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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@@ -1 +0,0 @@
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- module.exports = require("github:jspm/nodelibs-buffer@0.1.0/index");
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- module.exports = System._nodeRequire && System._nodeRequire('module');
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- module.exports = require("github:jspm/nodelibs-module@0.1.0/index");
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- module.exports = require("github:jspm/nodelibs-process@0.1.1/index");
@@ -1,58 +0,0 @@
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- amdefine is released under two licenses: new BSD, and MIT. You may pick the
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- license that best suits your development needs. The text of both licenses are
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- provided below.
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-
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-
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- The "New" BSD License:
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- ----------------------
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-
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- Copyright (c) 2011-2015, The Dojo Foundation
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- All rights reserved.
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-
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- Redistribution and use in source and binary forms, with or without
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- modification, are permitted provided that the following conditions are met:
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-
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- * Redistributions of source code must retain the above copyright notice, this
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- list of conditions and the following disclaimer.
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- * Redistributions in binary form must reproduce the above copyright notice,
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- this list of conditions and the following disclaimer in the documentation
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- and/or other materials provided with the distribution.
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- * Neither the name of the Dojo Foundation nor the names of its contributors
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- may be used to endorse or promote products derived from this software
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- without specific prior written permission.
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-
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- THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS" AND
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- ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE IMPLIED
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- WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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- DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT OWNER OR CONTRIBUTORS BE LIABLE
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- FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
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- DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
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- SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
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- CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
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- OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
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- OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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-
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-
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-
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- MIT License
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- -----------
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-
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- Copyright (c) 2011-2015, The Dojo Foundation
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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
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- in the Software without restriction, including without limitation the rights
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- to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
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- copies of the Software, and to permit persons to whom the Software is
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- furnished to do so, 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
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- all 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,
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- FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
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- AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
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- 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.
@@ -1,171 +0,0 @@
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- # amdefine
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-
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- A module that can be used to implement AMD's define() in Node. This allows you
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- to code to the AMD API and have the module work in node programs without
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- requiring those other programs to use AMD.
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-
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- ## Usage
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-
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- **1)** Update your package.json to indicate amdefine as a dependency:
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-
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- ```javascript
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- "dependencies": {
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- "amdefine": ">=0.1.0"
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- }
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- ```
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-
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- Then run `npm install` to get amdefine into your project.
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-
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- **2)** At the top of each module that uses define(), place this code:
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-
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- ```javascript
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- if (typeof define !== 'function') { var define = require('amdefine')(module) }
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- ```
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-
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- **Only use these snippets** when loading amdefine. If you preserve the basic structure,
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- with the braces, it will be stripped out when using the [RequireJS optimizer](#optimizer).
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-
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- You can add spaces, line breaks and even require amdefine with a local path, but
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- keep the rest of the structure to get the stripping behavior.
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-
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- As you may know, because `if` statements in JavaScript don't have their own scope, the var
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- declaration in the above snippet is made whether the `if` expression is truthy or not. If
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- RequireJS is loaded then the declaration is superfluous because `define` is already already
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- declared in the same scope in RequireJS. Fortunately JavaScript handles multiple `var`
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- declarations of the same variable in the same scope gracefully.
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-
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- If you want to deliver amdefine.js with your code rather than specifying it as a dependency
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- with npm, then just download the latest release and refer to it using a relative path:
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-
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- [Latest Version](https://github.com/jrburke/amdefine/raw/latest/amdefine.js)
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-
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- ### amdefine/intercept
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-
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- Consider this very experimental.
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-
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- Instead of pasting the piece of text for the amdefine setup of a `define`
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- variable in each module you create or consume, you can use `amdefine/intercept`
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- instead. It will automatically insert the above snippet in each .js file loaded
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- by Node.
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-
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- **Warning**: you should only use this if you are creating an application that
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- is consuming AMD style defined()'d modules that are distributed via npm and want
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- to run that code in Node.
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-
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- For library code where you are not sure if it will be used by others in Node or
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- in the browser, then explicitly depending on amdefine and placing the code
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- snippet above is suggested path, instead of using `amdefine/intercept`. The
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- intercept module affects all .js files loaded in the Node app, and it is
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- inconsiderate to modify global state like that unless you are also controlling
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- the top level app.
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-
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- #### Why distribute AMD-style modules via npm?
63
-
64
- npm has a lot of weaknesses for front-end use (installed layout is not great,
65
- should have better support for the `baseUrl + moduleID + '.js' style of loading,
66
- single file JS installs), but some people want a JS package manager and are
67
- willing to live with those constraints. If that is you, but still want to author
68
- in AMD style modules to get dynamic require([]), better direct source usage and
69
- powerful loader plugin support in the browser, then this tool can help.
70
-
71
- #### amdefine/intercept usage
72
-
73
- Just require it in your top level app module (for example index.js, server.js):
74
-
75
- ```javascript
76
- require('amdefine/intercept');
77
- ```
78
-
79
- The module does not return a value, so no need to assign the result to a local
80
- variable.
81
-
82
- Then just require() code as you normally would with Node's require(). Any .js
83
- loaded after the intercept require will have the amdefine check injected in
84
- the .js source as it is loaded. It does not modify the source on disk, just
85
- prepends some content to the text of the module as it is loaded by Node.
86
-
87
- #### How amdefine/intercept works
88
-
89
- It overrides the `Module._extensions['.js']` in Node to automatically prepend
90
- the amdefine snippet above. So, it will affect any .js file loaded by your
91
- app.
92
-
93
- ## define() usage
94
-
95
- It is best if you use the anonymous forms of define() in your module:
96
-
97
- ```javascript
98
- define(function (require) {
99
- var dependency = require('dependency');
100
- });
101
- ```
102
-
103
- or
104
-
105
- ```javascript
106
- define(['dependency'], function (dependency) {
107
-
108
- });
109
- ```
110
-
111
- ## RequireJS optimizer integration. <a name="optimizer"></name>
112
-
113
- Version 1.0.3 of the [RequireJS optimizer](http://requirejs.org/docs/optimization.html)
114
- will have support for stripping the `if (typeof define !== 'function')` check
115
- mentioned above, so you can include this snippet for code that runs in the
116
- browser, but avoid taking the cost of the if() statement once the code is
117
- optimized for deployment.
118
-
119
- ## Node 0.4 Support
120
-
121
- If you want to support Node 0.4, then add `require` as the second parameter to amdefine:
122
-
123
- ```javascript
124
- //Only if you want Node 0.4. If using 0.5 or later, use the above snippet.
125
- if (typeof define !== 'function') { var define = require('amdefine')(module, require) }
126
- ```
127
-
128
- ## Limitations
129
-
130
- ### Synchronous vs Asynchronous
131
-
132
- amdefine creates a define() function that is callable by your code. It will
133
- execute and trace dependencies and call the factory function *synchronously*,
134
- to keep the behavior in line with Node's synchronous dependency tracing.
135
-
136
- The exception: calling AMD's callback-style require() from inside a factory
137
- function. The require callback is called on process.nextTick():
138
-
139
- ```javascript
140
- define(function (require) {
141
- require(['a'], function(a) {
142
- //'a' is loaded synchronously, but
143
- //this callback is called on process.nextTick().
144
- });
145
- });
146
- ```
147
-
148
- ### Loader Plugins
149
-
150
- Loader plugins are supported as long as they call their load() callbacks
151
- synchronously. So ones that do network requests will not work. However plugins
152
- like [text](http://requirejs.org/docs/api.html#text) can load text files locally.
153
-
154
- The plugin API's `load.fromText()` is **not supported** in amdefine, so this means
155
- transpiler plugins like the [CoffeeScript loader plugin](https://github.com/jrburke/require-cs)
156
- will not work. This may be fixable, but it is a bit complex, and I do not have
157
- enough node-fu to figure it out yet. See the source for amdefine.js if you want
158
- to get an idea of the issues involved.
159
-
160
- ## Tests
161
-
162
- To run the tests, cd to **tests** and run:
163
-
164
- ```
165
- node all.js
166
- node all-intercept.js
167
- ```
168
-
169
- ## License
170
-
171
- New BSD and MIT. Check the LICENSE file for all the details.
@@ -1,200 +0,0 @@
1
- /* */
2
- (function(process) {
3
- 'use strict';
4
- function amdefine(module, requireFn) {
5
- 'use strict';
6
- var defineCache = {},
7
- loaderCache = {},
8
- alreadyCalled = false,
9
- path = require("path"),
10
- makeRequire,
11
- stringRequire;
12
- function trimDots(ary) {
13
- var i,
14
- part;
15
- for (i = 0; ary[i]; i += 1) {
16
- part = ary[i];
17
- if (part === '.') {
18
- ary.splice(i, 1);
19
- i -= 1;
20
- } else if (part === '..') {
21
- if (i === 1 && (ary[2] === '..' || ary[0] === '..')) {
22
- break;
23
- } else if (i > 0) {
24
- ary.splice(i - 1, 2);
25
- i -= 2;
26
- }
27
- }
28
- }
29
- }
30
- function normalize(name, baseName) {
31
- var baseParts;
32
- if (name && name.charAt(0) === '.') {
33
- if (baseName) {
34
- baseParts = baseName.split('/');
35
- baseParts = baseParts.slice(0, baseParts.length - 1);
36
- baseParts = baseParts.concat(name.split('/'));
37
- trimDots(baseParts);
38
- name = baseParts.join('/');
39
- }
40
- }
41
- return name;
42
- }
43
- function makeNormalize(relName) {
44
- return function(name) {
45
- return normalize(name, relName);
46
- };
47
- }
48
- function makeLoad(id) {
49
- function load(value) {
50
- loaderCache[id] = value;
51
- }
52
- load.fromText = function(id, text) {
53
- throw new Error('amdefine does not implement load.fromText');
54
- };
55
- return load;
56
- }
57
- makeRequire = function(systemRequire, exports, module, relId) {
58
- function amdRequire(deps, callback) {
59
- if (typeof deps === 'string') {
60
- return stringRequire(systemRequire, exports, module, deps, relId);
61
- } else {
62
- deps = deps.map(function(depName) {
63
- return stringRequire(systemRequire, exports, module, depName, relId);
64
- });
65
- if (callback) {
66
- process.nextTick(function() {
67
- callback.apply(null, deps);
68
- });
69
- }
70
- }
71
- }
72
- amdRequire.toUrl = function(filePath) {
73
- if (filePath.indexOf('.') === 0) {
74
- return normalize(filePath, path.dirname(module.filename));
75
- } else {
76
- return filePath;
77
- }
78
- };
79
- return amdRequire;
80
- };
81
- requireFn = requireFn || function req() {
82
- return module.require.apply(module, arguments);
83
- };
84
- function runFactory(id, deps, factory) {
85
- var r,
86
- e,
87
- m,
88
- result;
89
- if (id) {
90
- e = loaderCache[id] = {};
91
- m = {
92
- id: id,
93
- uri: __filename,
94
- exports: e
95
- };
96
- r = makeRequire(requireFn, e, m, id);
97
- } else {
98
- if (alreadyCalled) {
99
- throw new Error('amdefine with no module ID cannot be called more than once per file.');
100
- }
101
- alreadyCalled = true;
102
- e = module.exports;
103
- m = module;
104
- r = makeRequire(requireFn, e, m, module.id);
105
- }
106
- if (deps) {
107
- deps = deps.map(function(depName) {
108
- return r(depName);
109
- });
110
- }
111
- if (typeof factory === 'function') {
112
- result = factory.apply(m.exports, deps);
113
- } else {
114
- result = factory;
115
- }
116
- if (result !== undefined) {
117
- m.exports = result;
118
- if (id) {
119
- loaderCache[id] = m.exports;
120
- }
121
- }
122
- }
123
- stringRequire = function(systemRequire, exports, module, id, relId) {
124
- var index = id.indexOf('!'),
125
- originalId = id,
126
- prefix,
127
- plugin;
128
- if (index === -1) {
129
- id = normalize(id, relId);
130
- if (id === 'require') {
131
- return makeRequire(systemRequire, exports, module, relId);
132
- } else if (id === 'exports') {
133
- return exports;
134
- } else if (id === 'module') {
135
- return module;
136
- } else if (loaderCache.hasOwnProperty(id)) {
137
- return loaderCache[id];
138
- } else if (defineCache[id]) {
139
- runFactory.apply(null, defineCache[id]);
140
- return loaderCache[id];
141
- } else {
142
- if (systemRequire) {
143
- return systemRequire(originalId);
144
- } else {
145
- throw new Error('No module with ID: ' + id);
146
- }
147
- }
148
- } else {
149
- prefix = id.substring(0, index);
150
- id = id.substring(index + 1, id.length);
151
- plugin = stringRequire(systemRequire, exports, module, prefix, relId);
152
- if (plugin.normalize) {
153
- id = plugin.normalize(id, makeNormalize(relId));
154
- } else {
155
- id = normalize(id, relId);
156
- }
157
- if (loaderCache[id]) {
158
- return loaderCache[id];
159
- } else {
160
- plugin.load(id, makeRequire(systemRequire, exports, module, relId), makeLoad(id), {});
161
- return loaderCache[id];
162
- }
163
- }
164
- };
165
- function define(id, deps, factory) {
166
- if (Array.isArray(id)) {
167
- factory = deps;
168
- deps = id;
169
- id = undefined;
170
- } else if (typeof id !== 'string') {
171
- factory = id;
172
- id = deps = undefined;
173
- }
174
- if (deps && !Array.isArray(deps)) {
175
- factory = deps;
176
- deps = undefined;
177
- }
178
- if (!deps) {
179
- deps = ['require', 'exports', 'module'];
180
- }
181
- if (id) {
182
- defineCache[id] = [id, deps, factory];
183
- } else {
184
- runFactory(id, deps, factory);
185
- }
186
- }
187
- define.require = function(id) {
188
- if (loaderCache[id]) {
189
- return loaderCache[id];
190
- }
191
- if (defineCache[id]) {
192
- runFactory.apply(null, defineCache[id]);
193
- return loaderCache[id];
194
- }
195
- };
196
- define.amd = {};
197
- return define;
198
- }
199
- module.exports = amdefine;
200
- })(require("process"));
@@ -1,24 +0,0 @@
1
- /* */
2
- var inserted,
3
- Module = require("module"),
4
- fs = require("fs"),
5
- existingExtFn = Module._extensions['.js'],
6
- amdefineRegExp = /amdefine\.js/;
7
- inserted = "if (typeof define !== 'function') {var define = require('amdefine')(module)}";
8
- function stripBOM(content) {
9
- if (content.charCodeAt(0) === 0xFEFF) {
10
- content = content.slice(1);
11
- }
12
- return content;
13
- }
14
- function intercept(module, filename) {
15
- var content = stripBOM(fs.readFileSync(filename, 'utf8'));
16
- if (!amdefineRegExp.test(module.id)) {
17
- content = inserted + content;
18
- }
19
- module._compile(content, filename);
20
- }
21
- intercept._id = 'amdefine/intercept';
22
- if (!existingExtFn._id || existingExtFn._id !== intercept._id) {
23
- Module._extensions['.js'] = intercept;
24
- }
@@ -1,16 +0,0 @@
1
- {
2
- "name": "amdefine",
3
- "description": "Provide AMD's define() API for declaring modules in the AMD format",
4
- "version": "1.0.0",
5
- "homepage": "http://github.com/jrburke/amdefine",
6
- "author": "James Burke <jrburke@gmail.com> (http://github.com/jrburke)",
7
- "license": "BSD-3-Clause AND MIT",
8
- "repository": {
9
- "type": "git",
10
- "url": "https://github.com/jrburke/amdefine.git"
11
- },
12
- "main": "./amdefine.js",
13
- "engines": {
14
- "node": ">=0.4.2"
15
- }
16
- }
@@ -1 +0,0 @@
1
- module.exports = require("npm:amdefine@1.0.0/amdefine");
@@ -1,20 +0,0 @@
1
- Copyright (c) 2012 Andrew Nesbitt
2
-
3
- Permission is hereby granted, free of charge, to any person obtaining
4
- a copy of this software and associated documentation files (the
5
- "Software"), to deal in the Software without restriction, including
6
- without limitation the rights to use, copy, modify, merge, publish,
7
- distribute, sublicense, and/or sell copies of the Software, and to
8
- permit persons to whom the Software is furnished to do so, subject to
9
- the following conditions:
10
-
11
- The above copyright notice and this permission notice shall be
12
- included in all copies or substantial portions of the Software.
13
-
14
- THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
15
- EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF
16
- MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
17
- NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT HOLDERS BE
18
- LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY, WHETHER IN AN ACTION
19
- OF CONTRACT, TORT OR OTHERWISE, ARISING FROM, OUT OF OR IN CONNECTION
20
- WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE SOFTWARE.
@@ -1,30 +0,0 @@
1
- # Base62.js
2
- [![build status](https://secure.travis-ci.org/andrew/base62.js.png)](http://travis-ci.org/andrew/base62.js)
3
-
4
- A javascript Base62 encode/decoder for node.js
5
-
6
- ## Install
7
-
8
- npm install base62
9
-
10
- ## Usage
11
-
12
- Base62 = require('base62')
13
- Base62.encode(999) // 'g7'
14
- Base62.decode('g7') // 999
15
-
16
- ## Development
17
-
18
- Source hosted at [GitHub](http://github.com/andrew/base62.js).
19
- Report Issues/Feature requests on [GitHub Issues](http://github.com/andrew/split/base62.js).
20
-
21
- ### Note on Patches/Pull Requests
22
-
23
- * Fork the project.
24
- * Make your feature addition or bug fix.
25
- * Add tests for it. This is important so I don't break it in a future version unintentionally.
26
- * Send me a pull request. Bonus points for topic branches.
27
-
28
- ## Copyright
29
-
30
- Copyright (c) 2012 Andrew Nesbitt. See [LICENSE](https://github.com/andrew/base62.js/blob/master/LICENSE) for details.
@@ -1,28 +0,0 @@
1
- /* */
2
- var Base62 = (function (my) {
3
- my.chars = ["0", "1", "2", "3", "4", "5", "6", "7", "8", "9", "a", "b", "c", "d", "e", "f", "g", "h", "i", "j", "k", "l", "m", "n", "o", "p", "q", "r", "s", "t", "u", "v", "w", "x", "y", "z", "A", "B", "C", "D", "E", "F", "G", "H", "I", "J", "K", "L", "M", "N", "O", "P", "Q", "R", "S", "T", "U", "V", "W", "X", "Y", "Z"]
4
-
5
- my.encode = function(i){
6
- if (i === 0) {return '0'}
7
- var s = ''
8
- while (i > 0) {
9
- s = this.chars[i % 62] + s
10
- i = Math.floor(i/62)
11
- }
12
- return s
13
- };
14
- my.decode = function(a,b,c,d){
15
- for (
16
- b = c = (
17
- a === (/\W|_|^$/.test(a += "") || a)
18
- ) - 1;
19
- d = a.charCodeAt(c++);
20
- )
21
- b = b * 62 + d - [, 48, 29, 87][d >> 5];
22
- return b
23
- };
24
-
25
- return my;
26
- }({}));
27
-
28
- module.exports = Base62
@@ -1,21 +0,0 @@
1
- {
2
- "author": "Andrew Nesbitt <andrewnez@gmail.com> (http://andrew-nesbitt.com/)",
3
- "name": "base62",
4
- "description": "Javascript Base62 encode/decoder",
5
- "keywords": ["base-62"],
6
- "version": "0.1.1",
7
- "repository": {
8
- "type": "git",
9
- "url": "git://github.com/andrew/base62.js.git"
10
- },
11
- "main": "base62.js",
12
- "engines": {
13
- "node": "*"
14
- },
15
- "scripts": {
16
- "test": "mocha test"
17
- },
18
- "devDependencies": {
19
- "mocha": "1.7.x"
20
- }
21
- }
@@ -1,13 +0,0 @@
1
- /* */
2
- var assert = require("assert");
3
- var Base62 = require("../base62");
4
- describe("encode", function() {
5
- it("should encode a number to a Base62 string", function() {
6
- assert.equal(Base62.encode(999), 'g7');
7
- });
8
- });
9
- describe("decode", function() {
10
- it("should decode a number from a Base62 string", function() {
11
- assert.equal(Base62.decode('g7'), 999);
12
- });
13
- });
@@ -1 +0,0 @@
1
- module.exports = require("npm:base62@0.1.1/base62");