search_biomodel 0.1.2 → 1.0.0

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Files changed (1059) hide show
  1. data/Gemfile +1 -2
  2. data/Gemfile.lock +17 -3
  3. data/README.rdoc +9 -2
  4. data/VERSION +1 -1
  5. data/lib/search_biomodel.rb +11 -8
  6. data/search_biomodel.gemspec +1055 -9
  7. data/search_biomodel/ruby/1.8/bin/jeweler +19 -0
  8. data/search_biomodel/ruby/1.8/bin/nokogiri +19 -0
  9. data/search_biomodel/ruby/1.8/bin/rackup +19 -0
  10. data/search_biomodel/ruby/1.8/bin/rake +19 -0
  11. data/search_biomodel/ruby/1.8/bin/rcov +19 -0
  12. data/search_biomodel/ruby/1.8/cache/builder-3.0.0.gem +0 -0
  13. data/search_biomodel/ruby/1.8/cache/git-1.2.5.gem +0 -0
  14. data/search_biomodel/ruby/1.8/cache/gyoku-0.4.4.gem +0 -0
  15. data/search_biomodel/ruby/1.8/cache/httpi-0.9.4.gem +0 -0
  16. data/search_biomodel/ruby/1.8/cache/jeweler-1.6.2.gem +0 -0
  17. data/search_biomodel/ruby/1.8/cache/nokogiri-1.4.6.gem +0 -0
  18. data/search_biomodel/ruby/1.8/cache/nori-1.0.1.gem +0 -0
  19. data/search_biomodel/ruby/1.8/cache/pyu-ntlm-http-0.1.3.1.gem +0 -0
  20. data/search_biomodel/ruby/1.8/cache/rack-1.3.0.gem +0 -0
  21. data/search_biomodel/ruby/1.8/cache/rake-0.9.2.gem +0 -0
  22. data/search_biomodel/ruby/1.8/cache/rcov-0.9.9.gem +0 -0
  23. data/search_biomodel/ruby/1.8/cache/savon-0.9.2.gem +0 -0
  24. data/search_biomodel/ruby/1.8/gems/builder-3.0.0/CHANGES +89 -0
  25. data/search_biomodel/ruby/1.8/gems/builder-3.0.0/README +229 -0
  26. data/search_biomodel/ruby/1.8/gems/builder-3.0.0/README.rdoc +232 -0
  27. data/search_biomodel/ruby/1.8/gems/builder-3.0.0/Rakefile +296 -0
  28. data/search_biomodel/ruby/1.8/gems/builder-3.0.0/TAGS +55364 -0
  29. data/search_biomodel/ruby/1.8/gems/builder-3.0.0/lib/blankslate.rb +109 -0
  30. data/search_biomodel/ruby/1.8/gems/builder-3.0.0/lib/builder.rb +13 -0
  31. data/search_biomodel/ruby/1.8/gems/builder-3.0.0/lib/builder/blankslate.rb +23 -0
  32. data/search_biomodel/ruby/1.8/gems/builder-3.0.0/lib/builder/xchar.rb +197 -0
  33. data/search_biomodel/ruby/1.8/gems/builder-3.0.0/lib/builder/xmlbase.rb +160 -0
  34. data/search_biomodel/ruby/1.8/gems/builder-3.0.0/lib/builder/xmlevents.rb +63 -0
  35. data/search_biomodel/ruby/1.8/gems/builder-3.0.0/lib/builder/xmlmarkup.rb +334 -0
  36. data/search_biomodel/ruby/1.8/gems/builder-3.0.0/test/performance.rb +40 -0
  37. data/search_biomodel/ruby/1.8/gems/builder-3.0.0/test/preload.rb +39 -0
  38. data/search_biomodel/ruby/1.8/gems/builder-3.0.0/test/test_blankslate.rb +225 -0
  39. data/search_biomodel/ruby/1.8/gems/builder-3.0.0/test/test_cssbuilder.rb +125 -0
  40. data/search_biomodel/ruby/1.8/gems/builder-3.0.0/test/test_eventbuilder.rb +150 -0
  41. data/search_biomodel/ruby/1.8/gems/builder-3.0.0/test/test_markupbuilder.rb +546 -0
  42. data/search_biomodel/ruby/1.8/gems/builder-3.0.0/test/test_namecollision.rb +39 -0
  43. data/search_biomodel/ruby/1.8/gems/builder-3.0.0/test/test_xchar.rb +77 -0
  44. data/search_biomodel/ruby/1.8/gems/git-1.2.5/README +240 -0
  45. data/search_biomodel/ruby/1.8/gems/git-1.2.5/lib/git.rb +156 -0
  46. data/search_biomodel/ruby/1.8/gems/git-1.2.5/lib/git/author.rb +14 -0
  47. data/search_biomodel/ruby/1.8/gems/git-1.2.5/lib/git/base.rb +479 -0
  48. data/search_biomodel/ruby/1.8/gems/git-1.2.5/lib/git/branch.rb +104 -0
  49. data/search_biomodel/ruby/1.8/gems/git-1.2.5/lib/git/branches.rb +48 -0
  50. data/search_biomodel/ruby/1.8/gems/git-1.2.5/lib/git/diff.rb +146 -0
  51. data/search_biomodel/ruby/1.8/gems/git-1.2.5/lib/git/index.rb +5 -0
  52. data/search_biomodel/ruby/1.8/gems/git-1.2.5/lib/git/lib.rb +719 -0
  53. data/search_biomodel/ruby/1.8/gems/git-1.2.5/lib/git/log.rb +117 -0
  54. data/search_biomodel/ruby/1.8/gems/git-1.2.5/lib/git/object.rb +273 -0
  55. data/search_biomodel/ruby/1.8/gems/git-1.2.5/lib/git/path.rb +27 -0
  56. data/search_biomodel/ruby/1.8/gems/git-1.2.5/lib/git/remote.rb +40 -0
  57. data/search_biomodel/ruby/1.8/gems/git-1.2.5/lib/git/repository.rb +4 -0
  58. data/search_biomodel/ruby/1.8/gems/git-1.2.5/lib/git/stash.rb +27 -0
  59. data/search_biomodel/ruby/1.8/gems/git-1.2.5/lib/git/stashes.rb +44 -0
  60. data/search_biomodel/ruby/1.8/gems/git-1.2.5/lib/git/status.rb +110 -0
  61. data/search_biomodel/ruby/1.8/gems/git-1.2.5/lib/git/working_directory.rb +4 -0
  62. data/search_biomodel/ruby/1.8/gems/gyoku-0.4.4/.gemtest +0 -0
  63. data/search_biomodel/ruby/1.8/gems/gyoku-0.4.4/.gitignore +9 -0
  64. data/search_biomodel/ruby/1.8/gems/gyoku-0.4.4/.rspec +1 -0
  65. data/search_biomodel/ruby/1.8/gems/gyoku-0.4.4/.travis.yml +7 -0
  66. data/search_biomodel/ruby/1.8/gems/gyoku-0.4.4/CHANGELOG.md +55 -0
  67. data/search_biomodel/ruby/1.8/gems/gyoku-0.4.4/Gemfile +2 -0
  68. data/search_biomodel/ruby/1.8/gems/gyoku-0.4.4/LICENSE +20 -0
  69. data/search_biomodel/ruby/1.8/gems/gyoku-0.4.4/README.md +81 -0
  70. data/search_biomodel/ruby/1.8/gems/gyoku-0.4.4/Rakefile +11 -0
  71. data/search_biomodel/ruby/1.8/gems/gyoku-0.4.4/gyoku.gemspec +26 -0
  72. data/search_biomodel/ruby/1.8/gems/gyoku-0.4.4/lib/gyoku.rb +23 -0
  73. data/search_biomodel/ruby/1.8/gems/gyoku-0.4.4/lib/gyoku/array.rb +45 -0
  74. data/search_biomodel/ruby/1.8/gems/gyoku-0.4.4/lib/gyoku/core_ext/string.rb +19 -0
  75. data/search_biomodel/ruby/1.8/gems/gyoku-0.4.4/lib/gyoku/hash.rb +55 -0
  76. data/search_biomodel/ruby/1.8/gems/gyoku-0.4.4/lib/gyoku/version.rb +5 -0
  77. data/search_biomodel/ruby/1.8/gems/gyoku-0.4.4/lib/gyoku/xml_key.rb +63 -0
  78. data/search_biomodel/ruby/1.8/gems/gyoku-0.4.4/lib/gyoku/xml_value.rb +28 -0
  79. data/search_biomodel/ruby/1.8/gems/gyoku-0.4.4/spec/gyoku/array_spec.rb +53 -0
  80. data/search_biomodel/ruby/1.8/gems/gyoku-0.4.4/spec/gyoku/core_ext/string_spec.rb +17 -0
  81. data/search_biomodel/ruby/1.8/gems/gyoku-0.4.4/spec/gyoku/hash_spec.rb +160 -0
  82. data/search_biomodel/ruby/1.8/gems/gyoku-0.4.4/spec/gyoku/xml_key_spec.rb +77 -0
  83. data/search_biomodel/ruby/1.8/gems/gyoku-0.4.4/spec/gyoku/xml_value_spec.rb +49 -0
  84. data/search_biomodel/ruby/1.8/gems/gyoku-0.4.4/spec/gyoku_spec.rb +46 -0
  85. data/search_biomodel/ruby/1.8/gems/gyoku-0.4.4/spec/spec_helper.rb +2 -0
  86. data/search_biomodel/ruby/1.8/gems/httpi-0.9.4/.autotest +5 -0
  87. data/search_biomodel/ruby/1.8/gems/httpi-0.9.4/.gemtest +0 -0
  88. data/search_biomodel/ruby/1.8/gems/httpi-0.9.4/.gitignore +9 -0
  89. data/search_biomodel/ruby/1.8/gems/httpi-0.9.4/.rspec +1 -0
  90. data/search_biomodel/ruby/1.8/gems/httpi-0.9.4/.travis.yml +7 -0
  91. data/search_biomodel/ruby/1.8/gems/httpi-0.9.4/CHANGELOG.md +60 -0
  92. data/search_biomodel/ruby/1.8/gems/httpi-0.9.4/Gemfile +8 -0
  93. data/search_biomodel/ruby/1.8/gems/httpi-0.9.4/LICENSE +20 -0
  94. data/search_biomodel/ruby/1.8/gems/httpi-0.9.4/README.md +223 -0
  95. data/search_biomodel/ruby/1.8/gems/httpi-0.9.4/Rakefile +18 -0
  96. data/search_biomodel/ruby/1.8/gems/httpi-0.9.4/autotest/discover.rb +1 -0
  97. data/search_biomodel/ruby/1.8/gems/httpi-0.9.4/httpi.gemspec +28 -0
  98. data/search_biomodel/ruby/1.8/gems/httpi-0.9.4/lib/httpi.rb +198 -0
  99. data/search_biomodel/ruby/1.8/gems/httpi-0.9.4/lib/httpi/adapter.rb +67 -0
  100. data/search_biomodel/ruby/1.8/gems/httpi-0.9.4/lib/httpi/adapter/curb.rb +125 -0
  101. data/search_biomodel/ruby/1.8/gems/httpi-0.9.4/lib/httpi/adapter/httpclient.rb +98 -0
  102. data/search_biomodel/ruby/1.8/gems/httpi-0.9.4/lib/httpi/adapter/net_http.rb +117 -0
  103. data/search_biomodel/ruby/1.8/gems/httpi-0.9.4/lib/httpi/auth/config.rb +81 -0
  104. data/search_biomodel/ruby/1.8/gems/httpi-0.9.4/lib/httpi/auth/ssl.rb +91 -0
  105. data/search_biomodel/ruby/1.8/gems/httpi-0.9.4/lib/httpi/dime.rb +56 -0
  106. data/search_biomodel/ruby/1.8/gems/httpi-0.9.4/lib/httpi/request.rb +90 -0
  107. data/search_biomodel/ruby/1.8/gems/httpi-0.9.4/lib/httpi/response.rb +85 -0
  108. data/search_biomodel/ruby/1.8/gems/httpi-0.9.4/lib/httpi/version.rb +5 -0
  109. data/search_biomodel/ruby/1.8/gems/httpi-0.9.4/spec/fixtures/attachment.gif +0 -0
  110. data/search_biomodel/ruby/1.8/gems/httpi-0.9.4/spec/fixtures/client_cert.pem +16 -0
  111. data/search_biomodel/ruby/1.8/gems/httpi-0.9.4/spec/fixtures/client_key.pem +15 -0
  112. data/search_biomodel/ruby/1.8/gems/httpi-0.9.4/spec/fixtures/xml.gz +0 -0
  113. data/search_biomodel/ruby/1.8/gems/httpi-0.9.4/spec/fixtures/xml.xml +10 -0
  114. data/search_biomodel/ruby/1.8/gems/httpi-0.9.4/spec/fixtures/xml_dime.dime +0 -0
  115. data/search_biomodel/ruby/1.8/gems/httpi-0.9.4/spec/fixtures/xml_dime.xml +1 -0
  116. data/search_biomodel/ruby/1.8/gems/httpi-0.9.4/spec/httpi/adapter/curb_spec.rb +232 -0
  117. data/search_biomodel/ruby/1.8/gems/httpi-0.9.4/spec/httpi/adapter/httpclient_spec.rb +164 -0
  118. data/search_biomodel/ruby/1.8/gems/httpi-0.9.4/spec/httpi/adapter/net_http_spec.rb +142 -0
  119. data/search_biomodel/ruby/1.8/gems/httpi-0.9.4/spec/httpi/adapter_spec.rb +55 -0
  120. data/search_biomodel/ruby/1.8/gems/httpi-0.9.4/spec/httpi/auth/config_spec.rb +117 -0
  121. data/search_biomodel/ruby/1.8/gems/httpi-0.9.4/spec/httpi/auth/ssl_spec.rb +128 -0
  122. data/search_biomodel/ruby/1.8/gems/httpi-0.9.4/spec/httpi/httpi_spec.rb +284 -0
  123. data/search_biomodel/ruby/1.8/gems/httpi-0.9.4/spec/httpi/request_spec.rb +135 -0
  124. data/search_biomodel/ruby/1.8/gems/httpi-0.9.4/spec/httpi/response_spec.rb +125 -0
  125. data/search_biomodel/ruby/1.8/gems/httpi-0.9.4/spec/integration/request_spec.rb +95 -0
  126. data/search_biomodel/ruby/1.8/gems/httpi-0.9.4/spec/integration/server.rb +39 -0
  127. data/search_biomodel/ruby/1.8/gems/httpi-0.9.4/spec/spec_helper.rb +12 -0
  128. data/search_biomodel/ruby/1.8/gems/httpi-0.9.4/spec/support/fixture.rb +27 -0
  129. data/search_biomodel/ruby/1.8/gems/httpi-0.9.4/spec/support/matchers.rb +19 -0
  130. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/.document +8 -0
  131. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/ChangeLog.markdown +166 -0
  132. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/Gemfile +22 -0
  133. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/Gemfile.lock +59 -0
  134. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/LICENSE.txt +20 -0
  135. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/README.markdown +216 -0
  136. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/Rakefile +81 -0
  137. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/bin/jeweler +5 -0
  138. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/features/generator/cucumber.feature +103 -0
  139. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/features/generator/directory_layout.feature +86 -0
  140. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/features/generator/dotdocument.feature +13 -0
  141. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/features/generator/env_options.feature +9 -0
  142. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/features/generator/gemfile.feature +71 -0
  143. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/features/generator/git.feature +102 -0
  144. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/features/generator/license.feature +20 -0
  145. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/features/generator/rakefile.feature +158 -0
  146. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/features/generator/readme.feature +12 -0
  147. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/features/generator/test.feature +54 -0
  148. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/features/generator/test_helper.feature +149 -0
  149. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/features/placeholder.feature +5 -0
  150. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/features/step_definitions/debug_steps.rb +6 -0
  151. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/features/step_definitions/filesystem_steps.rb +70 -0
  152. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/features/step_definitions/generator_steps.rb +382 -0
  153. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/features/step_definitions/task_steps.rb +6 -0
  154. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/features/support/env.rb +42 -0
  155. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/features/tasks/build_gem.feature +9 -0
  156. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/features/tasks/version.feature +31 -0
  157. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/features/tasks/version_bumping.feature +49 -0
  158. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/jeweler.gemspec +244 -0
  159. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/lib/jeweler.rb +177 -0
  160. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/lib/jeweler/commands.rb +20 -0
  161. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/lib/jeweler/commands/build_gem.rb +36 -0
  162. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/lib/jeweler/commands/check_dependencies.rb +50 -0
  163. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/lib/jeweler/commands/install_gem.rb +31 -0
  164. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/lib/jeweler/commands/release_gemspec.rb +82 -0
  165. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/lib/jeweler/commands/release_to_git.rb +59 -0
  166. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/lib/jeweler/commands/release_to_rubygems.rb +28 -0
  167. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/lib/jeweler/commands/validate_gemspec.rb +30 -0
  168. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/lib/jeweler/commands/version/base.rb +55 -0
  169. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/lib/jeweler/commands/version/bump_major.rb +13 -0
  170. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/lib/jeweler/commands/version/bump_minor.rb +12 -0
  171. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/lib/jeweler/commands/version/bump_patch.rb +14 -0
  172. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/lib/jeweler/commands/version/write.rb +12 -0
  173. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/lib/jeweler/commands/write_gemspec.rb +39 -0
  174. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/lib/jeweler/errors.rb +8 -0
  175. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/lib/jeweler/gemcutter_tasks.rb +8 -0
  176. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/lib/jeweler/gemspec_helper.rb +87 -0
  177. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/lib/jeweler/generator.rb +287 -0
  178. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/lib/jeweler/generator/application.rb +61 -0
  179. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/lib/jeweler/generator/bacon_mixin.rb +43 -0
  180. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/lib/jeweler/generator/github_mixin.rb +29 -0
  181. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/lib/jeweler/generator/micronaut_mixin.rb +41 -0
  182. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/lib/jeweler/generator/minitest_mixin.rb +42 -0
  183. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/lib/jeweler/generator/options.rb +162 -0
  184. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/lib/jeweler/generator/rdoc_mixin.rb +9 -0
  185. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/lib/jeweler/generator/riot_mixin.rb +42 -0
  186. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/lib/jeweler/generator/rspec_mixin.rb +42 -0
  187. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/lib/jeweler/generator/shindo_mixin.rb +44 -0
  188. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/lib/jeweler/generator/shoulda_mixin.rb +42 -0
  189. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/lib/jeweler/generator/testspec_mixin.rb +42 -0
  190. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/lib/jeweler/generator/testunit_mixin.rb +39 -0
  191. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/lib/jeweler/generator/yard_mixin.rb +14 -0
  192. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/lib/jeweler/rubyforge_tasks.rb +95 -0
  193. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/lib/jeweler/rubygems_dot_org_tasks.rb +38 -0
  194. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/lib/jeweler/rubygems_tasks.rb +38 -0
  195. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/lib/jeweler/specification.rb +110 -0
  196. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/lib/jeweler/tasks.rb +224 -0
  197. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/lib/jeweler/templates/.document +5 -0
  198. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/lib/jeweler/templates/.gitignore +48 -0
  199. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/lib/jeweler/templates/Gemfile +12 -0
  200. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/lib/jeweler/templates/LICENSE.txt +20 -0
  201. data/search_biomodel/ruby/1.8/gems/jeweler-1.6.2/lib/jeweler/templates/README.rdoc +19 -0
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  911. data/search_biomodel/ruby/1.8/gems/rake-0.9.2/test/test_rake_task_manager_argument_resolution.rb +36 -0
  912. data/search_biomodel/ruby/1.8/gems/rake-0.9.2/test/test_rake_task_with_arguments.rb +162 -0
  913. data/search_biomodel/ruby/1.8/gems/rake-0.9.2/test/test_rake_test_task.rb +122 -0
  914. data/search_biomodel/ruby/1.8/gems/rake-0.9.2/test/test_rake_top_level_functions.rb +76 -0
  915. data/search_biomodel/ruby/1.8/gems/rake-0.9.2/test/test_rake_win32.rb +83 -0
  916. data/search_biomodel/ruby/1.8/gems/rake-0.9.2/test/test_sys.rb +20 -0
  917. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/BLURB +111 -0
  918. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/LICENSE +53 -0
  919. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/Rakefile +103 -0
  920. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/THANKS +110 -0
  921. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/bin/rcov +522 -0
  922. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/editor-extensions/rcov.el +131 -0
  923. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/editor-extensions/rcov.vim +38 -0
  924. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/ext/rcovrt/1.8/callsite.c +216 -0
  925. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/ext/rcovrt/1.8/rcovrt.c +294 -0
  926. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/ext/rcovrt/1.9/callsite.c +234 -0
  927. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/ext/rcovrt/1.9/rcovrt.c +264 -0
  928. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/ext/rcovrt/Makefile +157 -0
  929. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/ext/rcovrt/callsite.o +0 -0
  930. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/ext/rcovrt/extconf.rb +21 -0
  931. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/ext/rcovrt/rcovrt.o +0 -0
  932. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/ext/rcovrt/rcovrt.so +0 -0
  933. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/lib/rcov.rb +33 -0
  934. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/lib/rcov/call_site_analyzer.rb +225 -0
  935. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/lib/rcov/code_coverage_analyzer.rb +271 -0
  936. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/lib/rcov/coverage_info.rb +36 -0
  937. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/lib/rcov/differential_analyzer.rb +116 -0
  938. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/lib/rcov/file_statistics.rb +355 -0
  939. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/lib/rcov/formatters.rb +13 -0
  940. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/lib/rcov/formatters/base_formatter.rb +174 -0
  941. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/lib/rcov/formatters/failure_report.rb +15 -0
  942. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/lib/rcov/formatters/full_text_report.rb +48 -0
  943. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/lib/rcov/formatters/html_coverage.rb +274 -0
  944. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/lib/rcov/formatters/html_erb_template.rb +62 -0
  945. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/lib/rcov/formatters/text_coverage_diff.rb +193 -0
  946. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/lib/rcov/formatters/text_report.rb +32 -0
  947. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/lib/rcov/formatters/text_summary.rb +11 -0
  948. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/lib/rcov/lowlevel.rb +146 -0
  949. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/lib/rcov/rcovtask.rb +156 -0
  950. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/lib/rcov/templates/detail.html.erb +64 -0
  951. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/lib/rcov/templates/index.html.erb +93 -0
  952. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/lib/rcov/templates/jquery-1.3.2.min.js +19 -0
  953. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/lib/rcov/templates/jquery.tablesorter.min.js +15 -0
  954. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/lib/rcov/templates/print.css +12 -0
  955. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/lib/rcov/templates/rcov.js +42 -0
  956. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/lib/rcov/templates/screen.css +270 -0
  957. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/lib/rcov/version.rb +10 -0
  958. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/lib/rcovrt.so +0 -0
  959. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/setup.rb +1588 -0
  960. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/test/assets/sample_01.rb +7 -0
  961. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/test/assets/sample_02.rb +5 -0
  962. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/test/assets/sample_03.rb +20 -0
  963. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/test/assets/sample_04.rb +10 -0
  964. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/test/assets/sample_05-new.rb +17 -0
  965. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/test/assets/sample_05-old.rb +13 -0
  966. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/test/assets/sample_05.rb +17 -0
  967. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/test/assets/sample_06.rb +8 -0
  968. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/test/call_site_analyzer_test.rb +171 -0
  969. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/test/code_coverage_analyzer_test.rb +220 -0
  970. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/test/expected_coverage/diff-gcc-all.out +7 -0
  971. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/test/expected_coverage/diff-gcc-diff.out +11 -0
  972. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/test/expected_coverage/diff-gcc-original.out +5 -0
  973. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/test/expected_coverage/diff-no-color.out +12 -0
  974. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/test/expected_coverage/diff.out +12 -0
  975. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/test/expected_coverage/gcc-text.out +10 -0
  976. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/test/expected_coverage/sample_03_rb.html +651 -0
  977. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/test/expected_coverage/sample_03_rb.rb +28 -0
  978. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/test/expected_coverage/sample_04_rb.html +641 -0
  979. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/test/file_statistics_test.rb +471 -0
  980. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/test/functional_test.rb +91 -0
  981. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/test/test_helper.rb +4 -0
  982. data/search_biomodel/ruby/1.8/gems/rcov-0.9.9/test/turn_off_rcovrt.rb +4 -0
  983. data/search_biomodel/ruby/1.8/gems/savon-0.9.2/.gitignore +9 -0
  984. data/search_biomodel/ruby/1.8/gems/savon-0.9.2/.rspec +1 -0
  985. data/search_biomodel/ruby/1.8/gems/savon-0.9.2/.travis.yml +7 -0
  986. data/search_biomodel/ruby/1.8/gems/savon-0.9.2/.yardopts +2 -0
  987. data/search_biomodel/ruby/1.8/gems/savon-0.9.2/CHANGELOG.md +533 -0
  988. data/search_biomodel/ruby/1.8/gems/savon-0.9.2/Gemfile +4 -0
  989. data/search_biomodel/ruby/1.8/gems/savon-0.9.2/LICENSE +20 -0
  990. data/search_biomodel/ruby/1.8/gems/savon-0.9.2/README.md +39 -0
  991. data/search_biomodel/ruby/1.8/gems/savon-0.9.2/Rakefile +40 -0
  992. data/search_biomodel/ruby/1.8/gems/savon-0.9.2/lib/savon.rb +14 -0
  993. data/search_biomodel/ruby/1.8/gems/savon-0.9.2/lib/savon/client.rb +161 -0
  994. data/search_biomodel/ruby/1.8/gems/savon-0.9.2/lib/savon/core_ext/hash.rb +70 -0
  995. data/search_biomodel/ruby/1.8/gems/savon-0.9.2/lib/savon/core_ext/object.rb +14 -0
  996. data/search_biomodel/ruby/1.8/gems/savon-0.9.2/lib/savon/core_ext/string.rb +51 -0
  997. data/search_biomodel/ruby/1.8/gems/savon-0.9.2/lib/savon/core_ext/time.rb +22 -0
  998. data/search_biomodel/ruby/1.8/gems/savon-0.9.2/lib/savon/error.rb +6 -0
  999. data/search_biomodel/ruby/1.8/gems/savon-0.9.2/lib/savon/global.rb +83 -0
  1000. data/search_biomodel/ruby/1.8/gems/savon-0.9.2/lib/savon/http/error.rb +42 -0
  1001. data/search_biomodel/ruby/1.8/gems/savon-0.9.2/lib/savon/soap.rb +24 -0
  1002. data/search_biomodel/ruby/1.8/gems/savon-0.9.2/lib/savon/soap/fault.rb +59 -0
  1003. data/search_biomodel/ruby/1.8/gems/savon-0.9.2/lib/savon/soap/request.rb +61 -0
  1004. data/search_biomodel/ruby/1.8/gems/savon-0.9.2/lib/savon/soap/response.rb +85 -0
  1005. data/search_biomodel/ruby/1.8/gems/savon-0.9.2/lib/savon/soap/xml.rb +184 -0
  1006. data/search_biomodel/ruby/1.8/gems/savon-0.9.2/lib/savon/version.rb +5 -0
  1007. data/search_biomodel/ruby/1.8/gems/savon-0.9.2/lib/savon/wsdl/document.rb +112 -0
  1008. data/search_biomodel/ruby/1.8/gems/savon-0.9.2/lib/savon/wsdl/parser.rb +96 -0
  1009. data/search_biomodel/ruby/1.8/gems/savon-0.9.2/lib/savon/wsdl/request.rb +35 -0
  1010. data/search_biomodel/ruby/1.8/gems/savon-0.9.2/lib/savon/wsse.rb +156 -0
  1011. data/search_biomodel/ruby/1.8/gems/savon-0.9.2/savon.gemspec +30 -0
  1012. data/search_biomodel/ruby/1.8/gems/savon-0.9.2/spec/fixtures/gzip/message.gz +0 -0
  1013. data/search_biomodel/ruby/1.8/gems/savon-0.9.2/spec/fixtures/response/another_soap_fault.xml +14 -0
  1014. data/search_biomodel/ruby/1.8/gems/savon-0.9.2/spec/fixtures/response/authentication.xml +14 -0
  1015. data/search_biomodel/ruby/1.8/gems/savon-0.9.2/spec/fixtures/response/header.xml +13 -0
  1016. data/search_biomodel/ruby/1.8/gems/savon-0.9.2/spec/fixtures/response/list.xml +18 -0
  1017. data/search_biomodel/ruby/1.8/gems/savon-0.9.2/spec/fixtures/response/multi_ref.xml +39 -0
  1018. data/search_biomodel/ruby/1.8/gems/savon-0.9.2/spec/fixtures/response/soap_fault.xml +8 -0
  1019. data/search_biomodel/ruby/1.8/gems/savon-0.9.2/spec/fixtures/response/soap_fault12.xml +18 -0
  1020. data/search_biomodel/ruby/1.8/gems/savon-0.9.2/spec/fixtures/wsdl/authentication.xml +63 -0
  1021. data/search_biomodel/ruby/1.8/gems/savon-0.9.2/spec/fixtures/wsdl/geotrust.xml +156 -0
  1022. data/search_biomodel/ruby/1.8/gems/savon-0.9.2/spec/fixtures/wsdl/namespaced_actions.xml +307 -0
  1023. data/search_biomodel/ruby/1.8/gems/savon-0.9.2/spec/fixtures/wsdl/no_namespace.xml +115 -0
  1024. data/search_biomodel/ruby/1.8/gems/savon-0.9.2/spec/fixtures/wsdl/soap12.xml +11 -0
  1025. data/search_biomodel/ruby/1.8/gems/savon-0.9.2/spec/fixtures/wsdl/two_bindings.xml +25 -0
  1026. data/search_biomodel/ruby/1.8/gems/savon-0.9.2/spec/savon/client_spec.rb +354 -0
  1027. data/search_biomodel/ruby/1.8/gems/savon-0.9.2/spec/savon/core_ext/hash_spec.rb +121 -0
  1028. data/search_biomodel/ruby/1.8/gems/savon-0.9.2/spec/savon/core_ext/object_spec.rb +19 -0
  1029. data/search_biomodel/ruby/1.8/gems/savon-0.9.2/spec/savon/core_ext/string_spec.rb +57 -0
  1030. data/search_biomodel/ruby/1.8/gems/savon-0.9.2/spec/savon/core_ext/time_spec.rb +13 -0
  1031. data/search_biomodel/ruby/1.8/gems/savon-0.9.2/spec/savon/http/error_spec.rb +52 -0
  1032. data/search_biomodel/ruby/1.8/gems/savon-0.9.2/spec/savon/savon_spec.rb +85 -0
  1033. data/search_biomodel/ruby/1.8/gems/savon-0.9.2/spec/savon/soap/fault_spec.rb +89 -0
  1034. data/search_biomodel/ruby/1.8/gems/savon-0.9.2/spec/savon/soap/request_spec.rb +45 -0
  1035. data/search_biomodel/ruby/1.8/gems/savon-0.9.2/spec/savon/soap/response_spec.rb +181 -0
  1036. data/search_biomodel/ruby/1.8/gems/savon-0.9.2/spec/savon/soap/xml_spec.rb +341 -0
  1037. data/search_biomodel/ruby/1.8/gems/savon-0.9.2/spec/savon/soap_spec.rb +21 -0
  1038. data/search_biomodel/ruby/1.8/gems/savon-0.9.2/spec/savon/wsdl/document_spec.rb +132 -0
  1039. data/search_biomodel/ruby/1.8/gems/savon-0.9.2/spec/savon/wsdl/parser_spec.rb +107 -0
  1040. data/search_biomodel/ruby/1.8/gems/savon-0.9.2/spec/savon/wsdl/request_spec.rb +15 -0
  1041. data/search_biomodel/ruby/1.8/gems/savon-0.9.2/spec/savon/wsse_spec.rb +232 -0
  1042. data/search_biomodel/ruby/1.8/gems/savon-0.9.2/spec/spec_helper.rb +14 -0
  1043. data/search_biomodel/ruby/1.8/gems/savon-0.9.2/spec/support/endpoint.rb +25 -0
  1044. data/search_biomodel/ruby/1.8/gems/savon-0.9.2/spec/support/fixture.rb +37 -0
  1045. data/search_biomodel/ruby/1.8/specifications/builder-3.0.0.gemspec +36 -0
  1046. data/search_biomodel/ruby/1.8/specifications/git-1.2.5.gemspec +30 -0
  1047. data/search_biomodel/ruby/1.8/specifications/gyoku-0.4.4.gemspec +41 -0
  1048. data/search_biomodel/ruby/1.8/specifications/httpi-0.9.4.gemspec +49 -0
  1049. data/search_biomodel/ruby/1.8/specifications/jeweler-1.6.2.gemspec +79 -0
  1050. data/search_biomodel/ruby/1.8/specifications/nokogiri-1.4.6.gemspec +53 -0
  1051. data/search_biomodel/ruby/1.8/specifications/nori-1.0.1.gemspec +38 -0
  1052. data/search_biomodel/ruby/1.8/specifications/pyu-ntlm-http-0.1.3.1.gemspec +31 -0
  1053. data/search_biomodel/ruby/1.8/specifications/rack-1.3.0.gemspec +57 -0
  1054. data/search_biomodel/ruby/1.8/specifications/rake-0.9.2.gemspec +43 -0
  1055. data/search_biomodel/ruby/1.8/specifications/rcov-0.9.9.gemspec +34 -0
  1056. data/search_biomodel/ruby/1.8/specifications/savon-0.9.2.gemspec +55 -0
  1057. data/test/test_search_biomodel.rb +29 -4
  1058. metadata +1071 -36
  1059. data/test.rb +0 -1
@@ -0,0 +1,191 @@
1
+ # -*- ruby -*-
2
+
3
+ require 'rubygems'
4
+ gem 'hoe', '>= 2.1.0'
5
+ require 'hoe'
6
+
7
+ windows = RUBY_PLATFORM =~ /(mswin|mingw)/i
8
+ java = RUBY_PLATFORM =~ /java/
9
+
10
+ GENERATED_PARSER = "lib/nokogiri/css/parser.rb"
11
+ GENERATED_TOKENIZER = "lib/nokogiri/css/tokenizer.rb"
12
+ CROSS_DIR = File.join(File.dirname(__FILE__), 'tmp', 'cross')
13
+
14
+ # Make sure hoe-debugging is installed
15
+ Hoe.plugin :debugging
16
+ Hoe.plugin :git
17
+
18
+ HOE = Hoe.spec 'nokogiri' do
19
+ developer('Aaron Patterson', 'aaronp@rubyforge.org')
20
+ developer('Mike Dalessio', 'mike.dalessio@gmail.com')
21
+ self.readme_file = ['README', ENV['HLANG'], 'rdoc'].compact.join('.')
22
+ self.history_file = ['CHANGELOG', ENV['HLANG'], 'rdoc'].compact.join('.')
23
+ self.extra_rdoc_files = FileList['*.rdoc','ext/nokogiri/*.c']
24
+ self.clean_globs = [
25
+ "ext/nokogiri/*.dll",
26
+ 'lib/nokogiri/*.{o,so,bundle,a,log,dll}',
27
+ 'lib/nokogiri/nokogiri.rb',
28
+ 'lib/nokogiri/1.{8,9}',
29
+ GENERATED_PARSER,
30
+ GENERATED_TOKENIZER,
31
+ CROSS_DIR
32
+ ]
33
+
34
+ %w{ racc rexical rake-compiler }.each do |dep|
35
+ extra_dev_deps << [dep, '>= 0']
36
+ end
37
+ extra_dev_deps << ["minitest", ">= 1.6.0"]
38
+
39
+ self.spec_extras = { :extensions => ["ext/nokogiri/extconf.rb"] }
40
+
41
+ self.testlib = :minitest
42
+ end
43
+ Hoe.add_include_dirs '.'
44
+
45
+ task :ws_docs do
46
+ title = "#{HOE.name}-#{HOE.version} Documentation"
47
+
48
+ options = []
49
+ options << "--main=#{HOE.readme_file}"
50
+ options << '--format=activerecord'
51
+ options << '--threads=1'
52
+ options << "--title=#{title.inspect}"
53
+
54
+ options += HOE.spec.require_paths
55
+ options += HOE.spec.extra_rdoc_files
56
+ require 'rdoc/rdoc'
57
+ ENV['RAILS_ROOT'] ||= File.expand_path(File.join('..', 'nokogiri_ws'))
58
+ RDoc::RDoc.new.document options
59
+ end
60
+
61
+ unless java
62
+ gem 'rake-compiler', '>= 0.4.1'
63
+ require "rake/extensiontask"
64
+
65
+ RET = Rake::ExtensionTask.new("nokogiri", HOE.spec) do |ext|
66
+ ext.lib_dir = File.join(*['lib', 'nokogiri', ENV['FAT_DIR']].compact)
67
+
68
+ ext.config_options << ENV['EXTOPTS']
69
+ ext.cross_compile = true
70
+ ext.cross_platform = ["x86-mingw32", "x86-mswin32-60"]
71
+ ext.cross_config_options <<
72
+ "--with-xml2-include=#{File.join(CROSS_DIR, 'include', 'libxml2')}"
73
+ ext.cross_config_options <<
74
+ "--with-xml2-lib=#{File.join(CROSS_DIR, 'lib')}"
75
+ ext.cross_config_options << "--with-iconv-dir=#{CROSS_DIR}"
76
+ ext.cross_config_options << "--with-xslt-dir=#{CROSS_DIR}"
77
+ ext.cross_config_options << "--with-zlib-dir=#{CROSS_DIR}"
78
+ end
79
+ end
80
+
81
+ namespace :gem do
82
+ namespace :dev do
83
+ task :spec => [ GENERATED_PARSER, GENERATED_TOKENIZER ] do
84
+ File.open("#{HOE.name}.gemspec", 'w') do |f|
85
+ HOE.spec.version = "#{HOE.version}.#{Time.now.strftime("%Y%m%d%H%M%S")}"
86
+ f.write(HOE.spec.to_ruby)
87
+ end
88
+ end
89
+ end
90
+
91
+ desc "Build a gem targetted for JRuby"
92
+ task :jruby => ['gem:jruby:spec'] do
93
+ raise "ERROR: please run this task under jruby" unless java
94
+ system "gem build nokogiri.gemspec"
95
+ FileUtils.mkdir_p "pkg"
96
+ FileUtils.mv Dir.glob("nokogiri*-java.gem"), "pkg"
97
+ end
98
+
99
+ namespace :jruby do
100
+ task :spec => [GENERATED_PARSER, GENERATED_TOKENIZER, :"gem:jruby:dlls"] do
101
+ File.open("#{HOE.name}.gemspec", 'w') do |f|
102
+ HOE.spec.platform = 'java'
103
+ HOE.spec.files << GENERATED_PARSER
104
+ HOE.spec.files << GENERATED_TOKENIZER
105
+ HOE.spec.files += Dir["ext/nokogiri/*.dll"]
106
+ HOE.spec.extensions = []
107
+ HOE.spec.add_dependency 'weakling', '>= 0.0.3'
108
+ f.write(HOE.spec.to_ruby)
109
+ end
110
+ end
111
+
112
+ task :dlls do
113
+ def run cmd
114
+ puts(cmd) || system(cmd) || raise("command failed")
115
+ end
116
+
117
+ dlldir = "tmp/dlls"
118
+ FileUtils.mkdir_p dlldir
119
+ Dir.chdir dlldir do
120
+ unless File.exists? "nokogiri-1.4.3.1-java.gem"
121
+ run "wget http://rubygems.org/downloads/nokogiri-1.4.3.1-java.gem"
122
+ end
123
+ unless File.exists? "data.tar.gz"
124
+ run "tar -xf nokogiri-1.4.3.1-java.gem"
125
+ end
126
+ FileUtils.rm_rf "unpack"
127
+ FileUtils.mkdir "unpack"
128
+ Dir.chdir "unpack" do
129
+ run "tar -zxf ../data.tar.gz"
130
+ end
131
+ end
132
+
133
+ Dir["#{dlldir}/unpack/ext/nokogiri/*.dll"].each do |file|
134
+ cp file, "ext/nokogiri"
135
+ end
136
+ end
137
+ end
138
+
139
+ task :spec => ['gem:dev:spec']
140
+ end
141
+
142
+ file GENERATED_PARSER => "lib/nokogiri/css/parser.y" do |t|
143
+ racc = Config::CONFIG['target_os'] =~ /mswin32/ ? '' : `which racc`.strip
144
+ racc = "#{::Config::CONFIG['bindir']}/racc" if racc.empty?
145
+ sh "#{racc} -l -o #{t.name} #{t.prerequisites.first}"
146
+ end
147
+
148
+ file GENERATED_TOKENIZER => "lib/nokogiri/css/tokenizer.rex" do |t|
149
+ sh "rex --independent -o #{t.name} #{t.prerequisites.first}"
150
+ end
151
+
152
+ require 'tasks/test'
153
+ begin
154
+ require 'tasks/cross_compile' unless java
155
+ rescue RuntimeError => e
156
+ warn "WARNING: Could not perform some cross-compiling: #{e}"
157
+ end
158
+
159
+ desc "set environment variables to build and/or test with debug options"
160
+ task :debug do
161
+ ENV['NOKOGIRI_DEBUG'] = "true"
162
+ ENV['CFLAGS'] ||= ""
163
+ ENV['CFLAGS'] += " -DDEBUG"
164
+ end
165
+
166
+ # required_ruby_version
167
+
168
+ # Only do this on unix, since we can't build on windows
169
+ unless windows || java || ENV['NOKOGIRI_FFI']
170
+ [:compile, :check_manifest].each do |task_name|
171
+ Rake::Task[task_name].prerequisites << GENERATED_PARSER
172
+ Rake::Task[task_name].prerequisites << GENERATED_TOKENIZER
173
+ end
174
+
175
+ Rake::Task[:test].prerequisites << :compile
176
+ Rake::Task[:test].prerequisites << :check_extra_deps
177
+ if Hoe.plugins.include?(:debugging)
178
+ ['valgrind', 'valgrind:mem', 'valgrind:mem0'].each do |task_name|
179
+ Rake::Task["test:#{task_name}"].prerequisites << :compile
180
+ end
181
+ end
182
+ else
183
+ [:test, :check_manifest].each do |task_name|
184
+ if Rake::Task[task_name]
185
+ Rake::Task[task_name].prerequisites << GENERATED_PARSER
186
+ Rake::Task[task_name].prerequisites << GENERATED_TOKENIZER
187
+ end
188
+ end
189
+ end
190
+
191
+ # vim: syntax=Ruby
@@ -0,0 +1,54 @@
1
+ #!/usr/bin/env ruby
2
+ require 'optparse'
3
+ require 'open-uri'
4
+ require 'irb'
5
+ require 'uri'
6
+ require 'rubygems'
7
+ require 'nokogiri'
8
+
9
+ parse_class = Nokogiri
10
+ encoding = nil
11
+
12
+ opts = OptionParser.new do |opts|
13
+ opts.banner = "Nokogiri: an HTML, XML, SAX, and Reader parser"
14
+ opts.define_head "Usage: nokogiri <uri|path> [options]"
15
+ opts.separator ""
16
+ opts.separator "Examples:"
17
+ opts.separator " nokogiri http://www.ruby-lang.org/"
18
+ opts.separator " nokogiri ./public/index.html"
19
+ opts.separator ""
20
+ opts.separator "Options:"
21
+
22
+ opts.on("--type [TYPE]", [:xml, :html]) do |v|
23
+ parse_class = {:xml => Nokogiri::XML, :html => Nokogiri::HTML}[v]
24
+ end
25
+
26
+ opts.on("-E", "--encoding encoding", "Read as encoding (default #{encoding})") do |v|
27
+ encoding = v
28
+ end
29
+
30
+ opts.on_tail("-?", "--help", "Show this message") do
31
+ puts opts
32
+ exit
33
+ end
34
+
35
+ opts.on_tail("-v", "--version", "Show version") do
36
+ require 'yaml'
37
+ puts Nokogiri::VERSION_INFO.to_yaml
38
+ exit
39
+ end
40
+ end
41
+ opts.parse!
42
+
43
+ uri = ARGV.shift
44
+
45
+ if uri.to_s.strip.empty?
46
+ puts opts
47
+ exit 1
48
+ end
49
+
50
+ @doc = parse_class.parse(open(uri).read, nil, encoding)
51
+
52
+ puts "Your document is stored in @doc..."
53
+ IRB.start
54
+
@@ -0,0 +1,515 @@
1
+
2
+ SHELL = /bin/sh
3
+
4
+ #### Start of system configuration section. ####
5
+
6
+ srcdir = .
7
+ topdir = /usr/lib/ruby/1.8/x86_64-linux
8
+ hdrdir = $(topdir)
9
+ VPATH = $(srcdir):$(topdir):$(hdrdir)
10
+ exec_prefix = $(prefix)
11
+ prefix = $(DESTDIR)/usr
12
+ sharedstatedir = $(prefix)/com
13
+ mandir = $(prefix)/share/man
14
+ psdir = $(docdir)
15
+ oldincludedir = $(DESTDIR)/usr/include
16
+ localedir = $(datarootdir)/locale
17
+ bindir = $(exec_prefix)/bin
18
+ libexecdir = $(prefix)/lib/ruby1.8
19
+ sitedir = $(DESTDIR)/usr/local/lib/site_ruby
20
+ htmldir = $(docdir)
21
+ vendorarchdir = $(vendorlibdir)/$(sitearch)
22
+ includedir = $(prefix)/include
23
+ infodir = $(prefix)/share/info
24
+ vendorlibdir = $(vendordir)/$(ruby_version)
25
+ sysconfdir = $(DESTDIR)/etc
26
+ libdir = $(exec_prefix)/lib
27
+ sbindir = $(exec_prefix)/sbin
28
+ rubylibdir = $(libdir)/ruby/$(ruby_version)
29
+ docdir = $(datarootdir)/doc/$(PACKAGE)
30
+ dvidir = $(docdir)
31
+ vendordir = $(libdir)/ruby/vendor_ruby
32
+ datarootdir = $(prefix)/share
33
+ pdfdir = $(docdir)
34
+ archdir = $(rubylibdir)/$(arch)
35
+ sitearchdir = $(sitelibdir)/$(sitearch)
36
+ datadir = $(datarootdir)
37
+ localstatedir = $(DESTDIR)/var
38
+ sitelibdir = $(sitedir)/$(ruby_version)
39
+
40
+ CC = gcc
41
+ LIBRUBY = $(LIBRUBY_SO)
42
+ LIBRUBY_A = lib$(RUBY_SO_NAME)-static.a
43
+ LIBRUBYARG_SHARED = -l$(RUBY_SO_NAME)
44
+ LIBRUBYARG_STATIC = -l$(RUBY_SO_NAME)-static
45
+
46
+ RUBY_EXTCONF_H =
47
+ CFLAGS = -fPIC -fno-strict-aliasing -g -g -O2 -fPIC $(cflags) -g -DXP_UNIX -O3 -Wall -Wcast-qual -Wwrite-strings -Wconversion -Wmissing-noreturn -Winline
48
+ INCFLAGS = -I. -I. -I/usr/lib/ruby/1.8/x86_64-linux -I.
49
+ DEFS =
50
+ CPPFLAGS = -DHAVE_ICONV_OPEN -DHAVE_XMLFIRSTELEMENTCHILD -DHAVE_XMLRELAXNGSETPARSERSTRUCTUREDERRORS -DHAVE_XMLRELAXNGSETPARSERSTRUCTUREDERRORS -DHAVE_XMLRELAXNGSETVALIDSTRUCTUREDERRORS -DHAVE_XMLSCHEMASETVALIDSTRUCTUREDERRORS -DHAVE_XMLSCHEMASETPARSERSTRUCTUREDERRORS -I-I-I/opt/local/include -I-I-I/usr/local/include -I-I-I/usr/include -I-I-I/usr/include -I-I-I/usr/include/libxml2 -I/opt/local/include/libxml2 -I/usr/local/include/libxml2 -I-I/opt/local/include -I-I/usr/local/include -I-I/usr/include -I-I/usr/include -I-I/usr/include/libxml2 -I/opt/local/include -I/usr/local/include -I/usr/include -I/usr/include -I/usr/include/libxml2
51
+ CXXFLAGS = $(CFLAGS)
52
+ ldflags = -L. -Wl,-Bsymbolic-functions -rdynamic -Wl,-export-dynamic
53
+ dldflags =
54
+ archflag =
55
+ DLDFLAGS = $(ldflags) $(dldflags) $(archflag)
56
+ LDSHARED = $(CC) -shared
57
+ AR = ar
58
+ EXEEXT =
59
+
60
+ RUBY_INSTALL_NAME = ruby1.8
61
+ RUBY_SO_NAME = ruby1.8
62
+ arch = x86_64-linux
63
+ sitearch = x86_64-linux
64
+ ruby_version = 1.8
65
+ ruby = /usr/bin/ruby1.8
66
+ RUBY = $(ruby)
67
+ RM = rm -f
68
+ MAKEDIRS = mkdir -p
69
+ INSTALL = /usr/bin/install -c
70
+ INSTALL_PROG = $(INSTALL) -m 0755
71
+ INSTALL_DATA = $(INSTALL) -m 644
72
+ COPY = cp
73
+
74
+ #### End of system configuration section. ####
75
+
76
+ preload =
77
+
78
+ libpath = . $(libdir) /opt/local/lib /usr/local/lib /usr/lib
79
+ LIBPATH = -L. -L$(libdir) -L/opt/local/lib -L/usr/local/lib -L/usr/lib
80
+ DEFFILE =
81
+
82
+ CLEANFILES = mkmf.log
83
+ DISTCLEANFILES =
84
+
85
+ extout =
86
+ extout_prefix =
87
+ target_prefix = /nokogiri
88
+ LOCAL_LIBS =
89
+ LIBS = $(LIBRUBYARG_SHARED) -lexslt -lxslt -lxml2 -lpthread -lrt -ldl -lcrypt -lm -lc
90
+ SRCS = xml_relax_ng.c xml_entity_reference.c xml_entity_decl.c xml_cdata.c xml_encoding_handler.c xml_node.c xml_node_set.c xml_dtd.c html_entity_lookup.c html_sax_parser_context.c xml_xpath_context.c xml_libxml2_hacks.c xml_text.c xml_element_decl.c xml_reader.c xml_attribute_decl.c xml_sax_parser_context.c xslt_stylesheet.c xml_schema.c html_document.c xml_namespace.c html_element_description.c xml_processing_instruction.c xml_io.c nokogiri.c xml_attr.c xml_sax_parser.c xml_element_content.c xml_comment.c xml_syntax_error.c xml_document.c xml_document_fragment.c xml_sax_push_parser.c
91
+ OBJS = xml_relax_ng.o xml_entity_reference.o xml_entity_decl.o xml_cdata.o xml_encoding_handler.o xml_node.o xml_node_set.o xml_dtd.o html_entity_lookup.o html_sax_parser_context.o xml_xpath_context.o xml_libxml2_hacks.o xml_text.o xml_element_decl.o xml_reader.o xml_attribute_decl.o xml_sax_parser_context.o xslt_stylesheet.o xml_schema.o html_document.o xml_namespace.o html_element_description.o xml_processing_instruction.o xml_io.o nokogiri.o xml_attr.o xml_sax_parser.o xml_element_content.o xml_comment.o xml_syntax_error.o xml_document.o xml_document_fragment.o xml_sax_push_parser.o
92
+ TARGET = nokogiri
93
+ DLLIB = $(TARGET).so
94
+ EXTSTATIC =
95
+ STATIC_LIB =
96
+
97
+ BINDIR = $(bindir)
98
+ RUBYCOMMONDIR = $(sitedir)$(target_prefix)
99
+ RUBYLIBDIR = /home/cspc018/Work/Repos/gems/search_biomodel/search_biomodel/ruby/1.8/gems/nokogiri-1.4.6/lib$(target_prefix)
100
+ RUBYARCHDIR = /home/cspc018/Work/Repos/gems/search_biomodel/search_biomodel/ruby/1.8/gems/nokogiri-1.4.6/lib$(target_prefix)
101
+
102
+ TARGET_SO = $(DLLIB)
103
+ CLEANLIBS = $(TARGET).so $(TARGET).il? $(TARGET).tds $(TARGET).map
104
+ CLEANOBJS = *.o *.a *.s[ol] *.pdb *.exp *.bak
105
+
106
+ all: $(DLLIB)
107
+ static: $(STATIC_LIB)
108
+
109
+ clean:
110
+ @-$(RM) $(CLEANLIBS) $(CLEANOBJS) $(CLEANFILES)
111
+
112
+ distclean: clean
113
+ @-$(RM) Makefile $(RUBY_EXTCONF_H) conftest.* mkmf.log
114
+ @-$(RM) core ruby$(EXEEXT) *~ $(DISTCLEANFILES)
115
+
116
+ realclean: distclean
117
+ install: install-so install-rb
118
+
119
+ install-so: $(RUBYARCHDIR)
120
+ install-so: $(RUBYARCHDIR)/$(DLLIB)
121
+ $(RUBYARCHDIR)/$(DLLIB): $(DLLIB)
122
+ $(INSTALL_PROG) $(DLLIB) $(RUBYARCHDIR)
123
+ install-rb: pre-install-rb install-rb-default
124
+ install-rb-default: pre-install-rb-default
125
+ pre-install-rb: Makefile
126
+ pre-install-rb-default: Makefile
127
+ $(RUBYARCHDIR):
128
+ $(MAKEDIRS) $@
129
+
130
+ site-install: site-install-so site-install-rb
131
+ site-install-so: install-so
132
+ site-install-rb: install-rb
133
+
134
+ .SUFFIXES: .c .m .cc .cxx .cpp .C .o
135
+
136
+ .cc.o:
137
+ $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) -c $<
138
+
139
+ .cxx.o:
140
+ $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) -c $<
141
+
142
+ .cpp.o:
143
+ $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) -c $<
144
+
145
+ .C.o:
146
+ $(CXX) $(INCFLAGS) $(CPPFLAGS) $(CXXFLAGS) -c $<
147
+
148
+ .c.o:
149
+ $(CC) $(INCFLAGS) $(CPPFLAGS) $(CFLAGS) -c $<
150
+
151
+ $(DLLIB): $(OBJS) Makefile
152
+ @-$(RM) $@
153
+ $(LDSHARED) -o $@ $(OBJS) $(LIBPATH) $(DLDFLAGS) $(LOCAL_LIBS) $(LIBS)
154
+
155
+
156
+
157
+ ###
158
+ html_document.o: html_document.c html_document.h nokogiri.h xml_io.h \
159
+ xml_document.h html_entity_lookup.h xml_node.h xml_text.h \
160
+ xml_cdata.h xml_attr.h xml_processing_instruction.h \
161
+ xml_entity_reference.h xml_document_fragment.h xml_comment.h \
162
+ xml_node_set.h xml_dtd.h xml_attribute_decl.h xml_element_decl.h \
163
+ xml_entity_decl.h xml_xpath_context.h xml_element_content.h \
164
+ xml_sax_parser_context.h xml_sax_parser.h xml_sax_push_parser.h \
165
+ xml_reader.h html_sax_parser_context.h xslt_stylesheet.h \
166
+ xml_syntax_error.h xml_schema.h xml_relax_ng.h \
167
+ html_element_description.h xml_namespace.h xml_encoding_handler.h
168
+
169
+ html_element_description.o: html_element_description.c \
170
+ html_element_description.h nokogiri.h xml_io.h xml_document.h \
171
+ html_entity_lookup.h html_document.h xml_node.h xml_text.h \
172
+ xml_cdata.h xml_attr.h xml_processing_instruction.h \
173
+ xml_entity_reference.h xml_document_fragment.h xml_comment.h \
174
+ xml_node_set.h xml_dtd.h xml_attribute_decl.h xml_element_decl.h \
175
+ xml_entity_decl.h xml_xpath_context.h xml_element_content.h \
176
+ xml_sax_parser_context.h xml_sax_parser.h xml_sax_push_parser.h \
177
+ xml_reader.h html_sax_parser_context.h xslt_stylesheet.h \
178
+ xml_syntax_error.h xml_schema.h xml_relax_ng.h xml_namespace.h \
179
+ xml_encoding_handler.h
180
+
181
+ html_entity_lookup.o: html_entity_lookup.c html_entity_lookup.h \
182
+ nokogiri.h xml_io.h xml_document.h html_document.h xml_node.h \
183
+ xml_text.h xml_cdata.h xml_attr.h xml_processing_instruction.h \
184
+ xml_entity_reference.h xml_document_fragment.h xml_comment.h \
185
+ xml_node_set.h xml_dtd.h xml_attribute_decl.h xml_element_decl.h \
186
+ xml_entity_decl.h xml_xpath_context.h xml_element_content.h \
187
+ xml_sax_parser_context.h xml_sax_parser.h xml_sax_push_parser.h \
188
+ xml_reader.h html_sax_parser_context.h xslt_stylesheet.h \
189
+ xml_syntax_error.h xml_schema.h xml_relax_ng.h \
190
+ html_element_description.h xml_namespace.h xml_encoding_handler.h
191
+
192
+ html_sax_parser_context.o: html_sax_parser_context.c \
193
+ html_sax_parser_context.h nokogiri.h xml_io.h xml_document.h \
194
+ html_entity_lookup.h html_document.h xml_node.h xml_text.h \
195
+ xml_cdata.h xml_attr.h xml_processing_instruction.h \
196
+ xml_entity_reference.h xml_document_fragment.h xml_comment.h \
197
+ xml_node_set.h xml_dtd.h xml_attribute_decl.h xml_element_decl.h \
198
+ xml_entity_decl.h xml_xpath_context.h xml_element_content.h \
199
+ xml_sax_parser_context.h xml_sax_parser.h xml_sax_push_parser.h \
200
+ xml_reader.h xslt_stylesheet.h xml_syntax_error.h xml_schema.h \
201
+ xml_relax_ng.h html_element_description.h xml_namespace.h \
202
+ xml_encoding_handler.h
203
+
204
+ nokogiri.o: nokogiri.c nokogiri.h xml_io.h xml_document.h \
205
+ html_entity_lookup.h html_document.h xml_node.h xml_text.h \
206
+ xml_cdata.h xml_attr.h xml_processing_instruction.h \
207
+ xml_entity_reference.h xml_document_fragment.h xml_comment.h \
208
+ xml_node_set.h xml_dtd.h xml_attribute_decl.h xml_element_decl.h \
209
+ xml_entity_decl.h xml_xpath_context.h xml_element_content.h \
210
+ xml_sax_parser_context.h xml_sax_parser.h xml_sax_push_parser.h \
211
+ xml_reader.h html_sax_parser_context.h xslt_stylesheet.h \
212
+ xml_syntax_error.h xml_schema.h xml_relax_ng.h \
213
+ html_element_description.h xml_namespace.h xml_encoding_handler.h
214
+
215
+ xml_attr.o: xml_attr.c xml_attr.h nokogiri.h xml_io.h xml_document.h \
216
+ html_entity_lookup.h html_document.h xml_node.h xml_text.h \
217
+ xml_cdata.h xml_processing_instruction.h xml_entity_reference.h \
218
+ xml_document_fragment.h xml_comment.h xml_node_set.h xml_dtd.h \
219
+ xml_attribute_decl.h xml_element_decl.h xml_entity_decl.h \
220
+ xml_xpath_context.h xml_element_content.h xml_sax_parser_context.h \
221
+ xml_sax_parser.h xml_sax_push_parser.h xml_reader.h \
222
+ html_sax_parser_context.h xslt_stylesheet.h xml_syntax_error.h \
223
+ xml_schema.h xml_relax_ng.h html_element_description.h \
224
+ xml_namespace.h xml_encoding_handler.h
225
+
226
+ xml_attribute_decl.o: xml_attribute_decl.c xml_attribute_decl.h \
227
+ nokogiri.h xml_io.h xml_document.h html_entity_lookup.h \
228
+ html_document.h xml_node.h xml_text.h xml_cdata.h xml_attr.h \
229
+ xml_processing_instruction.h xml_entity_reference.h \
230
+ xml_document_fragment.h xml_comment.h xml_node_set.h xml_dtd.h \
231
+ xml_element_decl.h xml_entity_decl.h xml_xpath_context.h \
232
+ xml_element_content.h xml_sax_parser_context.h xml_sax_parser.h \
233
+ xml_sax_push_parser.h xml_reader.h html_sax_parser_context.h \
234
+ xslt_stylesheet.h xml_syntax_error.h xml_schema.h xml_relax_ng.h \
235
+ html_element_description.h xml_namespace.h xml_encoding_handler.h
236
+
237
+ xml_cdata.o: xml_cdata.c xml_cdata.h nokogiri.h xml_io.h \
238
+ xml_document.h html_entity_lookup.h html_document.h xml_node.h \
239
+ xml_text.h xml_attr.h xml_processing_instruction.h \
240
+ xml_entity_reference.h xml_document_fragment.h xml_comment.h \
241
+ xml_node_set.h xml_dtd.h xml_attribute_decl.h xml_element_decl.h \
242
+ xml_entity_decl.h xml_xpath_context.h xml_element_content.h \
243
+ xml_sax_parser_context.h xml_sax_parser.h xml_sax_push_parser.h \
244
+ xml_reader.h html_sax_parser_context.h xslt_stylesheet.h \
245
+ xml_syntax_error.h xml_schema.h xml_relax_ng.h \
246
+ html_element_description.h xml_namespace.h xml_encoding_handler.h
247
+
248
+ xml_comment.o: xml_comment.c xml_comment.h nokogiri.h xml_io.h \
249
+ xml_document.h html_entity_lookup.h html_document.h xml_node.h \
250
+ xml_text.h xml_cdata.h xml_attr.h xml_processing_instruction.h \
251
+ xml_entity_reference.h xml_document_fragment.h xml_node_set.h \
252
+ xml_dtd.h xml_attribute_decl.h xml_element_decl.h xml_entity_decl.h \
253
+ xml_xpath_context.h xml_element_content.h xml_sax_parser_context.h \
254
+ xml_sax_parser.h xml_sax_push_parser.h xml_reader.h \
255
+ html_sax_parser_context.h xslt_stylesheet.h xml_syntax_error.h \
256
+ xml_schema.h xml_relax_ng.h html_element_description.h \
257
+ xml_namespace.h xml_encoding_handler.h
258
+
259
+ xml_document.o: xml_document.c xml_document.h nokogiri.h xml_io.h \
260
+ html_entity_lookup.h html_document.h xml_node.h xml_text.h \
261
+ xml_cdata.h xml_attr.h xml_processing_instruction.h \
262
+ xml_entity_reference.h xml_document_fragment.h xml_comment.h \
263
+ xml_node_set.h xml_dtd.h xml_attribute_decl.h xml_element_decl.h \
264
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305
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328
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329
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339
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340
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341
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350
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351
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352
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357
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361
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362
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363
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367
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368
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372
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373
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379
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383
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384
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402
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405
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407
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412
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416
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417
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418
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422
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427
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435
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439
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450
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451
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452
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461
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472
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480
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484
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485
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491
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503
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506
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