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1 #!/usr/bin/env ruby
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2 $: << File.expand_path('../rubylib/lib', File.dirname(__FILE__))
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3 $: << File.expand_path('sparql/lib', File.dirname(__FILE__))
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4 require "galaxy_tool"
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5 require 'rubygems'
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6 require 'sparql'
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7 require 'rubyrdf'
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8
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9 class SPARQLExecutor < GalaxyTool::Base
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10
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11 option :endpoint,
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12 :short => "-e",
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13 :long => "--endpoint <URL>",
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14 :class => String,
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15 :description => "use <URL> as SPARQL endpoint.",
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16 :proc => proc {|arg| arg.strip },
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17 :required => true
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18
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19 option :query,
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20 :long => "--query-file <filepath>",
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21 :class => String,
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22 :description => "read query expression from <filepath>.",
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23 :proc => proc {|arg| File.read(arg).chomp },
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24 :required => true
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25
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26 option :query,
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27 :short => "-q",
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28 :long => "--query <expression>",
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29 :class => String,
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30 :description => "use <expression> as query expression.",
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31 :proc => proc {|arg| arg.chomp },
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32 :required => true
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33
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34 option_output :short => "-o",
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35 :long => "--output <filepath>",
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36 :description => "use <filepath> as output file path."
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37
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38 option_info :long => "--info <filepath>",
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39 :description => "use <filepath> as info file path. default is standard out (/dev/stdout)."
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40
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41 option_error_handler do |optparse, exception|
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42 $stderr.puts "Error: " + exception.message
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43 $stderr.puts optparse.help
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44 raise exception
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45 end
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46
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47 def info(info_out)
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48 info_out.puts "Execute SPARQL query. The endpoint is #{options[:endpoint]}.\n"
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49 end
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50
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51 def create_customized_client(endpoint)
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52 client = SPARQL::Client.new(endpoint)
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53
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54 def client.parsed_xml(content)
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55 REXML::Document.new(content).root
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56 end
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57
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58 def client.parse_xml(content)
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59 table = []
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60 xml = parsed_xml(content)
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61
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62 head = xml.elements['head']
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63 variables = head.elements.map do |variable|
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64 variable.attributes['name']
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65 end
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66 table << variables.map {|v| "?" + v }
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67
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68 case
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69 when boolean = xml.elements['boolean']
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70 boolean.text == 'true'
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71 when results = xml.elements['results']
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72 table += results.elements.map do |result|
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73 row = []
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74 result.elements.each do |binding|
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75 name = binding.attributes['name']
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76 value_node = binding.children.find {|n| !n.is_a?(REXML::Text) }
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77 value = parse_xml_value(value_node)
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78 row[variables.index(name)] = value
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79 end
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80 row
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81 end
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82 else
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83 raise NotImplementedError # TODO
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84 end
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85
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86 table
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87 end
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88
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89 def client.graph
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90 @graph ||= RDF::Graph::Memory.new
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91 end
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92
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93 def client.parse_xml_value(element)
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94 case element
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95 when REXML::Text
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96 element.value
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97 when REXML::Node
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98 case element.name.to_sym
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99 when :uri
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100 RDF::UriNode.new(element.text)
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101 when :literal
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102 RDF::PlainLiteralNode.new(element.text)
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103 when :bnode
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104 RDF::BlankNode.new(element.text, graph)
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105 else
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106 raise NotImplementedError # TODO
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107 end
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108 else
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109 raise NotImplementedError # TODO
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110 end
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111 end
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112
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113 client
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114 end
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115
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116 def search(client, query)
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117 client.query(query)
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118 end
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119
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120 def main(output)
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121 client = create_customized_client(options[:endpoint])
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122 search(client, options[:query]).each do |row|
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123 output.puts row.join("\t")
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124 end
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125 end
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126 end
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127
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128 if $0 == __FILE__
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129 SPARQLExecutor.new.run(ARGV)
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130 end
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