OCCAMS LIMS

A web application for managing a research samples

System Requirements

• Python 2.7+
• npm (globally installed with -g option) - bower - lessc
• redis
• PostgreSQL 9.5+

Authentication

Because many organizations have their politics of authentication, this app tries to not force any authentication paradigm on the client and instead uses repoze.who to allow clients to supply their own authentication via customized-organization-specific plugins.

For production, it is recommended you use a robust solution like LDAP, Active Directory, or a database of users.

For development, we'll be using a JSON document of users to allow us to create test users as neeeded.

Development

This application uses Docker to setup a development environment with dummy user accounts. It is recommended you familiarize yourself with some basic knowledge of how it works.

VirtualBox

Install Virtualbox from:

https://www.virtualbox.org/wiki/Downloads

This is required to install boot2docker on containers.

Machine and Compose

You will neeed to install Docker Compose and Machine in order so setup your environment. To do so, follow the instructions the following instructions based on your host environment:

• macOS: https://docs.docker.com/docker-for-mac/
• Windows: https://docs.docker.com/docker-for-windows/
• Linux: https://docs.docker.com/engine/installation/linux/

Installation

1. Provision a new Docker machine called "lims-develop" by running the following command:

   > docker-machine create -d virtualbox lims-develop
   

2. Point Docker to the development machine:

   > eval $(docker-machine env lims-develop)
   > docker-machine ls
   NAME              ACTIVE   DRIVER       STATE     URL                         SWARM   DOCKER    ERRORS
   lims-develop      *        virtualbox   Running   tcp://192.168.99.104:2376           v1.12.0
   

   Note the asterisk in the "ACTIVE" column.

3. Clone the application and build the containers:

   > git clone https://github.com/razorlabs/occams_lims
   > cd occams_lims
   > docker-compose build
   

   This will take a moment, so it's a good idea to refill on coffee at this time.

4. Back? Ok, spin up the containers, there will some additional building for dependencies, this is normal:

   > docker-compose up -d
   

5. Build the static assess:

   > docker-compose run app bower install
   

6. Build the database tables:

   > docker-compose run app occams_initdb develop.ini
   

7. Build the participant number generator tables:

   > docker-compose run app or_initdb develop.ini
   

8. Get the IP address of the machine and use it to navigate to http://the.ip.addr.es:3000/

   > docker-machine ip lims-develop
   

You now should have a working LIMS app.

Common Tasks

How do I add more users?

Modify the data setting in the [plugin:dev_users] section of the develop.ini file. There is already a test user there for you, so use that a template.

How do I run the tests?

Create a test user and database to run the tests.

> psql -U occams -h `docker-machine ip lims-develop` -c "CREATE USER test"
> psql -U occams -h `docker-machine ip lims-develop` -c "CREATE DATABASE test OWNER test"
> docker-compose run app py.test --db postgresql://test@postgres/test --redis redis://redis/9

How do I check the logs?

> docker-compose logs -f

How do I access the database?

Install the Postgres client on the host machine and run:

> psql -U occams -h `docker-machine ip lims-develop`

How do I restart the application?

> docker-compose restart app

How do I reset the database and start over again?

> docker-compose down
> docker volume rm occams_db
> docker-compose up -d
> docker-compose run app occams_initdb develop.ini