NGI Plate database

A tool for keeping track of plates used at NGI.

Location barcodes

Storage units (e.g. freezers and fridges), racks and positions within racks all have specific ID's described below:

• Full position barcode: R[NNNN]X[NN]Y[NN]
• Rack location only: R[NNNN]X00Y00
• Storage unit only: S[NNNN]

S: Storage unit, R: Rack, X/Y: position

Authentication

Login using password is not required. Users enter their scilifelab email address which is checked against the list of allowed users in StatusDB.

Back end

Tested on Apache (MAMP), PHP 7.1.1 and MySQL 5.6.35

Barcode generation: https://github.com/davidscotttufts/php-barcode

Front end

This site use the framework "Foundation" (http://foundation.zurb.com/), version 6.3.0. It also requires a JavaScript enabled browser.

Configuration

The necessary credentials for connecting to database, LIMS and StatusDB is added to the file config.php that's placed in the root directory:

<?php
$CONFIG=array(
	'mysql' => array(
		'user'   => '',
		'pass'   => '',
		'db'   => '',
		'server' => ''
	),
	'clarity' => array(
		'user'   => '',
		'pass'   => '',
		'uri'  => ''
	),
	'couch' => array(
		'user'   => '',
		'pass'   => '',
		'host'  => '',
		'port'  => '',
		'views'  => array(
			'users'  => '',
			'projects' => ''
		)
	),
	'uservalidation' => array(
		'salt'    => '',
		'useallowedlist' => TRUE,
		'roles'    => array('Disabled','User','Manager','Administrator')
	)
);

Database schema

The database structure can be created using the file db_init/init.sql. x

Developing using Docker

If you wish, you can use Docker to run this website on your computer for testing and development.

First, create a file in the root of this repository called config.php as described above, with the following MySQL credentials:

'mysql' => array(
	'user'   => 'platesdb_admin',
	'pass'   => '9jHdM4KM3uqD6EtuU7',
	'db'   => 'platesdb',
	'server' => 'db'
),

Then run docker compose up to fetch all requirements and create the containers. You should be able to visit the website in your browser at http://localhost:8888/

To stop the servers, just press + (windows / linux) / + (mac).