Sparrow

Command Line Interface

Sparrow is administered using the sparrow command-line interface. This command wraps application management, database management, and docker-compose orchestration subcommands in a single executable, simplifying basic management tasks.

Key commands:
  up                       Start sparrow and follow logs
  down                     Safely stop sparrow
  info                     Show information about the installation
  create-test-lab          Create an example installation of Sparrow
  run                      Run Sparrow tasks (alias to sparrow tasks
                           run)


Command groups:
  db                       Manage the sparrow database
  tasks                    Manage sparrow's task system
  test                     Run sparrow's test suite
  dev                      Helper commands for development
  docs                     Manage sparrow's documentation

Core commands:
  config                   Print configuration of backend
  create-user              Create an authorized user for the web frontend
  create-views             Recreate views only (without building rest of
                           schema)

  init                     Initialize database schema (non-destructive)
  list-users
  plugins                  Print a list of enabled plugins
  reset-password           Reset the password for an existing user
  shell                    Get a Python shell within the application

Plugin commands:
  import-earthchem         Import EarthChem vocabulary files
  import-pychron           Import PyChron Interpreted Age files.
  remove-audit-trail       Remove PGMemento audit trail
  show-interface           Show the import interface for a database model.
  tasks
  update-location-names    Update location names
  validate-data            Try to import data into the database to see if
                           errors are raised.


Container orchestration:
  compose                  Alias to docker-compose that respects
                           sparrow config

  attach                   Attach to the standard output of a container
  build                    Build Sparrow Docker images
  container-id
  logs
  shell                    Get an iPython or container shell
  psql                     Get a psql session to the database
  monitor                  Run a monitor
  printenv                 Print sparrow environment variables to a
                           file

  exec                     Quick shortcut to docker-compose exec
  status                   Get the status of the running Sparrow instance.
  kill                     Like sparrow down, but for people in a
                           hurry.

  test-runtime             Run tests for Sparrow
  restart                  Fully restart all sparrow containers

Some key commands:

• sparrow compose config: print out the entire Docker-compose configuration.
• sparrow restart: forces sparrow to restart and rebuild the docker containers.
• sparrow db: shows a list of the available commands for the sparrow database.
• sparrow tasks: shows a list of the available sparrow tasks, may not be a complete list and others can be seen on frontend.
• sparrow show-interface <schema-name>: shows the schema for a given data model (i.e sample).
• sparrow init: intializes the sparrow database. If the database doesn't exist this command will build the schemas and tables.

Container orchestration

Sparrow bundles an instance of docker-compose for container orchestration. All commands that are part of the compose interface can be used to access and manage containers that are part of a Sparrow installation.