sequenceserver 2.0.0 → 2.1.0

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Files changed (667) hide show
  1. checksums.yaml +4 -4
  2. data/lib/sequenceserver/api_errors.rb +24 -2
  3. data/lib/sequenceserver/blast/job.rb +41 -7
  4. data/lib/sequenceserver/blast/report.rb +36 -30
  5. data/lib/sequenceserver/config.rb +49 -27
  6. data/lib/sequenceserver/job.rb +13 -3
  7. data/lib/sequenceserver/job_remover.rb +25 -29
  8. data/lib/sequenceserver/refinements.rb +15 -0
  9. data/lib/sequenceserver/routes.rb +69 -7
  10. data/lib/sequenceserver/sequence.rb +8 -7
  11. data/lib/sequenceserver/sys.rb +2 -2
  12. data/lib/sequenceserver/version.rb +1 -1
  13. data/lib/sequenceserver/zip_file_generator.rb +56 -0
  14. data/lib/sequenceserver.rb +1 -0
  15. data/public/config.js +149 -143
  16. data/public/css/sequenceserver.css +44 -3
  17. data/public/css/sequenceserver.min.css +3 -3
  18. data/public/js/alignment_exporter.js +16 -8
  19. data/public/js/circos.js +370 -234
  20. data/public/js/cloud_share_modal.js +216 -0
  21. data/public/js/databases.js +144 -0
  22. data/public/js/databases_tree.js +42 -113
  23. data/public/js/dnd.js +164 -0
  24. data/public/js/error_modal.js +4 -11
  25. data/public/js/exporter.js +7 -3
  26. data/public/js/form.js +260 -0
  27. data/public/js/grapher.js +113 -106
  28. data/public/js/hit.js +80 -67
  29. data/public/js/hits_overview.js +2 -2
  30. data/public/js/hsp.js +343 -288
  31. data/public/js/jquery_world.js +4 -4
  32. data/public/js/mailto.js +36 -0
  33. data/public/js/options.js +84 -0
  34. data/public/js/query.js +319 -59
  35. data/public/js/report.js +315 -269
  36. data/public/js/report_root.js +75 -0
  37. data/public/js/search.js +28 -1011
  38. data/public/js/search_button.js +195 -0
  39. data/public/js/sequence.js +2409 -2411
  40. data/public/js/sequence_modal.js +152 -159
  41. data/public/js/share_url.js +23 -0
  42. data/public/js/sidebar.js +262 -83
  43. data/public/js/tests/database.spec.js +60 -0
  44. data/public/js/tests/mock_data/databases.json +91 -0
  45. data/public/js/tests/mock_data/long_response.json +269 -0
  46. data/public/js/tests/mock_data/short_response.json +2240 -0
  47. data/public/js/tests/report.spec.js +99 -0
  48. data/public/js/tests/search_button.spec.js +14 -0
  49. data/public/js/tests/search_query.spec.js +41 -0
  50. data/public/packages/circosJS@1.7.0.js +1640 -0
  51. data/public/packages/jquery-ui@1.11.4.js +16624 -0
  52. data/public/sequenceserver-report.min.js +2425 -19
  53. data/public/sequenceserver-search.min.js +2337 -15
  54. data/public/vendor/github/jspm/nodelibs-assert@0.1.0/index.js +2 -0
  55. data/public/vendor/github/jspm/{nodelibs-buffer@0.1.0 → nodelibs-assert@0.1.0}/package.json +1 -1
  56. data/public/vendor/github/jspm/nodelibs-assert@0.1.0.js +1 -0
  57. data/public/vendor/github/jspm/nodelibs-buffer@0.1.1/package.json +6 -0
  58. data/public/vendor/github/jspm/nodelibs-buffer@0.1.1.js +1 -0
  59. data/public/vendor/github/jspm/{nodelibs-process@0.1.1 → nodelibs-process@0.1.2}/package.json +2 -2
  60. data/public/vendor/github/jspm/nodelibs-process@0.1.2.js +1 -0
  61. data/public/vendor/github/jspm/nodelibs-vm@0.1.0/index.js +2 -0
  62. data/public/vendor/github/jspm/nodelibs-vm@0.1.0/package.json +6 -0
  63. data/public/vendor/github/jspm/nodelibs-vm@0.1.0.js +1 -0
  64. data/public/vendor/npm/assert@1.5.0/CHANGELOG.md +8 -0
  65. data/public/vendor/npm/assert@1.5.0/README.md +105 -0
  66. data/public/vendor/npm/assert@1.5.0/assert.js +327 -0
  67. data/public/vendor/npm/assert@1.5.0/package.json +32 -0
  68. data/public/vendor/npm/assert@1.5.0/test.js +288 -0
  69. data/public/vendor/npm/assert@1.5.0.js +1 -0
  70. data/public/vendor/npm/{base64-js@0.0.8/LICENSE.MIT → base64-js@1.5.1/LICENSE} +1 -1
  71. data/public/vendor/npm/{base64-js@0.0.8 → base64-js@1.5.1}/README.md +10 -7
  72. data/public/vendor/npm/base64-js@1.5.1/base64js.min.js +3 -0
  73. data/public/vendor/npm/base64-js@1.5.1/index.d.ts +3 -0
  74. data/public/vendor/npm/base64-js@1.5.1/index.js +151 -0
  75. data/public/vendor/npm/base64-js@1.5.1/package.json +47 -0
  76. data/public/vendor/npm/base64-js@1.5.1.js +1 -0
  77. data/public/vendor/npm/buffer@5.7.1/AUTHORS.md +70 -0
  78. data/public/vendor/npm/{buffer@3.4.3 → buffer@5.7.1}/README.md +111 -41
  79. data/public/vendor/npm/buffer@5.7.1/index.d.ts +186 -0
  80. data/public/vendor/npm/buffer@5.7.1/index.js +1817 -0
  81. data/public/vendor/npm/buffer@5.7.1/package.json +96 -0
  82. data/public/vendor/npm/buffer@5.7.1.js +1 -0
  83. data/public/vendor/npm/core-util-is@1.0.3/LICENSE +19 -0
  84. data/public/vendor/npm/core-util-is@1.0.3/lib/util.js +64 -0
  85. data/public/vendor/npm/{core-util-is@1.0.1 → core-util-is@1.0.3}/package.json +13 -1
  86. data/public/vendor/npm/core-util-is@1.0.3.js +1 -0
  87. data/public/vendor/npm/events@1.0.2/tests/add-listeners.js +2 -2
  88. data/public/vendor/npm/events@1.0.2/tests/check-listener-leaks.js +3 -3
  89. data/public/vendor/npm/events@1.0.2/tests/common.js +1 -1
  90. data/public/vendor/npm/events@1.0.2/tests/index.js +13 -13
  91. data/public/vendor/npm/events@1.0.2/tests/listeners-side-effects.js +2 -2
  92. data/public/vendor/npm/events@1.0.2/tests/listeners.js +2 -2
  93. data/public/vendor/npm/events@1.0.2/tests/max-listeners.js +2 -2
  94. data/public/vendor/npm/events@1.0.2/tests/modify-in-emit.js +2 -2
  95. data/public/vendor/npm/events@1.0.2/tests/num-args.js +2 -2
  96. data/public/vendor/npm/events@1.0.2/tests/once.js +2 -2
  97. data/public/vendor/npm/events@1.0.2/tests/remove-all-listeners.js +3 -3
  98. data/public/vendor/npm/events@1.0.2/tests/remove-listeners.js +3 -3
  99. data/public/vendor/npm/events@1.0.2/tests/set-max-listeners-side-effects.js +2 -2
  100. data/public/vendor/npm/events@1.0.2/tests/subclass.js +3 -3
  101. data/public/vendor/npm/events@1.0.2.js +1 -1
  102. data/public/vendor/npm/ieee754@1.2.1/LICENSE +11 -0
  103. data/public/vendor/npm/{ieee754@1.1.6 → ieee754@1.2.1}/README.md +12 -8
  104. data/public/vendor/npm/ieee754@1.2.1/index.d.ts +10 -0
  105. data/public/vendor/npm/{ieee754@1.1.6 → ieee754@1.2.1}/index.js +6 -6
  106. data/public/vendor/npm/ieee754@1.2.1/package.json +52 -0
  107. data/public/vendor/npm/ieee754@1.2.1.js +1 -0
  108. data/public/vendor/npm/{is-array@1.0.1 → indexof@0.0.1}/Makefile +3 -3
  109. data/public/vendor/npm/indexof@0.0.1/Readme.md +15 -0
  110. data/public/vendor/npm/indexof@0.0.1/component.json +10 -0
  111. data/public/vendor/npm/indexof@0.0.1/index.js +11 -0
  112. data/public/vendor/npm/indexof@0.0.1/package.json +12 -0
  113. data/public/vendor/npm/indexof@0.0.1.js +1 -0
  114. data/public/vendor/npm/inherits@2.0.1/inherits.js +1 -1
  115. data/public/vendor/npm/inherits@2.0.1.js +1 -1
  116. data/public/vendor/npm/isarray@0.0.1.js +1 -1
  117. data/public/vendor/npm/js-tokens@4.0.0/index.js +23 -0
  118. data/public/vendor/npm/js-tokens@4.0.0/package.json +30 -0
  119. data/public/vendor/npm/js-tokens@4.0.0.js +1 -0
  120. data/public/vendor/npm/loose-envify@1.4.0/LICENSE +21 -0
  121. data/public/vendor/npm/loose-envify@1.4.0/README.md +45 -0
  122. data/public/vendor/npm/loose-envify@1.4.0/cli.js +12 -0
  123. data/public/vendor/npm/loose-envify@1.4.0/custom.js +3 -0
  124. data/public/vendor/npm/loose-envify@1.4.0/index.js +5 -0
  125. data/public/vendor/npm/loose-envify@1.4.0/loose-envify.js +33 -0
  126. data/public/vendor/npm/loose-envify@1.4.0/package.json +36 -0
  127. data/public/vendor/npm/loose-envify@1.4.0/replace.js +52 -0
  128. data/public/vendor/npm/loose-envify@1.4.0.js +1 -0
  129. data/public/vendor/npm/object-assign@4.1.1/index.js +90 -0
  130. data/public/vendor/npm/object-assign@4.1.1/package.json +42 -0
  131. data/public/vendor/npm/object-assign@4.1.1.js +1 -0
  132. data/public/vendor/npm/path-browserify@0.0.0/index.js +1 -1
  133. data/public/vendor/npm/path-browserify@0.0.0.js +1 -1
  134. data/public/vendor/npm/{process@0.10.1 → process@0.11.10}/README.md +4 -1
  135. data/public/vendor/npm/process@0.11.10/browser.js +184 -0
  136. data/public/vendor/npm/{process@0.10.1 → process@0.11.10}/package.json +10 -1
  137. data/public/vendor/npm/process@0.11.10/test.js +185 -0
  138. data/public/vendor/npm/process@0.11.10.js +1 -0
  139. data/public/vendor/npm/react-dom@18.0.0/LICENSE +21 -0
  140. data/public/vendor/npm/react-dom@18.0.0/README.md +50 -0
  141. data/public/vendor/npm/react-dom@18.0.0/cjs/react-dom-server-legacy.browser.development.js +4771 -0
  142. data/public/vendor/npm/react-dom@18.0.0/cjs/react-dom-server-legacy.browser.production.min.js +85 -0
  143. data/public/vendor/npm/react-dom@18.0.0/cjs/react-dom-server-legacy.node.development.js +4813 -0
  144. data/public/vendor/npm/react-dom@18.0.0/cjs/react-dom-server-legacy.node.production.min.js +1705 -0
  145. data/public/vendor/npm/react-dom@18.0.0/cjs/react-dom-server.browser.development.js +4746 -0
  146. data/public/vendor/npm/react-dom@18.0.0/cjs/react-dom-server.browser.production.min.js +90 -0
  147. data/public/vendor/npm/react-dom@18.0.0/cjs/react-dom-server.node.development.js +4714 -0
  148. data/public/vendor/npm/react-dom@18.0.0/cjs/react-dom-server.node.production.min.js +1746 -0
  149. data/public/vendor/npm/react-dom@18.0.0/cjs/react-dom-test-utils.development.js +1017 -0
  150. data/public/vendor/npm/react-dom@18.0.0/cjs/react-dom-test-utils.production.min.js +617 -0
  151. data/public/vendor/npm/react-dom@18.0.0/cjs/react-dom.development.js +20092 -0
  152. data/public/vendor/npm/react-dom@18.0.0/cjs/react-dom.production.min.js +322 -0
  153. data/public/vendor/npm/react-dom@18.0.0/cjs/react-dom.profiling.min.js +364 -0
  154. data/public/vendor/npm/react-dom@18.0.0/client.js +27 -0
  155. data/public/vendor/npm/react-dom@18.0.0/index.js +23 -0
  156. data/public/vendor/npm/react-dom@18.0.0/package.json +62 -0
  157. data/public/vendor/npm/react-dom@18.0.0/profiling.js +23 -0
  158. data/public/vendor/npm/react-dom@18.0.0/server.browser.js +19 -0
  159. data/public/vendor/npm/react-dom@18.0.0/server.js +3 -0
  160. data/public/vendor/npm/react-dom@18.0.0/server.node.js +19 -0
  161. data/public/vendor/npm/react-dom@18.0.0/test-utils.js +9 -0
  162. data/public/vendor/npm/react-dom@18.0.0/umd/react-dom-server-legacy.browser.development.js +4770 -0
  163. data/public/vendor/npm/react-dom@18.0.0/umd/react-dom-server-legacy.browser.production.min.js +72 -0
  164. data/public/vendor/npm/react-dom@18.0.0/umd/react-dom-server.browser.development.js +4745 -0
  165. data/public/vendor/npm/react-dom@18.0.0/umd/react-dom-server.browser.production.min.js +74 -0
  166. data/public/vendor/npm/react-dom@18.0.0/umd/react-dom-test-utils.development.js +1013 -0
  167. data/public/vendor/npm/react-dom@18.0.0/umd/react-dom-test-utils.production.min.js +625 -0
  168. data/public/vendor/npm/react-dom@18.0.0/umd/react-dom.development.js +20106 -0
  169. data/public/vendor/npm/react-dom@18.0.0/umd/react-dom.production.min.js +269 -0
  170. data/public/vendor/npm/react-dom@18.0.0/umd/react-dom.profiling.min.js +285 -0
  171. data/public/vendor/npm/react-dom@18.0.0.js +1 -0
  172. data/public/vendor/npm/react@18.0.0/LICENSE +21 -0
  173. data/public/vendor/npm/react@18.0.0/README.md +13 -0
  174. data/public/vendor/npm/react@18.0.0/cjs/react-jsx-dev-runtime.development.js +837 -0
  175. data/public/vendor/npm/react@18.0.0/cjs/react-jsx-dev-runtime.production.min.js +10 -0
  176. data/public/vendor/npm/react@18.0.0/cjs/react-jsx-dev-runtime.profiling.min.js +10 -0
  177. data/public/vendor/npm/react@18.0.0/cjs/react-jsx-runtime.development.js +849 -0
  178. data/public/vendor/npm/react@18.0.0/cjs/react-jsx-runtime.production.min.js +38 -0
  179. data/public/vendor/npm/react@18.0.0/cjs/react-jsx-runtime.profiling.min.js +38 -0
  180. data/public/vendor/npm/react@18.0.0/cjs/react.development.js +1746 -0
  181. data/public/vendor/npm/react@18.0.0/cjs/react.production.min.js +26 -0
  182. data/public/vendor/npm/react@18.0.0/cjs/react.shared-subset.development.js +10 -0
  183. data/public/vendor/npm/react@18.0.0/cjs/react.shared-subset.production.min.js +12 -0
  184. data/public/vendor/npm/react@18.0.0/index.js +9 -0
  185. data/public/vendor/npm/react@18.0.0/jsx-dev-runtime.js +9 -0
  186. data/public/vendor/npm/react@18.0.0/jsx-runtime.js +9 -0
  187. data/public/vendor/npm/react@18.0.0/package.json +47 -0
  188. data/public/vendor/npm/react@18.0.0/react.shared-subset.js +9 -0
  189. data/public/vendor/npm/react@18.0.0/umd/react.development.js +2186 -0
  190. data/public/vendor/npm/react@18.0.0/umd/react.production.min.js +33 -0
  191. data/public/vendor/npm/react@18.0.0/umd/react.profiling.min.js +33 -0
  192. data/public/vendor/npm/react@18.0.0.js +1 -0
  193. data/public/vendor/npm/readable-stream@1.1.14/LICENSE +18 -0
  194. data/public/vendor/npm/readable-stream@1.1.14/duplex.js +2 -0
  195. data/public/vendor/npm/{readable-stream@1.1.13 → readable-stream@1.1.14}/lib/_stream_duplex.js +5 -5
  196. data/public/vendor/npm/{readable-stream@1.1.13 → readable-stream@1.1.14}/lib/_stream_passthrough.js +3 -3
  197. data/public/vendor/npm/{readable-stream@1.1.13 → readable-stream@1.1.14}/lib/_stream_readable.js +10 -10
  198. data/public/vendor/npm/{readable-stream@1.1.13 → readable-stream@1.1.14}/lib/_stream_transform.js +4 -4
  199. data/public/vendor/npm/{readable-stream@1.1.13 → readable-stream@1.1.14}/lib/_stream_writable.js +6 -6
  200. data/public/vendor/npm/{readable-stream@1.1.13 → readable-stream@1.1.14}/package.json +1 -1
  201. data/public/vendor/npm/readable-stream@1.1.14/passthrough.js +2 -0
  202. data/public/vendor/npm/readable-stream@1.1.14/readable.js +13 -0
  203. data/public/vendor/npm/readable-stream@1.1.14/transform.js +2 -0
  204. data/public/vendor/npm/readable-stream@1.1.14/writable.js +2 -0
  205. data/public/vendor/npm/readable-stream@1.1.14.js +1 -0
  206. data/public/vendor/npm/scheduler@0.21.0/LICENSE +21 -0
  207. data/public/vendor/npm/scheduler@0.21.0/README.md +9 -0
  208. data/public/vendor/npm/scheduler@0.21.0/cjs/scheduler-unstable_mock.development.js +530 -0
  209. data/public/vendor/npm/scheduler@0.21.0/cjs/scheduler-unstable_mock.production.min.js +20 -0
  210. data/public/vendor/npm/scheduler@0.21.0/cjs/scheduler-unstable_post_task.development.js +153 -0
  211. data/public/vendor/npm/scheduler@0.21.0/cjs/scheduler-unstable_post_task.production.min.js +14 -0
  212. data/public/vendor/npm/scheduler@0.21.0/cjs/scheduler.development.js +444 -0
  213. data/public/vendor/npm/scheduler@0.21.0/cjs/scheduler.production.min.js +19 -0
  214. data/public/vendor/npm/scheduler@0.21.0/index.js +9 -0
  215. data/public/vendor/npm/scheduler@0.21.0/package.json +36 -0
  216. data/public/vendor/npm/scheduler@0.21.0/umd/scheduler-unstable_mock.development.js +701 -0
  217. data/public/vendor/npm/scheduler@0.21.0/umd/scheduler-unstable_mock.production.min.js +21 -0
  218. data/public/vendor/npm/scheduler@0.21.0/umd/scheduler.development.js +154 -0
  219. data/public/vendor/npm/scheduler@0.21.0/umd/scheduler.production.min.js +148 -0
  220. data/public/vendor/npm/scheduler@0.21.0/umd/scheduler.profiling.min.js +148 -0
  221. data/public/vendor/npm/scheduler@0.21.0/unstable_mock.js +9 -0
  222. data/public/vendor/npm/scheduler@0.21.0/unstable_post_task.js +9 -0
  223. data/public/vendor/npm/scheduler@0.21.0.js +1 -0
  224. data/public/vendor/npm/stream-browserify@1.0.0/index.js +7 -7
  225. data/public/vendor/npm/stream-browserify@1.0.0/test/buf.js +5 -5
  226. data/public/vendor/npm/stream-browserify@1.0.0.js +1 -1
  227. data/public/vendor/npm/string_decoder@0.10.31/index.js +2 -2
  228. data/public/vendor/npm/string_decoder@0.10.31.js +1 -1
  229. data/public/vendor/npm/util@0.10.3/support/isBuffer.js +1 -1
  230. data/public/vendor/npm/util@0.10.3/test/browser/inspect.js +2 -2
  231. data/public/vendor/npm/util@0.10.3/test/browser/is.js +3 -3
  232. data/public/vendor/npm/util@0.10.3/test/node/debug.js +4 -4
  233. data/public/vendor/npm/util@0.10.3/test/node/format.js +2 -2
  234. data/public/vendor/npm/util@0.10.3/test/node/inspect.js +3 -3
  235. data/public/vendor/npm/util@0.10.3/test/node/log.js +3 -3
  236. data/public/vendor/npm/util@0.10.3/test/node/util.js +3 -3
  237. data/public/vendor/npm/util@0.10.3/util.js +3 -3
  238. data/public/vendor/npm/util@0.10.3.js +1 -1
  239. data/public/vendor/npm/vm-browserify@0.0.4/LICENSE +18 -0
  240. data/public/vendor/npm/vm-browserify@0.0.4/example/run/bundle.js +376 -0
  241. data/public/vendor/npm/vm-browserify@0.0.4/example/run/entry.js +6 -0
  242. data/public/vendor/npm/vm-browserify@0.0.4/example/run/index.html +9 -0
  243. data/public/vendor/npm/vm-browserify@0.0.4/example/run/server.js +6 -0
  244. data/public/vendor/npm/vm-browserify@0.0.4/index.js +139 -0
  245. data/public/vendor/npm/vm-browserify@0.0.4/package.json +46 -0
  246. data/public/vendor/npm/vm-browserify@0.0.4/readme.markdown +67 -0
  247. data/public/vendor/npm/vm-browserify@0.0.4/test/vm.js +34 -0
  248. data/public/vendor/npm/vm-browserify@0.0.4.js +1 -0
  249. data/public/vendor/npm/webshim@1.15.8/Gruntfile.js +4 -4
  250. data/public/vendor/npm/webshim@1.15.8/build/combobuild.js +2 -2
  251. data/public/vendor/npm/webshim@1.15.8/js-webshim/dev/shims/color-picker.js +1 -1
  252. data/public/vendor/npm/webshim@1.15.8/js-webshim/dev/shims/combos/10.js +1 -1
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  660. /data/public/vendor/github/jspm/{nodelibs-process@0.1.1 → nodelibs-process@0.1.2}/index.js +0 -0
  661. /data/public/vendor/npm/{readable-stream@1.1.13 → assert@1.5.0}/LICENSE +0 -0
  662. /data/public/vendor/npm/{buffer@3.4.3 → buffer@5.7.1}/LICENSE +0 -0
  663. /data/public/vendor/npm/{core-util-is@1.0.1 → core-util-is@1.0.3}/README.md +0 -0
  664. /data/public/vendor/npm/{process@0.10.1 → process@0.11.10}/LICENSE +0 -0
  665. /data/public/vendor/npm/{process@0.10.1 → process@0.11.10}/index.js +0 -0
  666. /data/public/vendor/npm/{readable-stream@1.1.13 → readable-stream@1.1.14}/README.md +0 -0
  667. /data/public/vendor/npm/{readable-stream@1.1.13 → readable-stream@1.1.14}/float.patch +0 -0
@@ -1,7 +1,7 @@
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  /* */
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- var assert = require("assert");
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- var context = require("vm").runInNewContext;
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- var util = require("../../util");
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+ var assert = require('assert');
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+ var context = require('vm').runInNewContext;
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+ var util = require('../../util');
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  assert.equal(true, util.isArray([]));
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  assert.equal(true, util.isArray(Array()));
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  assert.equal(true, util.isArray(new Array()));
@@ -391,7 +391,7 @@
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  return arg === null || typeof arg === 'boolean' || typeof arg === 'number' || typeof arg === 'string' || typeof arg === 'symbol' || typeof arg === 'undefined';
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  }
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  exports.isPrimitive = isPrimitive;
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- exports.isBuffer = require("./support/isBufferBrowser");
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+ exports.isBuffer = require('./support/isBufferBrowser');
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  function objectToString(o) {
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  return Object.prototype.toString.call(o);
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  }
@@ -407,7 +407,7 @@
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  exports.log = function() {
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  console.log('%s - %s', timestamp(), exports.format.apply(exports, arguments));
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  };
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- exports.inherits = require("inherits");
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+ exports.inherits = require('inherits');
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  exports._extend = function(origin, add) {
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  if (!add || !isObject(add))
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  return origin;
@@ -421,4 +421,4 @@
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  function hasOwnProperty(obj, prop) {
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  return Object.prototype.hasOwnProperty.call(obj, prop);
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  }
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- })(require("process"));
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+ })(require('process'));
@@ -1 +1 @@
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- module.exports = require("npm:util@0.10.3/util");
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+ module.exports = require("npm:util@0.10.3/util.js");
@@ -0,0 +1,18 @@
1
+ This software is released under the MIT license:
2
+
3
+ Permission is hereby granted, free of charge, to any person obtaining a copy of
4
+ this software and associated documentation files (the "Software"), to deal in
5
+ the Software without restriction, including without limitation the rights to
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+ use, copy, modify, merge, publish, distribute, sublicense, and/or sell copies of
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+ the Software, and to permit persons to whom the Software is furnished to do so,
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+ subject to the following conditions:
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+
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+ The above copyright notice and this permission notice shall be included in all
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+ copies or substantial portions of the Software.
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+
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+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
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+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY, FITNESS
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+ FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR
16
+ COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER
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+ IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN
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+ CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
@@ -0,0 +1,376 @@
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+ /* */
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+ (function(process) {
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+ var require = function(file, cwd) {
4
+ var resolved = require.resolve(file, cwd || '/');
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+ var mod = require.modules[resolved];
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+ if (!mod)
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+ throw new Error('Failed to resolve module ' + file + ', tried ' + resolved);
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+ var res = mod._cached ? mod._cached : mod();
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+ return res;
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+ };
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+ require.paths = [];
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+ require.modules = {};
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+ require.extensions = [".js", ".coffee"];
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+ require._core = {
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+ 'assert': true,
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+ 'events': true,
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+ 'fs': true,
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+ 'path': true,
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+ 'vm': true
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+ };
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+ require.resolve = (function() {
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+ return function(x, cwd) {
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+ if (!cwd)
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+ cwd = '/';
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+ if (require._core[x])
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+ return x;
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+ var path = require.modules.path();
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+ var y = cwd || '.';
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+ if (x.match(/^(?:\.\.?\/|\/)/)) {
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+ var m = loadAsFileSync(path.resolve(y, x)) || loadAsDirectorySync(path.resolve(y, x));
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+ if (m)
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+ return m;
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+ }
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+ var n = loadNodeModulesSync(x, y);
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+ if (n)
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+ return n;
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+ throw new Error("Cannot find module '" + x + "'");
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+ function loadAsFileSync(x) {
39
+ if (require.modules[x]) {
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+ return x;
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+ }
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+ for (var i = 0; i < require.extensions.length; i++) {
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+ var ext = require.extensions[i];
44
+ if (require.modules[x + ext])
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+ return x + ext;
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+ }
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+ }
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+ function loadAsDirectorySync(x) {
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+ x = x.replace(/\/+$/, '');
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+ var pkgfile = x + '/package.json';
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+ if (require.modules[pkgfile]) {
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+ var pkg = require.modules[pkgfile]();
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+ var b = pkg.browserify;
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+ if (typeof b === 'object' && b.main) {
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+ var m = loadAsFileSync(path.resolve(x, b.main));
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+ if (m)
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+ return m;
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+ } else if (typeof b === 'string') {
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+ var m = loadAsFileSync(path.resolve(x, b));
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+ if (m)
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+ return m;
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+ } else if (pkg.main) {
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+ var m = loadAsFileSync(path.resolve(x, pkg.main));
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+ if (m)
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+ return m;
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+ }
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+ }
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+ return loadAsFileSync(x + '/index');
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+ }
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+ function loadNodeModulesSync(x, start) {
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+ var dirs = nodeModulesPathsSync(start);
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+ for (var i = 0; i < dirs.length; i++) {
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+ var dir = dirs[i];
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+ var m = loadAsFileSync(dir + '/' + x);
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+ if (m)
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+ return m;
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+ var n = loadAsDirectorySync(dir + '/' + x);
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+ if (n)
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+ return n;
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+ }
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+ var m = loadAsFileSync(x);
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+ if (m)
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+ return m;
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+ }
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+ function nodeModulesPathsSync(start) {
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+ var parts;
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+ if (start === '/')
88
+ parts = [''];
89
+ else
90
+ parts = path.normalize(start).split('/');
91
+ var dirs = [];
92
+ for (var i = parts.length - 1; i >= 0; i--) {
93
+ if (parts[i] === 'node_modules')
94
+ continue;
95
+ var dir = parts.slice(0, i + 1).join('/') + '/node_modules';
96
+ dirs.push(dir);
97
+ }
98
+ return dirs;
99
+ }
100
+ };
101
+ })();
102
+ require.alias = function(from, to) {
103
+ var path = require.modules.path();
104
+ var res = null;
105
+ try {
106
+ res = require.resolve(from + '/package.json', '/');
107
+ } catch (err) {
108
+ res = require.resolve(from, '/');
109
+ }
110
+ var basedir = path.dirname(res);
111
+ var keys = (Object.keys || function(obj) {
112
+ var res = [];
113
+ for (var key in obj)
114
+ res.push(key);
115
+ return res;
116
+ })(require.modules);
117
+ for (var i = 0; i < keys.length; i++) {
118
+ var key = keys[i];
119
+ if (key.slice(0, basedir.length + 1) === basedir + '/') {
120
+ var f = key.slice(basedir.length);
121
+ require.modules[to + f] = require.modules[basedir + f];
122
+ } else if (key === basedir) {
123
+ require.modules[to] = require.modules[basedir];
124
+ }
125
+ }
126
+ };
127
+ require.define = function(filename, fn) {
128
+ var dirname = require._core[filename] ? '' : require.modules.path().dirname(filename);
129
+ ;
130
+ var require_ = function(file) {
131
+ return require(file, dirname);
132
+ };
133
+ require_.resolve = function(name) {
134
+ return require.resolve(name, dirname);
135
+ };
136
+ require_.modules = require.modules;
137
+ require_.define = require.define;
138
+ var module_ = {exports: {}};
139
+ require.modules[filename] = function() {
140
+ require.modules[filename]._cached = module_.exports;
141
+ fn.call(module_.exports, require_, module_, module_.exports, dirname, filename);
142
+ require.modules[filename]._cached = module_.exports;
143
+ return module_.exports;
144
+ };
145
+ };
146
+ if (typeof process === 'undefined')
147
+ process = {};
148
+ if (!process.nextTick)
149
+ process.nextTick = (function() {
150
+ var queue = [];
151
+ var canPost = typeof window !== 'undefined' && window.postMessage && window.addEventListener;
152
+ ;
153
+ if (canPost) {
154
+ window.addEventListener('message', function(ev) {
155
+ if (ev.source === window && ev.data === 'browserify-tick') {
156
+ ev.stopPropagation();
157
+ if (queue.length > 0) {
158
+ var fn = queue.shift();
159
+ fn();
160
+ }
161
+ }
162
+ }, true);
163
+ }
164
+ return function(fn) {
165
+ if (canPost) {
166
+ queue.push(fn);
167
+ window.postMessage('browserify-tick', '*');
168
+ } else
169
+ setTimeout(fn, 0);
170
+ };
171
+ })();
172
+ if (!process.title)
173
+ process.title = 'browser';
174
+ if (!process.binding)
175
+ process.binding = function(name) {
176
+ if (name === 'evals')
177
+ return require('vm');
178
+ else
179
+ throw new Error('No such module');
180
+ };
181
+ if (!process.cwd)
182
+ process.cwd = function() {
183
+ return '.';
184
+ };
185
+ require.define("path", function(require, module, exports, __dirname, __filename) {
186
+ function filter(xs, fn) {
187
+ var res = [];
188
+ for (var i = 0; i < xs.length; i++) {
189
+ if (fn(xs[i], i, xs))
190
+ res.push(xs[i]);
191
+ }
192
+ return res;
193
+ }
194
+ function normalizeArray(parts, allowAboveRoot) {
195
+ var up = 0;
196
+ for (var i = parts.length; i >= 0; i--) {
197
+ var last = parts[i];
198
+ if (last == '.') {
199
+ parts.splice(i, 1);
200
+ } else if (last === '..') {
201
+ parts.splice(i, 1);
202
+ up++;
203
+ } else if (up) {
204
+ parts.splice(i, 1);
205
+ up--;
206
+ }
207
+ }
208
+ if (allowAboveRoot) {
209
+ for (; up--; up) {
210
+ parts.unshift('..');
211
+ }
212
+ }
213
+ return parts;
214
+ }
215
+ var splitPathRe = /^(.+\/(?!$)|\/)?((?:.+?)?(\.[^.]*)?)$/;
216
+ exports.resolve = function() {
217
+ var resolvedPath = '',
218
+ resolvedAbsolute = false;
219
+ for (var i = arguments.length; i >= -1 && !resolvedAbsolute; i--) {
220
+ var path = (i >= 0) ? arguments[i] : process.cwd();
221
+ if (typeof path !== 'string' || !path) {
222
+ continue;
223
+ }
224
+ resolvedPath = path + '/' + resolvedPath;
225
+ resolvedAbsolute = path.charAt(0) === '/';
226
+ }
227
+ resolvedPath = normalizeArray(filter(resolvedPath.split('/'), function(p) {
228
+ return !!p;
229
+ }), !resolvedAbsolute).join('/');
230
+ return ((resolvedAbsolute ? '/' : '') + resolvedPath) || '.';
231
+ };
232
+ exports.normalize = function(path) {
233
+ var isAbsolute = path.charAt(0) === '/',
234
+ trailingSlash = path.slice(-1) === '/';
235
+ path = normalizeArray(filter(path.split('/'), function(p) {
236
+ return !!p;
237
+ }), !isAbsolute).join('/');
238
+ if (!path && !isAbsolute) {
239
+ path = '.';
240
+ }
241
+ if (path && trailingSlash) {
242
+ path += '/';
243
+ }
244
+ return (isAbsolute ? '/' : '') + path;
245
+ };
246
+ exports.join = function() {
247
+ var paths = Array.prototype.slice.call(arguments, 0);
248
+ return exports.normalize(filter(paths, function(p, index) {
249
+ return p && typeof p === 'string';
250
+ }).join('/'));
251
+ };
252
+ exports.dirname = function(path) {
253
+ var dir = splitPathRe.exec(path)[1] || '';
254
+ var isWindows = false;
255
+ if (!dir) {
256
+ return '.';
257
+ } else if (dir.length === 1 || (isWindows && dir.length <= 3 && dir.charAt(1) === ':')) {
258
+ return dir;
259
+ } else {
260
+ return dir.substring(0, dir.length - 1);
261
+ }
262
+ };
263
+ exports.basename = function(path, ext) {
264
+ var f = splitPathRe.exec(path)[2] || '';
265
+ if (ext && f.substr(-1 * ext.length) === ext) {
266
+ f = f.substr(0, f.length - ext.length);
267
+ }
268
+ return f;
269
+ };
270
+ exports.extname = function(path) {
271
+ return splitPathRe.exec(path)[3] || '';
272
+ };
273
+ });
274
+ require.define("vm", function(require, module, exports, __dirname, __filename) {
275
+ var Object_keys = function(obj) {
276
+ if (Object.keys)
277
+ return Object.keys(obj);
278
+ else {
279
+ var res = [];
280
+ for (var key in obj)
281
+ res.push(key);
282
+ return res;
283
+ }
284
+ };
285
+ var forEach = function(xs, fn) {
286
+ if (xs.forEach)
287
+ return xs.forEach(fn);
288
+ else
289
+ for (var i = 0; i < xs.length; i++) {
290
+ fn(xs[i], i, xs);
291
+ }
292
+ };
293
+ var Script = exports.Script = function NodeScript(code) {
294
+ if (!(this instanceof Script))
295
+ return new Script(code);
296
+ this.code = code;
297
+ };
298
+ var iframe = document.createElement('iframe');
299
+ if (!iframe.style)
300
+ iframe.style = {};
301
+ iframe.style.display = 'none';
302
+ var iframeCapable = true;
303
+ if (navigator.appName === 'Microsoft Internet Explorer') {
304
+ var m = navigator.appVersion.match(/\bMSIE (\d+\.\d+);/);
305
+ if (m && parseFloat(m[1]) <= 9.0) {
306
+ iframeCapable = false;
307
+ }
308
+ }
309
+ Script.prototype.runInNewContext = function(context) {
310
+ if (!context)
311
+ context = {};
312
+ if (!iframeCapable) {
313
+ var keys = Object_keys(context);
314
+ var args = [];
315
+ for (var i = 0; i < keys.length; i++) {
316
+ args.push(context[keys[i]]);
317
+ }
318
+ var fn = new Function(keys, 'return ' + this.code);
319
+ return fn.apply(null, args);
320
+ }
321
+ document.body.appendChild(iframe);
322
+ var win = iframe.contentWindow || (window.frames && window.frames[window.frames.length - 1]) || window[window.length - 1];
323
+ ;
324
+ forEach(Object_keys(context), function(key) {
325
+ win[key] = context[key];
326
+ iframe[key] = context[key];
327
+ });
328
+ if (win.eval) {
329
+ var res = win.eval(this.code);
330
+ } else {
331
+ iframe.setAttribute('src', 'javascript:__browserifyVmResult=(' + this.code + ')');
332
+ if ('__browserifyVmResult' in win) {
333
+ var res = win.__browserifyVmResult;
334
+ } else {
335
+ iframeCapable = false;
336
+ res = this.runInThisContext(context);
337
+ }
338
+ }
339
+ forEach(Object_keys(win), function(key) {
340
+ context[key] = win[key];
341
+ });
342
+ document.body.removeChild(iframe);
343
+ return res;
344
+ };
345
+ Script.prototype.runInThisContext = function() {
346
+ return eval(this.code);
347
+ };
348
+ Script.prototype.runInContext = function(context) {
349
+ return this.runInNewContext(context);
350
+ };
351
+ forEach(Object_keys(Script.prototype), function(name) {
352
+ exports[name] = Script[name] = function(code) {
353
+ var s = Script(code);
354
+ return s[name].apply(s, [].slice.call(arguments, 1));
355
+ };
356
+ });
357
+ exports.createScript = function(code) {
358
+ return exports.Script(code);
359
+ };
360
+ exports.createContext = Script.createContext = function(context) {
361
+ var copy = {};
362
+ forEach(Object_keys(context), function(key) {
363
+ copy[key] = context[key];
364
+ });
365
+ return copy;
366
+ };
367
+ });
368
+ require.define("/entry.js", function(require, module, exports, __dirname, __filename) {
369
+ var vm = require('vm');
370
+ $(function() {
371
+ var res = vm.runInNewContext('a + 5', {a: 100});
372
+ $('#res').text(res);
373
+ });
374
+ });
375
+ require('/entry');
376
+ })(require('process'));
@@ -0,0 +1,6 @@
1
+ /* */
2
+ var vm = require('vm');
3
+ $(function() {
4
+ var res = vm.runInNewContext('a + 5', {a: 100});
5
+ $('#res').text(res);
6
+ });
@@ -0,0 +1,9 @@
1
+ <html>
2
+ <head>
3
+ <script src="http://ajax.googleapis.com/ajax/libs/jquery/1.7.1/jquery.min.js"></script>
4
+ <script src="/bundle.js"></script>
5
+ </head>
6
+ <body>
7
+ result = <span id="res"></span>
8
+ </body>
9
+ </html>
@@ -0,0 +1,6 @@
1
+ /* */
2
+ var ecstatic = require('ecstatic')(__dirname);
3
+ var http = require('http');
4
+ http.createServer(ecstatic).listen(8000);
5
+ console.log('listening on :8000');
6
+ console.log('# remember to run browserify entry.js -o bundle.js');
@@ -0,0 +1,139 @@
1
+ /* */
2
+ var indexOf = require('indexof');
3
+
4
+ var Object_keys = function (obj) {
5
+ if (Object.keys) return Object.keys(obj)
6
+ else {
7
+ var res = [];
8
+ for (var key in obj) res.push(key)
9
+ return res;
10
+ }
11
+ };
12
+
13
+ var forEach = function (xs, fn) {
14
+ if (xs.forEach) return xs.forEach(fn)
15
+ else for (var i = 0; i < xs.length; i++) {
16
+ fn(xs[i], i, xs);
17
+ }
18
+ };
19
+
20
+ var defineProp = (function() {
21
+ try {
22
+ Object.defineProperty({}, '_', {});
23
+ return function(obj, name, value) {
24
+ Object.defineProperty(obj, name, {
25
+ writable: true,
26
+ enumerable: false,
27
+ configurable: true,
28
+ value: value
29
+ })
30
+ };
31
+ } catch(e) {
32
+ return function(obj, name, value) {
33
+ obj[name] = value;
34
+ };
35
+ }
36
+ }());
37
+
38
+ var globals = ['Array', 'Boolean', 'Date', 'Error', 'EvalError', 'Function',
39
+ 'Infinity', 'JSON', 'Math', 'NaN', 'Number', 'Object', 'RangeError',
40
+ 'ReferenceError', 'RegExp', 'String', 'SyntaxError', 'TypeError', 'URIError',
41
+ 'decodeURI', 'decodeURIComponent', 'encodeURI', 'encodeURIComponent', 'escape',
42
+ 'eval', 'isFinite', 'isNaN', 'parseFloat', 'parseInt', 'undefined', 'unescape'];
43
+
44
+ function Context() {}
45
+ Context.prototype = {};
46
+
47
+ var Script = exports.Script = function NodeScript (code) {
48
+ if (!(this instanceof Script)) return new Script(code);
49
+ this.code = code;
50
+ };
51
+
52
+ Script.prototype.runInContext = function (context) {
53
+ if (!(context instanceof Context)) {
54
+ throw new TypeError("needs a 'context' argument.");
55
+ }
56
+
57
+ var iframe = document.createElement('iframe');
58
+ if (!iframe.style) iframe.style = {};
59
+ iframe.style.display = 'none';
60
+
61
+ document.body.appendChild(iframe);
62
+
63
+ var win = iframe.contentWindow;
64
+ var wEval = win.eval, wExecScript = win.execScript;
65
+
66
+ if (!wEval && wExecScript) {
67
+ // win.eval() magically appears when this is called in IE:
68
+ wExecScript.call(win, 'null');
69
+ wEval = win.eval;
70
+ }
71
+
72
+ forEach(Object_keys(context), function (key) {
73
+ win[key] = context[key];
74
+ });
75
+ forEach(globals, function (key) {
76
+ if (context[key]) {
77
+ win[key] = context[key];
78
+ }
79
+ });
80
+
81
+ var winKeys = Object_keys(win);
82
+
83
+ var res = wEval.call(win, this.code);
84
+
85
+ forEach(Object_keys(win), function (key) {
86
+ // Avoid copying circular objects like `top` and `window` by only
87
+ // updating existing context properties or new properties in the `win`
88
+ // that was only introduced after the eval.
89
+ if (key in context || indexOf(winKeys, key) === -1) {
90
+ context[key] = win[key];
91
+ }
92
+ });
93
+
94
+ forEach(globals, function (key) {
95
+ if (!(key in context)) {
96
+ defineProp(context, key, win[key]);
97
+ }
98
+ });
99
+
100
+ document.body.removeChild(iframe);
101
+
102
+ return res;
103
+ };
104
+
105
+ Script.prototype.runInThisContext = function () {
106
+ return eval(this.code); // maybe...
107
+ };
108
+
109
+ Script.prototype.runInNewContext = function (context) {
110
+ var ctx = Script.createContext(context);
111
+ var res = this.runInContext(ctx);
112
+
113
+ forEach(Object_keys(ctx), function (key) {
114
+ context[key] = ctx[key];
115
+ });
116
+
117
+ return res;
118
+ };
119
+
120
+ forEach(Object_keys(Script.prototype), function (name) {
121
+ exports[name] = Script[name] = function (code) {
122
+ var s = Script(code);
123
+ return s[name].apply(s, [].slice.call(arguments, 1));
124
+ };
125
+ });
126
+
127
+ exports.createScript = function (code) {
128
+ return exports.Script(code);
129
+ };
130
+
131
+ exports.createContext = Script.createContext = function (context) {
132
+ var copy = new Context();
133
+ if(typeof context === 'object') {
134
+ forEach(Object_keys(context), function (key) {
135
+ copy[key] = context[key];
136
+ });
137
+ }
138
+ return copy;
139
+ };
@@ -0,0 +1,46 @@
1
+ {
2
+ "name": "vm-browserify",
3
+ "version": "0.0.4",
4
+ "description": "vm module for the browser",
5
+ "main": "index.js",
6
+ "repository": {
7
+ "type": "git",
8
+ "url": "http://github.com/substack/vm-browserify.git"
9
+ },
10
+ "keywords": [
11
+ "vm",
12
+ "browser",
13
+ "eval"
14
+ ],
15
+ "dependencies": {
16
+ "indexof": "0.0.1"
17
+ },
18
+ "devDependencies": {
19
+ "tape": "~2.3.2"
20
+ },
21
+ "author": {
22
+ "name": "James Halliday",
23
+ "email": "mail@substack.net",
24
+ "url": "http://substack.net"
25
+ },
26
+ "scripts": {
27
+ "test": "tap test/*.js"
28
+ },
29
+ "license": "MIT",
30
+ "testling": {
31
+ "files": "test/*.js",
32
+ "browsers": [
33
+ "ie/6..latest",
34
+ "firefox/16..latest",
35
+ "firefox/nightly",
36
+ "chrome/22..latest",
37
+ "chrome/canary",
38
+ "opera/12..latest",
39
+ "opera/next",
40
+ "safari/5.1..latest",
41
+ "ipad/6.0..latest",
42
+ "iphone/6.0..latest",
43
+ "android-browser/4.2..latest"
44
+ ]
45
+ }
46
+ }