sequenceserver 2.0.0 → 2.1.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
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
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  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
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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?
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-
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- npm has a lot of weaknesses for front-end use (installed layout is not great,
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- should have better support for the `baseUrl + moduleID + '.js' style of loading,
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- single file JS installs), but some people want a JS package manager and are
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- willing to live with those constraints. If that is you, but still want to author
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- in AMD style modules to get dynamic require([]), better direct source usage and
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- powerful loader plugin support in the browser, then this tool can help.
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-
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- #### amdefine/intercept usage
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-
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");