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@@ -131,78 +131,6 @@ TMPDIR also needs to be set correctly for the R script(s) (previously there was This project has a number of utility scripts that are needed in specific cirscumstances, and whose purpose is to support the operation of this application in one way or another. Have a look at the [Scripts.md file](./docs/Scripts.md] to see the details for each of the scripts that are available. -## Migrations - -**NOTE**: Do not create migration scripts manually. Use the processes indicated below. - -### Authentication/Authorisation Migrations - -The migration scripts for the authentication and authorisation system are in the *migrations/auth* folder in the root of the repository. - -To create an new migration script for the, do: - -```bash -$ yoyo new -m "<description of the migration>" ./migrations/auth/ -``` - -The command will ask whether you want to save the migration configuration, e.g. - -```bash -$ yoyo new --config=yoyo.auth.ini -m "testing a new migration" -Error: could not open editor! -Created file ./migrations/auth/20221103_02_HBzwk-testing-a-new-migration.py -Save migration configuration to yoyo.ini? -This is saved in plain text and contains your database password. - -Answering 'y' means you do not have to specify the migration source or database connection for future runs [yn]: -``` - -If you specify `y` then a file named yoyo.ini will be created in your current working directory, and you can refer to it to avoid providing the `./migrations/auth` explicitly. - -Now you can open and edit the scripts to provide the appropriate SQL statements to update or rollback your schema. - -### Running the Migrations - -To apply the migrations, you can do something like: - -```bash -$ yoyo apply --database="sqlite:////tmp/test-auth.db" ./migrations/auth/ - -[20221103_01_js9ub-initialise-the-auth-entic-oris-ation-database] -Shall I apply this migration? [Ynvdaqjk?]: Y - -[20221103_02_sGrIs-create-user-credentials-table] -Shall I apply this migration? [Ynvdaqjk?]: Y - -[20221108_01_CoxYh-create-the-groups-table] -Shall I apply this migration? [Ynvdaqjk?]: Y - -[20221108_02_wxTr9-create-privileges-table] -Shall I apply this migration? [Ynvdaqjk?]: Y - -... -``` - -If you have previously initialised the yoyo config file, you can put the database uri in the configuration file and just provide it to avoid the prompt to save the configuration. - -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 -$ flask apply-migrations -``` - -This expects that the following two configuration variables are set in the application: - -* `AUTH_MIGRATIONS`: path to the migration scripts -* `AUTH_DB`: path to the sqlite database file (will be created if absent) - -To enable you to run the OAuth2 server without HTTPS, you need to setup the -following environment variable(s): - -* `export AUTHLIB_INSECURE_TRANSPORT=true`: Allows you to run the Authlib server - without HTTPS on your development machine. - ## Example cURL Commands for OAuth2 In this section, we present some example request to the API using cURL to |