rdf2json 0.0.1
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- checksums.yaml +7 -0
- data/.document +5 -0
- data/.travis.yml +14 -0
- data/Gemfile +16 -0
- data/LICENSE.txt +20 -0
- data/README.md +50 -0
- data/README.rdoc +48 -0
- data/Rakefile +52 -0
- data/VERSION +1 -0
- data/bin/rdf2json +6 -0
- data/lib/rdf2json.rb +3 -0
- data/lib/rdf2json/rdf2json.rb +226 -0
- data/test/helper.rb +34 -0
- data/test/test_bio-rdf2json.rb +7 -0
- metadata +159 -0
checksums.yaml
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---
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SHA1:
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metadata.gz: 5b7bc9157133dd33407d3807be8d4e2ae8361424
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data.tar.gz: 4f22bddd6f50b8708d289f6699eaee564d7a0afe
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SHA512:
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metadata.gz: 4c0697837463e626dfc077ba4a0cd27ee7240fe6c3fcfdde29a3708edbf83689901e25f92ae266a8fe9a840fe34f6839c4363502b647fe207ef0fa2042908bb0
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data.tar.gz: ece185939cd4925b52632ca346653486905b91f185852845e5081dab6ca670de61df858795c2cbad5683bd2ebfaac23f845842185ac323412966ab8afb918b91
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data/.document
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data/.travis.yml
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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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- 2.0.0
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- 2.1.1
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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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# uncomment this line if your project needs to run something other than `rake`:
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# script: bundle exec rspec spec
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data/Gemfile
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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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gem "rdf", ">= 1.1.3"
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gem "json-ld", ">= 1.1.3"
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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 "simplecov", ">= 0"
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gem "jeweler", "~> 1.8.4"
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gem "bundler", ">= 1.0.21"
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gem "rdoc", "~> 3.12"
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end
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data/LICENSE.txt
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Copyright (c) 2014 Joachim Baran
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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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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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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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data/README.md
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# rdf2json
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[![Build Status](https://secure.travis-ci.org/joejimbo/rdf2json.png)](http://travis-ci.org/joejimbo/rdf2json)
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Reads RDF N-Triple/N-Quads that are sorted by subject and
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append a JSON/JSON-LD document per line in a designated
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output file.
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Usage: `rdf2json [options] --input filename.nt --output filename.json`
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#### Required options
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* `-i`, `--input FILE`: Input file for the conversion; either RDF N-Triples or N-Quads.
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* `-o`, `--output FILE`: Output file to which JSON-LD/JSON is appended.
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#### Options
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* `-m`, `--minimize`: Minimize JSON-LD to plain (semantically untyped) JSON.
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* `-n`, `--namespace [NAMESPACE]`: Alternative name for JSON-LD's "@id" key; replaces it; turns on `--minimize`
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* `-p`, `--prefix [PREFIX]`: Prefix that should be removed from keys; requires `--minimize`.
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* `-t`, `--triples`: Input file is in RDF N-Triples format.
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* `-q`, `--quads`: Input file is in RDF N-Quads format.
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#### Common options
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* `-h`, `--help`: Show this message.
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## Installation
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```sh
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gem install rdf2json
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```
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## Project home page
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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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http://github.com/joejimbo/rdf2json
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The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
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## Biogems.info
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This Biogem is published at (http://biogems.info/index.html#bio-rdf2json)
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## Copyright
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Copyright (c) 2014 Joachim Baran. See LICENSE.txt for further details.
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data/README.rdoc
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= bio-rdf2json
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{<img
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src="https://secure.travis-ci.org/joejimbo/bioruby-rdf2json.png"
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/>}[http://travis-ci.org/#!/joejimbo/bioruby-rdf2json]
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Full description goes here
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Note: this software is under active development!
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== Installation
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gem install bio-rdf2json
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== Usage
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== Developers
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To use the library
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require 'bio-rdf2json'
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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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== Project home page
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Information on the source tree, documentation, issues and how to contribute, see
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http://github.com/joejimbo/bioruby-rdf2json
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The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
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== Cite
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If you use this software, please cite one of
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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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== Biogems.info
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This Biogem is published at http://biogems.info/index.html#bio-rdf2json
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== Copyright
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Copyright (c) 2014 Joachim Baran. See LICENSE.txt for further details.
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data/Rakefile
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# encoding: utf-8
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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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require 'jeweler'
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Jeweler::Tasks.new do |gem|
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# gem is a Gem::Specification... see http://guides.rubygems.org/specification-reference/ for more options
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gem.name = "rdf2json"
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gem.homepage = "http://github.com/joejimbo/rdf2json"
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gem.license = "MIT"
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gem.summary = %Q{RDF N-Triples and N-Quads to JSON-LD or JSON converter.}
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gem.description = %Q{Converts RDF N-Triples and N-Quads files to either JSON-LD or JSON. Supports minimization of long URIs to shorter descriptive key names.}
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gem.email = 'joachim.baran@gmail.com'
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gem.authors = [ 'Joachim Baran' ]
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gem.executable = 'rdf2json'
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# dependencies defined in Gemfile
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end
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Jeweler::RubygemsDotOrgTasks.new
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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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desc "Code coverage detail"
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task :simplecov do
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ENV['COVERAGE'] = "true"
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Rake::Task['test'].execute
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end
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task :default => :test
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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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rdoc.rdoc_dir = 'rdoc'
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rdoc.title = "rdf2json #{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
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data/VERSION
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0.0.1
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data/bin/rdf2json
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data/lib/rdf2json.rb
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require 'rdf'
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require 'rdf/ntriples'
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require 'rdf/nquads'
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require 'json/ld'
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require 'optparse'
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module RDF2JSON
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def self.cli
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options = {}
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parser = OptionParser.new { |opts|
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opts.banner = 'Usage: rdf2json [options] --input filename.nt --output filename.json'
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opts.separator ''
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opts.separator 'Description: Reads RDF N-Triple/N-Quads that are sorted by subject and'
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opts.separator ' append a JSON/JSON-LD document per line in a designated'
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opts.separator ' output file.'
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opts.separator ''
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opts.separator 'Required:'
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opts.on('-i', '--input FILE', 'Input file for the conversion; either RDF N-Triples or N-Quads.') { |file|
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options[:input] = file
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}
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opts.on('-o', '--output FILE', 'Output file to which JSON-LD/JSON is appended.') { |file|
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options[:output] = file
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}
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opts.separator ''
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opts.separator 'Options:'
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opts.on('-m', '--minimize', 'Minimize JSON-LD to plain (semantically untyped) JSON.') { |minimize|
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options[:minimize] = true
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}
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opts.on('-n', '--namespace [NAMESPACE]', 'Alternative name for JSON-LD\'s "@id" key; replaces it; turns on --minimize') { |namespace|
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options[:minimize] = true
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options[:namespace] = namespace
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}
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opts.on('-p', '--prefix [PREFIX]', 'Prefix that should be removed from keys; requires --minimize.') { |prefix|
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options[:prefix] = prefix
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}
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opts.on('-t', '--triples', 'Input file is in RDF N-Triples format.') { |triples|
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options[:ntriples] = true
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}
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opts.on('-q', '--quads', 'Input file is in RDF N-Quads format.') { |quads|
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options[:nquads] = true
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}
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opts.separator ''
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opts.separator 'Common options:'
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opts.on_tail('-h', '--help', 'Show this message.') { |help|
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puts opts
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exit
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}
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}
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begin
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parser.parse!
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rescue
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puts parser
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exit 1
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end
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unless options.has_key?(:input) and options.has_key?(:output) then
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puts 'Error: Requires --input and --output parameters.'
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puts ''
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puts parser
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exit 2
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end
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if options.has_key?(:ntriples) and options.has_key?(:nquads) then
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puts 'Error: both --triples and --quads parameters were used.'
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puts ' Only one of the parameters may be provided for explicitly'
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puts ' setting the input fileformat.'
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puts ''
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puts parser
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exit 3
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end
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extension = File.extname(options[:input])
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if options.has_key?(:ntriples) then
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input_format = :ntriples
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elsif options.has_key?(:nquads) then
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input_format = :nquads
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elsif extension == '.nt' then
|
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input_format = :ntriples
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elsif extension == '.nq' then
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input_format = :nquads
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else
|
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puts 'Error: Cannot determine input file format by filename extension.'
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puts ' Recognized fileformat extensions are .nt and .nq for N-Triples'
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puts ' and N-Quads respectively. Use --triples or --quads options to'
|
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puts ' explicitly set the input fileformat (ignores filename extension'
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puts ' when one of those options is given.'
|
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puts ''
|
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puts parser
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exit 4
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end
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output_format = :jsonld
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output_format = :json if options[:minimize]
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+
|
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unless File.exist?(options[:input]) then
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puts 'Error: Input file (--input parameter) does not seem to exist.'
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puts ''
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puts parser
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exit 6
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end
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|
112
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begin
|
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# Why instantiate a Converter instance here? Well, for implementing parallelization later:
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Converter.new(options[:input], options[:output], input_format, output_format, options[:namespace], options[:prefix]).convert
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rescue Interrupt
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# The user hit Ctrl-C, which is okay and does not need error reporting.
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exit 0
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end
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end
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|
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class Converter
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|
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def initialize(input_filename, output_filename, input_format, output_format, namespace, prefix)
|
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@input_file = File.open(input_filename, 'r')
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@output_file = File.open(output_filename, 'a')
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@input_format = input_format
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@output_format = output_format
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@namespace = namespace
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@prefix = prefix
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end
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def convert
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no_of_lines = 0
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no_of_statements = 0
|
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read_errors = 0
|
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last_subject = nil
|
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+
subject_block = ''
|
138
|
+
|
139
|
+
@input_file.each_line { |line|
|
140
|
+
no_of_lines += 1
|
141
|
+
line.chomp!
|
142
|
+
|
143
|
+
subject = "#{line.sub(/>.*/, '')}>"
|
144
|
+
|
145
|
+
if subject == last_subject then
|
146
|
+
subject_block << line
|
147
|
+
else
|
148
|
+
stats = write_graph(subject_block)
|
149
|
+
no_of_statements += stats[:no_of_statements]
|
150
|
+
read_errors += stats[:read_errors]
|
151
|
+
subject_block = ''
|
152
|
+
end
|
153
|
+
|
154
|
+
last_subject = subject
|
155
|
+
}
|
156
|
+
|
157
|
+
stats = write_graph(subject_block)
|
158
|
+
no_of_statements += stats[:no_of_statements]
|
159
|
+
read_errors += stats[:read_errors]
|
160
|
+
|
161
|
+
puts "Total number of lines read : #{no_of_lines}"
|
162
|
+
puts "Statement read errors (N-Quads or N-Triples) : #{read_errors}"
|
163
|
+
puts "JSON/JSON-LD documents output : #{no_of_statements}"
|
164
|
+
end
|
165
|
+
|
166
|
+
def minify(jsonld_hash)
|
167
|
+
jsonld_hash.keys.each { |key|
|
168
|
+
if key == '@type' then
|
169
|
+
jsonld_hash.delete(key)
|
170
|
+
elsif @prefix and key.match(@prefix) then
|
171
|
+
shortened_key = key.sub(@prefix, '')
|
172
|
+
jsonld_hash[shortened_key] = jsonld_hash.delete(key)
|
173
|
+
key = shortened_key
|
174
|
+
end
|
175
|
+
|
176
|
+
if jsonld_hash[key].instance_of?(Array) then
|
177
|
+
jsonld_hash[key].each_index { |index|
|
178
|
+
if jsonld_hash[key][index].has_key?('@value') then
|
179
|
+
jsonld_hash[key][index] = jsonld_hash[key][index]['@value']
|
180
|
+
elsif jsonld_hash[key][index].has_key?('@id') then
|
181
|
+
jsonld_hash[key][index] = jsonld_hash[key][index]['@id']
|
182
|
+
end
|
183
|
+
}
|
184
|
+
elsif jsonld_hash[key].instance_of?(Hash) then
|
185
|
+
minify(jsonld_hash[key])
|
186
|
+
end
|
187
|
+
}
|
188
|
+
end
|
189
|
+
|
190
|
+
def write_graph(block)
|
191
|
+
return { :read_errors => 0, :no_of_statements => 0 } unless block and not block.empty?
|
192
|
+
|
193
|
+
block.gsub!("\\'", "'")
|
194
|
+
|
195
|
+
read_errors = 0
|
196
|
+
no_of_statements = 0
|
197
|
+
graph = RDF::Graph.new
|
198
|
+
RDF::Reader.for(@input_format).new(block) { |reader|
|
199
|
+
begin
|
200
|
+
reader.each_statement { |statement|
|
201
|
+
no_of_statements += 1
|
202
|
+
graph.insert(statement)
|
203
|
+
}
|
204
|
+
rescue RDF::ReaderError
|
205
|
+
read_errors += 1
|
206
|
+
end
|
207
|
+
}
|
208
|
+
|
209
|
+
JSON::LD::API::fromRdf(graph) { |document|
|
210
|
+
document.each{ |entity|
|
211
|
+
# Parsed JSON-LD representation:
|
212
|
+
entity = JSON.parse(entity.to_json)
|
213
|
+
|
214
|
+
entity[@namespace] = entity.delete('@id') if @namespace
|
215
|
+
minify(entity) if @output_format == :json
|
216
|
+
|
217
|
+
@output_file.puts entity.to_json
|
218
|
+
}
|
219
|
+
}
|
220
|
+
|
221
|
+
return { :read_errors => read_errors, :no_of_statements => no_of_statements }
|
222
|
+
end
|
223
|
+
|
224
|
+
end
|
225
|
+
|
226
|
+
end
|
data/test/helper.rb
ADDED
@@ -0,0 +1,34 @@
|
|
1
|
+
require 'simplecov'
|
2
|
+
|
3
|
+
module SimpleCov::Configuration
|
4
|
+
def clean_filters
|
5
|
+
@filters = []
|
6
|
+
end
|
7
|
+
end
|
8
|
+
|
9
|
+
SimpleCov.configure do
|
10
|
+
clean_filters
|
11
|
+
load_adapter 'test_frameworks'
|
12
|
+
end
|
13
|
+
|
14
|
+
ENV["COVERAGE"] && SimpleCov.start do
|
15
|
+
add_filter "/.rvm/"
|
16
|
+
end
|
17
|
+
require 'rubygems'
|
18
|
+
require 'bundler'
|
19
|
+
begin
|
20
|
+
Bundler.setup(:default, :development)
|
21
|
+
rescue Bundler::BundlerError => e
|
22
|
+
$stderr.puts e.message
|
23
|
+
$stderr.puts "Run `bundle install` to install missing gems"
|
24
|
+
exit e.status_code
|
25
|
+
end
|
26
|
+
require 'test/unit'
|
27
|
+
require 'shoulda'
|
28
|
+
|
29
|
+
$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
|
30
|
+
$LOAD_PATH.unshift(File.dirname(__FILE__))
|
31
|
+
require 'bio-rdf2json'
|
32
|
+
|
33
|
+
class Test::Unit::TestCase
|
34
|
+
end
|
metadata
ADDED
@@ -0,0 +1,159 @@
|
|
1
|
+
--- !ruby/object:Gem::Specification
|
2
|
+
name: rdf2json
|
3
|
+
version: !ruby/object:Gem::Version
|
4
|
+
version: 0.0.1
|
5
|
+
platform: ruby
|
6
|
+
authors:
|
7
|
+
- Joachim Baran
|
8
|
+
autorequire:
|
9
|
+
bindir: bin
|
10
|
+
cert_chain: []
|
11
|
+
date: 2014-05-20 00:00:00.000000000 Z
|
12
|
+
dependencies:
|
13
|
+
- !ruby/object:Gem::Dependency
|
14
|
+
name: rdf
|
15
|
+
requirement: !ruby/object:Gem::Requirement
|
16
|
+
requirements:
|
17
|
+
- - '>='
|
18
|
+
- !ruby/object:Gem::Version
|
19
|
+
version: 1.1.3
|
20
|
+
type: :runtime
|
21
|
+
prerelease: false
|
22
|
+
version_requirements: !ruby/object:Gem::Requirement
|
23
|
+
requirements:
|
24
|
+
- - '>='
|
25
|
+
- !ruby/object:Gem::Version
|
26
|
+
version: 1.1.3
|
27
|
+
- !ruby/object:Gem::Dependency
|
28
|
+
name: json-ld
|
29
|
+
requirement: !ruby/object:Gem::Requirement
|
30
|
+
requirements:
|
31
|
+
- - '>='
|
32
|
+
- !ruby/object:Gem::Version
|
33
|
+
version: 1.1.3
|
34
|
+
type: :runtime
|
35
|
+
prerelease: false
|
36
|
+
version_requirements: !ruby/object:Gem::Requirement
|
37
|
+
requirements:
|
38
|
+
- - '>='
|
39
|
+
- !ruby/object:Gem::Version
|
40
|
+
version: 1.1.3
|
41
|
+
- !ruby/object:Gem::Dependency
|
42
|
+
name: shoulda
|
43
|
+
requirement: !ruby/object:Gem::Requirement
|
44
|
+
requirements:
|
45
|
+
- - '>='
|
46
|
+
- !ruby/object:Gem::Version
|
47
|
+
version: '0'
|
48
|
+
type: :development
|
49
|
+
prerelease: false
|
50
|
+
version_requirements: !ruby/object:Gem::Requirement
|
51
|
+
requirements:
|
52
|
+
- - '>='
|
53
|
+
- !ruby/object:Gem::Version
|
54
|
+
version: '0'
|
55
|
+
- !ruby/object:Gem::Dependency
|
56
|
+
name: simplecov
|
57
|
+
requirement: !ruby/object:Gem::Requirement
|
58
|
+
requirements:
|
59
|
+
- - '>='
|
60
|
+
- !ruby/object:Gem::Version
|
61
|
+
version: '0'
|
62
|
+
type: :development
|
63
|
+
prerelease: false
|
64
|
+
version_requirements: !ruby/object:Gem::Requirement
|
65
|
+
requirements:
|
66
|
+
- - '>='
|
67
|
+
- !ruby/object:Gem::Version
|
68
|
+
version: '0'
|
69
|
+
- !ruby/object:Gem::Dependency
|
70
|
+
name: jeweler
|
71
|
+
requirement: !ruby/object:Gem::Requirement
|
72
|
+
requirements:
|
73
|
+
- - ~>
|
74
|
+
- !ruby/object:Gem::Version
|
75
|
+
version: 1.8.4
|
76
|
+
type: :development
|
77
|
+
prerelease: false
|
78
|
+
version_requirements: !ruby/object:Gem::Requirement
|
79
|
+
requirements:
|
80
|
+
- - ~>
|
81
|
+
- !ruby/object:Gem::Version
|
82
|
+
version: 1.8.4
|
83
|
+
- !ruby/object:Gem::Dependency
|
84
|
+
name: bundler
|
85
|
+
requirement: !ruby/object:Gem::Requirement
|
86
|
+
requirements:
|
87
|
+
- - '>='
|
88
|
+
- !ruby/object:Gem::Version
|
89
|
+
version: 1.0.21
|
90
|
+
type: :development
|
91
|
+
prerelease: false
|
92
|
+
version_requirements: !ruby/object:Gem::Requirement
|
93
|
+
requirements:
|
94
|
+
- - '>='
|
95
|
+
- !ruby/object:Gem::Version
|
96
|
+
version: 1.0.21
|
97
|
+
- !ruby/object:Gem::Dependency
|
98
|
+
name: rdoc
|
99
|
+
requirement: !ruby/object:Gem::Requirement
|
100
|
+
requirements:
|
101
|
+
- - ~>
|
102
|
+
- !ruby/object:Gem::Version
|
103
|
+
version: '3.12'
|
104
|
+
type: :development
|
105
|
+
prerelease: false
|
106
|
+
version_requirements: !ruby/object:Gem::Requirement
|
107
|
+
requirements:
|
108
|
+
- - ~>
|
109
|
+
- !ruby/object:Gem::Version
|
110
|
+
version: '3.12'
|
111
|
+
description: Converts RDF N-Triples and N-Quads files to either JSON-LD or JSON. Supports
|
112
|
+
minimization of long URIs to shorter descriptive key names.
|
113
|
+
email: joachim.baran@gmail.com
|
114
|
+
executables:
|
115
|
+
- rdf2json
|
116
|
+
extensions: []
|
117
|
+
extra_rdoc_files:
|
118
|
+
- LICENSE.txt
|
119
|
+
- README.md
|
120
|
+
- README.rdoc
|
121
|
+
files:
|
122
|
+
- .document
|
123
|
+
- .travis.yml
|
124
|
+
- Gemfile
|
125
|
+
- LICENSE.txt
|
126
|
+
- README.md
|
127
|
+
- README.rdoc
|
128
|
+
- Rakefile
|
129
|
+
- VERSION
|
130
|
+
- lib/rdf2json.rb
|
131
|
+
- lib/rdf2json/rdf2json.rb
|
132
|
+
- test/helper.rb
|
133
|
+
- test/test_bio-rdf2json.rb
|
134
|
+
- bin/rdf2json
|
135
|
+
homepage: http://github.com/joejimbo/rdf2json
|
136
|
+
licenses:
|
137
|
+
- MIT
|
138
|
+
metadata: {}
|
139
|
+
post_install_message:
|
140
|
+
rdoc_options: []
|
141
|
+
require_paths:
|
142
|
+
- lib
|
143
|
+
required_ruby_version: !ruby/object:Gem::Requirement
|
144
|
+
requirements:
|
145
|
+
- - '>='
|
146
|
+
- !ruby/object:Gem::Version
|
147
|
+
version: '0'
|
148
|
+
required_rubygems_version: !ruby/object:Gem::Requirement
|
149
|
+
requirements:
|
150
|
+
- - '>='
|
151
|
+
- !ruby/object:Gem::Version
|
152
|
+
version: '0'
|
153
|
+
requirements: []
|
154
|
+
rubyforge_project:
|
155
|
+
rubygems_version: 2.0.3
|
156
|
+
signing_key:
|
157
|
+
specification_version: 4
|
158
|
+
summary: RDF N-Triples and N-Quads to JSON-LD or JSON converter.
|
159
|
+
test_files: []
|