fishbook/docs/configuration.md

Project configuration

Database connection

• If you do not have access to a remote database server or want to run it locally, go to index for information on setting up the database server.

Suppose that you intend to work on a project named foo use the terminal to navigate to the project directory:

cd foo

To log into the database you need the host, the database name, the user name, and the password. Note, the selected user needs at least read access on the selected database (True? maybe also write?).

The root of the fishbook package contains a file called template_dj_local_conf.json. copy this file to your project folder, i.e. the location from which you call your scripts, remove the template_ prefix and fill in database.host, database.user, database.password.

The json template looks like this:

{
    "database.host": "yourhost",
    "database.user": "yourdatabaseusername",
    "database.password": "yourdatabaseuserpassword",
    "database.port": 3306,
    "loglevel": "DEBUG",
    "display.width": 14,
    "display.limit": 7,
    "safemode": false,
    "connection.init_function": null
}

Example

Let's assume you are working remotely, i.e. connecting to a remote database on a server that has the name foo.uni-xyz.de. The database is up and running and allows connections via port 3306 (the default). The database is called fish_db and the user credentials are name baz and password bar. The configuration file will look like this:

{
    "database.host": "foo.uni-xyz.de",
    "database.user": "bar",
    "database.password": "baz",
    "database.port": 3306,
    "loglevel": "DEBUG",
    "display.width": 14,
    "display.limit": 7,
    "safemode": false,
    "connection.init_function": null
}

In case you are working with a local database the database.host entry is "localhost". If you ommit database.user or database.password fishbook, respectively datajoint, will ask you for the user credentials every time you run your python scripts.

IMPORTANT: This configuration file is pure text and can be easily read by anyone. It must not be part of a public repository. Do not add it to your version control system!