rdf2json 0.0.1

checksums.yaml

@@ -0,0 +1,7 @@
+---
+SHA1:
+  metadata.gz: 5b7bc9157133dd33407d3807be8d4e2ae8361424
+  data.tar.gz: 4f22bddd6f50b8708d289f6699eaee564d7a0afe
+SHA512:
+  metadata.gz: 4c0697837463e626dfc077ba4a0cd27ee7240fe6c3fcfdde29a3708edbf83689901e25f92ae266a8fe9a840fe34f6839c4363502b647fe207ef0fa2042908bb0
+  data.tar.gz: ece185939cd4925b52632ca346653486905b91f185852845e5081dab6ca670de61df858795c2cbad5683bd2ebfaac23f845842185ac323412966ab8afb918b91

data/.document

@@ -0,0 +1,5 @@
+lib/**/*.rb
+bin/*
+- 
+features/**/*.feature
+LICENSE.txt

data/.travis.yml

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+language: ruby
+rvm:
+  - 1.9.2
+  - 1.9.3
+  - 2.0.0
+  - 2.1.1
+
+# - rbx-19mode
+#  - 1.8.7
+#  - jruby-18mode # JRuby in 1.8 mode
+#  - rbx-18mode
+
+# uncomment this line if your project needs to run something other than `rake`:
+# script: bundle exec rspec spec

data/Gemfile

@@ -0,0 +1,16 @@
+source "http://rubygems.org"
+# Add dependencies required to use your gem here.
+# Example:
+#   gem "activesupport", ">= 2.3.5"
+gem "rdf", ">= 1.1.3"
+gem "json-ld", ">= 1.1.3"
+
+# Add dependencies to develop your gem here.
+# Include everything needed to run rake, tests, features, etc.
+group :development do
+  gem "shoulda", ">= 0"
+  gem "simplecov", ">= 0"
+  gem "jeweler", "~> 1.8.4"
+  gem "bundler", ">= 1.0.21"
+  gem "rdoc", "~> 3.12"
+end

data/LICENSE.txt

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+Copyright (c) 2014 Joachim Baran
+
+Permission is hereby granted, free of charge, to any person obtaining
+a copy of this software and associated documentation files (the
+"Software"), to deal in the Software without restriction, including
+without limitation the rights to use, copy, modify, merge, publish,
+distribute, sublicense, and/or sell copies of the Software, and to
+permit persons to whom the Software is furnished to do so, subject to
+the following conditions:
+
+The above copyright notice and this permission notice shall be
+included in all copies or substantial portions of the Software.
+
+THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
+EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
+MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
+NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
+LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
+OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
+WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.

data/README.md

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+# rdf2json
+
+[![Build Status](https://secure.travis-ci.org/joejimbo/rdf2json.png)](http://travis-ci.org/joejimbo/rdf2json)
+
+Reads RDF N-Triple/N-Quads that are sorted by subject and
+append a JSON/JSON-LD document per line in a designated
+output file.
+
+Usage: `rdf2json [options] --input filename.nt --output filename.json`
+
+#### Required options
+
+*  `-i`, `--input FILE`: Input file for the conversion; either RDF N-Triples or N-Quads.
+*  `-o`, `--output FILE`: Output file to which JSON-LD/JSON is appended.
+
+#### Options
+
+*  `-m`, `--minimize`: Minimize JSON-LD to plain (semantically untyped) JSON.
+*  `-n`, `--namespace [NAMESPACE]`: Alternative name for JSON-LD's "@id" key; replaces it; turns on `--minimize`
+*  `-p`, `--prefix [PREFIX]`: Prefix that should be removed from keys; requires `--minimize`.
+*  `-t`, `--triples`: Input file is in RDF N-Triples format.
+*  `-q`, `--quads`: Input file is in RDF N-Quads format.
+
+#### Common options
+
+*  `-h`, `--help`: Show this message.
+
+## Installation
+
+```sh
+gem install rdf2json
+```
+
+## Project home page
+
+Information on the source tree, documentation, examples, issues and
+how to contribute, see
+
+  http://github.com/joejimbo/rdf2json
+
+The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
+
+## Biogems.info
+
+This Biogem is published at (http://biogems.info/index.html#bio-rdf2json)
+
+## Copyright
+
+Copyright (c) 2014 Joachim Baran. See LICENSE.txt for further details.
+

data/README.rdoc

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+= bio-rdf2json
+
+{<img
+src="https://secure.travis-ci.org/joejimbo/bioruby-rdf2json.png"
+/>}[http://travis-ci.org/#!/joejimbo/bioruby-rdf2json]
+
+Full description goes here
+
+Note: this software is under active development!
+
+== Installation
+
+        gem install bio-rdf2json
+
+== Usage
+
+== Developers
+
+To use the library 
+
+        require 'bio-rdf2json'
+
+The API doc is online. For more code examples see also the test files in
+the source tree.
+        
+== Project home page
+
+Information on the source tree, documentation, issues and how to contribute, see
+
+  http://github.com/joejimbo/bioruby-rdf2json
+
+The BioRuby community is on IRC server: irc.freenode.org, channel: #bioruby.
+
+== Cite
+
+  If you use this software, please cite one of
+ 
+* [BioRuby: bioinformatics software for the Ruby programming language](http://dx.doi.org/10.1093/bioinformatics/btq475)
+* [Biogem: an effective tool-based approach for scaling up open source software development in bioinformatics](http://dx.doi.org/10.1093/bioinformatics/bts080)
+
+== Biogems.info
+
+This Biogem is published at http://biogems.info/index.html#bio-rdf2json
+
+== Copyright
+
+Copyright (c) 2014 Joachim Baran. See LICENSE.txt for further details.
+

data/Rakefile

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+# encoding: utf-8
+
+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'rake'
+
+require 'jeweler'
+Jeweler::Tasks.new do |gem|
+  # gem is a Gem::Specification... see http://guides.rubygems.org/specification-reference/ for more options
+  gem.name = "rdf2json"
+  gem.homepage = "http://github.com/joejimbo/rdf2json"
+  gem.license = "MIT"
+  gem.summary = %Q{RDF N-Triples and N-Quads to JSON-LD or JSON converter.}
+  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.}
+  gem.email = 'joachim.baran@gmail.com'
+  gem.authors = [ 'Joachim Baran' ]
+  gem.executable = 'rdf2json'
+  # dependencies defined in Gemfile
+end
+Jeweler::RubygemsDotOrgTasks.new
+
+require 'rake/testtask'
+Rake::TestTask.new(:test) do |test|
+  test.libs << 'lib' << 'test'
+  test.pattern = 'test/**/test_*.rb'
+  test.verbose = true
+end
+
+desc "Code coverage detail"
+task :simplecov do
+  ENV['COVERAGE'] = "true"
+  Rake::Task['test'].execute
+end
+
+task :default => :test
+
+require 'rdoc/task'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "rdf2json #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+0.0.1

data/bin/rdf2json

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+#!/usr/bin/env ruby
+
+require 'rdf2json'
+
+RDF2JSON::cli
+

data/lib/rdf2json.rb

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+
+require 'rdf2json/rdf2json.rb'
+

data/lib/rdf2json/rdf2json.rb

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+
+require 'rdf'
+require 'rdf/ntriples'
+require 'rdf/nquads'
+require 'json/ld'
+require 'optparse'
+
+module RDF2JSON
+
+def self.cli
+  options = {}
+
+  parser = OptionParser.new { |opts|
+    opts.banner = 'Usage: rdf2json [options] --input filename.nt --output filename.json'
+
+    opts.separator ''
+    opts.separator 'Description: Reads RDF N-Triple/N-Quads that are sorted by subject and'
+    opts.separator '             append a JSON/JSON-LD document per line in a designated'
+    opts.separator '             output file.'
+    opts.separator ''
+    opts.separator 'Required:'
+
+    opts.on('-i', '--input FILE', 'Input file for the conversion; either RDF N-Triples or N-Quads.') { |file|
+      options[:input] = file
+    }
+    opts.on('-o', '--output FILE', 'Output file to which JSON-LD/JSON is appended.') { |file|
+      options[:output] = file
+    }
+
+    opts.separator ''
+    opts.separator 'Options:'
+
+    opts.on('-m', '--minimize', 'Minimize JSON-LD to plain (semantically untyped) JSON.') { |minimize|
+      options[:minimize] = true
+    }
+    opts.on('-n', '--namespace [NAMESPACE]', 'Alternative name for JSON-LD\'s "@id" key; replaces it; turns on --minimize') { |namespace|
+      options[:minimize] = true
+      options[:namespace] = namespace
+    }
+    opts.on('-p', '--prefix [PREFIX]', 'Prefix that should be removed from keys; requires --minimize.') { |prefix|
+      options[:prefix] = prefix
+    }
+    opts.on('-t', '--triples', 'Input file is in RDF N-Triples format.') { |triples|
+      options[:ntriples] = true
+    }
+    opts.on('-q', '--quads', 'Input file is in RDF N-Quads format.') { |quads|
+      options[:nquads] = true
+    }
+
+    opts.separator ''
+    opts.separator 'Common options:'
+
+    opts.on_tail('-h', '--help', 'Show this message.') { |help|
+      puts opts
+      exit
+    }
+  }
+
+  begin
+    parser.parse!
+  rescue
+    puts parser
+    exit 1
+  end
+
+  unless options.has_key?(:input) and options.has_key?(:output) then
+    puts 'Error: Requires --input and --output parameters.'
+    puts ''
+    puts parser
+    exit 2
+  end
+
+  if options.has_key?(:ntriples) and options.has_key?(:nquads) then
+    puts 'Error: both --triples and --quads parameters were used.'
+    puts '       Only one of the parameters may be provided for explicitly'
+    puts '       setting the input fileformat.'
+    puts ''
+    puts parser
+    exit 3
+  end
+
+  extension = File.extname(options[:input])
+  if options.has_key?(:ntriples) then
+    input_format = :ntriples
+  elsif options.has_key?(:nquads) then
+    input_format = :nquads
+  elsif extension == '.nt' then
+    input_format = :ntriples
+  elsif extension == '.nq' then
+    input_format = :nquads
+  else
+    puts 'Error: Cannot determine input file format by filename extension.'
+    puts '       Recognized fileformat extensions are .nt and .nq for N-Triples'
+    puts '       and N-Quads respectively. Use --triples or --quads options to'
+    puts '       explicitly set the input fileformat (ignores filename extension'
+    puts '       when one of those options is given.'
+    puts ''
+    puts parser
+    exit 4
+  end
+
+  output_format = :jsonld
+  output_format = :json if options[:minimize]
+
+  unless File.exist?(options[:input]) then
+    puts 'Error: Input file (--input parameter) does not seem to exist.'
+    puts ''
+    puts parser
+    exit 6
+  end
+
+  begin
+    # Why instantiate a Converter instance here? Well, for implementing parallelization later:
+    Converter.new(options[:input], options[:output], input_format, output_format, options[:namespace], options[:prefix]).convert
+  rescue Interrupt
+    # The user hit Ctrl-C, which is okay and does not need error reporting.
+    exit 0
+  end
+end
+
+class Converter
+
+  def initialize(input_filename, output_filename, input_format, output_format, namespace, prefix)
+    @input_file = File.open(input_filename, 'r')
+    @output_file = File.open(output_filename, 'a')
+    @input_format = input_format
+    @output_format = output_format
+    @namespace = namespace
+    @prefix = prefix
+  end
+
+  def convert
+    no_of_lines = 0
+    no_of_statements = 0
+    read_errors = 0
+    last_subject = nil
+    subject_block = ''
+
+    @input_file.each_line { |line|
+      no_of_lines += 1
+      line.chomp!
+
+      subject = "#{line.sub(/>.*/, '')}>"
+
+      if subject == last_subject then
+        subject_block << line
+      else
+        stats = write_graph(subject_block)
+        no_of_statements += stats[:no_of_statements]
+        read_errors += stats[:read_errors]
+        subject_block = ''
+      end
+
+      last_subject = subject
+    }
+
+    stats = write_graph(subject_block)
+    no_of_statements += stats[:no_of_statements]
+    read_errors += stats[:read_errors]
+
+    puts "Total number of lines read                   : #{no_of_lines}"
+    puts "Statement read errors (N-Quads or N-Triples) : #{read_errors}"
+    puts "JSON/JSON-LD documents output                : #{no_of_statements}"
+  end
+
+  def minify(jsonld_hash)
+    jsonld_hash.keys.each { |key|
+      if key == '@type' then
+        jsonld_hash.delete(key)
+      elsif @prefix and key.match(@prefix) then
+        shortened_key = key.sub(@prefix, '')
+        jsonld_hash[shortened_key] = jsonld_hash.delete(key)
+        key = shortened_key
+      end
+
+      if jsonld_hash[key].instance_of?(Array) then
+        jsonld_hash[key].each_index { |index|
+          if jsonld_hash[key][index].has_key?('@value') then
+            jsonld_hash[key][index] = jsonld_hash[key][index]['@value']
+          elsif jsonld_hash[key][index].has_key?('@id') then
+            jsonld_hash[key][index] = jsonld_hash[key][index]['@id']
+          end
+        }
+      elsif jsonld_hash[key].instance_of?(Hash) then
+        minify(jsonld_hash[key])
+      end
+    }
+  end
+
+  def write_graph(block)
+    return { :read_errors => 0, :no_of_statements => 0 } unless block and not block.empty?
+
+    block.gsub!("\\'", "'")
+
+    read_errors = 0
+    no_of_statements = 0
+    graph = RDF::Graph.new
+    RDF::Reader.for(@input_format).new(block) { |reader|
+      begin
+        reader.each_statement { |statement|
+          no_of_statements += 1
+          graph.insert(statement)
+        }
+      rescue RDF::ReaderError
+        read_errors += 1
+      end
+    }
+
+    JSON::LD::API::fromRdf(graph) { |document|
+      document.each{ |entity|
+        # Parsed JSON-LD representation:
+        entity = JSON.parse(entity.to_json)
+
+        entity[@namespace] = entity.delete('@id') if @namespace
+        minify(entity) if @output_format == :json
+
+        @output_file.puts entity.to_json
+      }
+    }
+
+    return { :read_errors => read_errors, :no_of_statements => no_of_statements }
+  end
+
+end
+
+end

data/test/helper.rb

@@ -0,0 +1,34 @@
+require 'simplecov'
+
+module SimpleCov::Configuration
+  def clean_filters
+    @filters = []
+  end
+end
+
+SimpleCov.configure do
+  clean_filters
+  load_adapter 'test_frameworks'
+end
+
+ENV["COVERAGE"] && SimpleCov.start do
+  add_filter "/.rvm/"
+end
+require 'rubygems'
+require 'bundler'
+begin
+  Bundler.setup(:default, :development)
+rescue Bundler::BundlerError => e
+  $stderr.puts e.message
+  $stderr.puts "Run `bundle install` to install missing gems"
+  exit e.status_code
+end
+require 'test/unit'
+require 'shoulda'
+
+$LOAD_PATH.unshift(File.join(File.dirname(__FILE__), '..', 'lib'))
+$LOAD_PATH.unshift(File.dirname(__FILE__))
+require 'bio-rdf2json'
+
+class Test::Unit::TestCase
+end

data/test/test_bio-rdf2json.rb

@@ -0,0 +1,7 @@
+require 'helper'
+
+class TestBioRdf2json < Test::Unit::TestCase
+  should "probably rename this file and start testing for real" do
+    flunk "hey buddy, you should probably rename this file and start testing for real"
+  end
+end

metadata

@@ -0,0 +1,159 @@
+--- !ruby/object:Gem::Specification
+name: rdf2json
+version: !ruby/object:Gem::Version
+  version: 0.0.1
+platform: ruby
+authors:
+- Joachim Baran
+autorequire: 
+bindir: bin
+cert_chain: []
+date: 2014-05-20 00:00:00.000000000 Z
+dependencies:
+- !ruby/object:Gem::Dependency
+  name: rdf
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: 1.1.3
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: 1.1.3
+- !ruby/object:Gem::Dependency
+  name: json-ld
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: 1.1.3
+  type: :runtime
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: 1.1.3
+- !ruby/object:Gem::Dependency
+  name: shoulda
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: simplecov
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: '0'
+- !ruby/object:Gem::Dependency
+  name: jeweler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.8.4
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: 1.8.4
+- !ruby/object:Gem::Dependency
+  name: bundler
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: 1.0.21
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - '>='
+      - !ruby/object:Gem::Version
+        version: 1.0.21
+- !ruby/object:Gem::Dependency
+  name: rdoc
+  requirement: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
+  type: :development
+  prerelease: false
+  version_requirements: !ruby/object:Gem::Requirement
+    requirements:
+    - - ~>
+      - !ruby/object:Gem::Version
+        version: '3.12'
+description: Converts RDF N-Triples and N-Quads files to either JSON-LD or JSON. Supports
+  minimization of long URIs to shorter descriptive key names.
+email: joachim.baran@gmail.com
+executables:
+- rdf2json
+extensions: []
+extra_rdoc_files:
+- LICENSE.txt
+- README.md
+- README.rdoc
+files:
+- .document
+- .travis.yml
+- Gemfile
+- LICENSE.txt
+- README.md
+- README.rdoc
+- Rakefile
+- VERSION
+- lib/rdf2json.rb
+- lib/rdf2json/rdf2json.rb
+- test/helper.rb
+- test/test_bio-rdf2json.rb
+- bin/rdf2json
+homepage: http://github.com/joejimbo/rdf2json
+licenses:
+- MIT
+metadata: {}
+post_install_message: 
+rdoc_options: []
+require_paths:
+- lib
+required_ruby_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+required_rubygems_version: !ruby/object:Gem::Requirement
+  requirements:
+  - - '>='
+    - !ruby/object:Gem::Version
+      version: '0'
+requirements: []
+rubyforge_project: 
+rubygems_version: 2.0.3
+signing_key: 
+specification_version: 4
+summary: RDF N-Triples and N-Quads to JSON-LD or JSON converter.
+test_files: []