togostanza 0.0.1

data/lib/togostanza/stanza/querying.rb

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+require 'sparql/client'
+
+module TogoStanza::Stanza
+  module Querying
+    MAPPINGS = {
+      togogenome: 'http://ep.dbcls.jp/sparql7',
+      uniprot:    'http://ep.dbcls.jp/sparql7',
+      go:         'http://ep.dbcls.jp/sparql7'
+    }
+
+    def query(endpoint, sparql)
+      client = SPARQL::Client.new(MAPPINGS[endpoint] || endpoint)
+
+      #Rails.logger.debug "SPARQL QUERY: \n#{sparql}"
+
+      client.query(sparql).map {|binding|
+        binding.each_with_object({}) {|(name, term), hash|
+          hash[name] = term.to_s
+        }
+      }
+    end
+
+    def uniprot_url_from_togogenome(gene_id)
+      # refseq の UniProt
+      # slr1311 の時 "http://purl.uniprot.org/refseq/NP_439906.1"
+      query(:togogenome, <<-SPARQL).first[:up]
+      PREFIX insdc: <http://insdc.org/owl/>
+      PREFIX idorg: <http://rdf.identifiers.org/database/>
+
+      SELECT DISTINCT ?up
+      FROM <http://togogenome.org/graph/refseq/>
+      WHERE {
+          ?s insdc:feature_locus_tag "#{gene_id}" .
+          ?s rdfs:seeAlso ?np .
+          ?s rdfs:seeAlso ?xref .
+          ?np rdf:type idorg:Protein .
+          BIND (STRAFTER(STR(?np), "ncbiprotein/") AS ?npid)
+          BIND (IRI(CONCAT("http://purl.uniprot.org/refseq/", ?npid)) AS ?up)
+      }
+      SPARQL
+    end
+  end
+end

data/lib/togostanza/stanza.rb

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+require 'active_support/all'
+
+module TogoStanza::Stanza
+  autoload :Base, 'togostanza/stanza/base'
+
+  class << self
+    def find(id)
+      "#{id.camelize}Stanza".constantize
+    end
+
+    def all
+      Base.descendants
+    end
+  end
+end

data/lib/togostanza/version.rb

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+module TogoStanza
+  VERSION = '0.0.1'
+end

data/lib/togostanza.rb

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+require 'togostanza/version'
+
+module TogoStanza
+  autoload :Application, 'togostanza/application'
+  autoload :CLI,         'togostanza/cli'
+  autoload :Markdown,    'togostanza/markdown'
+  autoload :Stanza,      'togostanza/stanza'
+end

data/public/assets/stanza.css

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+@charset "UTF-8";
+
+body {
+	background-color: transparent;
+	padding: 1px 2px 3px;
+	font-family: "Myriad Pro","Helvetica Neue",san-serif;
+	font-size: 16px;
+	line-height: 20px;
+}
+a {
+	color:#45b8cc;
+}
+
+ul, ol {
+	padding:0;
+	margin:0 0 0 16px;
+}
+dl {
+	margin: 0;
+	padding: 0;
+}
+dd {
+	margin: 0;
+}
+dt + dt, dd + dt,
+dt + dd, dd + dd {
+	margin-top: 8px;
+}
+
+
+body > .table, body > div {
+	-webkit-border-radius: 4px;
+	-moz-border-radius: 4px;
+	border-radius: 4px;
+	-webkit-box-shadow: 0 2px 2px rgba(0,0,0,.2);
+	-moz-box-shadow: 0 2px 2px rgba(0,0,0,.2);
+	box-shadow: 0 2px 2px rgba(0,0,0,.2);
+	background-color: #fff;
+}
+body > .table + .table, body > .table + div,
+body > div + .table, body > div + div {
+	margin-top: 5px;
+}
+
+body > div {
+	padding: 10px 20px;
+}
+
+body > .table {
+	border-style: solid;
+	border-color: rgba(0,0,0,0);
+	border-top-width: 5px;
+	border-bottom-width: 5px;
+	border-left-width: 0;
+	border-right-width: 0;
+}
+.table {
+	margin-bottom: 0;
+	word-break:break-all;
+}
+.table caption {
+	background-color: #8ac8d1;
+	text-align: left;
+	color: white;
+	font-size: 18px;
+	line-height: 22px;
+	height: 22px;
+	font-weight: bold;
+	padding: 10px 24px 4px;
+	margin: 0;
+	border-top-left-radius: 4px;
+	border-top-right-radius: 4px;
+}
+.table tr:before, .table tr:after {
+	content: "";
+	display: table-cell;
+	width: 20px;
+}
+.table thead th, .table thead td {
+	border-bottom: 1px solid #555;
+}
+.table th, .table td,
+.table > tbody > th, .table > tbody > td {
+	padding: 10px 4px;
+	line-height: 20px;
+	text-align: left;
+	vertical-align: top;
+	border-top: 1px solid #9fadad;
+}
+.table > tr:first-child > th, .table > tr:first-child > td,
+.table > tbody > tr:first-child > th, .table > tbody > tr:first-child > td {
+	border-top: none;
+}
+th > .table, td > .table {
+	margin: -10px -4px;
+	width: 100%;
+}
+th > .table > tbody > tr:before,
+td > .table > tbody > tr:before,
+th > .table > tbody > tr:after,
+td > .table > tbody > tr:after {
+	content: none;
+}
+.table li + li {
+	margin-top: 4px;
+}
+
+pre {
+	background-color:#daf1f5;
+	border:1px solid #ccc;
+	border:1px solid rgba(0,0,0,0.15);
+	padding: 8px 16px;
+}

data/public/assets/stanza.js

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+jQuery(function($) {
+  var RE = /^data-stanza-(.+)/
+
+  $('[data-stanza]').each(function(index) {
+    var $this  = $(this),
+        data   = $this.data(),
+        params = {};
+
+    $.each(this.attributes, function(i, attr) {
+      var key = (RE.exec(attr.name) || [])[1]
+
+      if (key) {
+        params[key.replace('-', '_')] = attr.value;
+      }
+    });
+
+    var src = data.stanza + '?' + $.param(params);
+
+    $('<iframe></iframe>')
+      .attr({src: src, frameborder: 0})
+      .attr({id: 'stanza-frame-' + index})
+      .attr({name: 'stanza-frame-' + index})
+      .width(data.stanzaWidth || '100%')
+      .height(data.stanzaHeight)
+      .appendTo($this);
+  });
+
+  window.onmessage = function(e) {
+    var message = JSON.parse(e.data),
+        iframe  = $('#' + message.id);
+
+    if (iframe.attr('style').search(/height/) === -1) {
+      iframe.height(message.height);
+    }
+  };
+});

data/spec/dummy/app.rb

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+$LOAD_PATH.unshift *Dir.glob(File.expand_path('../*_stanza/lib', __FILE__))
+
+require 'togostanza'
+require 'foo_stanza'
+require 'bar_stanza'
+
+class DummyApp < TogoStanza::Application
+end

data/spec/dummy/bar_stanza/help.md

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+# Bar

data/spec/dummy/bar_stanza/lib/bar_stanza.rb

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+require_relative '../stanza'
+
+BarStanza.root = File.expand_path('../..', __FILE__)

data/spec/dummy/bar_stanza/stanza.rb

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+class BarStanza < TogoStanza::Stanza::Base
+  property :name do
+    'bar'
+  end
+end

data/spec/dummy/bar_stanza/template.hbs

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+<p>hello from {{name}}</p>

data/spec/dummy/foo_stanza/help.md

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+# Foo

data/spec/dummy/foo_stanza/lib/foo_stanza.rb

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+require_relative '../stanza'
+
+FooStanza.root = File.expand_path('../..', __FILE__)

data/spec/dummy/foo_stanza/stanza.rb

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+class FooStanza < TogoStanza::Stanza::Base
+  property :name do
+    'foo'
+  end
+
+  resource :foo_resource do
+    {hello: 'world'}
+  end
+end

data/spec/dummy/foo_stanza/template.hbs

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+<p>hello from {{name}}</p>

data/spec/features/help_spec.rb

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+require 'spec_helper'
+
+describe 'Help' do
+  it 'should display FooStanza help' do
+    visit '/foo/help'
+    page.should have_css('h1', text: 'Foo')
+  end
+
+  it 'should display BarStanza help' do
+    visit '/bar/help'
+    page.should have_css('h1', text: 'Bar')
+  end
+end

data/spec/features/listing_spec.rb

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+require 'spec_helper'
+
+describe 'Listing' do
+  before do
+    visit '/'
+  end
+
+  it 'show all stanzas' do
+    page.should have_text('foo')
+    page.should have_text('bar')
+  end
+
+  it 'show link to help page' do
+    page.should have_link('help', href: '/foo/help')
+    page.should have_link('help', href: '/bar/help')
+  end
+end

data/spec/features/rendering_spec.rb

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+require 'spec_helper'
+
+describe 'Rendering' do
+  it 'should render FooStanza correctly' do
+    visit '/foo'
+    page.should have_content('hello from foo')
+  end
+
+  it 'should render BarStanza correctly' do
+    visit '/bar'
+    page.should have_content('hello from bar')
+  end
+end

data/spec/features/resource_spec.rb

@@ -0,0 +1,11 @@
+require 'spec_helper'
+
+describe 'Resource' do
+  before do
+    visit '/foo/resources/foo_resource'
+  end
+
+  it do
+    page.should have_content('{"hello":"world"}')
+  end
+end

data/spec/lib/togostanza/stanza/base_spec.rb

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+require 'spec_helper'
+
+describe TogoStanza::Stanza::Base do
+  describe '.property' do
+    let(:klass) { Class.new(TogoStanza::Stanza::Base) }
+
+    specify 'raise error when specify a value and block' do
+      expect {
+        klass.property :foo, 'bar' do
+          'baz'
+        end
+      }.to raise_error(ArgumentError)
+    end
+
+    specify 'raise error when neither specify a value nor block' do
+      expect {
+        klass.property :foo
+      }.to raise_error(ArgumentError)
+    end
+
+    specify 'allow specify a falsy value' do
+      klass.property :foo, false
+
+      klass.properties[:foo].should == false
+    end
+  end
+
+  describe '#context' do
+    let :klass do
+      Class.new(TogoStanza::Stanza::Base) {
+        property :foo do
+          'foo'
+        end
+
+        property :bar do |bar|
+          bar * 3
+        end
+
+        property :baz do
+          {
+            qux: 'quux'
+          }
+        end
+
+        property :foobar, 'foobar'
+
+        resource :do_not_evaluate do
+          raise
+        end
+      }
+    end
+
+    subject { klass.new(bar: 'bar').context }
+
+    its(:foo)    { should == 'foo' }
+    its(:bar)    { should == 'barbarbar' }
+    its(:baz)    { should == {'qux' => 'quux'} }
+    its(:foobar) { should == 'foobar' }
+  end
+
+  describe '#resource' do
+    let :klass do
+      Class.new(TogoStanza::Stanza::Base) {
+        resource :foo do
+          'foo'
+        end
+
+        resource :bar do |bar|
+          bar * 3
+        end
+      }
+    end
+
+    let(:stanza) { klass.new(bar: 'bar') }
+
+    specify { stanza.resource(:foo).should == 'foo' }
+    specify { stanza.resource(:bar).should == 'barbarbar' }
+  end
+end

data/spec/spec_helper.rb

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+ENV['RACK_ENV'] ||= 'test'
+
+require_relative 'dummy/app'
+
+require 'capybara'
+
+RSpec.configure do |config|
+  config.treat_symbols_as_metadata_keys_with_true_values = true
+  config.run_all_when_everything_filtered = true
+  config.filter_run :focus
+
+  config.order = 'random'
+
+  config.include Capybara::DSL
+end
+
+Capybara.app = DummyApp

data/templates/provider/Gemfile.erb

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+source 'https://rubygems.org'
+
+gem 'togostanza'

data/templates/provider/config.ru.erb

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+require 'bundler'
+Bundler.require
+
+map '/stanza' do
+  run TogoStanza::Application
+end

data/templates/stanza/Gemfile.erb

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+source 'https://rubygems.org'
+
+gemspec

data/templates/stanza/gemspec.erb

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+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+
+Gem::Specification.new do |spec|
+  spec.name          = '<%= file_name %>'
+  spec.version       = '0.0.1'
+  spec.authors       = ['TODO: Write your name']
+  spec.email         = ['TODO: Write your email address']
+  spec.summary       = %q{TODO: Write a short summary. Required.}
+  spec.description   = %q{TODO: Write a longer description. Optional.}
+  spec.homepage      = ''
+  spec.license       = 'MIT'
+
+  spec.files         = `git ls-files`.split($/)
+  spec.executables   = spec.files.grep(%r{^bin/}) { |f| File.basename(f) }
+  spec.test_files    = spec.files.grep(%r{^(test|spec|features)/})
+  spec.require_paths = ['lib']
+
+  spec.add_runtime_dependency 'togostanza'
+end

data/templates/stanza/help.md.erb

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+<%= title %>
+<%= '=' * title.size %>
+
+TODO: Write a stanza description
+
+## Parameters:
+
+(* = required)
+
+| Name             | Description                         |
+|------------------|-------------------------------------|
+| *data-stanza-foo | TODO: Write a parameter description |
+
+## Sample:
+
+```html
+<div data-stanza="<stanza url>"></div>
+```
+
+The above `<div>` will automatically embed the following Stanza in your HTML page.
+
+<div data-stanza="/stanza/<%= stanza_id %>"></div>

data/templates/stanza/lib.rb.erb

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+require 'togostanza'
+require_relative '../stanza'
+
+<%= class_name %>.root = File.expand_path('../..', __FILE__)

data/templates/stanza/stanza.rb.erb

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+class <%= class_name %> < TogoStanza::Stanza::Base
+  property :greeting do
+    'hello, world!'
+  end
+end

data/templates/stanza/template.hbs.erb

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+<!DOCTYPE html>
+
+<html>
+  <head>
+    <title><%= title %></title>
+    {{#each css_uri}}
+    <link rel="stylesheet" href="{{this}}" />
+    {{/each}}
+    <script src="//cdnjs.cloudflare.com/ajax/libs/jquery/1.8.3/jquery.min.js"></script>
+    <script src="//cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/2.2.2/bootstrap.min.js"></script>
+    {{adjust_iframe_height_script}}
+  </head>
+
+  <body>
+    <h1>{{greeting}}</h1>
+  </body>
+</html>

data/togostanza.gemspec

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+lib = File.expand_path('../lib', __FILE__)
+$LOAD_PATH.unshift(lib) unless $LOAD_PATH.include?(lib)
+require 'togostanza/version'
+
+Gem::Specification.new do |spec|
+  spec.name          = 'togostanza'
+  spec.version       = TogoStanza::VERSION
+  spec.authors       = ['Keita Urashima']
+  spec.email         = ['ursm@esm.co.jp']
+  spec.summary       = %q{Development tools of TogoStanza}
+  spec.homepage      = ''
+  spec.license       = 'MIT'
+
+  spec.files         = `git ls-files`.split($/)
+  spec.executables   = spec.files.grep(%r{^bin/}) {|f| File.basename(f) }
+  spec.test_files    = spec.files.grep(%r{^(test|spec|features)/})
+  spec.require_paths = ['lib']
+
+  spec.add_runtime_dependency 'activesupport'
+  spec.add_runtime_dependency 'flavour_saver'
+  spec.add_runtime_dependency 'haml'
+  spec.add_runtime_dependency 'hashie'
+  spec.add_runtime_dependency 'parallel'
+  spec.add_runtime_dependency 'redcarpet'
+  spec.add_runtime_dependency 'sinatra'
+  spec.add_runtime_dependency 'sinatra-contrib'
+  spec.add_runtime_dependency 'sparql-client'
+  spec.add_runtime_dependency 'thor'
+
+  spec.add_development_dependency 'appraisal'
+  spec.add_development_dependency 'bundler'
+  spec.add_development_dependency 'capybara'
+  spec.add_development_dependency 'rake'
+  spec.add_development_dependency 'rspec'
+
+  spec.required_ruby_version = '>= 1.9.3'
+end

data/views/index.haml

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+%h2 List of Stanzas
+
+%ul
+  - TogoStanza::Stanza.all.sort_by(&:id).each do |stanza|
+    %li
+      = stanza.id
+
+      != surround '(', ')' do
+        %a{href: path(stanza.id, :help)} help

data/views/layout.haml

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+!!!
+
+%html
+  %head
+    %meta(charset='utf-8')
+    %title= @page_title || 'Stanza'
+    %link(rel='stylesheet' href='//cdnjs.cloudflare.com/ajax/libs/twitter-bootstrap/2.2.2/css/bootstrap.min.css')
+    %link(rel='stylesheet' href='/stanza/assets/stanza.css')
+    %script(src='//cdnjs.cloudflare.com/ajax/libs/jquery/2.0.3/jquery.js')
+    %script(src='/stanza/assets/stanza.js')
+
+  %body
+    .container!~ yield