UPGRADE.md

Upgrading

Note: Namespace and annotation values are upgraded in BEL files.

Install Ruby (Windows)

1. Download RubyInstaller.
   • Versions 1.9.3 and 2.x.x are supported.
2. Install RubyInstaller version.
   • Enable the Add Ruby executables to your PATH option presented during installation.
3. Open a command prompt (Windows Key + R then type cmd).
   • Confirm installation by typing ruby -v.
   • The output should show the ruby version (e.g. ruby 2.0.0p451 (2014-02-24) [x64-mingw32]).

Continue with Install the bel gem.

Install Ruby (Mac OSX)

Option 1: Homebrew

1. Install with homebrew by typing brew install ruby.
2. Add ruby commands to your PATH.
   • Add to .bash_profile.
     • echo 'export PATH="/usr/local/Cellar/ruby/VERSION/bin:$PATH"' >> .bash_profile
   • Update environment by sourcing .bash_profile.
     • source ~/.bash_profile
3. Confirm installation by typing ruby -v.

Option 2: rbenv

• Install with homebrew.

  • brew update
  • brew install rbenv ruby-build
  • More details [here] (https://github.com/sstephenson/rbenv#homebrew-on-mac-os-x).

• Install with git.

  • Clone rbenv repository.
    • git clone https://github.com/sstephenson/rbenv.git ~/.rbenv
  • Add to .bash_profile.
    • echo 'export PATH="$HOME/.rbenv/bin:$PATH"' >> ~/.bash_profile
  • Enable shims and autocompletion from the terminal.
    • echo 'eval "$(rbenv init -)"' >> ~/.bash_profile
  • Clone ruby-build repository.
    • git clone https://github.com/sstephenson/ruby-build.git ~/.rbenv/plugins/ruby-build
  • More details [here] (https://github.com/sstephenson/rbenv#installation).

Continue with Install the bel gem.

Install Ruby (Linux)

Option 1: Install via package manager.

• Example installation with Ubuntu.
  • Type sudo apt-get install ruby in the terminal.

Option 2: rbenv

• Install with git.
  • Clone rbenv repository.
    • git clone https://github.com/sstephenson/rbenv.git ~/.rbenv
  • Add to .bash_profile.
    • echo 'export PATH="$HOME/.rbenv/bin:$PATH"' >> ~/.bash_profile
  • Enable shims and autocompletion from the terminal.
    • echo 'eval "$(rbenv init -)"' >> ~/.bash_profile
  • Clone ruby-build repository.
    • git clone https://github.com/sstephenson/ruby-build.git ~/.rbenv/plugins/ruby-build
  • More details [here] (https://github.com/sstephenson/rbenv#installation).

Continue with Install the bel gem.

## Install the _bel_ gem

1. Open a terminal or command prompt.
2. Use the gem command to install the bel gem.
   • gem install bel
3. You should see the following:

    Fetching: bel-0.3.0.gem (100%)
    Successfully installed bel-0.3.0
    Parsing documentation for bel-0.3.0
    Installing ri documentation for bel-0.3.0
    1 gem installed

4. Confirm you can access the bel command by type bel followed by the Enter/Return key.
5. Continue with Upgrading BEL.

## Upgrading BEL

1. Type bel upgrade help for details on the upgrade command.
2. Run command
   • Example 1 - convert a BEL file
     • `bel upgrade --bel small_corpus.bel --changelog "http://resource.belframework.org/belframework/20150611/change_log.json"
   • Example 2 - convert BEL from standard in
     • curl "http://resource.belframework.org/belframework/20131211/knowledge/small_corpus.bel" | bel upgrade --changelog "http://resource.belframework.org/belframework/20150611/change_log.json"
   • More details [here] (https://github.com/OpenBEL/bel.rb).
3. The upgraded BEL will be written to standard out. Simply redirect to a file after that.
   • bel upgrade ... > upgraded-version.bel

Issues

• If you have questions with bel upgrade or the bel gem please post to the [openbel-discuss] (https://groups.google.com/forum/#!forum/openbel-discuss) google group.
• If you encounter errors please post an issue to [github issues] (https://github.com/OpenBEL/bel.rb/issues).