sequenceserver 2.0.0 → 2.2.0

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Files changed (675) hide show
  1. checksums.yaml +4 -4
  2. data/bin/sequenceserver +7 -2
  3. data/lib/sequenceserver/api_errors.rb +24 -2
  4. data/lib/sequenceserver/blast/formatter.rb +13 -4
  5. data/lib/sequenceserver/blast/job.rb +41 -7
  6. data/lib/sequenceserver/blast/report.rb +69 -33
  7. data/lib/sequenceserver/config.rb +52 -27
  8. data/lib/sequenceserver/job.rb +13 -3
  9. data/lib/sequenceserver/job_remover.rb +25 -29
  10. data/lib/sequenceserver/makeblastdb.rb +80 -72
  11. data/lib/sequenceserver/pool.rb +1 -1
  12. data/lib/sequenceserver/refinements.rb +15 -0
  13. data/lib/sequenceserver/report.rb +1 -5
  14. data/lib/sequenceserver/routes.rb +92 -9
  15. data/lib/sequenceserver/sequence.rb +8 -7
  16. data/lib/sequenceserver/sys.rb +3 -3
  17. data/lib/sequenceserver/version.rb +1 -1
  18. data/lib/sequenceserver/zip_file_generator.rb +56 -0
  19. data/lib/sequenceserver.rb +9 -2
  20. data/public/config.js +149 -143
  21. data/public/css/sequenceserver.css +44 -3
  22. data/public/css/sequenceserver.min.css +3 -3
  23. data/public/js/alignment_exporter.js +16 -8
  24. data/public/js/circos.js +370 -234
  25. data/public/js/cloud_share_modal.js +216 -0
  26. data/public/js/databases.js +144 -0
  27. data/public/js/databases_tree.js +42 -113
  28. data/public/js/dnd.js +164 -0
  29. data/public/js/error_modal.js +4 -11
  30. data/public/js/exporter.js +7 -3
  31. data/public/js/form.js +260 -0
  32. data/public/js/grapher.js +113 -106
  33. data/public/js/hit.js +80 -67
  34. data/public/js/hits_overview.js +2 -2
  35. data/public/js/hsp.js +343 -288
  36. data/public/js/jquery_world.js +4 -4
  37. data/public/js/mailto.js +36 -0
  38. data/public/js/options.js +84 -0
  39. data/public/js/query.js +319 -59
  40. data/public/js/report.js +369 -269
  41. data/public/js/report_root.js +75 -0
  42. data/public/js/search.js +28 -1011
  43. data/public/js/search_button.js +195 -0
  44. data/public/js/sequence.js +2409 -2411
  45. data/public/js/sequence_modal.js +152 -159
  46. data/public/js/share_url.js +23 -0
  47. data/public/js/sidebar.js +262 -83
  48. data/public/js/tests/advanced_parameters.spec.js +36 -0
  49. data/public/js/tests/database.spec.js +60 -0
  50. data/public/js/tests/mock_data/databases.json +91 -0
  51. data/public/js/tests/mock_data/long_response.json +269 -0
  52. data/public/js/tests/mock_data/sequences.js +32 -0
  53. data/public/js/tests/mock_data/short_response.json +2240 -0
  54. data/public/js/tests/report.spec.js +155 -0
  55. data/public/js/tests/search_button.spec.js +14 -0
  56. data/public/js/tests/search_query.spec.js +58 -0
  57. data/public/js/visualisation_helpers.js +1 -1
  58. data/public/packages/circosJS@1.7.0.js +1640 -0
  59. data/public/packages/jquery-ui@1.11.4.js +16624 -0
  60. data/public/sequenceserver-report.min.js +2425 -19
  61. data/public/sequenceserver-search.min.js +2337 -15
  62. data/public/vendor/github/jspm/nodelibs-assert@0.1.0/index.js +2 -0
  63. data/public/vendor/github/jspm/{nodelibs-buffer@0.1.0 → nodelibs-assert@0.1.0}/package.json +1 -1
  64. data/public/vendor/github/jspm/nodelibs-assert@0.1.0.js +1 -0
  65. data/public/vendor/github/jspm/nodelibs-buffer@0.1.1/package.json +6 -0
  66. data/public/vendor/github/jspm/nodelibs-buffer@0.1.1.js +1 -0
  67. data/public/vendor/github/jspm/{nodelibs-process@0.1.1 → nodelibs-process@0.1.2}/package.json +2 -2
  68. data/public/vendor/github/jspm/nodelibs-process@0.1.2.js +1 -0
  69. data/public/vendor/github/jspm/nodelibs-vm@0.1.0/index.js +2 -0
  70. data/public/vendor/github/jspm/nodelibs-vm@0.1.0/package.json +6 -0
  71. data/public/vendor/github/jspm/nodelibs-vm@0.1.0.js +1 -0
  72. data/public/vendor/npm/assert@1.5.0/CHANGELOG.md +8 -0
  73. data/public/vendor/npm/assert@1.5.0/README.md +105 -0
  74. data/public/vendor/npm/assert@1.5.0/assert.js +327 -0
  75. data/public/vendor/npm/assert@1.5.0/package.json +32 -0
  76. data/public/vendor/npm/assert@1.5.0/test.js +288 -0
  77. data/public/vendor/npm/assert@1.5.0.js +1 -0
  78. data/public/vendor/npm/{base64-js@0.0.8/LICENSE.MIT → base64-js@1.5.1/LICENSE} +1 -1
  79. data/public/vendor/npm/{base64-js@0.0.8 → base64-js@1.5.1}/README.md +10 -7
  80. data/public/vendor/npm/base64-js@1.5.1/base64js.min.js +3 -0
  81. data/public/vendor/npm/base64-js@1.5.1/index.d.ts +3 -0
  82. data/public/vendor/npm/base64-js@1.5.1/index.js +151 -0
  83. data/public/vendor/npm/base64-js@1.5.1/package.json +47 -0
  84. data/public/vendor/npm/base64-js@1.5.1.js +1 -0
  85. data/public/vendor/npm/buffer@5.7.1/AUTHORS.md +70 -0
  86. data/public/vendor/npm/{buffer@3.4.3 → buffer@5.7.1}/README.md +111 -41
  87. data/public/vendor/npm/buffer@5.7.1/index.d.ts +186 -0
  88. data/public/vendor/npm/buffer@5.7.1/index.js +1817 -0
  89. data/public/vendor/npm/buffer@5.7.1/package.json +96 -0
  90. data/public/vendor/npm/buffer@5.7.1.js +1 -0
  91. data/public/vendor/npm/core-util-is@1.0.3/LICENSE +19 -0
  92. data/public/vendor/npm/core-util-is@1.0.3/lib/util.js +64 -0
  93. data/public/vendor/npm/{core-util-is@1.0.1 → core-util-is@1.0.3}/package.json +13 -1
  94. data/public/vendor/npm/core-util-is@1.0.3.js +1 -0
  95. data/public/vendor/npm/events@1.0.2/tests/add-listeners.js +2 -2
  96. data/public/vendor/npm/events@1.0.2/tests/check-listener-leaks.js +3 -3
  97. data/public/vendor/npm/events@1.0.2/tests/common.js +1 -1
  98. data/public/vendor/npm/events@1.0.2/tests/index.js +13 -13
  99. data/public/vendor/npm/events@1.0.2/tests/listeners-side-effects.js +2 -2
  100. data/public/vendor/npm/events@1.0.2/tests/listeners.js +2 -2
  101. data/public/vendor/npm/events@1.0.2/tests/max-listeners.js +2 -2
  102. data/public/vendor/npm/events@1.0.2/tests/modify-in-emit.js +2 -2
  103. data/public/vendor/npm/events@1.0.2/tests/num-args.js +2 -2
  104. data/public/vendor/npm/events@1.0.2/tests/once.js +2 -2
  105. data/public/vendor/npm/events@1.0.2/tests/remove-all-listeners.js +3 -3
  106. data/public/vendor/npm/events@1.0.2/tests/remove-listeners.js +3 -3
  107. data/public/vendor/npm/events@1.0.2/tests/set-max-listeners-side-effects.js +2 -2
  108. data/public/vendor/npm/events@1.0.2/tests/subclass.js +3 -3
  109. data/public/vendor/npm/events@1.0.2.js +1 -1
  110. data/public/vendor/npm/ieee754@1.2.1/LICENSE +11 -0
  111. data/public/vendor/npm/{ieee754@1.1.6 → ieee754@1.2.1}/README.md +12 -8
  112. data/public/vendor/npm/ieee754@1.2.1/index.d.ts +10 -0
  113. data/public/vendor/npm/{ieee754@1.1.6 → ieee754@1.2.1}/index.js +6 -6
  114. data/public/vendor/npm/ieee754@1.2.1/package.json +52 -0
  115. data/public/vendor/npm/ieee754@1.2.1.js +1 -0
  116. data/public/vendor/npm/{is-array@1.0.1 → indexof@0.0.1}/Makefile +3 -3
  117. data/public/vendor/npm/indexof@0.0.1/Readme.md +15 -0
  118. data/public/vendor/npm/indexof@0.0.1/component.json +10 -0
  119. data/public/vendor/npm/indexof@0.0.1/index.js +11 -0
  120. data/public/vendor/npm/indexof@0.0.1/package.json +12 -0
  121. data/public/vendor/npm/indexof@0.0.1.js +1 -0
  122. data/public/vendor/npm/inherits@2.0.1/inherits.js +1 -1
  123. data/public/vendor/npm/inherits@2.0.1.js +1 -1
  124. data/public/vendor/npm/isarray@0.0.1.js +1 -1
  125. data/public/vendor/npm/js-tokens@4.0.0/index.js +23 -0
  126. data/public/vendor/npm/js-tokens@4.0.0/package.json +30 -0
  127. data/public/vendor/npm/js-tokens@4.0.0.js +1 -0
  128. data/public/vendor/npm/loose-envify@1.4.0/LICENSE +21 -0
  129. data/public/vendor/npm/loose-envify@1.4.0/README.md +45 -0
  130. data/public/vendor/npm/loose-envify@1.4.0/cli.js +12 -0
  131. data/public/vendor/npm/loose-envify@1.4.0/custom.js +3 -0
  132. data/public/vendor/npm/loose-envify@1.4.0/index.js +5 -0
  133. data/public/vendor/npm/loose-envify@1.4.0/loose-envify.js +33 -0
  134. data/public/vendor/npm/loose-envify@1.4.0/package.json +36 -0
  135. data/public/vendor/npm/loose-envify@1.4.0/replace.js +52 -0
  136. data/public/vendor/npm/loose-envify@1.4.0.js +1 -0
  137. data/public/vendor/npm/object-assign@4.1.1/index.js +90 -0
  138. data/public/vendor/npm/object-assign@4.1.1/package.json +42 -0
  139. data/public/vendor/npm/object-assign@4.1.1.js +1 -0
  140. data/public/vendor/npm/path-browserify@0.0.0/index.js +1 -1
  141. data/public/vendor/npm/path-browserify@0.0.0.js +1 -1
  142. data/public/vendor/npm/{process@0.10.1 → process@0.11.10}/README.md +4 -1
  143. data/public/vendor/npm/process@0.11.10/browser.js +184 -0
  144. data/public/vendor/npm/{process@0.10.1 → process@0.11.10}/package.json +10 -1
  145. data/public/vendor/npm/process@0.11.10/test.js +185 -0
  146. data/public/vendor/npm/process@0.11.10.js +1 -0
  147. data/public/vendor/npm/react-dom@18.0.0/LICENSE +21 -0
  148. data/public/vendor/npm/react-dom@18.0.0/README.md +50 -0
  149. data/public/vendor/npm/react-dom@18.0.0/cjs/react-dom-server-legacy.browser.development.js +4771 -0
  150. data/public/vendor/npm/react-dom@18.0.0/cjs/react-dom-server-legacy.browser.production.min.js +85 -0
  151. data/public/vendor/npm/react-dom@18.0.0/cjs/react-dom-server-legacy.node.development.js +4813 -0
  152. data/public/vendor/npm/react-dom@18.0.0/cjs/react-dom-server-legacy.node.production.min.js +1705 -0
  153. data/public/vendor/npm/react-dom@18.0.0/cjs/react-dom-server.browser.development.js +4746 -0
  154. data/public/vendor/npm/react-dom@18.0.0/cjs/react-dom-server.browser.production.min.js +90 -0
  155. data/public/vendor/npm/react-dom@18.0.0/cjs/react-dom-server.node.development.js +4714 -0
  156. data/public/vendor/npm/react-dom@18.0.0/cjs/react-dom-server.node.production.min.js +1746 -0
  157. data/public/vendor/npm/react-dom@18.0.0/cjs/react-dom-test-utils.development.js +1017 -0
  158. data/public/vendor/npm/react-dom@18.0.0/cjs/react-dom-test-utils.production.min.js +617 -0
  159. data/public/vendor/npm/react-dom@18.0.0/cjs/react-dom.development.js +20092 -0
  160. data/public/vendor/npm/react-dom@18.0.0/cjs/react-dom.production.min.js +322 -0
  161. data/public/vendor/npm/react-dom@18.0.0/cjs/react-dom.profiling.min.js +364 -0
  162. data/public/vendor/npm/react-dom@18.0.0/client.js +27 -0
  163. data/public/vendor/npm/react-dom@18.0.0/index.js +23 -0
  164. data/public/vendor/npm/react-dom@18.0.0/package.json +62 -0
  165. data/public/vendor/npm/react-dom@18.0.0/profiling.js +23 -0
  166. data/public/vendor/npm/react-dom@18.0.0/server.browser.js +19 -0
  167. data/public/vendor/npm/react-dom@18.0.0/server.js +3 -0
  168. data/public/vendor/npm/react-dom@18.0.0/server.node.js +19 -0
  169. data/public/vendor/npm/react-dom@18.0.0/test-utils.js +9 -0
  170. data/public/vendor/npm/react-dom@18.0.0/umd/react-dom-server-legacy.browser.development.js +4770 -0
  171. data/public/vendor/npm/react-dom@18.0.0/umd/react-dom-server-legacy.browser.production.min.js +72 -0
  172. data/public/vendor/npm/react-dom@18.0.0/umd/react-dom-server.browser.development.js +4745 -0
  173. data/public/vendor/npm/react-dom@18.0.0/umd/react-dom-server.browser.production.min.js +74 -0
  174. data/public/vendor/npm/react-dom@18.0.0/umd/react-dom-test-utils.development.js +1013 -0
  175. data/public/vendor/npm/react-dom@18.0.0/umd/react-dom-test-utils.production.min.js +625 -0
  176. data/public/vendor/npm/react-dom@18.0.0/umd/react-dom.development.js +20106 -0
  177. data/public/vendor/npm/react-dom@18.0.0/umd/react-dom.production.min.js +269 -0
  178. data/public/vendor/npm/react-dom@18.0.0/umd/react-dom.profiling.min.js +285 -0
  179. data/public/vendor/npm/react-dom@18.0.0.js +1 -0
  180. data/public/vendor/npm/react@18.0.0/LICENSE +21 -0
  181. data/public/vendor/npm/react@18.0.0/README.md +13 -0
  182. data/public/vendor/npm/react@18.0.0/cjs/react-jsx-dev-runtime.development.js +837 -0
  183. data/public/vendor/npm/react@18.0.0/cjs/react-jsx-dev-runtime.production.min.js +10 -0
  184. data/public/vendor/npm/react@18.0.0/cjs/react-jsx-dev-runtime.profiling.min.js +10 -0
  185. data/public/vendor/npm/react@18.0.0/cjs/react-jsx-runtime.development.js +849 -0
  186. data/public/vendor/npm/react@18.0.0/cjs/react-jsx-runtime.production.min.js +38 -0
  187. data/public/vendor/npm/react@18.0.0/cjs/react-jsx-runtime.profiling.min.js +38 -0
  188. data/public/vendor/npm/react@18.0.0/cjs/react.development.js +1746 -0
  189. data/public/vendor/npm/react@18.0.0/cjs/react.production.min.js +26 -0
  190. data/public/vendor/npm/react@18.0.0/cjs/react.shared-subset.development.js +10 -0
  191. data/public/vendor/npm/react@18.0.0/cjs/react.shared-subset.production.min.js +12 -0
  192. data/public/vendor/npm/react@18.0.0/index.js +9 -0
  193. data/public/vendor/npm/react@18.0.0/jsx-dev-runtime.js +9 -0
  194. data/public/vendor/npm/react@18.0.0/jsx-runtime.js +9 -0
  195. data/public/vendor/npm/react@18.0.0/package.json +47 -0
  196. data/public/vendor/npm/react@18.0.0/react.shared-subset.js +9 -0
  197. data/public/vendor/npm/react@18.0.0/umd/react.development.js +2186 -0
  198. data/public/vendor/npm/react@18.0.0/umd/react.production.min.js +33 -0
  199. data/public/vendor/npm/react@18.0.0/umd/react.profiling.min.js +33 -0
  200. data/public/vendor/npm/react@18.0.0.js +1 -0
  201. data/public/vendor/npm/readable-stream@1.1.14/LICENSE +18 -0
  202. data/public/vendor/npm/readable-stream@1.1.14/duplex.js +2 -0
  203. data/public/vendor/npm/{readable-stream@1.1.13 → readable-stream@1.1.14}/lib/_stream_duplex.js +5 -5
  204. data/public/vendor/npm/{readable-stream@1.1.13 → readable-stream@1.1.14}/lib/_stream_passthrough.js +3 -3
  205. data/public/vendor/npm/{readable-stream@1.1.13 → readable-stream@1.1.14}/lib/_stream_readable.js +10 -10
  206. data/public/vendor/npm/{readable-stream@1.1.13 → readable-stream@1.1.14}/lib/_stream_transform.js +4 -4
  207. data/public/vendor/npm/{readable-stream@1.1.13 → readable-stream@1.1.14}/lib/_stream_writable.js +6 -6
  208. data/public/vendor/npm/{readable-stream@1.1.13 → readable-stream@1.1.14}/package.json +1 -1
  209. data/public/vendor/npm/readable-stream@1.1.14/passthrough.js +2 -0
  210. data/public/vendor/npm/readable-stream@1.1.14/readable.js +13 -0
  211. data/public/vendor/npm/readable-stream@1.1.14/transform.js +2 -0
  212. data/public/vendor/npm/readable-stream@1.1.14/writable.js +2 -0
  213. data/public/vendor/npm/readable-stream@1.1.14.js +1 -0
  214. data/public/vendor/npm/scheduler@0.21.0/LICENSE +21 -0
  215. data/public/vendor/npm/scheduler@0.21.0/README.md +9 -0
  216. data/public/vendor/npm/scheduler@0.21.0/cjs/scheduler-unstable_mock.development.js +530 -0
  217. data/public/vendor/npm/scheduler@0.21.0/cjs/scheduler-unstable_mock.production.min.js +20 -0
  218. data/public/vendor/npm/scheduler@0.21.0/cjs/scheduler-unstable_post_task.development.js +153 -0
  219. data/public/vendor/npm/scheduler@0.21.0/cjs/scheduler-unstable_post_task.production.min.js +14 -0
  220. data/public/vendor/npm/scheduler@0.21.0/cjs/scheduler.development.js +444 -0
  221. data/public/vendor/npm/scheduler@0.21.0/cjs/scheduler.production.min.js +19 -0
  222. data/public/vendor/npm/scheduler@0.21.0/index.js +9 -0
  223. data/public/vendor/npm/scheduler@0.21.0/package.json +36 -0
  224. data/public/vendor/npm/scheduler@0.21.0/umd/scheduler-unstable_mock.development.js +701 -0
  225. data/public/vendor/npm/scheduler@0.21.0/umd/scheduler-unstable_mock.production.min.js +21 -0
  226. data/public/vendor/npm/scheduler@0.21.0/umd/scheduler.development.js +154 -0
  227. data/public/vendor/npm/scheduler@0.21.0/umd/scheduler.production.min.js +148 -0
  228. data/public/vendor/npm/scheduler@0.21.0/umd/scheduler.profiling.min.js +148 -0
  229. data/public/vendor/npm/scheduler@0.21.0/unstable_mock.js +9 -0
  230. data/public/vendor/npm/scheduler@0.21.0/unstable_post_task.js +9 -0
  231. data/public/vendor/npm/scheduler@0.21.0.js +1 -0
  232. data/public/vendor/npm/stream-browserify@1.0.0/index.js +7 -7
  233. data/public/vendor/npm/stream-browserify@1.0.0/test/buf.js +5 -5
  234. data/public/vendor/npm/stream-browserify@1.0.0.js +1 -1
  235. data/public/vendor/npm/string_decoder@0.10.31/index.js +2 -2
  236. data/public/vendor/npm/string_decoder@0.10.31.js +1 -1
  237. data/public/vendor/npm/util@0.10.3/support/isBuffer.js +1 -1
  238. data/public/vendor/npm/util@0.10.3/test/browser/inspect.js +2 -2
  239. data/public/vendor/npm/util@0.10.3/test/browser/is.js +3 -3
  240. data/public/vendor/npm/util@0.10.3/test/node/debug.js +4 -4
  241. data/public/vendor/npm/util@0.10.3/test/node/format.js +2 -2
  242. data/public/vendor/npm/util@0.10.3/test/node/inspect.js +3 -3
  243. data/public/vendor/npm/util@0.10.3/test/node/log.js +3 -3
  244. data/public/vendor/npm/util@0.10.3/test/node/util.js +3 -3
  245. data/public/vendor/npm/util@0.10.3/util.js +3 -3
  246. data/public/vendor/npm/util@0.10.3.js +1 -1
  247. data/public/vendor/npm/vm-browserify@0.0.4/LICENSE +18 -0
  248. data/public/vendor/npm/vm-browserify@0.0.4/example/run/bundle.js +376 -0
  249. data/public/vendor/npm/vm-browserify@0.0.4/example/run/entry.js +6 -0
  250. data/public/vendor/npm/vm-browserify@0.0.4/example/run/index.html +9 -0
  251. data/public/vendor/npm/vm-browserify@0.0.4/example/run/server.js +6 -0
  252. data/public/vendor/npm/vm-browserify@0.0.4/index.js +139 -0
  253. data/public/vendor/npm/vm-browserify@0.0.4/package.json +46 -0
  254. data/public/vendor/npm/vm-browserify@0.0.4/readme.markdown +67 -0
  255. data/public/vendor/npm/vm-browserify@0.0.4/test/vm.js +34 -0
  256. data/public/vendor/npm/vm-browserify@0.0.4.js +1 -0
  257. data/public/vendor/npm/webshim@1.15.8/Gruntfile.js +4 -4
  258. data/public/vendor/npm/webshim@1.15.8/build/combobuild.js +2 -2
  259. data/public/vendor/npm/webshim@1.15.8/js-webshim/dev/shims/color-picker.js +1 -1
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  670. /data/public/vendor/npm/{buffer@3.4.3 → buffer@5.7.1}/LICENSE +0 -0
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  672. /data/public/vendor/npm/{process@0.10.1 → process@0.11.10}/LICENSE +0 -0
  673. /data/public/vendor/npm/{process@0.10.1 → process@0.11.10}/index.js +0 -0
  674. /data/public/vendor/npm/{readable-stream@1.1.13 → readable-stream@1.1.14}/README.md +0 -0
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@@ -0,0 +1,23 @@
1
+ // Copyright 2014, 2015, 2016, 2017, 2018 Simon Lydell
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+ // License: MIT. (See LICENSE.)
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+
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+ Object.defineProperty(exports, "__esModule", {
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+ value: true
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+ })
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+
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+ // This regex comes from regex.coffee, and is inserted here by generate-index.js
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+ // (run `npm run build`).
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+ exports.default = /((['"])(?:(?!\2|\\).|\\(?:\r\n|[\s\S]))*(\2)?|`(?:[^`\\$]|\\[\s\S]|\$(?!\{)|\$\{(?:[^{}]|\{[^}]*\}?)*\}?)*(`)?)|(\/\/.*)|(\/\*(?:[^*]|\*(?!\/))*(\*\/)?)|(\/(?!\*)(?:\[(?:(?![\]\\]).|\\.)*\]|(?![\/\]\\]).|\\.)+\/(?:(?!\s*(?:\b|[\u0080-\uFFFF$\\'"~({]|[+\-!](?!=)|\.?\d))|[gmiyus]{1,6}\b(?![\u0080-\uFFFF$\\]|\s*(?:[+\-*%&|^<>!=?({]|\/(?![\/*])))))|(0[xX][\da-fA-F]+|0[oO][0-7]+|0[bB][01]+|(?:\d*\.\d+|\d+\.?)(?:[eE][+-]?\d+)?)|((?!\d)(?:(?!\s)[$\w\u0080-\uFFFF]|\\u[\da-fA-F]{4}|\\u\{[\da-fA-F]+\})+)|(--|\+\+|&&|\|\||=>|\.{3}|(?:[+\-\/%&|^]|\*{1,2}|<{1,2}|>{1,3}|!=?|={1,2})=?|[?~.,:;[\](){}])|(\s+)|(^$|[\s\S])/g
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+
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+ exports.matchToToken = function(match) {
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+ var token = {type: "invalid", value: match[0], closed: undefined}
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+ if (match[ 1]) token.type = "string" , token.closed = !!(match[3] || match[4])
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+ else if (match[ 5]) token.type = "comment"
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+ else if (match[ 6]) token.type = "comment", token.closed = !!match[7]
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+ else if (match[ 8]) token.type = "regex"
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+ else if (match[ 9]) token.type = "number"
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+ else if (match[10]) token.type = "name"
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+ else if (match[11]) token.type = "punctuator"
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+ else if (match[12]) token.type = "whitespace"
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+ return token
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+ }
@@ -0,0 +1,30 @@
1
+ {
2
+ "name": "js-tokens",
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+ "version": "4.0.0",
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+ "author": "Simon Lydell",
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+ "license": "MIT",
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+ "description": "A regex that tokenizes JavaScript.",
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+ "keywords": [
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+ "JavaScript",
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+ "js",
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+ "token",
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+ "tokenize",
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+ "regex"
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+ ],
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+ "files": [
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+ "index.js"
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+ ],
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+ "repository": "lydell/js-tokens",
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+ "scripts": {
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+ "test": "mocha --ui tdd",
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+ "esprima-compare": "node esprima-compare ./index.js everything.js/es5.js",
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+ "build": "node generate-index.js",
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+ "dev": "npm run build && npm test"
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+ },
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+ "devDependencies": {
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+ "coffeescript": "2.1.1",
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+ "esprima": "4.0.0",
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+ "everything.js": "1.0.3",
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+ "mocha": "5.0.0"
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+ }
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+ }
@@ -0,0 +1 @@
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+ module.exports = require("npm:js-tokens@4.0.0/index");
@@ -0,0 +1,21 @@
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+ The MIT License (MIT)
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+
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+ Copyright (c) 2015 Andres Suarez <zertosh@gmail.com>
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+
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+ Permission is hereby granted, free of charge, to any person obtaining a copy
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+ of this software and associated documentation files (the "Software"), to deal
7
+ in the Software without restriction, including without limitation the rights
8
+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
9
+ copies of the Software, and to permit persons to whom the Software is
10
+ furnished to do so, subject to the following conditions:
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+
12
+ The above copyright notice and this permission notice shall be included in
13
+ all copies or substantial portions of the Software.
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+
15
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
16
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
17
+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
18
+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
19
+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
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+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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+ THE SOFTWARE.
@@ -0,0 +1,45 @@
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+ # loose-envify
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+
3
+ [![Build Status](https://travis-ci.org/zertosh/loose-envify.svg?branch=master)](https://travis-ci.org/zertosh/loose-envify)
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+
5
+ Fast (and loose) selective `process.env` replacer using [js-tokens](https://github.com/lydell/js-tokens) instead of an AST. Works just like [envify](https://github.com/hughsk/envify) but much faster.
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+
7
+ ## Gotchas
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+
9
+ * Doesn't handle broken syntax.
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+ * Doesn't look inside embedded expressions in template strings.
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+ - **this won't work:**
12
+ ```js
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+ console.log(`the current env is ${process.env.NODE_ENV}`);
14
+ ```
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+ * Doesn't replace oddly-spaced or oddly-commented expressions.
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+ - **this won't work:**
17
+ ```js
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+ console.log(process./*won't*/env./*work*/NODE_ENV);
19
+ ```
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+
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+ ## Usage/Options
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+
23
+ loose-envify has the exact same interface as [envify](https://github.com/hughsk/envify), including the CLI.
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+
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+ ## Benchmark
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+
27
+ ```
28
+ envify:
29
+
30
+ $ for i in {1..5}; do node bench/bench.js 'envify'; done
31
+ 708ms
32
+ 727ms
33
+ 791ms
34
+ 719ms
35
+ 720ms
36
+
37
+ loose-envify:
38
+
39
+ $ for i in {1..5}; do node bench/bench.js '../'; done
40
+ 51ms
41
+ 52ms
42
+ 52ms
43
+ 52ms
44
+ 52ms
45
+ ```
@@ -0,0 +1,12 @@
1
+ /* */
2
+ (function(process) {
3
+ 'use strict';
4
+ var looseEnvify = require('./index');
5
+ var fs = require('fs');
6
+ if (process.argv[2]) {
7
+ fs.createReadStream(process.argv[2], {encoding: 'utf8'}).pipe(looseEnvify(process.argv[2])).pipe(process.stdout);
8
+ } else {
9
+ process.stdin.resume();
10
+ process.stdin.pipe(looseEnvify(__filename)).pipe(process.stdout);
11
+ }
12
+ })(require('process'));
@@ -0,0 +1,3 @@
1
+ /* */
2
+ 'use strict';
3
+ module.exports = require('./loose-envify');
@@ -0,0 +1,5 @@
1
+ /* */
2
+ (function(process) {
3
+ 'use strict';
4
+ module.exports = require('./loose-envify')(process.env);
5
+ })(require('process'));
@@ -0,0 +1,33 @@
1
+ /* */
2
+ (function(process) {
3
+ 'use strict';
4
+ var stream = require('stream');
5
+ var util = require('util');
6
+ var replace = require('./replace');
7
+ var jsonExtRe = /\.json$/;
8
+ module.exports = function(rootEnv) {
9
+ rootEnv = rootEnv || process.env;
10
+ return function(file, trOpts) {
11
+ if (jsonExtRe.test(file)) {
12
+ return stream.PassThrough();
13
+ }
14
+ var envs = trOpts ? [rootEnv, trOpts] : [rootEnv];
15
+ return new LooseEnvify(envs);
16
+ };
17
+ };
18
+ function LooseEnvify(envs) {
19
+ stream.Transform.call(this);
20
+ this._data = '';
21
+ this._envs = envs;
22
+ }
23
+ util.inherits(LooseEnvify, stream.Transform);
24
+ LooseEnvify.prototype._transform = function(buf, enc, cb) {
25
+ this._data += buf;
26
+ cb();
27
+ };
28
+ LooseEnvify.prototype._flush = function(cb) {
29
+ var replaced = replace(this._data, this._envs);
30
+ this.push(replaced);
31
+ cb();
32
+ };
33
+ })(require('process'));
@@ -0,0 +1,36 @@
1
+ {
2
+ "name": "loose-envify",
3
+ "version": "1.4.0",
4
+ "description": "Fast (and loose) selective `process.env` replacer using js-tokens instead of an AST",
5
+ "keywords": [
6
+ "environment",
7
+ "variables",
8
+ "browserify",
9
+ "browserify-transform",
10
+ "transform",
11
+ "source",
12
+ "configuration"
13
+ ],
14
+ "homepage": "https://github.com/zertosh/loose-envify",
15
+ "license": "MIT",
16
+ "author": "Andres Suarez <zertosh@gmail.com>",
17
+ "main": "index.js",
18
+ "bin": {
19
+ "loose-envify": "cli.js"
20
+ },
21
+ "repository": {
22
+ "type": "git",
23
+ "url": "git://github.com/zertosh/loose-envify.git"
24
+ },
25
+ "scripts": {
26
+ "test": "tap test/*.js"
27
+ },
28
+ "dependencies": {
29
+ "js-tokens": "^3.0.0 || ^4.0.0"
30
+ },
31
+ "devDependencies": {
32
+ "browserify": "^13.1.1",
33
+ "envify": "^3.4.0",
34
+ "tap": "^8.0.0"
35
+ }
36
+ }
@@ -0,0 +1,52 @@
1
+ /* */
2
+ (function(process) {
3
+ 'use strict';
4
+ var jsTokens = require('js-tokens').default;
5
+ var processEnvRe = /\bprocess\.env\.[_$a-zA-Z][$\w]+\b/;
6
+ var spaceOrCommentRe = /^(?:\s|\/[/*])/;
7
+ function replace(src, envs) {
8
+ if (!processEnvRe.test(src)) {
9
+ return src;
10
+ }
11
+ var out = [];
12
+ var purge = envs.some(function(env) {
13
+ return env._ && env._.indexOf('purge') !== -1;
14
+ });
15
+ jsTokens.lastIndex = 0;
16
+ var parts = src.match(jsTokens);
17
+ for (var i = 0; i < parts.length; i++) {
18
+ if (parts[i] === 'process' && parts[i + 1] === '.' && parts[i + 2] === 'env' && parts[i + 3] === '.') {
19
+ var prevCodeToken = getAdjacentCodeToken(-1, parts, i);
20
+ var nextCodeToken = getAdjacentCodeToken(1, parts, i + 4);
21
+ var replacement = getReplacementString(envs, parts[i + 4], purge);
22
+ if (prevCodeToken !== '.' && nextCodeToken !== '.' && nextCodeToken !== '=' && typeof replacement === 'string') {
23
+ out.push(replacement);
24
+ i += 4;
25
+ continue;
26
+ }
27
+ }
28
+ out.push(parts[i]);
29
+ }
30
+ return out.join('');
31
+ }
32
+ function getAdjacentCodeToken(dir, parts, i) {
33
+ while (true) {
34
+ var part = parts[i += dir];
35
+ if (!spaceOrCommentRe.test(part)) {
36
+ return part;
37
+ }
38
+ }
39
+ }
40
+ function getReplacementString(envs, name, purge) {
41
+ for (var j = 0; j < envs.length; j++) {
42
+ var env = envs[j];
43
+ if (typeof env[name] !== 'undefined') {
44
+ return JSON.stringify(env[name]);
45
+ }
46
+ }
47
+ if (purge) {
48
+ return 'undefined';
49
+ }
50
+ }
51
+ module.exports = replace;
52
+ })(require('process'));
@@ -0,0 +1 @@
1
+ module.exports = require("npm:loose-envify@1.4.0/index.js");
@@ -0,0 +1,90 @@
1
+ /*
2
+ object-assign
3
+ (c) Sindre Sorhus
4
+ @license MIT
5
+ */
6
+
7
+ 'use strict';
8
+ /* eslint-disable no-unused-vars */
9
+ var getOwnPropertySymbols = Object.getOwnPropertySymbols;
10
+ var hasOwnProperty = Object.prototype.hasOwnProperty;
11
+ var propIsEnumerable = Object.prototype.propertyIsEnumerable;
12
+
13
+ function toObject(val) {
14
+ if (val === null || val === undefined) {
15
+ throw new TypeError('Object.assign cannot be called with null or undefined');
16
+ }
17
+
18
+ return Object(val);
19
+ }
20
+
21
+ function shouldUseNative() {
22
+ try {
23
+ if (!Object.assign) {
24
+ return false;
25
+ }
26
+
27
+ // Detect buggy property enumeration order in older V8 versions.
28
+
29
+ // https://bugs.chromium.org/p/v8/issues/detail?id=4118
30
+ var test1 = new String('abc'); // eslint-disable-line no-new-wrappers
31
+ test1[5] = 'de';
32
+ if (Object.getOwnPropertyNames(test1)[0] === '5') {
33
+ return false;
34
+ }
35
+
36
+ // https://bugs.chromium.org/p/v8/issues/detail?id=3056
37
+ var test2 = {};
38
+ for (var i = 0; i < 10; i++) {
39
+ test2['_' + String.fromCharCode(i)] = i;
40
+ }
41
+ var order2 = Object.getOwnPropertyNames(test2).map(function (n) {
42
+ return test2[n];
43
+ });
44
+ if (order2.join('') !== '0123456789') {
45
+ return false;
46
+ }
47
+
48
+ // https://bugs.chromium.org/p/v8/issues/detail?id=3056
49
+ var test3 = {};
50
+ 'abcdefghijklmnopqrst'.split('').forEach(function (letter) {
51
+ test3[letter] = letter;
52
+ });
53
+ if (Object.keys(Object.assign({}, test3)).join('') !==
54
+ 'abcdefghijklmnopqrst') {
55
+ return false;
56
+ }
57
+
58
+ return true;
59
+ } catch (err) {
60
+ // We don't expect any of the above to throw, but better to be safe.
61
+ return false;
62
+ }
63
+ }
64
+
65
+ module.exports = shouldUseNative() ? Object.assign : function (target, source) {
66
+ var from;
67
+ var to = toObject(target);
68
+ var symbols;
69
+
70
+ for (var s = 1; s < arguments.length; s++) {
71
+ from = Object(arguments[s]);
72
+
73
+ for (var key in from) {
74
+ if (hasOwnProperty.call(from, key)) {
75
+ to[key] = from[key];
76
+ }
77
+ }
78
+
79
+ if (getOwnPropertySymbols) {
80
+ symbols = getOwnPropertySymbols(from);
81
+ for (var i = 0; i < symbols.length; i++) {
82
+ if (propIsEnumerable.call(from, symbols[i])) {
83
+ to[symbols[i]] = from[symbols[i]];
84
+ }
85
+ }
86
+ }
87
+ }
88
+
89
+ return to;
90
+ };
@@ -0,0 +1,42 @@
1
+ {
2
+ "name": "object-assign",
3
+ "version": "4.1.1",
4
+ "description": "ES2015 `Object.assign()` ponyfill",
5
+ "license": "MIT",
6
+ "repository": "sindresorhus/object-assign",
7
+ "author": {
8
+ "name": "Sindre Sorhus",
9
+ "email": "sindresorhus@gmail.com",
10
+ "url": "sindresorhus.com"
11
+ },
12
+ "engines": {
13
+ "node": ">=0.10.0"
14
+ },
15
+ "scripts": {
16
+ "test": "xo && ava",
17
+ "bench": "matcha bench.js"
18
+ },
19
+ "files": [
20
+ "index.js"
21
+ ],
22
+ "keywords": [
23
+ "object",
24
+ "assign",
25
+ "extend",
26
+ "properties",
27
+ "es2015",
28
+ "ecmascript",
29
+ "harmony",
30
+ "ponyfill",
31
+ "prollyfill",
32
+ "polyfill",
33
+ "shim",
34
+ "browser"
35
+ ],
36
+ "devDependencies": {
37
+ "ava": "^0.16.0",
38
+ "lodash": "^4.16.4",
39
+ "matcha": "^0.7.0",
40
+ "xo": "^0.16.0"
41
+ }
42
+ }
@@ -0,0 +1 @@
1
+ module.exports = require("npm:object-assign@4.1.1/index");
@@ -146,4 +146,4 @@
146
146
  return str.substr(start, len);
147
147
  };
148
148
  ;
149
- })(require("process"));
149
+ })(require('process'));
@@ -1 +1 @@
1
- module.exports = require("npm:path-browserify@0.0.0/index");
1
+ module.exports = require("npm:path-browserify@0.0.0/index.js");
@@ -6,11 +6,14 @@ Works in node.js and browsers via the browser.js shim provided with the module.
6
6
 
7
7
  ## browser implementation
8
8
 
9
- The goal of this module is not to be a full-fledged alternative to the builtin process module. This module mostly exists to provide the nextTick functionality and nothing more. We keep this module lean because it will often be included by default by tools like browserify when it detects a module has used the `process` global.
9
+ The goal of this module is not to be a full-fledged alternative to the builtin process module. This module mostly exists to provide the nextTick functionality and little more. We keep this module lean because it will often be included by default by tools like browserify when it detects a module has used the `process` global.
10
+
11
+ It also exposes a "browser" member (i.e. `process.browser`) which is `true` in this implementation but `undefined` in node. This can be used in isomorphic code that adjusts it's behavior depending on which environment it's running in.
10
12
 
11
13
  If you are looking to provide other process methods, I suggest you monkey patch them onto the process global in your app. A list of user created patches is below.
12
14
 
13
15
  * [hrtime](https://github.com/kumavis/browser-process-hrtime)
16
+ * [stdout](https://github.com/kumavis/browser-stdout)
14
17
 
15
18
  ## package manager notes
16
19
 
@@ -0,0 +1,184 @@
1
+ // shim for using process in browser
2
+ var process = module.exports = {};
3
+
4
+ // cached from whatever global is present so that test runners that stub it
5
+ // don't break things. But we need to wrap it in a try catch in case it is
6
+ // wrapped in strict mode code which doesn't define any globals. It's inside a
7
+ // function because try/catches deoptimize in certain engines.
8
+
9
+ var cachedSetTimeout;
10
+ var cachedClearTimeout;
11
+
12
+ function defaultSetTimout() {
13
+ throw new Error('setTimeout has not been defined');
14
+ }
15
+ function defaultClearTimeout () {
16
+ throw new Error('clearTimeout has not been defined');
17
+ }
18
+ (function () {
19
+ try {
20
+ if (typeof setTimeout === 'function') {
21
+ cachedSetTimeout = setTimeout;
22
+ } else {
23
+ cachedSetTimeout = defaultSetTimout;
24
+ }
25
+ } catch (e) {
26
+ cachedSetTimeout = defaultSetTimout;
27
+ }
28
+ try {
29
+ if (typeof clearTimeout === 'function') {
30
+ cachedClearTimeout = clearTimeout;
31
+ } else {
32
+ cachedClearTimeout = defaultClearTimeout;
33
+ }
34
+ } catch (e) {
35
+ cachedClearTimeout = defaultClearTimeout;
36
+ }
37
+ } ())
38
+ function runTimeout(fun) {
39
+ if (cachedSetTimeout === setTimeout) {
40
+ //normal enviroments in sane situations
41
+ return setTimeout(fun, 0);
42
+ }
43
+ // if setTimeout wasn't available but was latter defined
44
+ if ((cachedSetTimeout === defaultSetTimout || !cachedSetTimeout) && setTimeout) {
45
+ cachedSetTimeout = setTimeout;
46
+ return setTimeout(fun, 0);
47
+ }
48
+ try {
49
+ // when when somebody has screwed with setTimeout but no I.E. maddness
50
+ return cachedSetTimeout(fun, 0);
51
+ } catch(e){
52
+ try {
53
+ // When we are in I.E. but the script has been evaled so I.E. doesn't trust the global object when called normally
54
+ return cachedSetTimeout.call(null, fun, 0);
55
+ } catch(e){
56
+ // same as above but when it's a version of I.E. that must have the global object for 'this', hopfully our context correct otherwise it will throw a global error
57
+ return cachedSetTimeout.call(this, fun, 0);
58
+ }
59
+ }
60
+
61
+
62
+ }
63
+ function runClearTimeout(marker) {
64
+ if (cachedClearTimeout === clearTimeout) {
65
+ //normal enviroments in sane situations
66
+ return clearTimeout(marker);
67
+ }
68
+ // if clearTimeout wasn't available but was latter defined
69
+ if ((cachedClearTimeout === defaultClearTimeout || !cachedClearTimeout) && clearTimeout) {
70
+ cachedClearTimeout = clearTimeout;
71
+ return clearTimeout(marker);
72
+ }
73
+ try {
74
+ // when when somebody has screwed with setTimeout but no I.E. maddness
75
+ return cachedClearTimeout(marker);
76
+ } catch (e){
77
+ try {
78
+ // When we are in I.E. but the script has been evaled so I.E. doesn't trust the global object when called normally
79
+ return cachedClearTimeout.call(null, marker);
80
+ } catch (e){
81
+ // same as above but when it's a version of I.E. that must have the global object for 'this', hopfully our context correct otherwise it will throw a global error.
82
+ // Some versions of I.E. have different rules for clearTimeout vs setTimeout
83
+ return cachedClearTimeout.call(this, marker);
84
+ }
85
+ }
86
+
87
+
88
+
89
+ }
90
+ var queue = [];
91
+ var draining = false;
92
+ var currentQueue;
93
+ var queueIndex = -1;
94
+
95
+ function cleanUpNextTick() {
96
+ if (!draining || !currentQueue) {
97
+ return;
98
+ }
99
+ draining = false;
100
+ if (currentQueue.length) {
101
+ queue = currentQueue.concat(queue);
102
+ } else {
103
+ queueIndex = -1;
104
+ }
105
+ if (queue.length) {
106
+ drainQueue();
107
+ }
108
+ }
109
+
110
+ function drainQueue() {
111
+ if (draining) {
112
+ return;
113
+ }
114
+ var timeout = runTimeout(cleanUpNextTick);
115
+ draining = true;
116
+
117
+ var len = queue.length;
118
+ while(len) {
119
+ currentQueue = queue;
120
+ queue = [];
121
+ while (++queueIndex < len) {
122
+ if (currentQueue) {
123
+ currentQueue[queueIndex].run();
124
+ }
125
+ }
126
+ queueIndex = -1;
127
+ len = queue.length;
128
+ }
129
+ currentQueue = null;
130
+ draining = false;
131
+ runClearTimeout(timeout);
132
+ }
133
+
134
+ process.nextTick = function (fun) {
135
+ var args = new Array(arguments.length - 1);
136
+ if (arguments.length > 1) {
137
+ for (var i = 1; i < arguments.length; i++) {
138
+ args[i - 1] = arguments[i];
139
+ }
140
+ }
141
+ queue.push(new Item(fun, args));
142
+ if (queue.length === 1 && !draining) {
143
+ runTimeout(drainQueue);
144
+ }
145
+ };
146
+
147
+ // v8 likes predictible objects
148
+ function Item(fun, array) {
149
+ this.fun = fun;
150
+ this.array = array;
151
+ }
152
+ Item.prototype.run = function () {
153
+ this.fun.apply(null, this.array);
154
+ };
155
+ process.title = 'browser';
156
+ process.browser = true;
157
+ process.env = {};
158
+ process.argv = [];
159
+ process.version = ''; // empty string to avoid regexp issues
160
+ process.versions = {};
161
+
162
+ function noop() {}
163
+
164
+ process.on = noop;
165
+ process.addListener = noop;
166
+ process.once = noop;
167
+ process.off = noop;
168
+ process.removeListener = noop;
169
+ process.removeAllListeners = noop;
170
+ process.emit = noop;
171
+ process.prependListener = noop;
172
+ process.prependOnceListener = noop;
173
+
174
+ process.listeners = function (name) { return [] }
175
+
176
+ process.binding = function (name) {
177
+ throw new Error('process.binding is not supported');
178
+ };
179
+
180
+ process.cwd = function () { return '/' };
181
+ process.chdir = function (dir) {
182
+ throw new Error('process.chdir is not supported');
183
+ };
184
+ process.umask = function() { return 0; };
@@ -5,14 +5,23 @@
5
5
  "keywords": [
6
6
  "process"
7
7
  ],
8
- "version": "0.10.1",
8
+ "scripts": {
9
+ "test": "mocha test.js",
10
+ "browser": "zuul --no-coverage --ui mocha-bdd --local 8080 -- test.js"
11
+ },
12
+ "version": "0.11.10",
9
13
  "repository": {
10
14
  "type": "git",
11
15
  "url": "git://github.com/shtylman/node-process.git"
12
16
  },
17
+ "license": "MIT",
13
18
  "browser": "./browser.js",
14
19
  "main": "./index.js",
15
20
  "engines": {
16
21
  "node": ">= 0.6.0"
22
+ },
23
+ "devDependencies": {
24
+ "mocha": "2.2.1",
25
+ "zuul": "^3.10.3"
17
26
  }
18
27
  }