Development

Getting started

  • Start a development environment in Docker, run make dev - you may need to do make build first
  • Populate the database by running make db or make db TEST_SET=.. if you want something else than the default data. See vardb/deposit/deposit_testdata.py#AVAILABLE_TESTSETS

To get visibility into what's happening in the browser client, start the Cerebral debugger (https://cerebraljs.com/docs/introduction/debugger.html). Enter any name ('ella' is a good name) and port 8585. This sets up a server listening on that part port. Open the app in the browser (refresh if the app was openen before starting Cerebral). The browser will connect to the Cerebral. Make sure the server port match the port configured in webui/src/js/index.js

Ops

Bringing up the production/development/demo/testing systems are handled by Make and supervisord. Look in Makefile and in ops/ for more information.

Migration

Whenever you make changes to the database model, you need to create migration scripts, so that the production database can be upgraded to the new version. We use Alembic to assist creating those scripts. Migration scripts are stored in src/vardb/datamodel/migration/alembic/. The current migration base is stored in src/vardb/datamodel/migration/ci_migration_base. This base serves as the base for which the migration scripts will be built against, and should represent the oldest database in production.

Create a new migration

  1. Make all your changes to the normal datamodel in src/vardb/datamodel/ and test them until you're satisfied. In general we don't want to make more migration scripts than necessary, so make sure things are proper.
  2. Make and enter a dev instance: make dev and make shell
  3. Inside it do:
    1. /ella/ella-cli database ci-migration-head (resets database to the migration base, then runs all the migrations)
    2. cd /ella/src/vardb/datamodel/migration/
    3. PYTHONPATH=../../.. alembic revision --autogenerate -m "Name of migration". This will look at the current datamodel and compare it against the database state, generating a migration script from the differences.
  4. Go over the created script, clean it up and test it (test-api-migration).

The migration scripts are far from perfect, so you need some knowledge of SQLAlchemy and Postgres to get it right. Known issues are Sequences and ENUMs, which have to be taken care of manually. Also remember to convert any data present in the database if necessary.

The test-api-migration part of the test suite will test also test database migrations, by running the api tests on a migrated database.

Manually testing the migrations

To manually test the migration scripts you can run the upgrade/downgrade parts of the various migrations:

  • $ ./ella-cli database ci-migration-base
  • $ ./ella-cli database upgrade e371dfeb38c1
  • $ ./ella-cli database upgrade 94a80b8848df
  • $ ./ella-cli database downgrade e371dfeb38c1

For migrations involving user generated data, it would be useful to run the migrations (both upgrade and downgrade) with the database populated through "real" use.

Typically you call make dbreset then interact with the application through the GUI. dbreset won't create the alembic table and the upgrade/downgrade scripts will fail.

So before manually running the upgrade/downgrade scripts, you need to create the alembic table and populate it with the corresponding version:

 CREATE TABLE alembic_version (version_num varchar)
 INSERT INTO alembic_version VALUES ([hash])

API documentation

The API is documented using apidocs supporting the OpenAPI specification (f.k.a. Swagger 2.0). You can see the specification here.

You can explore the ella's API at /api/v1/docs/ in you browser.

To document your resource, have a look at the current resources to see usage examples.

Under the hood, the resources and definitions (models) are loaded into apispec in api/v1/docs.py. The spec is made available at /api/v1/specs/. The definitions are generated automatically by apispec using it's Marshmallow plugin.

Last Updated: 12/4/2018, 12:41:18 PM