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README.md

PubAnnotation

A scalable and sharable storage system of literature annotation.

It is based on a production level DBMS, e.g., PostgreSQL, which makes it scaleable. Annotation data on PubAnnotation are shareable and comparable even if they come from different annotation projects.

Requirement

Please use it with

  • ruby version 2.3.4
  • Postgresql 9.0 or above, and
  • ElasticSearch 5 If your system does not already have an installation of ruby, you need to install it. Using rvm is generally a recommended way to install ruby in your system.

Installation

  1. git clone https://github.com/pubannotation/pubannotation.git
  2. cd pubannotation
  3. bundle install

Setup

  1. Edit config/database.yml as you like
  2. RAILE_ENV=production rake db:create
  3. RAILE_ENV=production rake db:migration
  4. RAILE_ENV=production rake assets:precompile

Deploy

rails s -e production

(You will encounter an error message with an instruction to set a secret key for devise. Please follow the instruction.)

License

The PubAnnotation repository (http://pubannotation.org) is freely available to anyone. The whole software system is also freely available under MIT license.

Deployment

Google authentication procedure

Execute the following ur in the browser and log in with the pubannotation specific user account.

https://console.developers.google.com/

Create a pubannotation project. Example:

pubannotation

Click link(Enable APIs and services) to activate the API library:

Gmail API

OAuth consent screen.

User Type:

External

application name:

pubannotation

Create authentication information(OAuth Client ID). Application type:

Web Application

After creating an OAuth client, client id and client secret are generated:

client id

99999999999-xx99x9xx9xxxxxx9x9xx9xx9xxxxxx.apps.googleusercontent.com

client secret

xxxxxxxxx9xxxx9xx9x9xx99

Add an approved redirect URI.

[Same URL as environment variable(pubannotation)]/users/auth/google_oauth2/callback

Create .env file.

cp .env.example .env

.env file settings.

CLIENT_ID=[Generated client id]
CLIENT_SECRET=[Generated client secret]

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