README.md

Copyright© 2017 Merck Sharp & Dohme Corp. a subsidiary of Merck & Co., Inc., Kenilworth, NJ, USA. Licensed under the Apache License, Version 2.0 (the "License"); you may not use this file except in compliance with the License. You may obtain a copy of the License at http://www.apache.org/licenses/LICENSE-2.0 Unless required by applicable law or agreed to in writing, software distributed under the License is distributed on an "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied. See the License for the specific language governing permissions and limitations under the License.

Linea

Linea is a DocGraph tool that is designed to be a digital catalogue of publically available healthcare related datasets.

Guidelines

Note: All of these come directly from the Linea readme when this readme was made. Most of these rules are still relevant, especially 2 and 5.1 .

Please observe the following rules when contributing to this project:

1. All code in the master branch is deployable, EC2 instances read from master anytime an instances is started
2. All development must occur in feature branches.
3. All code must be written test first using rspec.
4. You should push your branch changes to stash at least once a day, if not more.
5. Before pushing code or making a pull request, run the following:
   1. rake Linea:quality:rubocop and rake Linea:quality:slim to see if you have any quality issues to fix.
   2. rake Linea:security to see if you've introduced security issues

Deployment

Please see the associated deployment instructions file, linea_deployment_instructions.md.

Importing Previous Data

Please see the associated database migration instructions file, database_migration_instructions.md

Local Development

Local development requires the following to be installed:

• brew and Xcode command line utilities (when on Mac) - see http://brew.sh/
• rvm
• Git
• Ruby 2.2.5
• Postgres 9.3.x

Installing Ruby

If you're developing on a mac, you will need to install gnupg prior to install ruby and rvm:

brew install gnupg gnupg2

Install rvm:

# fetch key for rvm
command curl -sSL https://rvm.io/mpapis.asc | sudo gpg2 --import -

# install rvm
\curl -L https://get.rvm.io | bash -s stable

# add the rvm script to your .bash_profile 
echo "source $HOME/.rvm/scripts/rvm" >> ~/.bash_profile

# logout/login (to load rvm) or open another console window
# load latest rvm
rvm get head
rvm install 2.2.5 --patch railsexpress
rvm use 2.2.5@global
gem install bundler

Installing LauchRocket (mac)

LaunchRocket is a Mac PreferencePane that can be used to graphically start services such as ElasticSearch, Redis, MySQL, Postgresql, etc..

brew cask install launchrocket 

Installing ElasticSearch (mac)

brew install Caskroom/cask/java
brew install elasticsearch
brew info elasticsearch

If you would like to forgo using LaunchRocket, you can follow these instructions:

# To have launchd start elasticsearch at login:
ln -sfv /usr/local/opt/elasticsearch/*.plist ~/Library/LaunchAgents

# Then to load elasticsearch now:
launchctl load ~/Library/LaunchAgents/homebrew.mxcl.elasticsearch.plist

# Or, if you don't want/need launchctl, you can just run:
elasticsearch --config=/usr/local/opt/elasticsearch/config/elasticsearch.yml

Installing Postgres

The following assumes you have Homebrew installed.

Start by installing postgres:

brew update
brew install postgres
brew info postgres

Create a default database/confguration:

initdb /usr/local/var/postgres

Add the following to your ~/.bash_profile:

echo 'export PGHOST=localhost' >> ~/.bash_profile

Load the previous change with source ~/.bash_profile.

Installing redis

Infomation about redis: http://redis.io

• either use brew (brew install redis)

or

• download latest version somewhere (~/tmp for example)
• wget http://download.redis.io/releases/redis-3.2.0.tar.gz
• unpack redis-3.2.0.tar.gz
• run make
• start redis with src/redis-server

Installing sidekiq

gem install sidekiq

Environment Setup

The following assumes that SSH keys have been set up where this repository resides

Installing the gems and adding necessary files

# Get the latest code from stash
git clone repository link
cd Linea

# switch over to rvm 2.2.5@global if not already
rvm use 2.2.5@global

# copy over a few files
cp config/database.yml.sample config/database.yml
cp config/google_oauth.yml.sample config/google_oauth.yml
cp .env.example .env.development 
cp .env.example .env.test

# install the other gems via bundler
bundle install

If you receive errors with libv8 while trying to bundle install, follow these instructions:

brew tap homebrew/versions
brew install v8-315

gem install libv8 -v '3.16.14.13' -- --with-system-v8
gem install therubyracer -- --with-v8-dir=/usr/local/opt/v8-315

bundle install

Bootstrapping and starting up

Start Redis, Postgresql, and ElasticSearch from the LaunchRocket preference pane.

Bootstrapping

Open up the Linea project in the text editor of your choice. Navigate to bin/setup and uncomment lines 18 and 20.

In your open terminal window, execute:

bin/setup

Go back into bin/setup and recomment lines 18 and 20.

Startup

Open up a new terminal window in the Linea directory and start sidekiq:

bundle exec sidekiq –c 5 –e development –P ./tmp/sidekiq.pid –r ./ -q elastic –q sidekiq

Assuming that everything went well, you should now be able to launch Linea from the folder using

rails server

Linea should now be available in your web browser at http://localhost:3000.

Note

If you receive an error with Google Oauth after the server has been started and you attempt to log in, regenerate client id and client secret and edit the google_oauth.yml file as per the oauth section of the deployment instructions.