Brief description

NLims Controller is a Laboratory Information Management Systems' (LIMS) service which communicates with Eletronic Medical Record System (EMRS). It is used to exhange lab orders between these two systems. This README documents steps that are necessary to get the service up and running.

Requirements

• ruby ~> 2.5.3
• bundler ~> 2.1.4
• rails ~> 5.1.7
• 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 facility.

   Using your text editor open application.yml in config and provide district, facility_name and facility_code. Thus, your application.yml should look like this

   district: "Lilongwe"
   facility_name: "Kamuzu Central Hospital"
   facility_code: 'KCH'
   

3. Configure your database.

   While still in config folder, provide details of your mysql database in database.yml and 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: lims_db
   test:
         <<: *default
         database: lims_test
   .
   .
   .
   production:
         <<: *default
         database: nlims_production
         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:create
rails db:migrate
rails db:seed

NB: Database initialization is completed by a service called nlims_data_syncroniser. This service is used to sync data between two sites using couchdb.

Development

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

rails s -p 3010

Or using a passenger

passenger start -p 3010

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

How to use

1. Retrieve target labs.

   The following endpont is used to get a list of target labs from LIMS:

   Method: GET
   URL: http://your_host:3010/api/v1/retrieve_target_labs
   

2. Order tests

   The following endpoint is used to order tests in LIMS:

   Method: POST
   URL: http://your_host:3010/api/v1/create_order
   Payload: {
         "district"=>"Lilongwe",
         "health_facility_name"=>"Ntchisi District Hospital",
         "first_name"=>"Ted",
         "last_name"=>"Talk",
         "middle_name"=>"",
         "date_of_birth"=>"1994-05-15",
         "gender"=>"M",
         "national_patient_id"=>"P158602329249",
         "phone_number"=>"", 
         "who_order_test_last_name"=>"User", 
         "who_order_test_first_name"=>"Super", 
         "who_order_test_id"=>"1", 
         "order_location"=>"TB", 
         "date_sample_drawn"=>"2020-05-15T14:55:33.000+02:00", 
         "tests"=>["TB"], 
         "sample_priority"=>"Diagnosis", 
         "art_start_date"=>"not_applicable", 
         "sample_type"=>"Sputum", 
         "sample_status"=>"specimen_not_collected", 
         "target_lab"=>"Kamuzu Central Hospital", 
         "recommended_examination"=>nil, 
         "treatment_history"=>nil, 
         "sample_date"=>"2020-05-15", 
         "sending_facility"=>"Ntchisi District Hospital", 
         "time_line"=>"NA", 
         "requesting_clinician"=>"admin"
     }
   

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