Galaxy Webhooks

Contributors

Authors: Clemens Blank Martin Čech Björn Grüning

Questions

• What are Galaxy Webhooks?

• How to create them?

Objectives

• Discover what Galaxy Webhooks are

• Be able to create Webhooks

• Be able to add a Galaxy Webhook in a Galaxy instance

What are Galaxy Webhooks?

A system which can be used to attach new functionalities to predefined entry points in the Galaxy interface.

An accessible way to make isolated customisations to a Galaxy instance.

Entry point: masthead

Adds item to the top menu.

Entry point: tool/workflow submission

Shown after tool or workflow execution.

Entry point: tool-menu

Adds an entry to the tool form menu.

Entry point: history-menu

Adds an entry to the history menu.

What is a webhook made of?

• a config file in YAML format: config/<NAME>.yml
• optional: A Python helper file with access to the Galaxy trans object
  • helper/__init__.py
  • provides an API call at /api/webhooks/<WEBHOOK_NAME>/get_data
• optional: Additional JS and CSS code
  • static/script.js
  • static/styles.css

Example configuration YAML

<span id="trans_object
type:"><i class="fas fa-link" aria-hidden="true"></i> trans_object
type:
</span>
  - masthead
activate: true

icon: fa-user
tooltip: Show Username

function: >
  $.getJSON("/api/webhooks/trans_object/get_data", function(data) {
    alert('Username: ' + data.username);
  });

Definition of the configuration options

Example __init__.py

def main(trans, webhook):
    if trans.user:
        user = trans.user.username
    else:
        user = 'No user is logged in.'
    return {'username': user}

The return value can be read with a call to /api/webhooks/WEBHOOK_NAME/get_data

Want to integrate Webhooks in your Galaxy instance?

• Copy your Webhook to your Webhook directory on your Galaxy instance
  • default: config/plugins/webhooks
  • configurable via webhooks_dir in galaxy.yml
• Restart Galaxy. While developing, changes at the __init__.py file will be active immediately

Want to contribute?

• Create Webhooks and share them with the world!
  • on the main Galaxy repository
• Improve the Webhooks implementation
  • enhance existing entry points
  • add additional ones …
• Improve the documentation or training material
  • Documentation
  • Galaxy Training Network

Developing the Webhooks implementation

• Webhooks initialisation: lib/galaxy/webhooks/__init__.py
• JavaScript logic: client/galaxy/scripts/mvc/webhooks.js
• Entry points
  • client/galaxy/scripts/mvc/tool/tool-form.js
  • client/galaxy/scripts/mvc/tool/tool-form-composite.js
  • client/galaxy/scripts/mvc/history/options-menu.js
  • client/galaxy/scripts/layout/menu-js
• API: lib/galaxy/webapps/galaxy/api/webhooks.py
  • lib/galaxy/webapps/galaxy/buildapp.py

Key Points

• A Galaxy Webhook provides an easy way to customize the Galaxy UI with plugins
• Right now there are 4 entry points: tool, workflow, masthead, history-menu
• With a minimal amount of code you can extend Galaxy's user-interace.

Thank you!