README.md
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# Apache Taverna Databundle Viewer
[](https://codeclimate.com/github/Samhane/incubator-taverna-databundle-viewer)
[](https://codeclimate.com/github/Samhane/incubator-taverna-databundle-viewer/coverage)
[](https://semaphoreci.com/samhane/incubator-taverna-databundle-viewer)
Apache Taverna Databundle Viewer is planned as a web interface
for displaying
[Taverna databundles](https://github.com/apache/incubator-taverna-language/tree/master/taverna-databundle)
(workflow inputs/outputs/run), as produced by the
[Apache Taverna](http://taverna.incubator.apache.org/) workflow
system.
This module is **work in progress** as part of Google Summer of Code 2015.
You can see working prototype there: [DataBundleViewer](http://databundle.herokuapp.com/)
## License
(c) 2014-2015 Apache Software Foundation
This product includes software developed at The [Apache Software
Foundation](http://www.apache.org/).
Licensed under the [Apache License
2.0](https://www.apache.org/licenses/LICENSE-2.0), see the file
[LICENSE](LICENSE) for details.
The file [NOTICE](NOTICE) contain any additional attributions and
details about embedded third-party libraries and source code.
# Contribute
Please subscribe to and contact the
[dev@taverna](http://taverna.incubator.apache.org/community/lists#dev mailing list)
for any questions, suggestions and discussions about the
Apache Taverna Databundle Viewer.
Bugs and feature plannings are tracked in the Jira
[Issue tracker](https://issues.apache.org/jira/browse/TAVERNA/component/12326902)
under the `TAVERNA` component _GSOC Taverna Databundle Viewer_. Feel free
to add an issue!
To suggest changes to this source code, feel free to raise a
[GitHub pull request](https://github.com/apache/incubator-taverna-databundle-viewer/pulls).
Any contributions received are assumed to be covered by the [Apache License
2.0](https://www.apache.org/licenses/LICENSE-2.0). We might ask you
to sign a [Contributor License Agreement](https://www.apache.org/licenses/#clas)
before accepting a larger contribution.
# Building and install requirements
**Requirements**
* [rvm](https://rvm.io/rvm/install)
* ruby, installed with rvm (`rvm install 2.2.1`)
* [node](http://nodejs.org) ([on github](https://github.com/joyent/node))
* [bower](https://github.com/bower/bower) (>= 0.10.0) installed with npm
**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](https://console.developers.google.com/). 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](https://developers.facebook.com/)
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](https://aws.amazon.com/)
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](http://heroku.com/)
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](Gemfile) (gems) and in [bower.json](bower.json) (front-end assets)
Licenses to every dependency presented in [DEPENDENCY_LICENSES.md](DEPENDENCY_LICENSES.md) file
Main classes of the application:
1. [DataBundleDecorator](app/decorators/data_bundle_decorator.rb): access to data_bundle file as ro_bundle.
Methods for get inputs/outputs/intermediates values
2. [DataBundle](app/models/data_bundle.rb): necessary constants, and logic by extract data_bundle file after upload
Visualization component in [data_bundle.coffee](app/assets/javascripts/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