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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@@ -1,112 +0,0 @@
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- # Change Log
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-
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- ## 0.1.31
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-
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- * Delay parsing the mappings in SourceMapConsumer until queried for a source
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- location.
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-
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- * Support Sass source maps (which at the time of writing deviate from the spec
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- in small ways) in SourceMapConsumer.
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-
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- ## 0.1.30
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-
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- * Do not join source root with a source, when the source is a data URI.
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-
15
- * Extend the test runner to allow running single specific test files at a time.
16
-
17
- * Performance improvements in `SourceNode.prototype.walk` and
18
- `SourceMapConsumer.prototype.eachMapping`.
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-
20
- * Source map browser builds will now work inside Workers.
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-
22
- * Better error messages when attempting to add an invalid mapping to a
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- `SourceMapGenerator`.
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-
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- ## 0.1.29
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-
27
- * Allow duplicate entries in the `names` and `sources` arrays of source maps
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- (usually from TypeScript) we are parsing. Fixes github isse 72.
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-
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- ## 0.1.28
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-
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- * Skip duplicate mappings when creating source maps from SourceNode; github
33
- issue 75.
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-
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- ## 0.1.27
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-
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- * Don't throw an error when the `file` property is missing in SourceMapConsumer,
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- we don't use it anyway.
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-
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- ## 0.1.26
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-
42
- * Fix SourceNode.fromStringWithSourceMap for empty maps. Fixes github issue 70.
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-
44
- ## 0.1.25
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-
46
- * Make compatible with browserify
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-
48
- ## 0.1.24
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-
50
- * Fix issue with absolute paths and `file://` URIs. See
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- https://bugzilla.mozilla.org/show_bug.cgi?id=885597
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-
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- ## 0.1.23
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-
55
- * Fix issue with absolute paths and sourcesContent, github issue 64.
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-
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- ## 0.1.22
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-
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- * Ignore duplicate mappings in SourceMapGenerator. Fixes github issue 21.
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-
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- ## 0.1.21
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-
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- * Fixed handling of sources that start with a slash so that they are relative to
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- the source root's host.
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-
66
- ## 0.1.20
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-
68
- * Fixed github issue #43: absolute URLs aren't joined with the source root
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- anymore.
70
-
71
- ## 0.1.19
72
-
73
- * Using Travis CI to run tests.
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-
75
- ## 0.1.18
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-
77
- * Fixed a bug in the handling of sourceRoot.
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-
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- ## 0.1.17
80
-
81
- * Added SourceNode.fromStringWithSourceMap.
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-
83
- ## 0.1.16
84
-
85
- * Added missing documentation.
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-
87
- * Fixed the generating of empty mappings in SourceNode.
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-
89
- ## 0.1.15
90
-
91
- * Added SourceMapGenerator.applySourceMap.
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-
93
- ## 0.1.14
94
-
95
- * The sourceRoot is now handled consistently.
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-
97
- ## 0.1.13
98
-
99
- * Added SourceMapGenerator.fromSourceMap.
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-
101
- ## 0.1.12
102
-
103
- * SourceNode now generates empty mappings too.
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-
105
- ## 0.1.11
106
-
107
- * Added name support to SourceNode.
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-
109
- ## 0.1.10
110
-
111
- * Added sourcesContent support to the customer and generator.
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-
@@ -1,28 +0,0 @@
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-
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- Copyright (c) 2009-2011, Mozilla Foundation and contributors
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- All rights reserved.
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-
5
- Redistribution and use in source and binary forms, with or without
6
- modification, are permitted provided that the following conditions are met:
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-
8
- * Redistributions of source code must retain the above copyright notice, this
9
- list of conditions and the following disclaimer.
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-
11
- * Redistributions in binary form must reproduce the above copyright notice,
12
- this list of conditions and the following disclaimer in the documentation
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- and/or other materials provided with the distribution.
14
-
15
- * Neither the names of the Mozilla Foundation nor the names of project
16
- contributors may be used to endorse or promote products derived from this
17
- software without specific prior written permission.
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-
19
- 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
21
- WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
22
- DISCLAIMED. IN NO EVENT SHALL THE COPYRIGHT HOLDER OR CONTRIBUTORS BE LIABLE
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- FOR ANY DIRECT, INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL
24
- DAMAGES (INCLUDING, BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR
25
- SERVICES; LOSS OF USE, DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER
26
- CAUSED AND ON ANY THEORY OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY,
27
- OR TORT (INCLUDING NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE
28
- OF THIS SOFTWARE, EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
@@ -1,89 +0,0 @@
1
- /* */
2
- "format cjs";
3
- var path = require("path");
4
- var fs = require("fs");
5
- var copy = require("dryice").copy;
6
- function removeAmdefine(src) {
7
- src = String(src).replace(/if\s*\(typeof\s*define\s*!==\s*'function'\)\s*{\s*var\s*define\s*=\s*require\('amdefine'\)\(module,\s*require\);\s*}\s*/g, '');
8
- src = src.replace(/\b(define\(.*)('amdefine',?)/gm, '$1');
9
- return src;
10
- }
11
- removeAmdefine.onRead = true;
12
- function makeNonRelative(src) {
13
- return src.replace(/require\('.\//g, 'require(\'source-map/').replace(/\.\.\/\.\.\/lib\//g, '');
14
- }
15
- makeNonRelative.onRead = true;
16
- function buildBrowser() {
17
- console.log('\nCreating dist/source-map.js');
18
- var project = copy.createCommonJsProject({roots: [path.join(__dirname, 'lib')]});
19
- copy({
20
- source: ['build/mini-require.js', {
21
- project: project,
22
- require: ['source-map/source-map-generator', 'source-map/source-map-consumer', 'source-map/source-node']
23
- }, 'build/suffix-browser.js'],
24
- filter: [copy.filter.moduleDefines, removeAmdefine],
25
- dest: 'dist/source-map.js'
26
- });
27
- }
28
- function buildBrowserMin() {
29
- console.log('\nCreating dist/source-map.min.js');
30
- copy({
31
- source: 'dist/source-map.js',
32
- filter: copy.filter.uglifyjs,
33
- dest: 'dist/source-map.min.js'
34
- });
35
- }
36
- function buildFirefox() {
37
- console.log('\nCreating dist/SourceMap.jsm');
38
- var project = copy.createCommonJsProject({roots: [path.join(__dirname, 'lib')]});
39
- copy({
40
- source: ['build/prefix-source-map.jsm', {
41
- project: project,
42
- require: ['source-map/source-map-consumer', 'source-map/source-map-generator', 'source-map/source-node']
43
- }, 'build/suffix-source-map.jsm'],
44
- filter: [copy.filter.moduleDefines, removeAmdefine, makeNonRelative],
45
- dest: 'dist/SourceMap.jsm'
46
- });
47
- console.log('\nCreating dist/test/Utils.jsm');
48
- project = copy.createCommonJsProject({roots: [__dirname, path.join(__dirname, 'lib')]});
49
- copy({
50
- source: ['build/prefix-utils.jsm', 'build/assert-shim.js', {
51
- project: project,
52
- require: ['test/source-map/util']
53
- }, 'build/suffix-utils.jsm'],
54
- filter: [copy.filter.moduleDefines, removeAmdefine, makeNonRelative],
55
- dest: 'dist/test/Utils.jsm'
56
- });
57
- function isTestFile(f) {
58
- return /^test\-.*?\.js/.test(f);
59
- }
60
- var testFiles = fs.readdirSync(path.join(__dirname, 'test', 'source-map')).filter(isTestFile);
61
- testFiles.forEach(function(testFile) {
62
- console.log('\nCreating', path.join('dist', 'test', testFile.replace(/\-/g, '_')));
63
- copy({
64
- source: ['build/test-prefix.js', path.join('test', 'source-map', testFile), 'build/test-suffix.js'],
65
- filter: [removeAmdefine, makeNonRelative, function(input, source) {
66
- return input.replace('define(', 'define("' + path.join('test', 'source-map', testFile.replace(/\.js$/, '')) + '", ["require", "exports", "module"], ');
67
- }, function(input, source) {
68
- return input.replace('{THIS_MODULE}', function() {
69
- return "test/source-map/" + testFile.replace(/\.js$/, '');
70
- });
71
- }],
72
- dest: path.join('dist', 'test', testFile.replace(/\-/g, '_'))
73
- });
74
- });
75
- }
76
- function ensureDir(name) {
77
- var dirExists = false;
78
- try {
79
- dirExists = fs.statSync(name).isDirectory();
80
- } catch (err) {}
81
- if (!dirExists) {
82
- fs.mkdirSync(name, 0777);
83
- }
84
- }
85
- ensureDir("dist");
86
- ensureDir("dist/test");
87
- buildFirefox();
88
- buildBrowser();
89
- buildBrowserMin();
@@ -1,434 +0,0 @@
1
- # Source Map
2
-
3
- This is a library to generate and consume the source map format
4
- [described here][format].
5
-
6
- This library is written in the Asynchronous Module Definition format, and works
7
- in the following environments:
8
-
9
- * Modern Browsers supporting ECMAScript 5 (either after the build, or with an
10
- AMD loader such as RequireJS)
11
-
12
- * Inside Firefox (as a JSM file, after the build)
13
-
14
- * With NodeJS versions 0.8.X and higher
15
-
16
- ## Node
17
-
18
- $ npm install source-map
19
-
20
- ## Building from Source (for everywhere else)
21
-
22
- Install Node and then run
23
-
24
- $ git clone https://fitzgen@github.com/mozilla/source-map.git
25
- $ cd source-map
26
- $ npm link .
27
-
28
- Next, run
29
-
30
- $ node Makefile.dryice.js
31
-
32
- This should spew a bunch of stuff to stdout, and create the following files:
33
-
34
- * `dist/source-map.js` - The unminified browser version.
35
-
36
- * `dist/source-map.min.js` - The minified browser version.
37
-
38
- * `dist/SourceMap.jsm` - The JavaScript Module for inclusion in Firefox source.
39
-
40
- ## Examples
41
-
42
- ### Consuming a source map
43
-
44
- var rawSourceMap = {
45
- version: 3,
46
- file: 'min.js',
47
- names: ['bar', 'baz', 'n'],
48
- sources: ['one.js', 'two.js'],
49
- sourceRoot: 'http://example.com/www/js/',
50
- mappings: 'CAAC,IAAI,IAAM,SAAUA,GAClB,OAAOC,IAAID;CCDb,IAAI,IAAM,SAAUE,GAClB,OAAOA'
51
- };
52
-
53
- var smc = new SourceMapConsumer(rawSourceMap);
54
-
55
- console.log(smc.sources);
56
- // [ 'http://example.com/www/js/one.js',
57
- // 'http://example.com/www/js/two.js' ]
58
-
59
- console.log(smc.originalPositionFor({
60
- line: 2,
61
- column: 28
62
- }));
63
- // { source: 'http://example.com/www/js/two.js',
64
- // line: 2,
65
- // column: 10,
66
- // name: 'n' }
67
-
68
- console.log(smc.generatedPositionFor({
69
- source: 'http://example.com/www/js/two.js',
70
- line: 2,
71
- column: 10
72
- }));
73
- // { line: 2, column: 28 }
74
-
75
- smc.eachMapping(function (m) {
76
- // ...
77
- });
78
-
79
- ### Generating a source map
80
-
81
- In depth guide:
82
- [**Compiling to JavaScript, and Debugging with Source Maps**](https://hacks.mozilla.org/2013/05/compiling-to-javascript-and-debugging-with-source-maps/)
83
-
84
- #### With SourceNode (high level API)
85
-
86
- function compile(ast) {
87
- switch (ast.type) {
88
- case 'BinaryExpression':
89
- return new SourceNode(
90
- ast.location.line,
91
- ast.location.column,
92
- ast.location.source,
93
- [compile(ast.left), " + ", compile(ast.right)]
94
- );
95
- case 'Literal':
96
- return new SourceNode(
97
- ast.location.line,
98
- ast.location.column,
99
- ast.location.source,
100
- String(ast.value)
101
- );
102
- // ...
103
- default:
104
- throw new Error("Bad AST");
105
- }
106
- }
107
-
108
- var ast = parse("40 + 2", "add.js");
109
- console.log(compile(ast).toStringWithSourceMap({
110
- file: 'add.js'
111
- }));
112
- // { code: '40 + 2',
113
- // map: [object SourceMapGenerator] }
114
-
115
- #### With SourceMapGenerator (low level API)
116
-
117
- var map = new SourceMapGenerator({
118
- file: "source-mapped.js"
119
- });
120
-
121
- map.addMapping({
122
- generated: {
123
- line: 10,
124
- column: 35
125
- },
126
- source: "foo.js",
127
- original: {
128
- line: 33,
129
- column: 2
130
- },
131
- name: "christopher"
132
- });
133
-
134
- console.log(map.toString());
135
- // '{"version":3,"file":"source-mapped.js","sources":["foo.js"],"names":["christopher"],"mappings":";;;;;;;;;mCAgCEA"}'
136
-
137
- ## API
138
-
139
- Get a reference to the module:
140
-
141
- // NodeJS
142
- var sourceMap = require('source-map');
143
-
144
- // Browser builds
145
- var sourceMap = window.sourceMap;
146
-
147
- // Inside Firefox
148
- let sourceMap = {};
149
- Components.utils.import('resource:///modules/devtools/SourceMap.jsm', sourceMap);
150
-
151
- ### SourceMapConsumer
152
-
153
- A SourceMapConsumer instance represents a parsed source map which we can query
154
- for information about the original file positions by giving it a file position
155
- in the generated source.
156
-
157
- #### new SourceMapConsumer(rawSourceMap)
158
-
159
- The only parameter is the raw source map (either as a string which can be
160
- `JSON.parse`'d, or an object). According to the spec, source maps have the
161
- following attributes:
162
-
163
- * `version`: Which version of the source map spec this map is following.
164
-
165
- * `sources`: An array of URLs to the original source files.
166
-
167
- * `names`: An array of identifiers which can be referrenced by individual
168
- mappings.
169
-
170
- * `sourceRoot`: Optional. The URL root from which all sources are relative.
171
-
172
- * `sourcesContent`: Optional. An array of contents of the original source files.
173
-
174
- * `mappings`: A string of base64 VLQs which contain the actual mappings.
175
-
176
- * `file`: The generated filename this source map is associated with.
177
-
178
- #### SourceMapConsumer.prototype.originalPositionFor(generatedPosition)
179
-
180
- Returns the original source, line, and column information for the generated
181
- source's line and column positions provided. The only argument is an object with
182
- the following properties:
183
-
184
- * `line`: The line number in the generated source.
185
-
186
- * `column`: The column number in the generated source.
187
-
188
- and an object is returned with the following properties:
189
-
190
- * `source`: The original source file, or null if this information is not
191
- available.
192
-
193
- * `line`: The line number in the original source, or null if this information is
194
- not available.
195
-
196
- * `column`: The column number in the original source, or null or null if this
197
- information is not available.
198
-
199
- * `name`: The original identifier, or null if this information is not available.
200
-
201
- #### SourceMapConsumer.prototype.generatedPositionFor(originalPosition)
202
-
203
- Returns the generated line and column information for the original source,
204
- line, and column positions provided. The only argument is an object with
205
- the following properties:
206
-
207
- * `source`: The filename of the original source.
208
-
209
- * `line`: The line number in the original source.
210
-
211
- * `column`: The column number in the original source.
212
-
213
- and an object is returned with the following properties:
214
-
215
- * `line`: The line number in the generated source, or null.
216
-
217
- * `column`: The column number in the generated source, or null.
218
-
219
- #### SourceMapConsumer.prototype.sourceContentFor(source)
220
-
221
- Returns the original source content for the source provided. The only
222
- argument is the URL of the original source file.
223
-
224
- #### SourceMapConsumer.prototype.eachMapping(callback, context, order)
225
-
226
- Iterate over each mapping between an original source/line/column and a
227
- generated line/column in this source map.
228
-
229
- * `callback`: The function that is called with each mapping. Mappings have the
230
- form `{ source, generatedLine, generatedColumn, originalLine, originalColumn,
231
- name }`
232
-
233
- * `context`: Optional. If specified, this object will be the value of `this`
234
- every time that `callback` is called.
235
-
236
- * `order`: Either `SourceMapConsumer.GENERATED_ORDER` or
237
- `SourceMapConsumer.ORIGINAL_ORDER`. Specifies whether you want to iterate over
238
- the mappings sorted by the generated file's line/column order or the
239
- original's source/line/column order, respectively. Defaults to
240
- `SourceMapConsumer.GENERATED_ORDER`.
241
-
242
- ### SourceMapGenerator
243
-
244
- An instance of the SourceMapGenerator represents a source map which is being
245
- built incrementally.
246
-
247
- #### new SourceMapGenerator(startOfSourceMap)
248
-
249
- To create a new one, you must pass an object with the following properties:
250
-
251
- * `file`: The filename of the generated source that this source map is
252
- associated with.
253
-
254
- * `sourceRoot`: An optional root for all relative URLs in this source map.
255
-
256
- #### SourceMapGenerator.fromSourceMap(sourceMapConsumer)
257
-
258
- Creates a new SourceMapGenerator based on a SourceMapConsumer
259
-
260
- * `sourceMapConsumer` The SourceMap.
261
-
262
- #### SourceMapGenerator.prototype.addMapping(mapping)
263
-
264
- Add a single mapping from original source line and column to the generated
265
- source's line and column for this source map being created. The mapping object
266
- should have the following properties:
267
-
268
- * `generated`: An object with the generated line and column positions.
269
-
270
- * `original`: An object with the original line and column positions.
271
-
272
- * `source`: The original source file (relative to the sourceRoot).
273
-
274
- * `name`: An optional original token name for this mapping.
275
-
276
- #### SourceMapGenerator.prototype.setSourceContent(sourceFile, sourceContent)
277
-
278
- Set the source content for an original source file.
279
-
280
- * `sourceFile` the URL of the original source file.
281
-
282
- * `sourceContent` the content of the source file.
283
-
284
- #### SourceMapGenerator.prototype.applySourceMap(sourceMapConsumer[, sourceFile])
285
-
286
- Applies a SourceMap for a source file to the SourceMap.
287
- Each mapping to the supplied source file is rewritten using the
288
- supplied SourceMap. Note: The resolution for the resulting mappings
289
- is the minimium of this map and the supplied map.
290
-
291
- * `sourceMapConsumer`: The SourceMap to be applied.
292
-
293
- * `sourceFile`: Optional. The filename of the source file.
294
- If omitted, sourceMapConsumer.file will be used.
295
-
296
- #### SourceMapGenerator.prototype.toString()
297
-
298
- Renders the source map being generated to a string.
299
-
300
- ### SourceNode
301
-
302
- SourceNodes provide a way to abstract over interpolating and/or concatenating
303
- snippets of generated JavaScript source code, while maintaining the line and
304
- column information associated between those snippets and the original source
305
- code. This is useful as the final intermediate representation a compiler might
306
- use before outputting the generated JS and source map.
307
-
308
- #### new SourceNode(line, column, source[, chunk[, name]])
309
-
310
- * `line`: The original line number associated with this source node, or null if
311
- it isn't associated with an original line.
312
-
313
- * `column`: The original column number associated with this source node, or null
314
- if it isn't associated with an original column.
315
-
316
- * `source`: The original source's filename.
317
-
318
- * `chunk`: Optional. Is immediately passed to `SourceNode.prototype.add`, see
319
- below.
320
-
321
- * `name`: Optional. The original identifier.
322
-
323
- #### SourceNode.fromStringWithSourceMap(code, sourceMapConsumer)
324
-
325
- Creates a SourceNode from generated code and a SourceMapConsumer.
326
-
327
- * `code`: The generated code
328
-
329
- * `sourceMapConsumer` The SourceMap for the generated code
330
-
331
- #### SourceNode.prototype.add(chunk)
332
-
333
- Add a chunk of generated JS to this source node.
334
-
335
- * `chunk`: A string snippet of generated JS code, another instance of
336
- `SourceNode`, or an array where each member is one of those things.
337
-
338
- #### SourceNode.prototype.prepend(chunk)
339
-
340
- Prepend a chunk of generated JS to this source node.
341
-
342
- * `chunk`: A string snippet of generated JS code, another instance of
343
- `SourceNode`, or an array where each member is one of those things.
344
-
345
- #### SourceNode.prototype.setSourceContent(sourceFile, sourceContent)
346
-
347
- Set the source content for a source file. This will be added to the
348
- `SourceMap` in the `sourcesContent` field.
349
-
350
- * `sourceFile`: The filename of the source file
351
-
352
- * `sourceContent`: The content of the source file
353
-
354
- #### SourceNode.prototype.walk(fn)
355
-
356
- Walk over the tree of JS snippets in this node and its children. The walking
357
- function is called once for each snippet of JS and is passed that snippet and
358
- the its original associated source's line/column location.
359
-
360
- * `fn`: The traversal function.
361
-
362
- #### SourceNode.prototype.walkSourceContents(fn)
363
-
364
- Walk over the tree of SourceNodes. The walking function is called for each
365
- source file content and is passed the filename and source content.
366
-
367
- * `fn`: The traversal function.
368
-
369
- #### SourceNode.prototype.join(sep)
370
-
371
- Like `Array.prototype.join` except for SourceNodes. Inserts the separator
372
- between each of this source node's children.
373
-
374
- * `sep`: The separator.
375
-
376
- #### SourceNode.prototype.replaceRight(pattern, replacement)
377
-
378
- Call `String.prototype.replace` on the very right-most source snippet. Useful
379
- for trimming whitespace from the end of a source node, etc.
380
-
381
- * `pattern`: The pattern to replace.
382
-
383
- * `replacement`: The thing to replace the pattern with.
384
-
385
- #### SourceNode.prototype.toString()
386
-
387
- Return the string representation of this source node. Walks over the tree and
388
- concatenates all the various snippets together to one string.
389
-
390
- ### SourceNode.prototype.toStringWithSourceMap(startOfSourceMap)
391
-
392
- Returns the string representation of this tree of source nodes, plus a
393
- SourceMapGenerator which contains all the mappings between the generated and
394
- original sources.
395
-
396
- The arguments are the same as those to `new SourceMapGenerator`.
397
-
398
- ## Tests
399
-
400
- [![Build Status](https://travis-ci.org/mozilla/source-map.png?branch=master)](https://travis-ci.org/mozilla/source-map)
401
-
402
- Install NodeJS version 0.8.0 or greater, then run `node test/run-tests.js`.
403
-
404
- To add new tests, create a new file named `test/test-<your new test name>.js`
405
- and export your test functions with names that start with "test", for example
406
-
407
- exports["test doing the foo bar"] = function (assert, util) {
408
- ...
409
- };
410
-
411
- The new test will be located automatically when you run the suite.
412
-
413
- The `util` argument is the test utility module located at `test/source-map/util`.
414
-
415
- The `assert` argument is a cut down version of node's assert module. You have
416
- access to the following assertion functions:
417
-
418
- * `doesNotThrow`
419
-
420
- * `equal`
421
-
422
- * `ok`
423
-
424
- * `strictEqual`
425
-
426
- * `throws`
427
-
428
- (The reason for the restricted set of test functions is because we need the
429
- tests to run inside Firefox's test suite as well and so the assert module is
430
- shimmed in that environment. See `build/assert-shim.js`.)
431
-
432
- [format]: https://docs.google.com/document/d/1U1RGAehQwRypUTovF1KRlpiOFze0b-_2gc6fAH0KY0k/edit
433
- [feature]: https://wiki.mozilla.org/DevTools/Features/SourceMap
434
- [Dryice]: https://github.com/mozilla/dryice