%s] User %s not updated" % (str(options.action), str(options.user))) + if options.action == 'renew': + user.renew_apikey() + user = BmajUser(user.user['id']) + print("[%s] User %s, successfully renewed API key: '%s'" % + (str(options.action), str(user.user['id']), str(user.user['apikey']))) + if options.action == 'view': + print(tabulate([["User", "Email", "API Key", "LDAP"], + [str(user.user['id']), str(user.user['email']), + str(user.user['apikey']), str(user.user['is_ldap'])]], + headers="firstrow", tablefmt="psql")) + sys.exit(0) + +if __name__ == '__main__': + main() diff --git a/biomaj_user/__init__.py b/biomaj_user/__init__.py new file mode 100644 index 0000000..e69de29 diff --git a/biomaj_user/biomaj_user_service.py b/biomaj_user/biomaj_user_service.py new file mode 100644 index 0000000..a584a56 --- /dev/null +++ b/biomaj_user/biomaj_user_service.py @@ -0,0 +1,132 @@ +import ssl +import os +import random +import string +import yaml +from flask import Flask +from flask import jsonify +from flask import request +from flask import abort +import consul + +from biomaj_user.user import BmajUser +from biomaj_core.utils import Utils + +config_file = 'config.yml' +if 'BIOMAJ_CONFIG' in os.environ: + config_file = os.environ['BIOMAJ_CONFIG'] + +config = None +with open(config_file, 'r') as ymlfile: + config = yaml.load(ymlfile) + Utils.service_config_override(config) + +BmajUser.set_config(config) + +app = Flask(__name__) + + +def consul_declare(config): + if config['consul']['host']: + consul_agent = consul.Consul(host=config['consul']['host']) + consul_agent.agent.service.register('biomaj-user', service_id=config['consul']['id'], address=config['web']['hostname'], port=config['web']['port'], tags=['biomaj']) + check = consul.Check.http(url='http://' + config['web']['hostname'] + ':' + str(config['web']['port']) + '/api/user', interval=20) + consul_agent.agent.check.register(config['consul']['id'] + '_check', check=check, service_id=config['consul']['id']) + + +consul_declare(config) + + [email protected]('/api/user', methods=['GET']) +def ping(): + return jsonify({'msg': 'pong'}) + + [email protected]('/api/user/info/user', methods=['GET']) +def list_users(): + ''' + List users + ''' + users = BmajUser.list() + for user in users: + del user['_id'] + del user['hashed_password'] + return jsonify({'users': users}) + + [email protected]('/api/user/info/user/<user>', methods=['GET']) +def get_user(user): + ''' + Get user info + ''' + user = BmajUser(user) + if not user.user: + abort(404) + del user.user['_id'] + if 'hashed_password' in user.user: + del user.user['hashed_password'] + return jsonify({'user': user.user}) + + [email protected]('/api/user/info/user/<user>', methods=['POST']) +def create_user(user): + ''' + Create a user + ''' + user = BmajUser(user) + param = request.get_json() + if 'password' not in param: + param['password'] = ''.join(random.SystemRandom().choice(string.ascii_uppercase + string.digits) for _ in range(10)) + if 'email' not in param: + param['email'] = None + if not user.user: + user.create(password=param['password'], email=param['email']) + del user.user['_id'] + if 'hashed_password' in user.user: + del user.user['hashed_password'] + return jsonify({'user': user.user, 'password': param['password']}) + + [email protected]('/api/user/bind/user/<user>', methods=['POST']) +def bind_user(user): + ''' + Bind a user with his password or API Key. Post parameters dict: + + {'type': 'password|apikey', 'value': 'XXXX'} + + + ''' + user = BmajUser(user) + params = request.get_json() + check = False + if params['type'] == 'password': + check = user.check_password(params['value']) + else: + check = user.check_apikey(params['value']) + if not check: + abort(401) + del user.user['_id'] + if 'hashed_password' in user.user: + del user.user['hashed_password'] + return jsonify({'user': user.user}) + + [email protected]('/api/user/info/apikey/<apikey>', methods=['GET']) +def get_user_by_apikey(apikey): + ''' + Get a user from his api key + ''' + user = BmajUser.get_user_by_apikey(apikey) + if user: + del user['_id'] + if 'hashed_password' in user: + del user['hashed_password'] + return jsonify({'user': user}) + + +if __name__ == "__main__": + context = None + if config['tls']['cert']: + context = ssl.SSLContext(ssl.PROTOCOL_TLSv1_2) + context.load_cert_chain(config['tls']['cert'], config['tls']['key']) + app.run(host='0.0.0.0', port=config['web']['port'], ssl_context=context, threaded=True, debug=config['web']['debug']) diff --git a/biomaj_user/user.py b/biomaj_user/user.py new file mode 100644 index 0000000..626b9af --- /dev/null +++ b/biomaj_user/user.py @@ -0,0 +1,187 @@ +from builtins import str +from builtins import object +import bcrypt +import logging +import random +import string + +from pymongo import MongoClient + + +class BmajUser(object): + """ + Biomaj User + """ + + config = None + + client = None + db = None + banks = None + users = None + + @staticmethod + def set_config(config): + BmajUser.config = config + BmajUser.client = MongoClient(BmajUser.config['mongo']['url']) + BmajUser.db = BmajUser.client[BmajUser.config['mongo']['db']] + BmajUser.banks = BmajUser.db.banks + BmajUser.users = BmajUser.db.users + + @staticmethod + def get_user_by_apikey(apikey): + return BmajUser.users.find_one({'apikey': apikey}) + + def __init__(self, user): + self.id = user + self.user = BmajUser.users.find_one({'id': user}) + + ldap_server = None + con = None + if not self.user and BmajUser.config['ldap']['host']: + # Check if in ldap + from ldap3 import Server, Connection, STRATEGY_SYNC, SEARCH_SCOPE_WHOLE_SUBTREE, GET_ALL_INFO + try: + ldap_host = BmajUser.config['ldap']['host'] + ldap_port = BmajUser.config['ldap']['port'] + ldap_server = Server(ldap_host, port=ldap_port, get_info=GET_ALL_INFO) + con = Connection(ldap_server, auto_bind=True, client_strategy=STRATEGY_SYNC, check_names=True) + except Exception as err: + logging.error(str(err)) + self.user = None + ldap_dn = BmajUser.config['ldap']['dn'] + base_dn = 'ou=People,' + ldap_dn + ldapfilter = "(&(|(uid=" + user + ")(mail=" + user + ")))" + try: + attrs = ['mail'] + con.search(base_dn, ldapfilter, SEARCH_SCOPE_WHOLE_SUBTREE, attributes=attrs) + if con.response: + ldapMail = None + for r in con.response: + # user_dn = str(r['dn']) + if 'mail' not in r['attributes']: + logging.error('Mail not set for user ' + user) + else: + ldapMail = r['attributes']['mail'][0] + self.user = { + 'id': user, + 'email': ldapMail, + 'is_ldap': True, + 'apikey': ''.join(random.SystemRandom().choice(string.ascii_uppercase + string.digits) for _ in range(10)) + } + self.user['_id'] = self.users.insert(self.user) + + else: + self.user = None + except Exception as err: + logging.error(str(err)) + if con: + con.unbind() + + @staticmethod + def user_remove(user_name): + """ + Remove a user from db + + :param user_name: user name + :type user_name: str + """ + BmajUser.users.remove({'id': user_name}) + + @staticmethod + def list(): + """ + Get users + """ + users = [] + user_list = BmajUser.users.find() + for user in user_list: + users.append(user) + return users + + def check_apikey(self, apikey): + if self.user is None: + return False + if 'apikey' not in self.user: + return False + if self.user['apikey'] == apikey: + return True + else: + return False + + def check_password(self, password): + if self.user is None: + return False + + if self.user['is_ldap']: + con = None + ldap_server = None + + from ldap3 import Server, Connection, AUTH_SIMPLE, STRATEGY_SYNC, SEARCH_SCOPE_WHOLE_SUBTREE, GET_ALL_INFO + from ldap3.core.exceptions import LDAPBindError + try: + ldap_host = BmajUser.config['ldap']['host'] + ldap_port = BmajUser.config['ldap']['port'] + ldap_server = Server(ldap_host, port=ldap_port, get_info=GET_ALL_INFO) + con = Connection(ldap_server, auto_bind=True, client_strategy=STRATEGY_SYNC, check_names=True) + except Exception as err: + logging.error(str(err)) + return False + ldap_dn = BmajUser.config['ldap']['dn'] + base_dn = 'ou=People,' + ldap_dn + ldapfilter = "(&(|(uid=" + self.user['id'] + ")(mail=" + self.user['id'] + ")))" + + try: + attrs = ['mail'] + con.search(base_dn, ldapfilter, SEARCH_SCOPE_WHOLE_SUBTREE, attributes=attrs) + user_dn = None + # ldapMail = None + # ldapHomeDirectory = None + for r in con.response: + user_dn = str(r['dn']) + # ldapMail = r['attributes']['mail'][0] + + con.unbind() + con = Connection(ldap_server, auto_bind=True, read_only=True, client_strategy=STRATEGY_SYNC, user=user_dn, password=password, authentication=AUTH_SIMPLE, check_names=True) + con.unbind() + + if user_dn: + return True + except LDAPBindError as err: + logging.error('Bind error: ' + str(err)) + return False + except Exception as err: + logging.error('Bind error: ' + str(err)) + return False + + else: + hashed = bcrypt.hashpw(password, self.user['hashed_password']) + if hashed == self.user['hashed_password']: + return True + else: + return False + + def remove(self): + if self.user is None: + return False + BmajUser.users.remove({'_id': self.user['_id']}) + return True + + def create(self, password, email=''): + """ + Create a new user + """ + hashed = bcrypt.hashpw(password, bcrypt.gensalt()) + if self.user is None: + self.user = { + 'id': self.id, + 'hashed_password': hashed, + 'email': email, + 'is_ldap': False, + 'apikey': ''.join(random.SystemRandom().choice(string.ascii_uppercase + string.digits) for _ in range(10)) + } + self.user['_id'] = BmajUser.users.insert(self.user) + + def renew_apikey(self): + api_key = ''.join(random.SystemRandom().choice(string.ascii_uppercase + string.digits) for _ in range(10)) + BmajUser.users.update({'_id': self.user['_id']}, {'$set': {'apikey': api_key}}) diff --git a/biomaj_user/wsgi.py b/biomaj_user/wsgi.py new file mode 100644 index 0000000..0bd2115 --- /dev/null +++ b/biomaj_user/wsgi.py @@ -0,0 +1,4 @@ +from biomaj_user.biomaj_user_service import app + +if __name__ == "__main__": + app.run() diff --git a/config.yml b/config.yml new file mode 100644 index 0000000..ee890d8 --- /dev/null +++ b/config.yml @@ -0,0 +1,44 @@ +mongo: + url: 'mongodb://localhost:27017' + db: 'biomaj_user' + +ldap: + host: null + port: 389 + dn: null + + +consul: + host: null + # Unique agent identifier name among biomaj downloaders + id: 'biomaj_user_agent' + +web: + debug: true + port: 5070 + local_endpoint: 'http://127.0.0.1:5070' + +tls: + key: null + cert: null + +log_config: + 'version': 1 + 'formatters': + 'generic': + 'format': '%(asctime)s %(levelname)-5.5s [%(name)s][%(threadName)s] %(message)s' + 'handlers': + 'console': + 'class': 'logging.StreamHandler' + 'formatter': 'generic' + 'level': 'DEBUG' + 'loggers': + 'root': + 'level': 'INFO' + 'handlers': + - 'console' + 'biomaj': + 'level': 'DEBUG' + 'handlers': + - 'console' + 'disable_existing_loggers': False diff --git a/requirements.txt b/requirements.txt new file mode 100644 index 0000000..681d030 --- /dev/null +++ b/requirements.txt @@ -0,0 +1,10 @@ +biomaj_core +nose +mock +ldap3==1.4.0 +pymongo +py-bcrypt +flask +python-consul +tabulate +PyYAML diff --git a/setup.cfg b/setup.cfg new file mode 100644 index 0000000..3c6e79c --- /dev/null +++ b/setup.cfg @@ -0,0 +1,2 @@ +[bdist_wheel] +universal=1 diff --git a/setup.py b/setup.py new file mode 100644 index 0000000..48a6d78 --- /dev/null +++ b/setup.py @@ -0,0 +1,64 @@ +try: + from setuptools import setup, find_packages +except ImportError: + from distutils.core import setup + +from distutils.command.install import install +import os + + +here = os.path.abspath(os.path.dirname(__file__)) +with open(os.path.join(here, 'README.md')) as f: + README = f.read() +with open(os.path.join(here, 'CHANGES.txt')) as f: + CHANGES = f.read() + + +config = { + 'description': 'BioMAJ user management library', + 'long_description': README + '\n\n' + CHANGES, + 'author': 'Olivier Sallou', + 'url': 'http://biomaj.genouest.org', + 'download_url': 'http://biomaj.genouest.org', + 'author_email': '[email protected]', + 'version': '3.0.5', + 'classifiers': [ + # How mature is this project? Common values are + # 3 - Alpha + # 4 - Beta + # 5 - Production/Stable + 'Development Status :: 5 - Production/Stable', + 'Environment :: Console', + 'Natural Language :: English', + 'Operating System :: POSIX :: Linux', + # Indicate who your project is intended for + 'Intended Audience :: Science/Research', + 'Topic :: Scientific/Engineering :: Bio-Informatics', + # Pick your license as you wish (should match "license" above) + 'License :: OSI Approved :: GNU Affero General Public License v3 or later (AGPLv3+)', + # Specify the Python versions you support here. In particular, ensure + # that you indicate whether you support Python 2, Python 3 or both. + 'Programming Language :: Python :: 2', + 'Programming Language :: Python :: 2.7', + 'Programming Language :: Python :: 3', + 'Programming Language :: Python :: 3.4' + ], + 'install_requires': [ + 'ldap3==1.4.0', + 'pymongo', + 'py-bcrypt', + 'flask', + 'PyYAML', + 'tabulate', + 'python-consul', + 'biomaj_core' + ], + 'tests_require': ['nose', 'mock'], + 'test_suite': 'nose.collector', + 'packages': find_packages(), + 'include_package_data': True, + 'scripts': ['bin/biomaj-users.py'], + 'name': 'biomaj_user' +} + +setup(**config) diff --git a/tests/biomaj_tests.py b/tests/biomaj_tests.py new file mode 100644 index 0000000..f16b062 --- /dev/null +++ b/tests/biomaj_tests.py @@ -0,0 +1,207 @@ +from nose.tools import * +from nose.plugins.attrib import attr + +import json +import shutil +import os +import tempfile +import logging +import copy +import stat +import time + +from mock import patch + +from optparse import OptionParser + +from biomaj_core.config import BiomajConfig +from biomaj_core.utils import Utils + +from biomaj_user.user import BmajUser + +import unittest + +class UtilsForTest(): + """ + Copy properties files to a temp directory and update properties to + use a temp directory + """ + + def __init__(self): + """ + Setup the temp dirs and files. + """ + self.global_properties = None + self.bank_properties = None + + self.test_dir = tempfile.mkdtemp('biomaj') + + self.conf_dir =os.path.join(self.test_dir,'conf') + if not os.path.exists(self.conf_dir): + os.makedirs(self.conf_dir) + self.data_dir =os.path.join(self.test_dir,'data') + if not os.path.exists(self.data_dir): + os.makedirs(self.data_dir) + self.log_dir =os.path.join(self.test_dir,'log') + if not os.path.exists(self.log_dir): + os.makedirs(self.log_dir) + self.process_dir =os.path.join(self.test_dir,'process') + if not os.path.exists(self.process_dir): + os.makedirs(self.process_dir) + self.lock_dir =os.path.join(self.test_dir,'lock') + if not os.path.exists(self.lock_dir): + os.makedirs(self.lock_dir) + self.cache_dir =os.path.join(self.test_dir,'cache') + if not os.path.exists(self.cache_dir): + os.makedirs(self.cache_dir) + + + if self.global_properties is None: + self.__copy_global_properties() + + + def clean(self): + """ + Deletes temp directory + """ + shutil.rmtree(self.test_dir) + + + def __copy_global_properties(self): + if self.global_properties is not None: + return + self.global_properties = os.path.join(self.conf_dir,'global.properties') + curdir = os.path.dirname(os.path.realpath(__file__)) + global_template = os.path.join(curdir,'global.properties') + fout = open(self.global_properties,'w') + with open(global_template,'r') as fin: + for line in fin: + if line.startswith('conf.dir'): + fout.write("conf.dir="+self.conf_dir+"\n") + elif line.startswith('log.dir'): + fout.write("log.dir="+self.log_dir+"\n") + elif line.startswith('data.dir'): + fout.write("data.dir="+self.data_dir+"\n") + elif line.startswith('process.dir'): + fout.write("process.dir="+self.process_dir+"\n") + elif line.startswith('lock.dir'): + fout.write("lock.dir="+self.lock_dir+"\n") + else: + fout.write(line) + fout.close() + + +class MockLdapConn(object): + + ldap_user = 'biomajldap' + ldap_user_email = '[email protected]' + + STRATEGY_SYNC = 0 + AUTH_SIMPLE = 0 + STRATEGY_SYNC = 0 + STRATEGY_ASYNC_THREADED = 0 + SEARCH_SCOPE_WHOLE_SUBTREE = 0 + GET_ALL_INFO = 0 + + @staticmethod + def Server(ldap_host, port, get_info): + return None + + @staticmethod + def Connection(ldap_server, auto_bind=True, read_only=True, client_strategy=0, user=None, password=None, authentication=0,check_names=True): + if user is not None and password is not None: + if password == 'notest': + #raise ldap3.core.exceptions.LDAPBindError('no bind') + return None + return MockLdapConn(ldap_server) + + def __init__(self, url=None): + #self.ldap_user = 'biomajldap' + #self.ldap_user_email = '[email protected]' + pass + + def search(self, base_dn, filter, scope, attributes=[]): + if MockLdapConn.ldap_user in filter: + self.response = [{'dn': MockLdapConn.ldap_user, 'attributes': {'mail': [MockLdapConn.ldap_user_email]}}] + return [(MockLdapConn.ldap_user, {'mail': [MockLdapConn.ldap_user_email]})] + else: + raise Exception('no match') + + def unbind(self): + pass + + +@attr('user') +class TestUser(unittest.TestCase): + """ + Test user management + """ + + def setUp(self): + self.utils = UtilsForTest() + self.curdir = os.path.dirname(os.path.realpath(__file__)) + BiomajConfig.load_config(self.utils.global_properties, allow_user_config=False) + config = { + 'mongo': { + 'url': BiomajConfig.global_config.get('GENERAL', 'db.url'), + 'db': BiomajConfig.global_config.get('GENERAL', 'db.name') + }, + 'ldap': { + 'host': BiomajConfig.global_config.get('GENERAL', 'ldap.host'), + 'port': int(BiomajConfig.global_config.get('GENERAL', 'ldap.port')), + 'dn': BiomajConfig.global_config.get('GENERAL', 'ldap.dn') + } + } + BmajUser.set_config(config) + + def tearDown(self): + self.utils.clean() + + @patch('ldap3.Connection') + def test_get_user(self, initialize_mock): + mockldap = MockLdapConn() + initialize_mock.return_value = MockLdapConn.Connection(None, None, None, None) + user = BmajUser('biomaj') + self.assertTrue(user.user is None) + user.remove() + + @patch('ldap3.Connection') + def test_create_user(self, initialize_mock): + mockldap = MockLdapConn() + initialize_mock.return_value = MockLdapConn.Connection(None, None, None, None) + user = BmajUser('biomaj') + user.create('test', '[email protected]') + self.assertTrue(user.user['email'] == '[email protected]') + user.remove() + + @patch('ldap3.Connection') + def test_check_password(self, initialize_mock): + mockldap = MockLdapConn() + initialize_mock.return_value = MockLdapConn.Connection(None, None, None, None) + user = BmajUser('biomaj') + user.create('test', '[email protected]') + self.assertTrue(user.check_password('test')) + user.remove() + + @patch('ldap3.Connection') + def test_ldap_user(self, initialize_mock): + mockldap = MockLdapConn() + initialize_mock.return_value = MockLdapConn.Connection(None, None, None, None) + user = BmajUser('biomajldap') + self.assertTrue(user.user['is_ldap'] == True) + self.assertTrue(user.user['_id'] is not None) + self.assertTrue(user.check_password('test')) + user.remove() + + @patch('ldap3.Connection') + def test_api_renew(self, initialize_mock): + mockldap = MockLdapConn() + initialize_mock.return_value = MockLdapConn.Connection(None, None, None, None) + user = BmajUser('biomajldap') + apikey = user.user['apikey'] + user = BmajUser('biomajldap') + self.assertTrue(user.user['apikey'] == apikey) + user.renew_apikey() + user = BmajUser('biomajldap') + self.assertTrue(user.user['apikey'] != apikey) + user.remove() diff --git a/tests/global.properties b/tests/global.properties new file mode 100644 index 0000000..75cb02c --- /dev/null +++ b/tests/global.properties @@ -0,0 +1,123 @@ +[GENERAL] +test=1 +conf.dir=/tmp/biomaj/config +log.dir=/tmp/biomaj/log +process.dir=/tmp/biomaj/process +#The root directory where all databases are stored. +#If your data is not stored under one directory hirearchy +#you can override this value in the database properties file. +data.dir=/tmp/biomaj/ +lock.dir=/tmp/biomaj/lock +cache.dir=/tmp/biomaj/cache + +db.url=mongodb://localhost:27017 +db.name=biomaj_test + +use_ldap=1 +ldap.host=localhost +ldap.port=389 +ldap.dn=nodomain + +# Use ElasticSearch for index/search capabilities +use_elastic=0 +#Comma separated list of elasticsearch nodes host1,host2:port2 +elastic_nodes=localhost +elastic_index=biomaj_test + +celery.queue=biomaj +celery.broker=mongodb://localhost:27017/biomaj_celery + +# Get directory stats (can be time consuming depending on number of files etc...) +data.stats=1 + +# List of user admin (linux user id, comma separated) +admin= + +# Auto publish on updates (do not need publish flag, can be ovveriden in bank property file) +auto_publish=0 + +######################## +# Global properties file + + +#To override these settings for a specific database go to its +#properties file and uncomment or add the specific line you want +#to override. + +#---------------- +# Mail Configuration +#--------------- +#Uncomment thes lines if you want receive mail when the workflow is finished + +mail.smtp.host= +mail.admin= +mail.from= + +#--------------------- +#Proxy authentification +#--------------------- +#proxyHost= +#proxyPort= +#proxyUser= +#proxyPassword= + +#Number of thread for processes +bank.num.threads=2 + +#Number of threads to use for downloading +files.num.threads=4 + +#to keep more than one release increase this value +keep.old.version=0 + +#---------------------- +# Release configuration +#---------------------- +release.separator=_ + +#The historic log file is generated in log/ +#define level information for output : DEBUG,INFO,WARN,ERR +historic.logfile.level=DEBUG + +#http.parse.dir.line=<a[\s]+href="([\S]+)/".*alt="\[DIR\]">.*([\d]{2}-[\w\d]{2,5}-[\d]{4}\s[\d]{2}:[\d]{2}) +http.parse.dir.line=<img[\s]+src="[\S]+"[\s]+alt="\[DIR\]"[\s]*/?>[\s]*<a[\s]+href="([\S]+)/"[\s]*>.*([\d]{2}-[\w\d]{2,5}-[\d]{4}\s[\d]{2}:[\d]{2}) +http.parse.file.line=<img[\s]+src="[\S]+"[\s]+alt="\[[\s]+\]"[\s]*/?>[\s]<a[\s]+href="([\S]+)".*([\d]{2}-[\w\d]{2,5}-[\d]{4}\s[\d]{2}:[\d]{2})[\s]+([\d\.]+[MKG]{0,1}) + +http.group.dir.name=1 +http.group.dir.date=2 +http.group.file.name=1 +http.group.file.date=2 +http.group.file.size=3 + + +# Bank default access +visibility.default=public + + +[loggers] +keys = root, biomaj + +[handlers] +keys = console + +[formatters] +keys = generic + +[logger_root] +level = INFO +handlers = console + +[logger_biomaj] +level = DEBUG +handlers = console +qualname = biomaj +propagate=0 + +[handler_console] +class = StreamHandler +args = (sys.stderr,) +level = DEBUG +formatter = generic + +[formatter_generic] +format = %(asctime)s %(levelname)-5.5s [%(name)s][%(threadName)s] %(message)s -- Alioth's /usr/local/bin/git-commit-notice on /srv/git.debian.org/git/debian-med/biomaj3-user.git _______________________________________________ debian-med-commit mailing list [email protected] http://lists.alioth.debian.org/cgi-bin/mailman/listinfo/debian-med-commit
