Brief description

Nlims Data Suncroniser is a Laboratory Information Management System (LIMS) service which is used to exchange data between two sites. The exchange is done through Couchdb, using its sync functionality and MySQL. Data is exchanged, first, between MySQL and Couchdb before Couchdb syncronises with another CouchDB in another facility or site.

-Therefore, in order for syncing data from couchdb to couchdb, you have to add the sites through the user interface of this module. Two sites will have to be added, thus the site at which module is being installed, and the other site. The other site will probably be the molecular laboratory centre were the testing of the samples will be done.

Dependancy

• Nlims Controller
• iBLIS

Requirements

• Ruby ~> 2.5.1
• Rails ~> 5.2.1
• Bundler ~> 2.1.4
• Gem ~> 2.7.6
• MySQL ~> 5.7
• CouchDB ~> 3.1.0

Configuration

1. Rename .example files in config.

   From the commandline, moved into config directory then rename all files with .example by removing the .example extension from then.

   Here is the command:

   cd config
   cp database.yml.example database.yml
   cp application.yml.example application.yml
   cp couchdb.yml.example couchdb.yml
   cp secrets.yml.example secrets.yml

2. Configure your site / facility.

   Using your text editor open application.yml in config and provide name of your site / facility, site code, district and target lab where your data will be pushing and pulling data to and fro. Thus, your application.yml should look like this

   site_name: "Martin Preuss Centre"
   site_code: "MPC"
   district: 'Lilongwe'
   target_lab: "Kamuzu Central Hospital"
   

3. Configure your database.

   This section requires that nlims_controller be installed and running. While still in config folder, provide details of your nlims_controller mysql database in database.yml and nlims_controller couchdb in couchdb.yml respectively.

   For database.yml, replace username with the username of your mysql and password with the password of your mysql.

   Here is the example:

   default: &default
         adapter: mysql2
         encoding: utf8
         pool: <%= ENV.fetch("RAILS_MAX_THREADS") { 5 } %>
         username: your_username
         password: your_password
         socket: /var/run/mysqld/mysqld.sock
   .
   .
   .
   development:
         <<: *default
         database: your_nlims_database
   test:
         <<: *default
         database: your_nlims_test_database
   .
   .
   .
   production:
         <<: *default
         database: your_nlims_production_database
         username: your_username
         password: <%= ENV['NLIMS_DATABASE_PASSWORD'] %>
   

   In couchdb, provide details of your couchdb including protocol (whether http or https), port (normally runs on 5984, but can be replaced with your couchdb port), host, database name in form of prefix and suffix (for example, if your database name is "lims_database" then your prefix will be "lims" and "database" will be your suffix, but if your database is just "lims" then "lims" will be your prefix and no suffix), username and password.

   Here is an example of how your couchdb.yml will be:

   development: &development
         protocol: 'http'
         host: your_host
         port: 5984
         prefix: nlims
         suffix: repo
         username: your_username
         password: your_password
    
   test:
         <<: *development
         suffix: test
          production:
         <<: *development
         protocol: 'http'
   

Installation

Install ruby gems by running the following command:

bundle install

Initiate database by running this command;

rails db:migrate
rails db:seed

Development

To run the application in development server, type the following in commandline:

rails s -p 3011

Or using a passenger

passenger start -p 3011

Test

Production

To deploy the application in production you can either use nginx or apache2 servers. Nginx is recommended since it has been tested and approved by our deployment team.

1. Initialize database

   To initialize database for development, in the database.yml folder in production block, provide the name of the database and the username. In your commandline type the following (replacing your_password with your actual password of mysql database):

   export NLIMS_DATABASE_PASSWORD='your_password'
   

   Then run the following commands to create, migrate and seed data into your database:

   rails db:create RAILS_ENV=production
   rails db:migrate RAILS_ENV=production
   rails db:seed RAILS_ENV=production

2. Deploy

Contribution

We are very much willing to have your contributions. Contact BHT software development team @ [email protected] for such arrangements.

Issues

Issues with the system can be logged on directy here on git. You can also contact BHT software support team @ [email protected].

License

MPL-2.0