From 257eaefb9228aae69ef1fb32efd03e0cda278750 Mon Sep 17 00:00:00 2001
From: Arthur Le Bars <arthur.le-bars@sb-roscoff.fr>
Date: Tue, 19 Jan 2021 17:11:01 +0100
Subject: [PATCH] removed duplicated files
---
docker_compose_generator.py | 73 ----
metadata_generator.py | 36 --
templates/authelia_phaeoexplorer_config.yml | 355 --------------------
3 files changed, 464 deletions(-)
delete mode 100755 docker_compose_generator.py
delete mode 100755 metadata_generator.py
delete mode 100644 templates/authelia_phaeoexplorer_config.yml
diff --git a/docker_compose_generator.py b/docker_compose_generator.py
deleted file mode 100755
index 92f8cb9..0000000
--- a/docker_compose_generator.py
+++ /dev/null
@@ -1,73 +0,0 @@
-#!/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()
diff --git a/metadata_generator.py b/metadata_generator.py
deleted file mode 100755
index c03ff0c..0000000
--- a/metadata_generator.py
+++ /dev/null
@@ -1,36 +0,0 @@
-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
diff --git a/templates/authelia_phaeoexplorer_config.yml b/templates/authelia_phaeoexplorer_config.yml
deleted file mode 100644
index 535590a..0000000
--- a/templates/authelia_phaeoexplorer_config.yml
+++ /dev/null
@@ -1,355 +0,0 @@
-###############################################################
-# 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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