diff --git a/docs/database.md b/docs/database.md index f3fddbd9a4d5f0e753f14b2561bf3aa1de728208..ea9d4576df3aabd49a72c822fde7e00b0e4f2948 100644 --- a/docs/database.md +++ b/docs/database.md @@ -1,4 +1,4 @@ -# Database +# Configuration database ## Introduction @@ -7,14 +7,116 @@ To run anis-server need at least two databases: - One database to store the configuration - At least one database containing datasets -## Configuration database +Here we will explain how the configuration database works. + +## Purpose of the database Anis-server 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. + - The Access rights on datasets (users and roles). ## Schema + + +## Settings + +By default anis-server is configured to connect to a postgres 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 php container. + + + +Here is the list of options concerning the configuration database : + +- `DATABASE_DEV_MODE`: Default to `1` in development mode and to `0` in production mode +- `DATABASE_CO_DRIVER`: 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 configuration database +- `DATABASE_CO_USER`: User name used to connect to the anis-server configuration database +- `DATABASE_CO_PASSWORD`: Password used to connect to the anis-server configuration 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](https://www.doctrine-project.org). + +Anis server stores the different doctrine entities in the `src/Entity` folder and each file corresponds to a table in the configuration database. + + + +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 file (see installation). + +You must be at the root of the anis-server directory. +And you can then enter into the anis-server container by typing the following command: + +```bash +$ make shell +``` + +Once in the container you can type the following command to execute doctrine-cli: + +```bash +$ ./vendor/bin/doctrine +``` + +What you see are the different operations you can perform. + + + +## 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: + +```bash +$ ./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: + +```bash +$ ./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: + +```bash +$ ./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: + +```bash +$ ./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: + +```bash +$ ./vendor/bin/doctrine orm:generate-proxies +``` diff --git a/docs/extra.css b/docs/extra.css new file mode 100644 index 0000000000000000000000000000000000000000..ae79377e8ac3f30c22cc287b3233d623cebaa0fc --- /dev/null +++ b/docs/extra.css @@ -0,0 +1,10 @@ +img[src*='#left'] { + float: left; +} +img[src*='#right'] { + float: right; +} +img[src*='#center'] { + display: block; + margin: auto; +} \ No newline at end of file diff --git a/docs/img/anis_v3_logo300.png b/docs/img/anis_v3_logo300.png new file mode 100755 index 0000000000000000000000000000000000000000..50a0355b5a9b5ca9ee9017973d3e3b338af2cbf2 Binary files /dev/null and b/docs/img/anis_v3_logo300.png differ diff --git a/docs/img/database_connection_settings.png b/docs/img/database_connection_settings.png new file mode 100755 index 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You can use, modify and/ or redistribute the software under the terms of the CeCILL license as circulated by CEA, CNRS and INRIA at the following URL -[https://cecill.info](https://cecill.info) and / or below. +[https://cecill.info](https://cecill.info/index.en.html). ## Authors diff --git a/mkdocs.yml b/mkdocs.yml index a35e26230865399c7a437959f544e54146fcdd3b..e04c21d5093c1b8e68b12a05c7b9d041f2c55e8e 100644 --- a/mkdocs.yml +++ b/mkdocs.yml @@ -1,9 +1,10 @@ site_name: ANIS Documentation dev_addr: 0.0.0.0:8888 theme: readthedocs +extra_css: [extra.css] nav: - Overview: index.md - Installation: installation.md - - Database: database.md + - Configuration database: database.md - Configuration: configuration.md - Search: search.md \ No newline at end of file