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| -rw-r--r-- | README.md | 4 | ||||
| -rw-r--r-- | docs/Scripts.md | 109 | ||||
| -rw-r--r-- | main.py | 6 | ||||
| -rw-r--r-- | scripts/migrate_existing_data.py | 12 |
4 files changed, 127 insertions, 4 deletions
@@ -127,6 +127,10 @@ These configurations should be set in an external config file, pointed to with t TMPDIR also needs to be set correctly for the R script(s) (previously there was an issue with it being set to /tmp instead of ~/genenetwork3/tmp) +## Command-Line Utility Scripts + +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. diff --git a/docs/Scripts.md b/docs/Scripts.md new file mode 100644 index 0000000..5164277 --- /dev/null +++ b/docs/Scripts.md @@ -0,0 +1,109 @@ +# CLI Utility Scripts + +This documents the various utility scripts that are provided with the project +whose purposes are to support the operation of the application in one way or +another. + +To get a list of the available scripts/flask commands that can be run, do: + +```sh +FLASK_APP="main.py" flask --help +``` + +With that, you should get a list of commands, which as of 2023-05-26 are: + +```sh +. . . output truncated to save space ... + +Commands: + apply-migrations Apply the dabasase migrations. + assign-system-admin Assign user with ID `user_id` administrator role. + init-dev-clients Initialise a development client for OAuth2 sessions. + init-dev-users Initialise development users for OAuth2 sessions. + routes Show the routes for the app. + run Run a development server. + shell Run a shell in the app context. +``` + +*NB*: You can simply do `export FLASK_APP="main.py"` at the beginning of your +shell session and then just run the commands without prepending with the +`FLASK_APP="main.py"` declaration. + +## Setting a User as System Administrator + +Once you have registered the user with the new (as of 2023-05-26) +auth(entic|oris)ation system, you can then proceed to specify that the user is +going to be a system administrator of the system. + +You will need to retrieve the users identifier (UUID) from the system; say the +UUID you get for the user is `5b15ef01-a9d7-4ee4-9a38-fe9dd1d871b8`, you can +then set that user as a system administrator by running: + +```sh +FLASK_APP="main.py" flask assign-system-admin 5b15ef01-a9d7-4ee4-9a38-fe9dd1d871b8 +``` + +## Make Existing Data Publicly Visible + +This will only act on any existing data that is not already linked with a user +group in the new auth system. + +This can be run using flask with + +```sh +FLASK_APP="main.py" flask make-data-public +``` + +which will use the application's configuration settings for the +auth(entic|oris)ation database and the MariaDB database. + +You could also run the script directly with: + +```sh +python3 -m scripts.migrate_existing_data AUTHDBPATH MYSQLDBURI +``` + +where `AUTHDBPATH` and `MYSQLDBURI` are replaced with the appropriate values, +e.g. + +```sh +python3 -m scripts.migrate_existing_data \ + /home/frederick/genenetwork/gn3_files/db/auth.db \ + mysql://webqtlout:webqtlout@127.0.0.1:3307/db_webqtl +``` + +## List Available Routes + +```sh +FLASK_APP="main.py" flask routes +``` + +## Drop Into a Python Shell + +```sh +FLASK_APP="main.py" flask shell +``` + +## Development Scripts + +The commands in this section are meant for easing development and are not to be +run in a production environment. + +### Setting up a Sample User for Development + +```sh +FLASK_APP="main.py" flask init-dev-users +``` + +That will initialise your development database with a development user with the +following details: + +- User ID: 0ad1917c-57da-46dc-b79e-c81c91e5b928 +- Email: test@development.user +- Password: testpasswd + +### Setting up Sample OAuth2 Client for Development + +```sh +FLASK_APP="main.py" flask init-dev-clients +``` @@ -108,6 +108,12 @@ def assign_system_admin(user_id: uuid.UUID): file=sys.stderr) sys.exit(1) +@app.cli.command() +def make_data_public(): + """Make existing data that is not assigned to any group publicly visible.""" + from scripts.migrate_existing_data import entry + entry(app.config["AUTH_DB"], app.config["SQL_URI"]) + ##### END: CLI Commands ##### if __name__ == '__main__': diff --git a/scripts/migrate_existing_data.py b/scripts/migrate_existing_data.py index 5c7e568..5097488 100644 --- a/scripts/migrate_existing_data.py +++ b/scripts/migrate_existing_data.py @@ -336,10 +336,7 @@ def assign_data_to_resource(authconn, bioconn, resource: Resource): return assigner_fns[resource.resource_category.resource_category_key]( authconn, bioconn, resource) -@click.command() -@click.argument("authdbpath") # "Path to the Auth(entic|oris)ation database" -@click.argument("mysqldburi") # "URI to the MySQL database with the biology data" -def run(authdbpath, mysqldburi): +def entry(authdbpath, mysqldburi): """Entry-point for data migration.""" if not Path(authdbpath).exists(): print( @@ -360,5 +357,12 @@ def run(authdbpath, mysqldburi): print(dnf.args[0], file=sys.stderr) sys.exit(1) +@click.command() +@click.argument("authdbpath") # "Path to the Auth(entic|oris)ation database" +@click.argument("mysqldburi") # "URI to the MySQL database with the biology data" +def run(authdbpath, mysqldburi): + """Setup command-line arguments.""" + entry(authdbpath, mysqldburi) + if __name__ == "__main__": run() # pylint: disable=[no-value-for-parameter] |