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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@@ -1,58 +0,0 @@
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- /* */
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- "format cjs";
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- /* -*- Mode: js; js-indent-level: 2; -*- */
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- /*
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- * Copyright 2011 Mozilla Foundation and contributors
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- * Licensed under the New BSD license. See LICENSE or:
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- * http://opensource.org/licenses/BSD-3-Clause
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- */
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- define('test/source-map/assert', ['exports'], function (exports) {
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-
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- let do_throw = function (msg) {
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- throw new Error(msg);
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- };
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-
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- exports.init = function (throw_fn) {
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-
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- try {
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- fn();
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- }
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- catch (e) {
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- do_throw(e.message);
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- }
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- };
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-
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- exports.equal = function (actual, expected, msg) {
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- msg = msg || String(actual) + ' != ' + String(expected);
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- if (actual != expected) {
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- do_throw(msg);
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- }
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- };
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-
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- exports.ok = function (val, msg) {
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- msg = msg || String(val) + ' is falsey';
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- if (!Boolean(val)) {
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- do_throw(msg);
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- }
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- };
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-
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- msg = msg || String(actual) + ' !== ' + String(expected);
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- if (actual !== expected) {
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- do_throw(msg);
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- }
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- };
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-
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- catch (e) {
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- };
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- });
@@ -1,154 +0,0 @@
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- /* */
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- "format cjs";
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- /* -*- Mode: js; js-indent-level: 2; -*- */
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- /*
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- * Copyright 2011 Mozilla Foundation and contributors
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- * Licensed under the New BSD license. See LICENSE or:
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- * http://opensource.org/licenses/BSD-3-Clause
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- */
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-
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- /**
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- * Define a module along with a payload.
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- * @param {string} moduleName Name for the payload
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- * @param {ignored} deps Ignored. For compatibility with CommonJS AMD Spec
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- * @param {function} payload Function with (require, exports, module) params
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- */
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- function define(moduleName, deps, payload) {
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- if (typeof moduleName != "string") {
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- throw new TypeError('Expected string, got: ' + moduleName);
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- }
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-
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- if (arguments.length == 2) {
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- payload = deps;
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- }
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-
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- if (moduleName in define.modules) {
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- throw new Error("Module already defined: " + moduleName);
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- }
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- define.modules[moduleName] = payload;
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- };
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-
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- /**
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- * The global store of un-instantiated modules
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- */
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- define.modules = {};
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-
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-
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- /**
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- * We invoke require() in the context of a Domain so we can have multiple
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- * This contrasts with JSMs which are singletons, Domains allows us to
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- * optionally load a CommonJS module twice with separate data each time.
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- * Perhaps you want 2 command lines with a different set of commands in each,
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- * for example.
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- */
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- function Domain() {
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- this.modules = {};
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- this._currentModule = null;
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- }
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-
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- (function () {
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-
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- /**
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- * Lookup module names and resolve them by calling the definition function if
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- * needed.
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- * There are 2 ways to call this, either with an array of dependencies and a
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- * callback to call when the dependencies are found (which can happen
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- * asynchronously in an in-page context) or with a single string an no callback
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- * where the dependency is resolved synchronously and returned.
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- * The API is designed to be compatible with the CommonJS AMD spec and
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- * RequireJS.
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- * @param {string[]|string} deps A name, or names for the payload
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- * @param {function|undefined} callback Function to call when the dependencies
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- * are resolved
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- * @return {undefined|object} The module required or undefined for
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- * array/callback method
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- */
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- Domain.prototype.require = function(deps, callback) {
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- if (Array.isArray(deps)) {
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- var params = deps.map(function(dep) {
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- return this.lookup(dep);
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- }, this);
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- if (callback) {
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- callback.apply(null, params);
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- return undefined;
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- }
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- else {
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- return this.lookup(deps);
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- }
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- };
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-
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- function normalize(path) {
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- var i = 1;
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- while (i < bits.length) {
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- bits.splice(i-1, 1);
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- i++;
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- }
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- }
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- return bits.join('/');
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- }
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-
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- function join(a, b) {
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- a = a.trim();
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- b = b.trim();
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- if (/^\//.test(b)) {
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- return b;
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- } else {
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- return a.replace(/\/*$/, '/') + b;
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- }
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- }
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-
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- function dirname(path) {
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- var bits = path.split('/');
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- bits.pop();
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- return bits.join('/');
111
- }
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-
113
- /**
114
- * Lookup module names and resolve them by calling the definition function if
115
- * needed.
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- * @param {string} moduleName A name for the payload to lookup
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- * @return {object} The module specified by aModuleName or null if not found.
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- */
119
- Domain.prototype.lookup = function(moduleName) {
120
- if (/^\./.test(moduleName)) {
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- moduleName = normalize(join(dirname(this._currentModule), moduleName));
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- }
123
-
124
- if (moduleName in this.modules) {
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- var module = this.modules[moduleName];
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- return module;
127
- }
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-
129
- if (!(moduleName in define.modules)) {
130
- throw new Error("Module not defined: " + moduleName);
131
- }
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-
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- var module = define.modules[moduleName];
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-
135
- if (typeof module == "function") {
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- var exports = {};
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- var previousModule = this._currentModule;
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- this._currentModule = moduleName;
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- module(this.require.bind(this), exports, { id: moduleName, uri: "" });
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- this._currentModule = previousModule;
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- module = exports;
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- }
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-
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- // cache the resulting module object for next time
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- this.modules[moduleName] = module;
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-
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- return module;
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- };
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-
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- }());
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-
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- define.Domain = Domain;
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- define.globalDomain = new Domain();
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- var require = define.globalDomain.require.bind(define.globalDomain);
@@ -1,20 +0,0 @@
1
- /* -*- Mode: js; js-indent-level: 2; -*- */
2
- /*
3
- * Copyright 2011 Mozilla Foundation and contributors
4
- * Licensed under the New BSD license. See LICENSE or:
5
- * http://opensource.org/licenses/BSD-3-Clause
6
- */
7
-
8
- /*
9
- * WARNING!
10
- *
11
- * Do not edit this file directly, it is built from the sources at
12
- * https://github.com/mozilla/source-map/
13
- */
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-
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- ///////////////////////////////////////////////////////////////////////////////
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-
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-
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- this.EXPORTED_SYMBOLS = [ "SourceMapConsumer", "SourceMapGenerator", "SourceNode" ];
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-
20
- Components.utils.import('resource://gre/modules/devtools/Require.jsm');
@@ -1,18 +0,0 @@
1
- /* -*- Mode: js; js-indent-level: 2; -*- */
2
- /*
3
- * Copyright 2011 Mozilla Foundation and contributors
4
- * Licensed under the New BSD license. See LICENSE or:
5
- * http://opensource.org/licenses/BSD-3-Clause
6
- */
7
-
8
- /*
9
- * WARNING!
10
- *
11
- * Do not edit this file directly, it is built from the sources at
12
- * https://github.com/mozilla/source-map/
13
- */
14
-
15
- Components.utils.import('resource://gre/modules/devtools/Require.jsm');
16
- Components.utils.import('resource://gre/modules/devtools/SourceMap.jsm');
17
-
18
- this.EXPORTED_SYMBOLS = [ "define", "runSourceMapTests" ];
@@ -1,8 +0,0 @@
1
- /* -*- Mode: js; js-indent-level: 2; -*- */
2
- ///////////////////////////////////////////////////////////////////////////////
3
-
4
- this.sourceMap = {
5
- SourceMapConsumer: require('source-map/source-map-consumer').SourceMapConsumer,
6
- SourceMapGenerator: require('source-map/source-map-generator').SourceMapGenerator,
7
- SourceNode: require('source-map/source-node').SourceNode
8
- };
@@ -1,6 +0,0 @@
1
- /* -*- Mode: js; js-indent-level: 2; -*- */
2
- ///////////////////////////////////////////////////////////////////////////////
3
-
4
- this.SourceMapConsumer = require('source-map/source-map-consumer').SourceMapConsumer;
5
- this.SourceMapGenerator = require('source-map/source-map-generator').SourceMapGenerator;
6
- this.SourceNode = require('source-map/source-node').SourceNode;
@@ -1,21 +0,0 @@
1
- /* -*- Mode: js; js-indent-level: 2; -*- */
2
- /*
3
- * Copyright 2011 Mozilla Foundation and contributors
4
- * Licensed under the New BSD license. See LICENSE or:
5
- * http://opensource.org/licenses/BSD-3-Clause
6
- */
7
- function runSourceMapTests(modName, do_throw) {
8
- let mod = require(modName);
9
- let assert = require('test/source-map/assert');
10
- let util = require('test/source-map/util');
11
-
12
- assert.init(do_throw);
13
-
14
- for (let k in mod) {
15
- if (/^test/.test(k)) {
16
- mod[k](assert, util);
17
- }
18
- }
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-
20
- }
21
- this.runSourceMapTests = runSourceMapTests;
@@ -1,10 +0,0 @@
1
- /* */
2
- "format cjs";
3
- /*
4
- * WARNING!
5
- *
6
- * Do not edit this file directly, it is built from the sources at
7
- * https://github.com/mozilla/source-map/
8
- */
9
-
10
- Components.utils.import('resource://test/Utils.jsm');
@@ -1,5 +0,0 @@
1
- /* */
2
- "format cjs";
3
- function run_test() {
4
- runSourceMapTests('{THIS_MODULE}', do_throw);
5
- }
@@ -1,49 +0,0 @@
1
- /* */
2
- "format cjs";
3
- if (typeof define !== 'function') {
4
- var define = require("amdefine")(module, require);
5
- }
6
- define(function(require, exports, module) {
7
- var util = require("./util");
8
- function ArraySet() {
9
- this._array = [];
10
- this._set = {};
11
- }
12
- ArraySet.fromArray = function ArraySet_fromArray(aArray, aAllowDuplicates) {
13
- var set = new ArraySet();
14
- for (var i = 0,
15
- len = aArray.length; i < len; i++) {
16
- set.add(aArray[i], aAllowDuplicates);
17
- }
18
- return set;
19
- };
20
- ArraySet.prototype.add = function ArraySet_add(aStr, aAllowDuplicates) {
21
- var isDuplicate = this.has(aStr);
22
- var idx = this._array.length;
23
- if (!isDuplicate || aAllowDuplicates) {
24
- this._array.push(aStr);
25
- }
26
- if (!isDuplicate) {
27
- this._set[util.toSetString(aStr)] = idx;
28
- }
29
- };
30
- ArraySet.prototype.has = function ArraySet_has(aStr) {
31
- return Object.prototype.hasOwnProperty.call(this._set, util.toSetString(aStr));
32
- };
33
- ArraySet.prototype.indexOf = function ArraySet_indexOf(aStr) {
34
- if (this.has(aStr)) {
35
- return this._set[util.toSetString(aStr)];
36
- }
37
- throw new Error('"' + aStr + '" is not in the set.');
38
- };
39
- ArraySet.prototype.at = function ArraySet_at(aIdx) {
40
- if (aIdx >= 0 && aIdx < this._array.length) {
41
- return this._array[aIdx];
42
- }
43
- throw new Error('No element indexed by ' + aIdx);
44
- };
45
- ArraySet.prototype.toArray = function ArraySet_toArray() {
46
- return this._array.slice();
47
- };
48
- exports.ArraySet = ArraySet;
49
- });
@@ -1,56 +0,0 @@
1
- /* */
2
- "format cjs";
3
- if (typeof define !== 'function') {
4
- var define = require("amdefine")(module, require);
5
- }
6
- define(function(require, exports, module) {
7
- var base64 = require("./base64");
8
- var VLQ_BASE_SHIFT = 5;
9
- var VLQ_BASE = 1 << VLQ_BASE_SHIFT;
10
- var VLQ_BASE_MASK = VLQ_BASE - 1;
11
- var VLQ_CONTINUATION_BIT = VLQ_BASE;
12
- function toVLQSigned(aValue) {
13
- return aValue < 0 ? ((-aValue) << 1) + 1 : (aValue << 1) + 0;
14
- }
15
- function fromVLQSigned(aValue) {
16
- var isNegative = (aValue & 1) === 1;
17
- var shifted = aValue >> 1;
18
- return isNegative ? -shifted : shifted;
19
- }
20
- exports.encode = function base64VLQ_encode(aValue) {
21
- var encoded = "";
22
- var digit;
23
- var vlq = toVLQSigned(aValue);
24
- do {
25
- digit = vlq & VLQ_BASE_MASK;
26
- vlq >>>= VLQ_BASE_SHIFT;
27
- if (vlq > 0) {
28
- digit |= VLQ_CONTINUATION_BIT;
29
- }
30
- encoded += base64.encode(digit);
31
- } while (vlq > 0);
32
- return encoded;
33
- };
34
- exports.decode = function base64VLQ_decode(aStr) {
35
- var i = 0;
36
- var strLen = aStr.length;
37
- var result = 0;
38
- var shift = 0;
39
- var continuation,
40
- digit;
41
- do {
42
- if (i >= strLen) {
43
- throw new Error("Expected more digits in base 64 VLQ value.");
44
- }
45
- digit = base64.decode(aStr.charAt(i++));
46
- continuation = !!(digit & VLQ_CONTINUATION_BIT);
47
- digit &= VLQ_BASE_MASK;
48
- result = result + (digit << shift);
49
- shift += VLQ_BASE_SHIFT;
50
- } while (continuation);
51
- return {
52
- value: fromVLQSigned(result),
53
- rest: aStr.slice(i)
54
- };
55
- };
56
- });
@@ -1,44 +0,0 @@
1
- /* */
2
- "format cjs";
3
- /* -*- Mode: js; js-indent-level: 2; -*- */
4
- /*
5
- * Copyright 2011 Mozilla Foundation and contributors
6
- * Licensed under the New BSD license. See LICENSE or:
7
- * http://opensource.org/licenses/BSD-3-Clause
8
- */
9
- if (typeof define !== 'function') {
10
- var define = require('amdefine')(module, require);
11
- }
12
- define(function (require, exports, module) {
13
-
14
- var charToIntMap = {};
15
- var intToCharMap = {};
16
-
17
- 'ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklmnopqrstuvwxyz0123456789+/'
18
- .split('')
19
- .forEach(function (ch, index) {
20
- charToIntMap[ch] = index;
21
- intToCharMap[index] = ch;
22
- });
23
-
24
- /**
25
- * Encode an integer in the range of 0 to 63 to a single base 64 digit.
26
- */
27
- exports.encode = function base64_encode(aNumber) {
28
- if (aNumber in intToCharMap) {
29
- return intToCharMap[aNumber];
30
- }
31
- throw new TypeError("Must be between 0 and 63: " + aNumber);
32
- };
33
-
34
- /**
35
- * Decode a single base 64 digit to an integer.
36
- */
37
- exports.decode = function base64_decode(aChar) {
38
- if (aChar in charToIntMap) {
39
- return charToIntMap[aChar];
40
- }
41
- throw new TypeError("Not a valid base 64 digit: " + aChar);
42
- };
43
-
44
- });
@@ -1,83 +0,0 @@
1
- /* */
2
- "format cjs";
3
- /* -*- Mode: js; js-indent-level: 2; -*- */
4
- /*
5
- * Copyright 2011 Mozilla Foundation and contributors
6
- * Licensed under the New BSD license. See LICENSE or:
7
- * http://opensource.org/licenses/BSD-3-Clause
8
- */
9
- if (typeof define !== 'function') {
10
- var define = require('amdefine')(module, require);
11
- }
12
- define(function (require, exports, module) {
13
-
14
- /**
15
- * Recursive implementation of binary search.
16
- *
17
- * @param aLow Indices here and lower do not contain the needle.
18
- * @param aHigh Indices here and higher do not contain the needle.
19
- * @param aNeedle The element being searched for.
20
- * @param aHaystack The non-empty array being searched.
21
- * @param aCompare Function which takes two elements and returns -1, 0, or 1.
22
- */
23
- function recursiveSearch(aLow, aHigh, aNeedle, aHaystack, aCompare) {
24
- // This function terminates when one of the following is true:
25
- //
26
- // 1. We find the exact element we are looking for.
27
- //
28
- // 2. We did not find the exact element, but we can return the next
29
- // closest element that is less than that element.
30
- //
31
- // 3. We did not find the exact element, and there is no next-closest
32
- // element which is less than the one we are searching for, so we
33
- // return null.
34
- var mid = Math.floor((aHigh - aLow) / 2) + aLow;
35
- var cmp = aCompare(aNeedle, aHaystack[mid], true);
36
- if (cmp === 0) {
37
- // Found the element we are looking for.
38
- return aHaystack[mid];
39
- }
40
- else if (cmp > 0) {
41
- // aHaystack[mid] is greater than our needle.
42
- if (aHigh - mid > 1) {
43
- // The element is in the upper half.
44
- return recursiveSearch(mid, aHigh, aNeedle, aHaystack, aCompare);
45
- }
46
- // We did not find an exact match, return the next closest one
47
- // (termination case 2).
48
- return aHaystack[mid];
49
- }
50
- else {
51
- // aHaystack[mid] is less than our needle.
52
- if (mid - aLow > 1) {
53
- // The element is in the lower half.
54
- return recursiveSearch(aLow, mid, aNeedle, aHaystack, aCompare);
55
- }
56
- // The exact needle element was not found in this haystack. Determine if
57
- // we are in termination case (2) or (3) and return the appropriate thing.
58
- return aLow < 0
59
- ? null
60
- : aHaystack[aLow];
61
- }
62
- }
63
-
64
- /**
65
- * This is an implementation of binary search which will always try and return
66
- * the next lowest value checked if there is no exact hit. This is because
67
- * mappings between original and generated line/col pairs are single points,
68
- * and there is an implicit region between each of them, so a miss just means
69
- * that you aren't on the very start of a region.
70
- *
71
- * @param aNeedle The element you are looking for.
72
- * @param aHaystack The array that is being searched.
73
- * @param aCompare A function which takes the needle and an element in the
74
- * array and returns -1, 0, or 1 depending on whether the needle is less
75
- * than, equal to, or greater than the element, respectively.
76
- */
77
- exports.search = function search(aNeedle, aHaystack, aCompare) {
78
- return aHaystack.length > 0
79
- ? recursiveSearch(-1, aHaystack.length, aNeedle, aHaystack, aCompare)
80
- : null;
81
- };
82
-
83
- });