For more information and further documentation please see here
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 [email protected] and a password of Chopchop1234 (case sensitive).
- Python >= 3.4
- 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)
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.
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.
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 "$(pyenv init -)"
Install Python 3.
pyenv install 3.6.5
Create a virtual environment.
pyenv virtualenv 3.6.5 biorepo-portal
Activate that virtual environment for the current directory.
pyenv local biorepo-portal
For macOS, there is a handy application named Postgres which does all the setup for you. It can be installed using Homebrew.
brew cask install postgres
When you first open the application, click the little icon on the bottom to expand a side-drawer that will allow you to add a database, since you don't want to use the default version 10 database you are offered. From there it is pretty easy to initialize and start a new version 9 database.
Use the following to make the PostgreSQL 9 binaries available in your PATH before, for example, installing the required psycopg2 python package dependency. You may want to add this line to your shell setup script.
export PATH=/Applications/Postgres.app/Contents/Versions/9.6/bin:$PATH
On macOS using Homebrew.
brew install redis
Start a Redis server.
redis-server /usr/local/etc/redis.conf