Metamodel database

Introduction

To run anis need at least two databases:

  • One database to store the configuration (metamodel database)
  • At least one database containing datasets

Here we will explain how the metamodel database works.

Purpose of the database

Anis needs a database to store all the configuration :

  • The available business database(s) that should contain the shared datasets.
  • The different scientific projects.
  • The shared datasets and their attributes.
  • The access rights on datasets (groups_datasets).

Schema

database_schema

Settings

By default anis-server is configured to connect to a PostgreSQL database created during the first launch of docker-compose. The docker compose integrates a PostgreSQL database server named db. You can find the docker-compose.yml file at the root of the anis-server project.

The database settings connection are given in the environment variables of the server container.

php_settings.png

Here is the list of options concerning the metamodel database :

  • DATABASE_DEV_MODE: Default to 1 in development mode and to 0 in production mode
  • DATABASE_CO_DRIVER: Doctrine pdo driver used to connect to the database
  • DATABASE_CO_HOST: Database server host
  • DATABASE_CO_PORT: Database server listening port
  • DATABASE_CO_DBNAME: Name of the anis-server metamodel database
  • DATABASE_CO_USER: User name used to connect to the anis-server metamodel database
  • DATABASE_CO_PASSWORD: Password used to connect to the anis-server metamodel database

You are free to change this configuration to connect to another database.

Doctrine entities

Anis server uses a tool called doctrine to generate the database from the code. You can find more information on the official website: https://www.doctrine-project.org.

Anis server stores the different doctrine entities in the server/src/Entity folder and each file corresponds to a table in the metamodel database.

doctrine_entities

If you want to change the structure of the database you must edit or add entities. But be careful for each change you will have to re-generate the database and the doctrine proxies.

Doctrine command-line tool

You can use the doctrine command-line tool to perform most of the operations. To run the tool you must have launched anis-server with the docker-compose.yml file (see installation).

You must be at the root of the anis directory. And you can then enter into the server container by typing the following command:

$ make shell_server

Once in the container you can type the following command to execute doctrine-cli:

$ ./vendor/bin/doctrine

What you see are the different operations you can perform.

doctrine_cli_operations

Validate schema

If you have performed operations on entities you must ensure that the database schema remains valid. Doctrine then proposes a command to perform that:

$ ./vendor/bin/doctrine orm:validate-schema

Create database

If the tables of your database are not yet generated you must ask doctrine to create them with the following command:

$ ./vendor/bin/doctrine orm:schema-tool:create

Drop database

If the tables of your database are already generated but you want to start from a blank database you can type the following command:

$ ./vendor/bin/doctrine orm:schema-tool:drop

Update database

If you have made changes to your entities you must update the database with the following command:

$ ./vendor/bin/doctrine orm:schema-tool:update

Generate proxies

If you have made changes to your entities you must also update the doctrine entities proxies. The doctrine entities proxies are used to improve the performance of requests. To regenerate them type the following command:

$ ./vendor/bin/doctrine orm:generate-proxies