Release 2.0 (merge dev to master)

General

• Reorganize repository
• Fix verbosity mode
• Fix logs details
• Update README.md
• Update the "help" option in the scripts
• Update examples
• Factorize and optimize code
• Create file constants.py containing the constant variables

Input organisms.yml file

• Change root structure (a list instead of a dictionary, the name parameter is added to the species dictionary sp_dict)
• Add parameter main_species. Useful when there are multiple strains for the same species: set to yes to define the strain used as home for JBrowse
• Parameters species, genus, strain, sex, common will be sanitized (removing " ", "-", "(", ")", "'")
• Add jinja2 template

Input config file

• Change root structure (one-level dictionary)
• Add parameters authelia_secrets_env_path and authelia_db_postgres_password required for Authelia
• Change the name of some parameters (galaxy_persist_data, tripal_banner_path, jbrowse_menu_url)
• Remove unused apollo parameters (webapollo_user, webapollo_password)

Step "init"

• Update templates files
• Fix the copy of the specified banner
• Write galaxy_nginx.conf only if needed

Step "get data"

• Prefix data filenames with g_species_s
• Add the last modification date of the source file to the gff filename

Step "load data"

• Use Bioblend function upload_from_galaxy_fs() instead of upload_from_local() (to enable symlink, instead of copy)

Step "run workflow Phaeoexplorer"

• Development of a workflow loading fasta and gff files to Chado, Tripal and JBrowse, for one or two organisms of the same species

examples/authelia_config.yml

@@ -16,7 +16,7 @@ log_level: info
 # 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: XXXXXXXXXXXXXXXXX
+#jwt_secret: XXXXXXXXXXXXXXXXX
 
 # Default redirection URL
 #
@@ -82,7 +82,7 @@ authentication_backend:
 #    skip_verify: false
 
     # The base dn for every entries
-#    base_dn: dc=genouest,dc=org
+#    base_dn: dc=domain,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
@@ -196,7 +196,7 @@ 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
+  default_policy: deny
 
   rules:
     # The login portal is freely accessible (redirectino loop otherwise)
@@ -213,12 +213,9 @@ access_control:
     - domain: localhost
       resources:
         - "^/traefik/.*$"
+        - "^/api/.*$"
       policy: one_factor
       subject: "group:ldap_admin"
-    - domain: localhost
-      resources:
-        - "^/traefik/.*$"
-      policy: deny
 
     # All galaxies are restricted to a group from ldap
     - domain: localhost
@@ -237,22 +234,17 @@ access_control:
         - "^/sp/genus_species/.*$"
       policy: one_factor
       subject: "group:gspecies"
-    - domain: localhost
-      resources:
-        - "^/sp/genus_species/.*$"
-      policy: deny
-
 
 # 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_replaceme_session
+  name: authelia_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
+#  secret: WXXXXXXXXXXXXXXXXXXXcXXXXXXXXXXXXXX
 
   # The time in seconds before the cookie expires and session is reset.
   expiration: 3600000 # 1000 hour
@@ -271,7 +263,7 @@ session:
   # 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: replaceme.org
+  domain: domain.org
 
   # The redis connection details
   redis:
@@ -342,7 +334,7 @@ notifier:
     host: smtp-server-hostname
     port: 25
     disable_require_tls: true
-    sender: replace@me.fr
+    sender: replace@domain.org
 
   # 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