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.

Please use it with

• ruby version 3.4.1,
• Postgresql 9.0 or above,
• ElasticSearch 5 or above, and
• redis

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.

$ brew install redis

Start redis-server by specifying the location of redis.conf.

$ redis-server /usr/local/etc/redis.conf

1. git clone https://github.com/pubannotation/pubannotation.git
2. cd pubannotation
3. bin/setup

This project uses RSpec for testing. To run the tests, execute:

bundle exec rspec

Start the worker by specifying the location of sidekiq.yml.

By starting a worker by specifying a queue, only Jobs that belong to that queue can be executed.

# Start sidekiq
$ bundle exec sidekiq -C config/sidekiq.yml

# Start by specifying a queue
$ bundle exec sidekiq -C config/sidekiq.yml -q general

rails s -e production

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

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

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

cp .env.example .env

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

Access the Google reCAPTCHA site and log in with your Google account.

https://www.google.com/recaptcha/admin/create

The first screen that opens is the paid Enterprise version.
Click "Switch to create a legacy key" to switch to the free version.

Switch to create a legacy key

Enter the required information.

label:

pubannotation

reCAPTCHA type:

v2 "I'm not a robot" checkbox

domain:
Add your domain, example:

example.com

After you register your site, site_key and secret_key are generated.
Add keys to .env file to use reCAPTCHA on your app.

RECAPTCHA_SITE_KEY=[Generated site key]
RECAPTCHA_SECRET_KEY=[Generated secret key]

Sending a POST request to /textae with an annotation in the body returns a URL that generates HTML with the annotation opened in TextAE.
Specify JSON or SimpleInlineTextAnnotationFormat annotation to the body.

Please specify the content-type according to the body.

curl --globoff -X POST https://pubannotation.org/textae \
  -H "Content-Type: application/json" \
  -d '{
         "text": "Elon Musk is a member of the PayPal Mafia.",
         "denotations":[
           {"span":{"begin": 0, "end": 9}, "obj":"Person"}
         ]
       }'

curl -X POST https://pubannotation.org/textae \
  -H "Content-Type: text/plain" \
  -d "[Elon Musk][Person] is a member of the PayPal Mafia.

      [Person]: https://example.com/Person"

Notes:
If you want to specify BODY from a file, you need to send the data in binary format to keep the newlines.

curl example:
Use --data-binary option instead of -d

curl -X POST http://pubannotation.org/textae \
  -H "Content-Type: text/plain" \
  --data-binary @sample.txt