TeamTat

Publication

Rezarta Islamaj, Dongseop Kwon, Sun Kim, Zhiyong Lu, TeamTat: a collaborative text annotation tool, Nucleic Acids Research, 2020, gkaa333, https://doi.org/10.1093/nar/gkaa333

How to build

Prerequisite

You need to install the following software packages in your server or computer.

Ruby 2.5
MySQL 5.7
Git
NodeJS

For more detailed instructions, please find the following articles.

before Install

We need to install Docsplit to process PDF properly. http://documentcloud.github.io/docsplit/

apt-get install -y graphicsmagick
apt-get install -y poppler-utils poppler-data
apt-get install -y ghostscript
apt-get install -y pdftk

Basic Setup

Download the source code from the Git repository. Currently the repository is private. So you need a permission to access it. Soon, it will be transferred to a public repository such as NCBI GitHub repository.

  git clone [email protected]:ncbi-nlp/TeamTat.git

Configure config/database.yml
You need to generate a new key and secrets. First, remove the credential file, then you need to input the following information.

rm ./config/credentials.yml.enc
EDITOR=vim rails credentials:edit

example

secret_key_base: << your secret key: will be auto-generated >>
google:
  client_id: << your google OAuth 2.0 client id - need for google login >>
  secret: << your google OAuth 2.0 client secret >>
recaptcha:
  site_key: << your recaptcha site key - for prevent spammer >> 
  secret: << your recaptcha secret - for prevent spammer >>
mailgun:
  key: << your mailgun key - for sending email from the server >>

You can generate your own google id from https://console.developers.google.com and reCAPTCHA key from https://www.google.com/recaptcha/admin.

Install ruby packages and create database

bundle install
rake db:create
rake db:migrate

Run the server on the local computer

rails s

Open the site from you web browser, such as Google Chrome

http://localhost:3000

Deploy

The basic setup is suitable only for testing or small group. If you want to use the software in a production environment, you need to deploy the software. Please refer the following links for the detailed.

Deploy Ruby On Rails: Ubuntu 18.04 Bionic Beaver in 2019 https://gorails.com/deploy/ubuntu/
Deploying a Rails Application to Elastic Beanstalk: https://docs.aws.amazon.com/elasticbeanstalk/latest/dg/ruby-rails-tutorial.html

Appendix: Deploy with Capistrano

https://capistranorb.com/documentation/getting-started/authentication-and-authorisation/ Add deploy user to the remote

root@remote $ adduser deploy
root@remote $ passwd -l deploy

root@remote $ su - deploy
deploy@remote $ cd ~
deploy@remote $ mkdir .ssh
deploy@remote $ echo "ssh-rsa jccXJ/JRfGxnkh/8iL........dbfCH/9cDiKa0Dw8XGAo01mU/w== /Users/me/.ssh/id_rsa" >> .ssh/authorized_keys
deploy@remote $ chmod 700 .ssh
deploy@remote $ chmod 600 .ssh/authorized_keys

Ubuntu 19.04 https://gorails.com/setup/ubuntu/19.04

sudo apt install curl
curl -sL https://deb.nodesource.com/setup_12.x | sudo -E bash -
curl -sS https://dl.yarnpkg.com/debian/pubkey.gpg | sudo apt-key add -
echo "deb https://dl.yarnpkg.com/debian/ stable main" | sudo tee /etc/apt/sources.list.d/yarn.list

sudo apt-get update
sudo apt-get install -y git-core zlib1g-dev build-essential libssl-dev libreadline-dev libyaml-dev libsqlite3-dev sqlite3 libxml2-dev libxslt1-dev libcurl4-openssl-dev software-properties-common libffi-dev nodejs yarn

sudo apt-get -y install mysql-server mysql-client libmysqlclient-dev

sudo apt-get -y install nginx
sudo ufw app list
sudo ufw allow 'Nginx FULL'
sudo service nginx start

cd
su - deploy

git clone https://github.com/rbenv/rbenv.git ~/.rbenv
echo 'export PATH="$HOME/.rbenv/bin:$PATH"' >> ~/.bashrc
echo 'eval "$(rbenv init -)"' >> ~/.bashrc
exec $SHELL

git clone https://github.com/rbenv/ruby-build.git ~/.rbenv/plugins/ruby-build
echo 'export PATH="$HOME/.rbenv/plugins/ruby-build/bin:$PATH"' >> ~/.bashrc
exec $SHELL

rbenv install 2.5.1
rbenv global 2.5.1
ruby -v

gem install bundler
gem install bundler -v '2.0.1'
gem install rails -v 5.2.3

Database Setup

sudo mysql_secure_installation
mysql -u root -p
CREATE DATABASE pubqrator_production CHARACTER SET utf8mb4 COLLATE utf8mb4_unicode_ci;
CREATE USER IF NOT EXISTS 'deploy'@'localhost' IDENTIFIED BY '$omeFancyPassword123';
GRANT ALL PRIVILEGES ON pubqrator_production.* TO 'deploy'@'localhost';
FLUSH PRIVILEGES;

Deploy with Capistrano

ssh-add
cap production deploy

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ncbi-nlp / TeamTat

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