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https://github.com/jywarren/spectral-workbench

Web-based tools for collecting, analyzing, and sharing data from a DIY spectrometer
https://github.com/jywarren/spectral-workbench

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Web-based tools for collecting, analyzing, and sharing data from a DIY spectrometer

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README 

        
# Spectral Workbench



Copyright 2011-2016 Public Lab

publiclab.org | spectralworkbench.org



![tests](https://travis-ci.org/publiclab/spectral-workbench.svg)



Spectral Workbench is an open-source tool to perform low-cost spectral analysis and to share those results online. It consists of a Ruby on Rails web application for publishing, archiving, discussing, and analyzing spectra online -- running at http://spectralworkbench.org



Read about how to build and use your own spectrometer with this software here: http://publiclab.org/wiki/spectrometer



****



## Simple installation with Cloud9



1. If you have a GitHub account, visit https://c9.io and log in with the GitHub button.

2. Fork this repository to your own GitHub account, creating a `yourname/spectral-workbench` project.

3. Name your project, then (order important!) choose the **Ruby** template, THEN enter `yourname/spectral-workbench` in the "Clone from Git or Mercurial URL" field, and press **Create Workspace** 

4. In the command line prompt at the bottom of the page, type `./install_cloud9.sh` and press enter.

5. Enter your username when prompted, and click "Run Project" when it's done.

6. You're done! Go to the URL shown!



****



## Installation



The app now runs on Ruby 1.9.3 up to Ruby 2.1.2 (preferred), and Rails 3.2.x, and uses Bundler for gem management and Bower for static asset management.  



### Prerequisites:



Recommended; for an Ubuntu/Debian system. Varies slightly for mac/fedora/etc



Install a database, if necessary:



`sudo apt-get install mysql-server`



**Note:** You will have to update the `config/database.yml` file appropriately. The example file assumes usage of SQLite. For which you need not install MySQL.



RMagick dependencies are required for processing uploaded spectrum images: `apt-get install imagemagick ruby-rmagick libmagickwand-dev libmagick++-dev`



* On Fedora/centOs: `yum install ImageMagick-devel`

* On mac, you can use Homebrew: `brew install imagemagick`



Install rvm for Ruby management (http://rvm.io)



`curl -L https://get.rvm.io | bash -s stable`



**Note:** At this point during the process, you may want to log out and log back in, or open a new terminal window; RVM will then properly load in your environment. 



**Ubuntu users:** You may need to enable `Run command as a login shell` in Ubuntu's Terminal, under Profile Preferences > Title and Command. Then close the terminal and reopen it.



Then, use RVM to install version 2.1.2 of Ruby:



`rvm install 2.1.2`



You'll also need **bower** which is available through NPM. To install NPM, you can run:



`sudo apt-get install npm`



However, on Ubuntu, you may need to also install the `nodejs-legacy` package, as due to a naming collision, some versions of Ubuntu already have an unrelated package called `node`. To do this, run:



`sudo apt-get install nodejs-legacy`



Once NPM is installed, you should be able to run:



`sudo npm install -g bower`



### Installation steps:



1. Download a copy of the source with `git clone https://github.com/publiclab/spectral-workbench.git` 

2. Install gems with `bundle install` from the rails root folder. You may need to run `bundle update` if you have older gems in your environment.

3. Copy and configure config/database.yml from config/database.yml.example, using a new empty databse you've created. Do the same thing for config/config.yml file copying it from config/config.yml.example file.

4. Initialize database with `bundle exec rake db:setup`

5. Install static assets (like external javascript libraries, fonts) with `bower install` 

6. Start rails with `bundle exec passenger start` from the Rails root and open http://localhost:3000 in a web browser. (For some, just `passenger start` will work; adding `bundle exec` ensures you're using the version of passenger you just installed with Bundler.)



Sign in instructions:



*  Create a account at PublicLab.org and use that username to log in.

*  Then you will be redirected to publiclab.org to "approve" a use of the openid identity.

*  Note that this applies for development environment as well. 



## Bugs and support



To report bugs and request features, please use the GitHub issue tracker provided at http://github.com/publiclab/spectral-workbench/issues 



For additional support, join the Public Laboratory website and mailing list at http://publiclab.org/lists or for urgent requests, email [email protected]



For questions related to the use of this software and your open source spectrometer, the same page links to the "plots-spectrometry" group. 



## API



Using your secret API token on your SpectralWorkbench.org profile, you can submit spectral via the API in JSON format:



POST to "https://spectralworkbench.org/spectrums.json"



The required parameters are: 



```json

{"spectrum": {

  "title": "Test spectrum",

  "data_type": "json",

  "data": [

    {"average": 64.3, "r": 69, "g": 46, "b": 78, "wavelength": 269.089 },

    {"average": 63.3, "r": 71, "g": 45, "b": 74, "wavelength": 277.718 },

    {"average": 64,   "r": 71, "g": 47, "b": 74, "wavelength": 291.524 },

    {"average": 64,   "r": 68, "g": 49, "b": 75, "wavelength": 303.604 }

  ]},

  "token": "00000000"

}

```



This will return a path (from the root URL by default) to the spectrum, as in: `/spectrums/12345`



## Developers



Development is occurring at https://github.com/publiclab/spectral-workbench/; please fork and submit pull requests; for more guidelines on contributing to Public Lab projects, see http://publiclab.org/wiki/contributing-to-public-lab-software



If you're a developer, consider joining the Public Lab developer list, also at http://publiclab.org/wiki/developers



### Testing



Before submitting changes, please run tests with `rake test` to ensure that your code passes.



Also run `rake jasmine` and navigate to http://localhost:8888 to check client-side tests.



New tests are also appreciated to increase coverage; Rails tests are in /test and Jasmine tests (JavaScript tests) are in /spec.



****



## License



Spectral Workbench is free software: you can redistribute it and/or modify

it under the terms of the GNU General Public License as published by

the Free Software Foundation, either version 3 of the License, or

(at your option) any later version.



Spectral Workbench is distributed in the hope that it will be useful,

but WITHOUT ANY WARRANTY; without even the implied warranty of

MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE.  See the

GNU General Public License for more details.



You should have received a copy of the GNU General Public License

along with Spectral Workbench.  If not, see .