bio-rdf 0.0.1.pre1

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
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+ lib/**/*.rb
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+ bin/*
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+ -
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+ features/**/*.feature
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+ LICENSE.txt
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+ language: ruby
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+ rvm:
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+ - 1.9.2
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+ - 1.9.3
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+ - jruby-19mode # JRuby in 1.9 mode
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+ - rbx-19mode
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+ # - 1.8.7
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+ # - jruby-18mode # JRuby in 1.8 mode
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+ # - rbx-18mode
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+
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+ # uncomment this line if your project needs to run something other than `rake`:
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+ # script: bundle exec rspec spec
data/Gemfile ADDED
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+ source "http://rubygems.org"
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+ # Add dependencies required to use your gem here.
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+ # Example:
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+ # gem "activesupport", ">= 2.3.5"
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+
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+ # Add dependencies to develop your gem here.
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+ # Include everything needed to run rake, tests, features, etc.
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+ group :development do
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+ gem "shoulda", ">= 0"
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+ gem "rdoc", "~> 3.12"
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+ gem "bundler", "~> 1.0.0"
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+ gem "jeweler", "~> 1.8.3"
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+ gem "bio", ">= 1.4.2"
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+ gem "rdoc", "~> 3.12"
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+ end
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+ Copyright (c) 2012 Pjotr Prins
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+
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+ Permission is hereby granted, free of charge, to any person obtaining
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+ a copy of this software and associated documentation files (the
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+ "Software"), to deal in the Software without restriction, including
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+ without limitation the rights to use, copy, modify, merge, publish,
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+ distribute, sublicense, and/or sell copies of the Software, and to
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+ permit persons to whom the Software is furnished to do so, subject to
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+ the following conditions:
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+
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+ The above copyright notice and this permission notice shall be
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+ included in all copies or substantial portions of the Software.
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+
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+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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+ EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
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+ MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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+ NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
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+ LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
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+ OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
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+ WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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+ # bio-rdf
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+
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+ [![Build Status](https://secure.travis-ci.org/pjotrp/bioruby-rdf.png)](http://travis-ci.org/pjotrp/bioruby-rdf)
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+
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+ Full description goes here
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+
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+ Note: this software is under active development!
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+
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+ ## Installation
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+
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+ ```sh
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+ gem install bio-rdf
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+ ```
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+
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+ ## Usage
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+
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+ ```ruby
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+ require 'bio-rdf
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+ ```
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+
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+ The API doc is online. For more code examples see the test files in
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+ the source tree.
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+
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+ ## Project home page
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+
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+ Information on the source tree, documentation, examples, issues and
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+ how to contribute, see
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+
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+ http://github.com/pjotrp/bioruby-rdf
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+
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+ ## Cite
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+
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+ If you use this software, please cite one of
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+
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+ * [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
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+ * [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
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+
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+ ## Biogems.info
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+
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+ This Biogem is published at [#bio-rdf](http://biogems.info/index.html)
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+
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+ ## Copyright
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+
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+ Copyright (c) 2012 Pjotr Prins. See LICENSE.txt for further details.
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+
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+ = bio-rdf
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+
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+ {<img
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+ src="https://secure.travis-ci.org/pjotrp/bioruby-rdf.png"
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+ />}[http://travis-ci.org/#!/pjotrp/bioruby-rdf]
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+
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+ Full description goes here
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+
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+ Note: this software is under active development!
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+
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+ == Installation
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+
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+ gem install bio-rdf
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+
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+ == Usage
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+
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+ == Developers
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+
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+ To use the library
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+
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+ require 'bio-rdf
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+
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+ The API doc is online. For more code examples see also the test files in
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+ the source tree.
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+
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+ == Project home page
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+
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+ Information on the source tree, documentation, issues and how to contribute, see
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+
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+ http://github.com/pjotrp/bioruby-rdf
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+
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+ == Cite
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+
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+ If you use this software, please cite one of
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+
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+ * [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
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+ * [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
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+
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+ == Biogems.info
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+
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+ This Biogem is published at http://biogems.info/index.html#bio-rdf
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+
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+ == Copyright
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+
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+ Copyright (c) 2012 Pjotr Prins. See LICENSE.txt for further details.
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+
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+ # encoding: utf-8
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+
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+ require 'rubygems'
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+ require 'bundler'
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+ begin
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+ Bundler.setup(:default, :development)
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+ rescue Bundler::BundlerError => e
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+ $stderr.puts e.message
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+ $stderr.puts "Run `bundle install` to install missing gems"
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+ exit e.status_code
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+ end
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+ require 'rake'
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+
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+ require 'jeweler'
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+ Jeweler::Tasks.new do |gem|
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+ # gem is a Gem::Specification... see http://docs.rubygems.org/read/chapter/20 for more options
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+ gem.name = "bio-rdf"
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+ gem.homepage = "http://github.com/pjotrp/bioruby-rdf"
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+ gem.license = "MIT"
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+ gem.summary = %Q{Bioinformatics triple-store support}
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+ gem.description = %Q{Store relationships in a triple-store, such as gene enrichment and QTL, and use this information for inference and causality}
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+ gem.email = "pjotr.public01@thebird.nl"
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+ gem.authors = ["Pjotr Prins", "Anurag Priyam"]
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+ # dependencies defined in Gemfile
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+ end
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+ Jeweler::RubygemsDotOrgTasks.new
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+
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+ require 'rake/testtask'
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+ Rake::TestTask.new(:test) do |test|
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+ test.libs << 'lib' << 'test'
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+ test.pattern = 'test/**/test_*.rb'
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+ test.verbose = true
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+ end
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+
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+ task :default => :test
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+
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+ require 'rdoc/task'
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+ Rake::RDocTask.new do |rdoc|
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+ version = File.exist?('VERSION') ? File.read('VERSION') : ""
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+
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+ rdoc.rdoc_dir = 'rdoc'
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+ rdoc.title = "bio-rdf #{version}"
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+ rdoc.rdoc_files.include('README*')
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+ rdoc.rdoc_files.include('lib/**/*.rb')
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+ end
data/VERSION ADDED
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+ 0.0.1.pre1
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+ #!/usr/bin/env ruby
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+ #
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+ # BioRuby bio-rdf Plugin BioRdf
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+ # Author:: Pjotr Prins
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+ # Copyright:: 2012
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+
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+ USAGE = "Describe bio-rdf"
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+
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+ if ARGV.size == 0
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+ print USAGE
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+ end
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+
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+ require 'bio-rdf'
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+ require 'optparse'
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+
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+ # Uncomment when using the bio-logger
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+ # require 'bio-logger'
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+ # Bio::Log::CLI.logger('stderr')
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+ # Bio::Log::CLI.trace('info')
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+
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+ options = {:example_switch=>false,:show_help=>false}
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+ opts = OptionParser.new do |o|
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+ o.banner = "Usage: #{File.basename($0)} [options] reponame\ne.g. #{File.basename($0)} the-perfect-gem"
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+
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+ o.on('--example_parameter [EXAMPLE_PARAMETER]', 'TODO: put a description for the PARAMETER') do |example_parameter|
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+ # TODO: your logic here, below an example
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+ options[:example_parameter] = 'this is a parameter'
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+ end
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+
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+ o.separator ""
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+ o.on("--switch-example", 'TODO: put a description for the SWITCH') do
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+ # TODO: your logic here, below an example
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+ self[:example_switch] = true
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+ end
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+
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+ # Uncomment the following when using the bio-logger
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+ # o.separator ""
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+ # o.on("--logger filename",String,"Log to file (default stderr)") do | name |
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+ # Bio::Log::CLI.logger(name)
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+ # end
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+ #
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+ # o.on("--trace options",String,"Set log level (default INFO, see bio-logger)") do | s |
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+ # Bio::Log::CLI.trace(s)
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+ # end
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+ #
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+ # o.on("-q", "--quiet", "Run quietly") do |q|
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+ # Bio::Log::CLI.trace('error')
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+ # end
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+ #
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+ # o.on("-v", "--verbose", "Run verbosely") do |v|
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+ # Bio::Log::CLI.trace('info')
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+ # end
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+ #
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+ # o.on("--debug", "Show debug messages") do |v|
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+ # Bio::Log::CLI.trace('debug')
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+ # end
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+
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+ o.separator ""
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+ o.on_tail('-h', '--help', 'display this help and exit') do
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+ options[:show_help] = true
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+ end
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+ end
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+
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+ begin
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+ opts.parse!(ARGV)
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+
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+ # Uncomment the following when using the bio-logger
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+ # Bio::Log::CLI.configure('bio-rdf')
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+
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+ # TODO: your code here
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+ # use options for your logic
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+ rescue OptionParser::InvalidOption => e
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+ options[:invalid_argument] = e.message
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+ end
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+ # Please require your code below, respecting the naming conventions in the
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+ # bioruby directory tree.
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+ #
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+ # For example, say you have a plugin named bio-plugin, the only uncommented
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+ # line in this file would be
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+ #
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+ # require 'bio/bio-plugin/plugin'
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+ #
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+ # In this file only require other files. Avoid other source code.
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+
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+ require 'bio-rdf/rdf.rb'
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+
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+ module BioRdf
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+
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+ end
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+ require 'rubygems'
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+ require 'bundler'
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+ begin
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+ Bundler.setup(:default, :development)
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+ rescue Bundler::BundlerError => e
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+ $stderr.puts e.message
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+ $stderr.puts "Run `bundle install` to install missing gems"
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+ exit e.status_code
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+ end
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+ require 'test/unit'
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+ require 'shoulda'
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+
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+ $LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
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+ $LOAD_PATH.unshift(File.dirname(__FILE__))
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+ require 'bio-rdf'
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+
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+ class Test::Unit::TestCase
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+ end
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+ require 'helper'
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+
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+ class TestBioRdf < Test::Unit::TestCase
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+ should "probably rename this file and start testing for real" do
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+ flunk "hey buddy, you should probably rename this file and start testing for real"
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+ end
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+ end
metadata ADDED
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+ --- !ruby/object:Gem::Specification
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+ name: bio-rdf
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+ version: !ruby/object:Gem::Version
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+ version: 0.0.1.pre1
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+ prerelease: 6
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+ platform: ruby
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+ authors:
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+ - Pjotr Prins
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+ - Anurag Priyam
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+ autorequire:
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+ bindir: bin
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+ cert_chain: []
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+ date: 2012-04-07 00:00:00.000000000Z
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+ dependencies:
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+ - !ruby/object:Gem::Dependency
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+ name: shoulda
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+ requirement: &16197900 !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - ! '>='
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+ - !ruby/object:Gem::Version
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+ version: '0'
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+ type: :development
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+ prerelease: false
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+ version_requirements: *16197900
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+ - !ruby/object:Gem::Dependency
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+ name: rdoc
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+ requirement: &16196760 !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - ~>
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+ - !ruby/object:Gem::Version
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+ version: '3.12'
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+ type: :development
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+ prerelease: false
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+ version_requirements: *16196760
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+ - !ruby/object:Gem::Dependency
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+ name: bundler
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+ requirement: &16195560 !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - ~>
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+ - !ruby/object:Gem::Version
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+ version: 1.0.0
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+ type: :development
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+ prerelease: false
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+ version_requirements: *16195560
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+ - !ruby/object:Gem::Dependency
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+ name: jeweler
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+ requirement: &16194300 !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - ~>
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+ - !ruby/object:Gem::Version
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+ version: 1.8.3
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+ type: :development
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+ prerelease: false
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+ version_requirements: *16194300
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+ - !ruby/object:Gem::Dependency
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+ name: bio
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+ requirement: &16193260 !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - ! '>='
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+ - !ruby/object:Gem::Version
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+ version: 1.4.2
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+ type: :development
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+ prerelease: false
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+ version_requirements: *16193260
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+ - !ruby/object:Gem::Dependency
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+ name: rdoc
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+ requirement: &16192040 !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - ~>
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+ - !ruby/object:Gem::Version
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+ version: '3.12'
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+ type: :development
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+ prerelease: false
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+ version_requirements: *16192040
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+ description: Store relationships in a triple-store, such as gene enrichment and QTL,
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+ and use this information for inference and causality
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+ email: pjotr.public01@thebird.nl
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+ executables:
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+ - bio-rdf
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+ extensions: []
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+ extra_rdoc_files:
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+ - LICENSE.txt
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+ - README.md
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+ - README.rdoc
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+ files:
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+ - .document
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+ - .travis.yml
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+ - Gemfile
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+ - LICENSE.txt
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+ - README.md
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+ - README.rdoc
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+ - Rakefile
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+ - VERSION
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+ - bin/bio-rdf
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+ - lib/bio-rdf.rb
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+ - lib/bio-rdf/rdf.rb
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+ - test/helper.rb
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+ - test/test_bio-rdf.rb
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+ homepage: http://github.com/pjotrp/bioruby-rdf
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+ licenses:
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+ - MIT
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+ post_install_message:
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+ rdoc_options: []
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+ require_paths:
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+ - lib
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+ required_ruby_version: !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - ! '>='
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+ - !ruby/object:Gem::Version
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+ version: '0'
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+ segments:
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+ - 0
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+ hash: -868237054466869818
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+ required_rubygems_version: !ruby/object:Gem::Requirement
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+ none: false
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+ requirements:
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+ - - ! '>'
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+ - !ruby/object:Gem::Version
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+ version: 1.3.1
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+ requirements: []
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+ rubyforge_project:
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+ rubygems_version: 1.8.10
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+ signing_key:
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+ specification_version: 3
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+ summary: Bioinformatics triple-store support
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+ test_files: []