jats 0.1.0

checksums.yaml

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+---
+SHA1:
+  metadata.gz: 313ee2fe8532319f7b1aab77c0121a269c0d017f
+  data.tar.gz: d4087afdd6b0283a194543aaae98e927f22d23a8
+SHA512:
+  metadata.gz: 64d2aa4db8e064376a1fae73d8353ac32f2c42cb97b60a346d5255c62d68434a6f8f2bc49faea637b8a1d9af1e984ecc8421f1b6304c6b9720921ec3b8732ba0
+  data.tar.gz: dfab7e8bfa74b242ca15f1d692aef6e5ad4329b9565bab0c16f941e800ceee715ceed009795c0b80b05cf7d7a250ad9f7f84e12b373bf116a0f80da6bd09d6f7

data/.document

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+lib/**/*.rb
+bin/*
+- 
+features/**/*.feature
+LICENSE.txt

data/.rspec

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+--color
+--format progress

data/Gemfile

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+source "http://rubygems.org"
+
+group :development do
+  gem "rspec", ">= 0"
+  gem "rdoc", "~> 3.12"
+  gem "bundler", "~> 1.0"
+  gem "jeweler", "~> 1.8.7"
+  gem "simplecov", ">= 0"
+  gem 'guard'
+  gem 'guard-rspec'
+end

data/Gemfile.lock

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+GEM
+  remote: http://rubygems.org/
+  specs:
+    addressable (2.3.5)
+    builder (3.2.2)
+    coderay (1.0.9)
+    diff-lcs (1.2.4)
+    faraday (0.8.8)
+      multipart-post (~> 1.2.0)
+    ffi (1.9.0)
+    formatador (0.2.4)
+    git (1.2.6)
+    github_api (0.10.1)
+      addressable
+      faraday (~> 0.8.1)
+      hashie (>= 1.2)
+      multi_json (~> 1.4)
+      nokogiri (~> 1.5.2)
+      oauth2
+    guard (1.8.2)
+      formatador (>= 0.2.4)
+      listen (>= 1.0.0)
+      lumberjack (>= 1.0.2)
+      pry (>= 0.9.10)
+      thor (>= 0.14.6)
+    guard-rspec (3.0.2)
+      guard (>= 1.8)
+      rspec (~> 2.13)
+    hashie (2.0.5)
+    highline (1.6.19)
+    httpauth (0.2.0)
+    jeweler (1.8.7)
+      builder
+      bundler (~> 1.0)
+      git (>= 1.2.5)
+      github_api (= 0.10.1)
+      highline (>= 1.6.15)
+      nokogiri (= 1.5.10)
+      rake
+      rdoc
+    json (1.8.0)
+    jwt (0.1.8)
+      multi_json (>= 1.5)
+    listen (1.3.0)
+      rb-fsevent (>= 0.9.3)
+      rb-inotify (>= 0.9)
+      rb-kqueue (>= 0.2)
+    lumberjack (1.0.4)
+    method_source (0.8.2)
+    multi_json (1.7.9)
+    multi_xml (0.5.5)
+    multipart-post (1.2.0)
+    nokogiri (1.5.10)
+    oauth2 (0.9.2)
+      faraday (~> 0.8)
+      httpauth (~> 0.2)
+      jwt (~> 0.1.4)
+      multi_json (~> 1.0)
+      multi_xml (~> 0.5)
+      rack (~> 1.2)
+    pry (0.9.12.2)
+      coderay (~> 1.0.5)
+      method_source (~> 0.8)
+      slop (~> 3.4)
+    rack (1.5.2)
+    rake (10.1.0)
+    rb-fsevent (0.9.3)
+    rb-inotify (0.9.1)
+      ffi (>= 0.5.0)
+    rb-kqueue (0.2.0)
+      ffi (>= 0.5.0)
+    rdoc (3.12.2)
+      json (~> 1.4)
+    rspec (2.14.1)
+      rspec-core (~> 2.14.0)
+      rspec-expectations (~> 2.14.0)
+      rspec-mocks (~> 2.14.0)
+    rspec-core (2.14.5)
+    rspec-expectations (2.14.2)
+      diff-lcs (>= 1.1.3, < 2.0)
+    rspec-mocks (2.14.3)
+    simplecov (0.7.1)
+      multi_json (~> 1.0)
+      simplecov-html (~> 0.7.1)
+    simplecov-html (0.7.1)
+    slop (3.4.6)
+    thor (0.18.1)
+
+PLATFORMS
+  ruby
+
+DEPENDENCIES
+  bundler (~> 1.0)
+  guard
+  guard-rspec
+  jeweler (~> 1.8.7)
+  rdoc (~> 3.12)
+  rspec
+  simplecov

data/Guardfile

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+# A sample Guardfile
+# More info at https://github.com/guard/guard#readme
+
+guard :rspec do
+  watch(%r{^spec/.+_spec\.rb$})
+  watch(%r{^lib/(.+)\.rb$})     { |m| "spec/lib/#{m[1]}_spec.rb" }
+  watch('spec/spec_helper.rb')  { "spec" }
+
+  # Rails example
+  watch(%r{^app/(.+)\.rb$})                           { |m| "spec/#{m[1]}_spec.rb" }
+  watch(%r{^app/(.*)(\.erb|\.haml)$})                 { |m| "spec/#{m[1]}#{m[2]}_spec.rb" }
+  watch(%r{^app/controllers/(.+)_(controller)\.rb$})  { |m| ["spec/routing/#{m[1]}_routing_spec.rb", "spec/#{m[2]}s/#{m[1]}_#{m[2]}_spec.rb", "spec/acceptance/#{m[1]}_spec.rb"] }
+  watch(%r{^spec/support/(.+)\.rb$})                  { "spec" }
+  watch('config/routes.rb')                           { "spec/routing" }
+  watch('app/controllers/application_controller.rb')  { "spec/controllers" }
+
+  # Capybara features specs
+  watch(%r{^app/views/(.+)/.*\.(erb|haml)$})          { |m| "spec/features/#{m[1]}_spec.rb" }
+
+  # Turnip features and steps
+  watch(%r{^spec/acceptance/(.+)\.feature$})
+  watch(%r{^spec/acceptance/steps/(.+)_steps\.rb$})   { |m| Dir[File.join("**/#{m[1]}.feature")][0] || 'spec/acceptance' }
+end
+

data/LICENSE.txt

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+Copyright (c) 2013 Bart Zonneveld
+
+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.rdoc

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+= jats
+
+Description goes here.
+
+== Contributing to jats
+ 
+* Check out the latest master to make sure the feature hasn't been implemented or the bug hasn't been fixed yet.
+* Check out the issue tracker to make sure someone already hasn't requested it and/or contributed it.
+* Fork the project.
+* Start a feature/bugfix branch.
+* Commit and push until you are happy with your contribution.
+* Make sure to add tests for it. This is important so I don't break it in a future version unintentionally.
+* Please try not to mess with the Rakefile, version, or history. If you want to have your own version, or is otherwise necessary, that is fine, but please isolate to its own commit so I can cherry-pick around it.
+
+== Copyright
+
+Copyright (c) 2013 Bart Zonneveld. 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://docs.rubygems.org/read/chapter/20 for more options
+  gem.name = "jats"
+  gem.homepage = "http://github.com/bartzon/jats"
+  gem.license = "MIT"
+  gem.summary = %Q{Parse Journal Publishing Tag Set into sensible Ruby}
+  gem.description = %Q{This gem converts a Journal Publishing Tag Set (Jats) XML file into a ruby hash compatible with the Lens document format}
+  gem.email = "bart@madebyhiro.com"
+  gem.authors = ["Bart Zonneveld"]
+  # dependencies defined in Gemfile
+end
+Jeweler::RubygemsDotOrgTasks.new
+
+require 'rspec'
+require 'rspec/core/rake_task'
+RSpec::Core::RakeTask.new(:spec)
+task :default => :spec
+
+require 'rdoc/task'
+Rake::RDocTask.new do |rdoc|
+  version = File.exist?('VERSION') ? File.read('VERSION') : ""
+
+  rdoc.rdoc_dir = 'rdoc'
+  rdoc.title = "jats #{version}"
+  rdoc.rdoc_files.include('README*')
+  rdoc.rdoc_files.include('lib/**/*.rb')
+end

data/VERSION

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+0.1.0

data/jats.gemspec

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+# Generated by jeweler
+# DO NOT EDIT THIS FILE DIRECTLY
+# Instead, edit Jeweler::Tasks in Rakefile, and run 'rake gemspec'
+# -*- encoding: utf-8 -*-
+
+Gem::Specification.new do |s|
+  s.name = "jats"
+  s.version = "0.1.0"
+
+  s.required_rubygems_version = Gem::Requirement.new(">= 0") if s.respond_to? :required_rubygems_version=
+  s.authors = ["Bart Zonneveld"]
+  s.date = "2013-08-22"
+  s.description = "This gem converts a Journal Publishing Tag Set (Jats) XML file into a ruby hash compatible with the Lens document format"
+  s.email = "bart@madebyhiro.com"
+  s.extra_rdoc_files = [
+    "LICENSE.txt",
+    "README.rdoc"
+  ]
+  s.files = [
+    ".document",
+    ".rspec",
+    "Gemfile",
+    "Gemfile.lock",
+    "Guardfile",
+    "LICENSE.txt",
+    "README.rdoc",
+    "Rakefile",
+    "VERSION",
+    "jats.gemspec",
+    "lib/jats.rb",
+    "lib/jats/affiliation.rb",
+    "lib/jats/annotation.rb",
+    "lib/jats/article.rb",
+    "lib/jats/body.rb",
+    "lib/jats/figure.rb",
+    "lib/jats/front.rb",
+    "lib/jats/heading.rb",
+    "lib/jats/node.rb",
+    "lib/jats/person.rb",
+    "lib/jats/text.rb",
+    "spec/fixtures/affiliation.xml",
+    "spec/fixtures/annotation.xml",
+    "spec/fixtures/bmj_sample.xml",
+    "spec/fixtures/figure.xml",
+    "spec/fixtures/heading.xml",
+    "spec/fixtures/peerj.xml",
+    "spec/fixtures/person.xml",
+    "spec/fixtures/plos_one.xml",
+    "spec/fixtures/pnas_sample.xml",
+    "spec/fixtures/text.xml",
+    "spec/jats/affiliation_spec.rb",
+    "spec/jats/annotation_spec.rb",
+    "spec/jats/article_spec.rb",
+    "spec/jats/body_spec.rb",
+    "spec/jats/figure_spec.rb",
+    "spec/jats/front_spec.rb",
+    "spec/jats/heading_spec.rb",
+    "spec/jats/node_spec.rb",
+    "spec/jats/person_spec.rb",
+    "spec/jats/text_spec.rb",
+    "spec/jats_spec.rb",
+    "spec/spec_helper.rb"
+  ]
+  s.homepage = "http://github.com/bartzon/jats"
+  s.licenses = ["MIT"]
+  s.require_paths = ["lib"]
+  s.rubygems_version = "2.0.6"
+  s.summary = "Parse Journal Publishing Tag Set into sensible Ruby"
+
+  if s.respond_to? :specification_version then
+    s.specification_version = 4
+
+    if Gem::Version.new(Gem::VERSION) >= Gem::Version.new('1.2.0') then
+      s.add_development_dependency(%q<rspec>, [">= 0"])
+      s.add_development_dependency(%q<rdoc>, ["~> 3.12"])
+      s.add_development_dependency(%q<bundler>, ["~> 1.0"])
+      s.add_development_dependency(%q<jeweler>, ["~> 1.8.7"])
+      s.add_development_dependency(%q<simplecov>, [">= 0"])
+      s.add_development_dependency(%q<guard>, [">= 0"])
+      s.add_development_dependency(%q<guard-rspec>, [">= 0"])
+    else
+      s.add_dependency(%q<rspec>, [">= 0"])
+      s.add_dependency(%q<rdoc>, ["~> 3.12"])
+      s.add_dependency(%q<bundler>, ["~> 1.0"])
+      s.add_dependency(%q<jeweler>, ["~> 1.8.7"])
+      s.add_dependency(%q<simplecov>, [">= 0"])
+      s.add_dependency(%q<guard>, [">= 0"])
+      s.add_dependency(%q<guard-rspec>, [">= 0"])
+    end
+  else
+    s.add_dependency(%q<rspec>, [">= 0"])
+    s.add_dependency(%q<rdoc>, ["~> 3.12"])
+    s.add_dependency(%q<bundler>, ["~> 1.0"])
+    s.add_dependency(%q<jeweler>, ["~> 1.8.7"])
+    s.add_dependency(%q<simplecov>, [">= 0"])
+    s.add_dependency(%q<guard>, [">= 0"])
+    s.add_dependency(%q<guard-rspec>, [">= 0"])
+  end
+end
+

data/lib/jats.rb

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+module Jats
+  autoload :Article,     'jats/article'
+
+  autoload :Front,       'jats/front'
+  autoload :Body,        'jats/body'
+
+  autoload :Node,        'jats/node'
+  autoload :Person,      'jats/person'
+  autoload :Heading,     'jats/heading'
+  autoload :Text,        'jats/text'
+  autoload :Figure,      'jats/figure'
+  autoload :Annotation,  'jats/annotation'
+  autoload :Affiliation, 'jats/affiliation'
+
+end

data/lib/jats/affiliation.rb

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+module Jats
+  class Affiliation < Node
+    def to_hash
+      {
+        label:      xml.css('label').text,
+        department: xml.css('institution').text.gsub(/^\W+|\W+$/, ''),
+        address:    xml.css('addr-line').text,
+        country:    xml.css('country').text
+      }
+    end
+  end
+end
+

data/lib/jats/annotation.rb

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+module Jats
+  class Annotation < Node
+    attr_accessor :source
+
+    def attributes
+      rid = xml['rid']
+      id  = rid.gsub('ref-', '')
+
+      {
+        source:  source,
+        content: xml.text,
+        target:  "article:bib#{id}"
+      }
+    end
+  end
+end
+

data/lib/jats/article.rb

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+module Jats
+  class Article
+    include Front
+    include Body
+
+    attr_accessor :xml, :doc
+
+    def self.from_xml(xml)
+      new(xml).parse
+    end
+
+    def initialize(xml=nil)
+      @xml = xml
+      @doc = { properties: {} }
+      @doc[:nodes] = {}
+      @doc[:views] = { content: [] }
+    end
+
+    def add_to_outline(node)
+      doc[:views][:content] << node.name
+    end
+
+    def add_node(node)
+      doc[:nodes].merge!(node.to_hash)
+    end
+
+    def parse_back
+      # TODO implement
+    end
+
+    def parse
+      parse_front
+      parse_body
+      parse_back
+      doc
+    end
+  end
+end

data/lib/jats/body.rb

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+module Jats
+  module Body
+    def parse_sec(xml)
+      sec = Heading.from_xml(xml)
+      add_to_outline(sec)
+      add_node(sec)
+    end
+
+    def parse_p(xml)
+      p = Text.from_xml(xml)
+      add_to_outline(p)
+      add_node(p)
+      p.annotations.each { |a| add_node(a) }
+    end
+
+    def parse_fig(xml)
+      fig = Figure.from_xml(xml)
+      add_to_outline(fig)
+      add_node(fig)
+    end
+
+    def nodes
+      xml.xpath('//sec | //sec /p | //fig')
+    end
+
+    def parse_body
+      nodes.each do |node|
+        next if node.text?
+
+        if respond_to?("parse_#{node.name}")
+          self.send("parse_#{node.name}", node)
+        end
+      end
+
+      doc
+    end
+  end
+end
+