Spectral Workbench

Copyright Public Lab publiclab.org | spectralworkbench.org

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

The core library for analyzing and manipulating spectral data has been spun out into its own self-contained JavaScript module, at https://github.com/publiclab/spectral-workbench.js, which is then included into this application. To use Spectral Workbench on the commandline, try that out!

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

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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!

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Installation

The app now runs on Ruby 2.6.6 up to Ruby 2.6.x (preferred), and Rails 5.2.x, and uses Bundler for gem management and Yarn 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 2.6.6 of Ruby:

rvm install 2.6.6

You'll also need yarn 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 yarn

• On mac, you can use Homebrew: brew install yarn

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 database with cp config/database.yml.example config/database.yml. Similarly, configure cp config/config.yml.example config/config.yml
4. Initialize database with bundle exec rake db:setup
5. Install static assets (like external javascript libraries, fonts) with yarn 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:

{"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.

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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 http://www.gnu.org/licenses/.