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Diffstat (limited to 'README.md')
| -rw-r--r-- | README.md | 39 |
1 files changed, 34 insertions, 5 deletions
@@ -14,7 +14,7 @@ The recommended way to pass configuration values to the application is via a configuration file passed in via the `GN_AUTH_CONF` environment variable. This variable simply holds the path to the configuration file, e.g. ```sh -export GN_AUTH_CONF="${HOME}/genenetwork/configs/gn_auth_conf.py" +export GN_AUTH_CONF="${HOME}/genenetwork/configs/gn_auth_conf.conf" ``` The settings in the file above will override @@ -186,7 +186,7 @@ If you have previously initialised the yoyo config file, you can put the databas As a convenience, and to enable the CI/CD to apply the migrations automatically, I have provided a flask cli command that can be run with: ```bash -$ export FLASK_APP=main.py +$ export FLASK_APP=wsgi.py $ flask apply-migrations ``` @@ -205,17 +205,46 @@ following environment variable(s): ### Development +For initial set up, you need a custom configuration file that will contain +custom local_settings. At minimum it can contain: + +```python +# contents for local_settings saved at /absolute/path/to/local_settings_file.conf +SQL_URI = "mysql://user:password@localhost/db_name" # mysql uri +AUTH_DB = "/absolute/path/to/auth.db/" # path to sqlite db file +# path to file containings SECRETS key. +# Note: this path is also used to determine the jwks location +GN_AUTH_SECRETS = "/home/rookie/gn_data/gn2_files/secrets.conf" +``` + +Here's an example `secrets.conf` file: + +```python +SECRET_KEY = "qQIrgiK29kXZU6v8D09y4uw_sk8I4cqgNZniYUrRoUk" +``` + +and you set up the oauth clients using: + +``` +export FLASK_DEBUG=1 AUTHLIB_INSECURE_TRANSPORT=1 OAUTHLIB_INSECURE_TRANSPORT=1 FLASK_APP=gn_auth/wsgi +export GN_AUTH_CONF=/absolute/path/to/local_settings_file.conf +# this sets up a user and client +flask init-dev-clients --client-uri http://localhost:gn2_port_number +``` + To run the application during development: ```sh export FLASK_DEBUG=1 -export FLASK_APP="main.py" +export FLASK_APP="wsgi.py" export AUTHLIB_INSECURE_TRANSPORT=true -export GN_AUTH_CONF="${HOME}/genenetwork/configs/gn_auth_conf.py" +export GN_AUTH_CONF="/absolute/path/to/local_settings_file.conf" flask run --port=8081 ``` -replace the `GN_AUTH_CONF` file with the correct path for your environment. +You can test this by attemptiong to log in to your local GN2 using credentials +defined by the dummy user you set up (see the function `__init_dev_users__` in +`/gn_auth/wsgi.py`). ### Production |