OpenBEL/bel_parser

Parser for Biolgical Expression Language.

bel_parser

The bel_parser gem implements BEL specifications (currently 1.0 and 2.0) and BEL Script nanopub format.

Installation

gem install bel_parser

Motivation

The motivation for this library is to provide the building blocks to implement BEL specifications more easily. This includes:

• Recognizing input to Abstract Syntax Trees
• Applying syntax validation relative to a BEL specification.
• Applying signature validation relative to a BEL specification.
• Conversion of Abstract Syntax Trees to a Nanopub object model.

Currently BEL 1.0 and 2.0 specifications are implemented.

Getting Started

bel_parser provides a Ruby library and a set of command-line tools.

Command-line tools:

1. bel2_debug_ast

Writes the AST output recognized from the input.

usage: bel2_debug_ast (Then enter a line at a time)

usage: bel2_debug_ast --file file.bel

2. bel2_validator

Validate the syntax and semantics of the AST recognized from the input.

usage: bel2_validator (Then enter a line at a time)

usage: bel2_validator --file file.bel --specification 2.0

3. bel2_upgrade

Upgrades BEL statements from 1.0 to 2.0.

usage: bel2_upgrade (Then enter a line at a time)

usage: bel2_upgrade --file file.bel

Development / Deployment

Development for the next release should be performed on the next branch. When the new changes are complete, functional, and tested they should be merged over to the master branch.

To make a release, perform the following steps:

• Update the version in the VERSION file.

• Add a new version with list of changes in the CHANGELOG file. This file is modelled after http://keepachangelog.com/.

• Build the Ruby and Java versions of the gem:

  Ruby: gem build .gemspec

  Java: jruby -S gem build .gemspec

• Create a release on GitHub with both gems and a summary of the changes in this version.

• Push both gems to RubyGems:

  gem push bel_parser-VERSION.gem

  gem push bel_parser-VERSION-java.gem