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Commit 257eaefb authored by Arthur Le Bars's avatar Arthur Le Bars
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removed duplicated files

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docker_compose_generator.py deleted 100755 → 0
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#!/usr/bin/env python3
# -*- coding: utf-8 -*-
import os
import argparse
import logging
# import yaml
# import ruamel.yaml
# import json
"""
docker-compose_generator.py
This method will write a formatted docker-compose.yml for the specified organism (only requires genus and species)
"""
class DockerComposeGenerator:
def __init__(self):
self.mode = None
self.genus = None
self.species = None
self.organism_template = None
self.traefik_template = None
self.outdir = None
def generate(self):
if self.organism_template is None:
self.organism_template = str(os.getcwd() + "/templates/compose_template.yml")
else:
with open(self.organism_template, 'r') as infile:
organism_content = list()
for line in infile:
# Replace placeholders by the genus and species
organism_content.append(line.replace("genus_species", str(self.genus.lower() + "_" + self.species)).replace("Genus species", str(self.genus + " " + self.species)).replace("Genus/species", str(self.genus + "/" + self.species)).replace("gspecies", str(self.genus.lower()[0] + self.species)))
self.write_yml(content=organism_content)
if self.traefik_template is None:
self.traefik_template = str(os.getcwd() + "/templates/compose_template.yml")
else:
with open(self.traefik_template, 'r') as infile:
traefik_content = list()
for line in infile:
# Replace placeholders by the genus and species
traefik_content.append(line.replace("genus_species", str(self.genus.lower() + "_" + self.species)).replace("Genus species", str(self.genus + " " + self.species)).replace("Genus/species", str(self.genus + "/" + self.species)).replace("gspecies", str(self.genus.lower()[0] + self.species)))
self.write_yml(content=traefik_content)
def write_yml(self, content):
with open(self.outdir + "/docker-compose.yml", 'w') as outfile:
for line in content:
outfile.write(line)
if __name__ == "__main__":
parser = argparse.ArgumentParser(description="Generator of docker-compose.yml for GGA automated integration "
"following the templates available @ "
"https://gitlab.inria.fr/abretaud/genodock_demo/")
parser.add_argument("-g", "--genus", type=str, help="input genus")
parser.add_argument("-s", "--species", type=str, help="input species")
parser.add_argument("-o", "--organism-template", type=str, help="input organism template docker-compose.yml (compose or stack), optional")
parser.add_argument("-t", "--traefik-template", type=str, help="input organism template docker-compose.yml (compose or stack), optional")
parser.add_argument("-m", "--main-dir", type=str, help="where to write the output traefik docker-compose.yml (defaults to cd, autoload places it in main directory)")
parser.add_argument("-d", "--organism-dir", type=str, help="where to write the output organism docker-compose.yml (defaults to cd, autoload places it in organism directory)")
args = parser.parse_args()
dc_generator = DockerComposeGenerator()
dc_generator.genus = args.genus
dc_generator.species = args.species
if args.template:
dc_generator.template = args.template
dc_generator.outdir = args.outdir
dc_generator.generate()
metadata_generator.py deleted 100755 → 0
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− 36
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import os
import logging
import yaml
"""
Metadata generator for gga_auto_load
Creates a file that summarizes actions taken by the autoload script (e.g what was done in the dedicated galaxy instance)
This organism metadata file is located in the metadata directory of the organism directory (i.e /genus_species/metadata)
By default, will also create/update a general metadata file (located in the parent directory i.e where all the organisms
directories are located)
TODO: move inside autoload
Metadata format: .yml
"""
class MetadataGenerator:
def __init__(self, maindir):
self.maindir = maindir
self.genus = None
self.species = None
self.metadata = None
self.do_update = False
self.date = "01/01/2020"
# def read_metadata(self):
# for label, content in metadata.items():
# print("FOO")
def write_metadata(self):
with open(self.maindir + "/main_metadata.yml", "a") as metadata:
metadata.write("\n\nAdded " + self.genus + " " + self.species + "")
\ No newline at end of file
templates/authelia_phaeoexplorer_config.yml deleted 100644 → 0
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###############################################################
# Authelia configuration #
###############################################################
# The host and port to listen on
host: 0.0.0.0
port: 9091
# tls_key: /var/lib/authelia/ssl/key.pem
# tls_cert: /var/lib/authelia/ssl/cert.pem
# Level of verbosity for logs: info, debug, trace
log_level: info
## File path where the logs will be written. If not set logs are written to stdout.
# log_file_path: /var/log/authelia
# The secret used to generate JWT tokens when validating user identity by
# email confirmation.
# This secret can also be set using the env variables AUTHELIA_JWT_SECRET
jwt_secret: secret
# Default redirection URL
#
# If user tries to authenticate without any referer, Authelia
# does not know where to redirect the user to at the end of the
# authentication process.
# This parameter allows you to specify the default redirection
# URL Authelia will use in such a case.
#
# Note: this parameter is optional. If not provided, user won't
# be redirected upon successful authentication.
default_redirection_url: https://localhost/
# Google Analytics Tracking ID to track the usage of the portal
# using a Google Analytics dashboard.
#
## google_analytics: UA-00000-01
# TOTP Settings
#
# Parameters used for TOTP generation
#totp:
# The issuer name displayed in the Authenticator application of your choice
# See: https://github.com/google/google-authenticator/wiki/Key-Uri-Format for more info on issuer names
#issuer: authelia.com
# The period in seconds a one-time password is current for. Changing this will require all users to register
# their TOTP applications again.
# Warning: before changing period read the docs link below.
#period: 30
# The skew controls number of one-time passwords either side of the current one that are valid.
# Warning: before changing skew read the docs link below.
#skew: 1
# See: https://docs.authelia.com/configuration/one-time-password.html#period-and-skew to read the documentation.
# Duo Push API
#
# Parameters used to contact the Duo API. Those are generated when you protect an application
# of type "Partner Auth API" in the management panel.
#duo_api:
#hostname: api-123456789.example.com
#integration_key: ABCDEF
# This secret can also be set using the env variables AUTHELIA_DUO_API_SECRET_KEY
#secret_key: 1234567890abcdefghifjkl
# The authentication backend to use for verifying user passwords
# and retrieve information such as email address and groups
# users belong to.
#
# There are two supported backends: 'ldap' and 'file'.
authentication_backend:
# Disable both the HTML element and the API for reset password functionality
disable_reset_password: true
# LDAP backend configuration.
#
# This backend allows Authelia to be scaled to more
# than one instance and therefore is recommended for
# production.
# ldap:
# The url to the ldap server. Scheme can be ldap:// or ldaps://
url: ldap://ldap.sb-roscoff.fr/o=sb-roscoff,c=fr?uid?sub?
# Skip verifying the server certificate (to allow self-signed certificate).
skip_verify: false
# The base dn for every entries
# base_dn: dc=genouest,dc=org
# The attribute holding the username of the user. This attribute is used to populate
# the username in the session information. It was introduced due to #561 to handle case
# insensitive search queries.
# For you information, Microsoft Active Directory usually uses 'sAMAccountName' and OpenLDAP
# usually uses 'uid'
username_attribute: uid
# An additional dn to define the scope to all users
# additional_users_dn: ou=users
# The users filter used in search queries to find the user profile based on input filled in login form.
# Various placeholders are available to represent the user input and back reference other options of the configuration:
# - {input} is a placeholder replaced by what the user inputs in the login form.
# - {username_attribute} is a placeholder replaced by what is configured in `username_attribute`.
# - {mail_attribute} is a placeholder replaced by what is configured in `mail_attribute`.
# - DON'T USE - {0} is an alias for {input} supported for backward compatibility but it will be deprecated in later versions, so please don't use it.
#
# Recommended settings are as follows:
# - Microsoft Active Directory: (&({username_attribute}={input})(objectCategory=person)(objectClass=user))
# - OpenLDAP: (&({username_attribute}={input})(objectClass=person))' or '(&({username_attribute}={input})(objectClass=inetOrgPerson))
#
# To allow sign in both with username and email, one can use a filter like
# (&(|({username_attribute}={input})({mail_attribute}={input}))(objectClass=person))
users_filter: (&({username_attribute}={input})(objectClass=abimsPerson)(isActive=TRUE))
# An additional dn to define the scope of groups
# additional_groups_dn: ou=groups
# The groups filter used in search queries to find the groups of the user.
# - {input} is a placeholder replaced by what the user inputs in the login form.
# - {username} is a placeholder replace by the username stored in LDAP (based on `username_attribute`).
# - {dn} is a matcher replaced by the user distinguished name, aka, user DN.
# - {username_attribute} is a placeholder replaced by what is configured in `username_attribute`.
# - {mail_attribute} is a placeholder replaced by what is configured in `mail_attribute`.
# - DON'T USE - {0} is an alias for {input} supported for backward compatibility but it will be deprecated in later versions, so please don't use it.
# - DON'T USE - {1} is an alias for {username} supported for backward compatibility but it will be deprecated in later version, so please don't use it.
# groups_filter: (&(member={dn})(objectclass=bipaaGroup))
# The attribute holding the name of the group
# group_name_attribute: cn
# The attribute holding the mail address of the user
# mail_attribute: mail
# The username and password of the admin user.
user: cn=admin,dc=abims,dc=org
# This secret can also be set using the env variables AUTHELIA_AUTHENTICATION_BACKEND_LDAP_PASSWORD
password: dev
# File backend configuration.
#
# With this backend, the users database is stored in a file
# which is updated when users reset their passwords.
# Therefore, this backend is meant to be used in a dev environment
# and not in production since it prevents Authelia to be scaled to
# more than one instance. The options under password_options have sane
# defaults, and as it has security implications it is highly recommended
# you leave the default values. Before considering changing these settings
# please read the docs page below:
# https://docs.authelia.com/configuration/authentication/file.html#password-hash-algorithm-tuning
#
# file:
# path: ./users_database.yml
file:
path: ./users.yml
password_options:
algorithm: argon2id
iterations: 1
key_length: 32
salt_length: 16
memory: 1024
parallelism: 8
# Access Control
#
# Access control is a list of rules defining the authorizations applied for one
# resource to users or group of users.
#
# If 'access_control' is not defined, ACL rules are disabled and the 'bypass'
# rule is applied, i.e., access is allowed to anyone. Otherwise restrictions follow
# the rules defined.
#
# Note: One can use the wildcard * to match any subdomain.
# It must stand at the beginning of the pattern. (example: *.mydomain.com)
#
# Note: You must put patterns containing wildcards between simple quotes for the YAML
# to be syntactically correct.
#
# Definition: A 'rule' is an object with the following keys: 'domain', 'subject',
# 'policy' and 'resources'.
#
# - 'domain' defines which domain or set of domains the rule applies to.
#
# - 'subject' defines the subject to apply authorizations to. This parameter is
# optional and matching any user if not provided. If provided, the parameter
# represents either a user or a group. It should be of the form 'user:<username>'
# or 'group:<groupname>'.
#
# - 'policy' is the policy to apply to resources. It must be either 'bypass',
# 'one_factor', 'two_factor' or 'deny'.
#
# - 'resources' is a list of regular expressions that matches a set of resources to
# apply the policy to. This parameter is optional and matches any resource if not
# provided.
#
# Note: the order of the rules is important. The first policy matching
# (domain, resource, subject) applies.
access_control:
# Default policy can either be 'bypass', 'one_factor', 'two_factor' or 'deny'.
# It is the policy applied to any resource if there is no policy to be applied
# to the user.
default_policy: bypass
rules:
# The login portal is freely accessible (redirectino loop otherwise)
- domain: auth.example.org
policy: bypass
# Apollo needs to be authenticated
- domain: localhost
resources:
- "^/apollo/.*$"
policy: allow
# traefik dashboard is restricted to a group from ldap
- domain: localhost
resources:
- "^/traefik/.*$"
policy: allow
subject: "group:ldap_admin"
- domain: allow
resources:
- "^/traefik/.*$"
policy: allow
# All galaxies are restricted to a group from ldap
- domain: localhost
resources:
- "^/sp/.+/galaxy/.*$"
policy: one_factor
subject: "group:ldap_admin"
- domain: localhost
resources:
- "^/sp/.+/galaxy$"
policy: allow
# A genome restricted to an ldap group
- domain: localhost
resources:
- "^/sp/genus_species/.*$"
policy: one_factor
subject: "group:gspecies"
- domain: localhost
resources:
- "^/sp/genus_species/.*$"
policy: allow
# Configuration of session cookies
#
# The session cookies identify the user once logged in.
session:
# The name of the session cookie. (default: authelia_session).
name: authelia_abims_session
# The secret to encrypt the session data. This is only used with Redis.
# This secret can also be set using the env variables AUTHELIA_SESSION_SECRET
secret: WXXXXXXXXXXXXXXXXXXXcXXXXXXXXXXXXXX
# The time in seconds before the cookie expires and session is reset.
expiration: 3600000 # 1000 hour
# The inactivity time in seconds before the session is reset.
# abretaud: We get an Unauthorized message when reaching this threshold => disabling by making > cookie lifetime
inactivity: 3700000 # 5 minutes
# The remember me duration.
# Value of 0 disables remember me.
# Value is in seconds, or duration notation. See: https://docs.authelia.com/configuration/index.html#duration-notation-format
# Longer periods are considered less secure because a stolen cookie will last longer giving attackers more time to spy
# or attack. Currently the default is 1M or 1 month.
remember_me_duration: 1M
# The domain to protect.
# Note: the authenticator must also be in that domain. If empty, the cookie
# is restricted to the subdomain of the issuer.
domain: genouest.org
# The redis connection details
redis:
host: authelia-redis
port: 6379
# This secret can also be set using the env variables AUTHELIA_SESSION_REDIS_PASSWORD
#password: authelia
# This is the Redis DB Index https://redis.io/commands/select (sometimes referred to as database number, DB, etc).
#database_index: 0
# Configuration of the authentication regulation mechanism.
#
# This mechanism prevents attackers from brute forcing the first factor.
# It bans the user if too many attempts are done in a short period of
# time.
regulation:
# The number of failed login attempts before user is banned.
# Set it to 0 to disable regulation.
max_retries: 3
# The time range during which the user can attempt login before being banned.
# The user is banned if the authentication failed 'max_retries' times in a 'find_time' seconds window.
# Find Time accepts duration notation. See: https://docs.authelia.com/configuration/index.html#duration-notation-format
find_time: 2m
# The length of time before a banned user can login again.
# Ban Time accepts duration notation. See: https://docs.authelia.com/configuration/index.html#duration-notation-format
ban_time: 5m
# Configuration of the storage backend used to store data and secrets.
#
# You must use only an available configuration: local, mysql, postgres
storage:
postgres:
host: authelia-db
port: 5432
database: postgres
username: postgres
# # This secret can also be set using the env variables AUTHELIA_STORAGE_POSTGRES_PASSWORD
password: XXXXXXXX
# Configuration of the notification system.
#
# Notifications are sent to users when they require a password reset, a u2f
# registration or a TOTP registration.
# Use only an available configuration: filesystem, gmail
notifier:
# For testing purpose, notifications can be sent in a file
## filesystem:
## filename: /tmp/authelia/notification.txt
# Use a SMTP server for sending notifications. Authelia uses PLAIN or LOGIN method to authenticate.
# [Security] By default Authelia will:
# - force all SMTP connections over TLS including unauthenticated connections
# - use the disable_require_tls boolean value to disable this requirement (only works for unauthenticated connections)
# - validate the SMTP server x509 certificate during the TLS handshake against the hosts trusted certificates
# - trusted_cert option:
# - this is a string value, that may specify the path of a PEM format cert, it is completely optional
# - if it is not set, a blank string, or an invalid path; will still trust the host machine/containers cert store
# - defaults to the host machine (or docker container's) trusted certificate chain for validation
# - use the trusted_cert string value to specify the path of a PEM format public cert to trust in addition to the hosts trusted certificates
# - use the disable_verify_cert boolean value to disable the validation (prefer the trusted_cert option as it's more secure)
smtp:
#username: test
# This secret can also be set using the env variables AUTHELIA_NOTIFIER_SMTP_PASSWORD
#password: password
#secure: false
host: smtp-server-hostname
port: 25
disable_require_tls: true
sender: abims@sb-roscoff.fr
# Sending an email using a Gmail account is as simple as the next section.
# You need to create an app password by following: https://support.google.com/accounts/answer/185833?hl=en
## smtp:
## username: myaccount@gmail.com
## # This secret can also be set using the env variables AUTHELIA_NOTIFIER_SMTP_PASSWORD
## password: yourapppassword
## sender: admin@example.com
## host: smtp.gmail.com
## port: 587
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