[med-svn] [biomaj3-user] 01/02: New upstream version 3.0.5
Olivier Sallou
osallou at debian.org
Thu Aug 17 14:43:51 UTC 2017
This is an automated email from the git hooks/post-receive script.
osallou pushed a commit to branch master
in repository biomaj3-user.
commit 52b77bd5a2f1b1e0ad94612b680051080adec3e4
Author: Olivier Sallou <osallou at debian.org>
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
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+to the third party based on the extent of your activity of conveying
+the work, and under which the third party grants, to any of the
+parties who would receive the covered work from you, a discriminatory
+patent license (a) in connection with copies of the covered work
+conveyed by you (or copies made from those copies), or (b) primarily
+for and in connection with specific products or compilations that
+contain the covered work, unless you entered into that arrangement,
+or that patent license was granted, prior to 28 March 2007.
+
+ Nothing in this License shall be construed as excluding or limiting
+any implied license or other defenses to infringement that may
+otherwise be available to you under applicable patent law.
+
+ 12. No Surrender of Others' Freedom.
+
+ If conditions are imposed on you (whether by court order, agreement or
+otherwise) that contradict the conditions of this License, they do not
+excuse you from the conditions of this License. If you cannot convey a
+covered work so as to satisfy simultaneously your obligations under this
+License and any other pertinent obligations, then as a consequence you may
+not convey it at all. For example, if you agree to terms that obligate you
+to collect a royalty for further conveying from those to whom you convey
+the Program, the only way you could satisfy both those terms and this
+License would be to refrain entirely from conveying the Program.
+
+ 13. Remote Network Interaction; Use with the GNU General Public License.
+
+ Notwithstanding any other provision of this License, if you modify the
+Program, your modified version must prominently offer all users
+interacting with it remotely through a computer network (if your version
+supports such interaction) an opportunity to receive the Corresponding
+Source of your version by providing access to the Corresponding Source
+from a network server at no charge, through some standard or customary
+means of facilitating copying of software. This Corresponding Source
+shall include the Corresponding Source for any work covered by version 3
+of the GNU General Public License that is incorporated pursuant to the
+following paragraph.
+
+ Notwithstanding any other provision of this License, you have
+permission to link or combine any covered work with a work licensed
+under version 3 of the GNU General Public License into a single
+combined work, and to convey the resulting work. The terms of this
+License will continue to apply to the part which is the covered work,
+but the work with which it is combined will remain governed by version
+3 of the GNU General Public License.
+
+ 14. Revised Versions of this License.
+
+ The Free Software Foundation may publish revised and/or new versions of
+the GNU Affero General Public License from time to time. Such new versions
+will be similar in spirit to the present version, but may differ in detail to
+address new problems or concerns.
+
+ Each version is given a distinguishing version number. If the
+Program specifies that a certain numbered version of the GNU Affero General
+Public License "or any later version" applies to it, you have the
+option of following the terms and conditions either of that numbered
+version or of any later version published by the Free Software
+Foundation. If the Program does not specify a version number of the
+GNU Affero General Public License, you may choose any version ever published
+by the Free Software Foundation.
+
+ If the Program specifies that a proxy can decide which future
+versions of the GNU Affero General Public License can be used, that proxy's
+public statement of acceptance of a version permanently authorizes you
+to choose that version for the Program.
+
+ Later license versions may give you additional or different
+permissions. However, no additional obligations are imposed on any
+author or copyright holder as a result of your choosing to follow a
+later version.
+
+ 15. Disclaimer of Warranty.
+
+ THERE IS NO WARRANTY FOR THE PROGRAM, TO THE EXTENT PERMITTED BY
+APPLICABLE LAW. EXCEPT WHEN OTHERWISE STATED IN WRITING THE COPYRIGHT
+HOLDERS AND/OR OTHER PARTIES PROVIDE THE PROGRAM "AS IS" WITHOUT WARRANTY
+OF ANY KIND, EITHER EXPRESSED OR IMPLIED, INCLUDING, BUT NOT LIMITED TO,
+THE IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR
+PURPOSE. THE ENTIRE RISK AS TO THE QUALITY AND PERFORMANCE OF THE PROGRAM
+IS WITH YOU. SHOULD THE PROGRAM PROVE DEFECTIVE, YOU ASSUME THE COST OF
+ALL NECESSARY SERVICING, REPAIR OR CORRECTION.
+
+ 16. Limitation of Liability.
+
+ IN NO EVENT UNLESS REQUIRED BY APPLICABLE LAW OR AGREED TO IN WRITING
+WILL ANY COPYRIGHT HOLDER, OR ANY OTHER PARTY WHO MODIFIES AND/OR CONVEYS
+THE PROGRAM AS PERMITTED ABOVE, BE LIABLE TO YOU FOR DAMAGES, INCLUDING ANY
+GENERAL, SPECIAL, INCIDENTAL OR CONSEQUENTIAL DAMAGES ARISING OUT OF THE
+USE OR INABILITY TO USE THE PROGRAM (INCLUDING BUT NOT LIMITED TO LOSS OF
+DATA OR DATA BEING RENDERED INACCURATE OR LOSSES SUSTAINED BY YOU OR THIRD
+PARTIES OR A FAILURE OF THE PROGRAM TO OPERATE WITH ANY OTHER PROGRAMS),
+EVEN IF SUCH HOLDER OR OTHER PARTY HAS BEEN ADVISED OF THE POSSIBILITY OF
+SUCH DAMAGES.
+
+ 17. Interpretation of Sections 15 and 16.
+
+ If the disclaimer of warranty and limitation of liability provided
+above cannot be given local legal effect according to their terms,
+reviewing courts shall apply local law that most closely approximates
+an absolute waiver of all civil liability in connection with the
+Program, unless a warranty or assumption of liability accompanies a
+copy of the Program in return for a fee.
+
+ END OF TERMS AND CONDITIONS
+
+ How to Apply These Terms to Your New Programs
+
+ If you develop a new program, and you want it to be of the greatest
+possible use to the public, the best way to achieve this is to make it
+free software which everyone can redistribute and change under these terms.
+
+ To do so, attach the following notices to the program. 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)
+
+
+ at app.route('/api/user', methods=['GET'])
+def ping():
+ return jsonify({'msg': 'pong'})
+
+
+ at app.route('/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})
+
+
+ at app.route('/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})
+
+
+ at app.route('/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']})
+
+
+ at app.route('/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})
+
+
+ at app.route('/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': 'olivier.sallou at irisa.fr',
+ '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 = 'bldap at no-reply.org'
+
+ 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 = 'bldap at no-reply.org'
+ 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
+
+
+ at 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', 'test at no-reply.org')
+ self.assertTrue(user.user['email'] == 'test at no-reply.org')
+ 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', 'test at no-reply.org')
+ 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
--
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