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The Biorepository Portal Project

CircleCI ReadTheDocs

For more information and further documentation please see here

Quickstart

Requirements

The Biorepository Portal contains a docker-compose file which defines a brp service to quickly spin up a demonstration instance of the portal. This demo consists of the Portal itself, redis, as well as a companion instance of electronic Honest Broker.

Run:

docker-compose up brp

Demonstration accounts for both the Portal and the eHB have a user name of admin@email.chop.edu and a password of Chopchop1234 (case sensitive).

Installation

Requirements

  • Python >= 3.4

Recommended

  • Postgres >= 9.4, < 10
  • Redis >= 3.0.5

To build front-end components

  • Node >= 5.4.0 [instructions]
  • npm >= 3.3.12 (packaged with Node)

Contributions

Please lint all code contributions using flake8 according to the .flake8 configuration file found in the root of this repository.

Please write tests for contributions when applicable and run the included test suite before submitting a pull request.

Testing

Install the required python packages. Best practice is to do this in a virtual environment, which must be using Python 3. A PostgreSQL 9 pg_config binary must be available in your PATH.

pip install -r requirements.txt -r requirements-dev.txt

Create a local configuration file. This file assumes you have a PostgreSQL 9 server running on port 5432 and a Redis server running on port 6379.

cp test.env_example test.env

Point the Django configuration at the test configuration file.

export APP_ENV=test

Run the unit tests.

./manage.py test

There should only be 5 failing tests, which all relate to LDAP integration.

Helpful Hints

Install Python 3

Install pyenv and pyenv-virtualenv (on macOS using Homebrew).

brew install pyenv pyenv-virtualenv

Initialize pyenv. You may (probably) want to add this line to your shell setup script.

eval "$(pyenv init -)"

Install Python 3.

pyenv install 3.6.5

Create a virtual environment.

pyenv virtualenv 3.6.5 biorepo-portal

Activate that virtual environment for the current directory.

pyenv local biorepo-portal

Install PostgreSQL 9

For macOS, there is a handy application named Postgres which does all the setup for you. It can be installed using Homebrew.

brew cask install postgres

When you first open the application, click the little icon on the bottom to expand a side-drawer that will allow you to add a database, since you don't want to use the default version 10 database you are offered. From there it is pretty easy to initialize and start a new version 9 database.

Use the following to make the PostgreSQL 9 binaries available in your PATH before, for example, installing the required psycopg2 python package dependency. You may want to add this line to your shell setup script.

export PATH=/Applications/Postgres.app/Contents/Versions/9.6/bin:$PATH

Install Redis

On macOS using Homebrew.

brew install redis

Start a Redis server.

redis-server /usr/local/etc/redis.conf