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LOCAL_INSTALL.md

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Localhost setup on OSX 10.11.6

Overview

To develop on pFDA locally you need to manually add a new user and organization. Because when you first get started in a new system, there is no existing user. So you can't log in to provision new accounts. This requires manually "bootstrapping" the situation in steps described in pFDA localhost user.

Install

Setup for localhost development on MacOS

  • Install XCode
    • Search and install XCode from the App Store.
  • Install Apple Command Line Tools
    • Open XCode (this just needs to run once to initialize it) and close it.
    • Install XCode command line tools by running xcode-select --install in the terminal.
  • Install Homebrew
    • /usr/bin/ruby -e "$(curl -fsSL https://raw.githubusercontent.com/Homebrew/install/master/install)"
    • Run brew update to make sure all your formulas are current
  • Install RVM
    • gpg --keyserver hkp://keys.gnupg.net --recv-keys 409B6B1796C275462A1703113804BB82D39DC0E3
    • \curl -sSL https://get.rvm.io | bash -s stable
  • Install ruby
    • rvm install 2.2.3
  • Install bundler
    • gem install bundler
    • to keep the current bundler version from Gemfile.lock:
      • gem install bundler -v 1.16.6
  • Update the libv8 gem before bundle i:
    • gem install libv8 -v '3.16.14.13' -- --with-system-v8
  • Install git
    • brew install git
  • Set up git ssh
    • ssh-keygen -t rsa -b 4096 -C "your_email@dnanexus.com"
    • Use pbcopy < ~/.ssh/id_rsa.pub to add SSH key to github here
  • Set up git config
    • git config --global core.editor "vim"
    • git config --global user.email “your_email@dnanexus.com”
    • git config --global user.name “FirstName LastName”
    • git config --global push.default simple

Docker setup

  • Install Docker and Docker-Compose. See instructions
  • Install gems
    • docker-compose run web bundle install
  • Prepare db
    • docker-compose run web bundle exec rake db:create
    • docker-compose run web bundle exec rake db:schema:load
  • start rails server
    • docker-compose up
  • start rails console
    • docker compose exec web bundle exec rails c

pFDA setup

  • Clone Repo
    • git clone git@github.com:dnanexus/precision-fda.git
  • bundle install
  • bundle exec rake db:schema:load

Issues

On your first bundle, you may have issues installing the libv8 and therubyracer gems. See here for potential solutions. Try bundle update libv8.

Create a User and Org, and other required records by running

The dxuser of the user record must match your DNAnexus username, and the handle of the org record must match the DNAnexus org handle without the pfda.. prefix, i.e. floranteorg.

pFDA running

  • start rails server
  • start rails console
    • bundle exec rails c

Dev team Backend Testing

  • Run all tests

    • bundle exec rspec

  • Run tests with Rspec Guard

    • bundle exec guard

  • To exit from Guard mode:

    • exit

  • Check current code coverage:

    • open coverage/index.html