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apache / incubator-taverna-databundle-viewer

Mirror of Apache Taverna Databundle Viewer (Incubating)

Mirrored from https://github.com/apache/incubator-taverna-databundle-viewer.git
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  1. 630d616 Taverna retired from Apache Incubator by Stian Soiland-Reyes · 4 years, 9 months ago master
  2. 8f5eab9 might also need libwebkit-dev by Stian Soiland-Reyes · 6 years ago apache-retire-2020-03-12
  3. 4883e6f attempt to disable Gemfile.lock by Stian Soiland-Reyes · 7 years ago
  4. ec7f94a Update for omniauth to latest (1.8.1) rather than frozen at 1.3.1 by Ian Dunlop · 7 years ago
  5. 2f44592 Update nokogiri by Stian Soiland-Reyes · 7 years ago

Taverna Project Retired

tl;dr: The Taverna code base is no longer maintained and is provided here for archival purposes.

From 2014 till 2020 this code base was maintained by the Apache Incubator project Apache Taverna (incubating) (see web archive and podling status).

In 2020 the Taverna community voted to retire Taverna as a project and withdraw the code base from the Apache Software Foundation.

This code base remains available under the Apache License 2.0 (see License below), but is now simply called Taverna rather than Apache Taverna (incubating).

While the code base is no longer actively maintained, Pull Requests are welcome to the GitHub organization taverna, which may infrequently be considered by remaining volunteer caretakers.

Previous releases

This code base has not yet been formally released.

Apache Taverna Databundle Viewer

Code Climate Test Coverage Build Status

Apache Taverna Databundle Viewer is planned as a web interface for displaying Taverna databundles (workflow inputs/outputs/run), as produced by the Apache Taverna workflow system.

This module is work in progress as part of Google Summer of Code 2015.

You can see working prototype there: DataBundleViewer

License

(c) 2014-2020 Apache Software Foundation

This product includes software developed at The Apache Software Foundation.

Licensed under the Apache License 2.0, see the file LICENSE for details.

The file NOTICE contain any additional attributions and details about embedded third-party libraries and source code.

Contribute

Any contributions received are assumed to be covered by the Apache License 2.0. We might ask you to sign a Contributor License Agreement before accepting a larger contribution.

Building and install requirements

Requirements

  • rvm
  • ruby, installed with rvm (rvm install 2.2.1)
  • node (on github)
  • bower (>= 0.10.0) installed with npm
  • libwebkit-dev or equivalent, try sudo apt install libwebkit-dev qt4-qmake libqt4-dev

Set up

  1. Run bin/setup to install dependencies, create and set up database. By default used PostgreSQL
  2. Run rake bower:install to install front-end assets

Set up omniauth

Google omniauth:

  1. Visit Console google. Click by link APIs & auth -> Credentials -> Create new Client ID
  2. Set Redirect URIs as http://yoursite.com/users/auth/google_oauth2/callback
  3. Enable Google+ API. Click by link APIs & auth -> Google+ API -> Enable API
  4. Set up environmental variables GOOGLE_CLIENT_ID, GOOGLE_CLIENT_SECRET

Facebook omniauth:

  1. Visit Developers Facebook
  2. Click by My Apps -> Add a New App
  3. Visit Settings -> Advanced. Fill in field Valid OAuth redirect URIs with http://yoursite.com/users/auth/facebook/callback
  4. Set up environmental variables FACEBOOK_CLIENT_ID, FACEBOOK_CLIENT_SECRET

Set up the AWS S3 for storage files in production environment

  1. Visit AWS Console
  2. Open the Amazon S3 console.
  3. Click Create Bucket.
  4. In the Create a Bucket dialog box enter a name and select a region.
  5. Click on the name of your account (it is located in the top right corner of the console). Then, in the expanded drop-down list, select Security Credentials.
  6. Click the Get Started with IAM Users button.
  7. Click the Create New Users
  8. Enter User Name(s) and click the Create
  9. Click the Download Credentials
  10. Set up environmental variables S3_KEY, S3_SECRET, S3_REGION, S3_ASSET_URL, S3_BUCKET_NAME

Ways to set up environmental variables

  1. Set Unix Environment Variables
  2. Use a local .env file. Template you can find in .env.example file
  3. Set environmental variables as parameters to command rails s

Don't forget: Keeping Environment Variables Private

Usage

In development environment

  1. Run server with command rails s
  2. Open in the browser a address http://localhost:3000

In production environment

  1. Run rake assets:precompile
  2. Run server with command RAILS_ENV=production rails s
  3. Open in the browser a address http://localhost:3000

Also you can deploy this application to Heroku

For upload new databundle file, you need to be logged in. You may log in with your facebook or google account, or register in DataBundle viewer site.

When you logged in, you can upload databundle file in box ‘New Databundle’. Enter name for the databundle and choose file to upload.

After click on ‘Save’ you will see information about workflow run:

  1. Workflow name
  2. Authors of the workflow
  3. Titles
  4. Description

And also you will see dataflow diagram of workflow run. You can click on edges of the graph to see what value produced by this step

Documentation

Dependencies listed in Gemfile (gems) and in bower.json (front-end assets)

Licenses to every dependency presented in DEPENDENCY_LICENSES.md file

Main classes of the application:

  1. DataBundleDecorator: access to data_bundle file as ro_bundle. Methods for get inputs/outputs/intermediates values

  2. DataBundle: necessary constants, and logic by extract data_bundle file after upload

Visualization component in data_bundle.coffee

Todo

  1. Better visualization

  2. Show intermediates run results with taverna-prov

  3. Docker image with auto install dependencies and run server