#+TITLE: Configurations for GeneNetwork2 Service
#+OPTIONS: toc:3

* Configuration Variables

** Basic Configurations

- *GN_VERSION*: The current version of GN2
- *GN2_PROXY*: URL to the GN2 proxy service
- *GN_SERVER_URL*:  URL to the GN3 REST API server
- *GN2_BASE_URL*: ??
- *GN2_BRANCH_URL*:
- *SERVER_PORT*: The port on which to run GN2. This is passed on to Flask.
- *SECRET_HMAC_CODE*:
- *GENENETWORK_FILES*: Base directory for all static data files
- *HOME*: The home directory of the user that GN2 runs as

** Redis Configurations

- *REDIS_URL*: The url to use to connect to the running redis instance
- *USE_REDIS*: Redis caching


** Database (MySQL) Configurations

- *SQL_URI*: The URI to the database server in the form
   ~mysql://<username>:<password>@<host>:<port>/<dbname>~. Replace the items in
    the angle brackets with the appropriate values for each item.
- *SQL_ALCHEMY_POOL_RECYCLE*: Probably obsoleted - the use of ORMs (ha/i)s
   be(en/ing) phased off

# ---- Flask configuration (see website)
** Flask-Specific Configurations
- *TRAP_BAD_REQUEST_ERRORS*:
- *SECURITY_CONFIRMABLE*:
- *SECURITY_TRACKABLE*:
- *SECURITY_REGISTERABLE*:
- *SECURITY_RECOVERABLE*:
- *SECURITY_EMAIL_SENDER*:
- *SECURITY_POST_LOGIN_VIEW*:

** External Services

*** GitHub Configurations

- *GITHUB_CLIENT_ID*: Client identifier key for GitHub OAuth authentication
- *GITHUB_CLIENT_SECRET*: Client authentication token for github
- *GITHUB_AUTH_URL*: The url to use for authenticating the client (GN2) with
  GitHub. Default: https://github.com/login/oauth/authorize
- *GITHUB_API_URL*: Once the client (GN2) is authenticated with GitHub, this URI
  is the used to authenticate users using GitHub. The default value is
   https://api.github.com/user

*** ORCID Configurations

- *ORCID_CLIENT_ID*: Client identifier key for ORCID OAuth authentication
- *ORCID_CLIENT_SECRET*: Client authentication token for ORCID
- *ORCID_AUTH_URL*: The url to use for authenticating the client (GN2) with
  ORCID. Default: https://orcid.org/oauth/authorize
- *ORCID_TOKEN_URL*: The URI to acquire a token once GN2 has been authenticated
  with ORCID. This token is used to authenticate users with the ORCID service.
  The default value is https://orcid.org/oauth/token

** Mail Configurations
- *SMTP_CONNECT*:
- *SMTP_USERNAME*:
- *SMTP_PASSWORD*:

** Javascript Configurations
- *JS_GN_PATH*: Path to local javascript libraries for development purposes only.
   See [[./development.org]] for more details

** External Commands Configurations
- *REAPER_COMMAND*: The path to the reaper command/executable

** Behavioral Settings
# ---- Behavioural settings (defaults) note that logger and log levels can
#      be overridden at the module level and with enviroment settings
- *WEBSERVER_MODE*: Determines how the service is run.
  If the value is ~DEBUG~, the service is run in debug mode - debug tools are
  activated for the application.
  If the value is ~DEV~, the service is run in development mode; logging is
  activated.
- *WEBSERVER_BRANDING*: Probably unused - verify and remove.
- *WEBSERVER_DEPLOY*: Probably unused - verify and remove.
- *WEBSERVER_URL*: Probably unused - verify and remove.
- *LOG_LEVEL*:
- *LOG_LEVEL_DEBUG*:
- *LOG_SQL*:
- *LOG_SQL_ALCHEMY*:
- *LOG_BENCH*:
- *USE_GN_SERVER*: ??