sequenceserver 2.0.0.rc8 → 2.1.0

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Files changed (758) hide show
  1. checksums.yaml +4 -4
  2. data/bin/sequenceserver +22 -30
  3. data/lib/sequenceserver/api_errors.rb +29 -3
  4. data/lib/sequenceserver/blast/constants.rb +1 -1
  5. data/lib/sequenceserver/blast/hit.rb +5 -16
  6. data/lib/sequenceserver/blast/job.rb +49 -24
  7. data/lib/sequenceserver/blast/report.rb +38 -30
  8. data/lib/sequenceserver/config.rb +52 -27
  9. data/lib/sequenceserver/database.rb +69 -9
  10. data/lib/sequenceserver/job.rb +14 -4
  11. data/lib/sequenceserver/job_remover.rb +25 -29
  12. data/lib/sequenceserver/makeblastdb.rb +40 -45
  13. data/lib/sequenceserver/refinements.rb +15 -0
  14. data/lib/sequenceserver/routes.rb +70 -4
  15. data/lib/sequenceserver/sequence.rb +8 -7
  16. data/lib/sequenceserver/sys.rb +2 -2
  17. data/lib/sequenceserver/version.rb +1 -1
  18. data/lib/sequenceserver/zip_file_generator.rb +56 -0
  19. data/lib/sequenceserver.rb +16 -11
  20. data/public/config.js +62 -55
  21. data/public/css/fonts.css +23 -22
  22. data/public/css/grapher.css +598 -594
  23. data/public/css/sequenceserver.css +130 -27
  24. data/public/css/sequenceserver.min.css +3 -3
  25. data/public/js/alignment_exporter.js +30 -22
  26. data/public/js/circos.js +370 -234
  27. data/public/js/cloud_share_modal.js +216 -0
  28. data/public/js/databases.js +144 -0
  29. data/public/js/databases_tree.js +144 -0
  30. data/public/js/dnd.js +164 -0
  31. data/public/js/download_fasta.js +1 -1
  32. data/public/js/error_modal.js +4 -11
  33. data/public/js/exporter.js +7 -3
  34. data/public/js/form.js +260 -0
  35. data/public/js/grapher.js +113 -106
  36. data/public/js/hit.js +84 -67
  37. data/public/js/hits_overview.js +3 -3
  38. data/public/js/hsp.js +343 -288
  39. data/public/js/jquery_world.js +4 -4
  40. data/public/js/length_distribution.js +5 -5
  41. data/public/js/mailto.js +36 -0
  42. data/public/js/options.js +84 -0
  43. data/public/js/query.js +321 -64
  44. data/public/js/report.js +322 -288
  45. data/public/js/report_root.js +75 -0
  46. data/public/js/search.js +28 -992
  47. data/public/js/search_button.js +195 -0
  48. data/public/js/sequence.js +2409 -2411
  49. data/public/js/sequence_modal.js +152 -159
  50. data/public/js/share_url.js +23 -0
  51. data/public/js/sidebar.js +265 -86
  52. data/public/js/svgExporter.js +12 -12
  53. data/public/js/tests/database.spec.js +60 -0
  54. data/public/js/tests/mock_data/databases.json +91 -0
  55. data/public/js/tests/mock_data/long_response.json +269 -0
  56. data/public/js/tests/mock_data/short_response.json +2240 -0
  57. data/public/js/tests/report.spec.js +99 -0
  58. data/public/js/tests/search_button.spec.js +14 -0
  59. data/public/js/tests/search_query.spec.js +41 -0
  60. data/public/js/visualisation_helpers.js +4 -5
  61. data/public/packages/circosJS@1.7.0.js +1640 -0
  62. data/public/packages/jquery-ui@1.11.4.js +16624 -0
  63. data/public/sequenceserver-report.min.js +2425 -19
  64. data/public/sequenceserver-search.min.js +2337 -11
  65. data/public/vendor/github/jspm/nodelibs-assert@0.1.0/index.js +2 -0
  66. data/public/vendor/github/jspm/{nodelibs-buffer@0.1.0 → nodelibs-assert@0.1.0}/package.json +1 -1
  67. data/public/vendor/github/jspm/nodelibs-assert@0.1.0.js +1 -0
  68. data/public/vendor/github/jspm/nodelibs-buffer@0.1.1/package.json +6 -0
  69. data/public/vendor/github/jspm/nodelibs-buffer@0.1.1.js +1 -0
  70. data/public/vendor/github/jspm/{nodelibs-process@0.1.1 → nodelibs-process@0.1.2}/package.json +2 -2
  71. data/public/vendor/github/jspm/nodelibs-process@0.1.2.js +1 -0
  72. data/public/vendor/github/jspm/nodelibs-vm@0.1.0/index.js +2 -0
  73. data/public/vendor/github/jspm/nodelibs-vm@0.1.0/package.json +6 -0
  74. data/public/vendor/github/jspm/nodelibs-vm@0.1.0.js +1 -0
  75. data/public/vendor/github/vakata/jstree@3.3.8/LICENSE-MIT +22 -0
  76. data/public/vendor/github/vakata/jstree@3.3.8/README.md +663 -0
  77. data/public/vendor/github/vakata/jstree@3.3.8/bower.json +33 -0
  78. data/public/vendor/github/vakata/jstree@3.3.8/component.json +28 -0
  79. data/public/vendor/github/vakata/jstree@3.3.8/composer.json +46 -0
  80. data/public/vendor/github/vakata/jstree@3.3.8/demo/README.md +2 -0
  81. data/public/vendor/github/vakata/jstree@3.3.8/demo/basic/index.html +146 -0
  82. data/public/vendor/github/vakata/jstree@3.3.8/demo/basic/root.json +1 -0
  83. data/public/vendor/github/vakata/jstree@3.3.8/dist/jstree.js +8612 -0
  84. data/public/vendor/github/vakata/jstree@3.3.8/dist/jstree.min.js +6 -0
  85. data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default/32px.png +0 -0
  86. data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default/40px.png +0 -0
  87. data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default/style.css +1102 -0
  88. data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default/style.min.css +1 -0
  89. data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default/throbber.gif +0 -0
  90. data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default-dark/32px.png +0 -0
  91. data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default-dark/40px.png +0 -0
  92. data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default-dark/style.css +1146 -0
  93. data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default-dark/style.min.css +1 -0
  94. data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default-dark/throbber.gif +0 -0
  95. data/public/vendor/github/vakata/jstree@3.3.8/gruntfile.js +242 -0
  96. data/public/vendor/github/vakata/jstree@3.3.8/jstree.jquery.json +28 -0
  97. data/public/vendor/github/vakata/jstree@3.3.8/package.json +58 -0
  98. data/public/vendor/github/vakata/jstree@3.3.8/src/intro.js +14 -0
  99. data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.changed.js +69 -0
  100. data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.checkbox.js +976 -0
  101. data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.conditionalselect.js +38 -0
  102. data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.contextmenu.js +661 -0
  103. data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.dnd.js +669 -0
  104. data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.js +4931 -0
  105. data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.massload.js +137 -0
  106. data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.search.js +421 -0
  107. data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.sort.js +74 -0
  108. data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.state.js +138 -0
  109. data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.types.js +372 -0
  110. data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.unique.js +164 -0
  111. data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.wholerow.js +122 -0
  112. data/public/vendor/github/vakata/jstree@3.3.8/src/misc.js +656 -0
  113. data/public/vendor/github/vakata/jstree@3.3.8/src/outro.js +1 -0
  114. data/public/vendor/github/vakata/jstree@3.3.8/src/sample.js +93 -0
  115. data/public/vendor/github/vakata/jstree@3.3.8/src/themes/base.less +93 -0
  116. data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default/32px.png +0 -0
  117. data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default/40px.png +0 -0
  118. data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default/style.css +1102 -0
  119. data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default/style.less +22 -0
  120. data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default/throbber.gif +0 -0
  121. data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default-dark/32px.png +0 -0
  122. data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default-dark/40px.png +0 -0
  123. data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default-dark/style.css +1146 -0
  124. data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default-dark/style.less +50 -0
  125. data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default-dark/throbber.gif +0 -0
  126. data/public/vendor/github/vakata/jstree@3.3.8/src/themes/main.less +77 -0
  127. data/public/vendor/github/vakata/jstree@3.3.8/src/themes/mixins.less +104 -0
  128. data/public/vendor/github/vakata/jstree@3.3.8/src/themes/responsive.less +67 -0
  129. data/public/vendor/github/vakata/jstree@3.3.8/src/vakata-jstree.js +38 -0
  130. data/public/vendor/github/vakata/jstree@3.3.8/test/unit/index.html +16 -0
  131. data/public/vendor/github/vakata/jstree@3.3.8/test/unit/libs/qunit.css +244 -0
  132. data/public/vendor/github/vakata/jstree@3.3.8/test/unit/libs/qunit.js +2212 -0
  133. data/public/vendor/github/vakata/jstree@3.3.8/test/unit/test.js +11 -0
  134. data/public/vendor/github/vakata/jstree@3.3.8/test/visual/desktop/index.html +44 -0
  135. data/public/vendor/github/vakata/jstree@3.3.8/test/visual/mobile/index.html +42 -0
  136. data/public/vendor/github/vakata/jstree@3.3.8/test/visual/screenshots/desktop/desktop.png +0 -0
  137. data/public/vendor/github/vakata/jstree@3.3.8/test/visual/screenshots/desktop/home.png +0 -0
  138. data/public/vendor/github/vakata/jstree@3.3.8/test/visual/screenshots/mobile/home.png +0 -0
  139. data/public/vendor/github/vakata/jstree@3.3.8/test/visual/screenshots/mobile/mobile.png +0 -0
  140. data/public/vendor/github/vakata/jstree@3.3.8.js +3 -0
  141. data/public/vendor/npm/assert@1.5.0/CHANGELOG.md +8 -0
  142. data/public/vendor/npm/assert@1.5.0/README.md +105 -0
  143. data/public/vendor/npm/assert@1.5.0/assert.js +327 -0
  144. data/public/vendor/npm/assert@1.5.0/package.json +32 -0
  145. data/public/vendor/npm/assert@1.5.0/test.js +288 -0
  146. data/public/vendor/npm/assert@1.5.0.js +1 -0
  147. data/public/vendor/npm/{base64-js@0.0.8/LICENSE.MIT → base64-js@1.5.1/LICENSE} +1 -1
  148. data/public/vendor/npm/{base64-js@0.0.8 → base64-js@1.5.1}/README.md +10 -7
  149. data/public/vendor/npm/base64-js@1.5.1/base64js.min.js +3 -0
  150. data/public/vendor/npm/base64-js@1.5.1/index.d.ts +3 -0
  151. data/public/vendor/npm/base64-js@1.5.1/index.js +151 -0
  152. data/public/vendor/npm/base64-js@1.5.1/package.json +47 -0
  153. data/public/vendor/npm/base64-js@1.5.1.js +1 -0
  154. data/public/vendor/npm/buffer@5.7.1/AUTHORS.md +70 -0
  155. data/public/vendor/npm/{buffer@3.4.3 → buffer@5.7.1}/README.md +111 -41
  156. data/public/vendor/npm/buffer@5.7.1/index.d.ts +186 -0
  157. data/public/vendor/npm/buffer@5.7.1/index.js +1817 -0
  158. data/public/vendor/npm/buffer@5.7.1/package.json +96 -0
  159. data/public/vendor/npm/buffer@5.7.1.js +1 -0
  160. data/public/vendor/npm/core-util-is@1.0.3/LICENSE +19 -0
  161. data/public/vendor/npm/core-util-is@1.0.3/lib/util.js +64 -0
  162. data/public/vendor/npm/{core-util-is@1.0.1 → core-util-is@1.0.3}/package.json +13 -1
  163. data/public/vendor/npm/core-util-is@1.0.3.js +1 -0
  164. data/public/vendor/npm/events@1.0.2/tests/add-listeners.js +2 -2
  165. data/public/vendor/npm/events@1.0.2/tests/check-listener-leaks.js +3 -3
  166. data/public/vendor/npm/events@1.0.2/tests/common.js +1 -1
  167. data/public/vendor/npm/events@1.0.2/tests/index.js +13 -13
  168. data/public/vendor/npm/events@1.0.2/tests/listeners-side-effects.js +2 -2
  169. data/public/vendor/npm/events@1.0.2/tests/listeners.js +2 -2
  170. data/public/vendor/npm/events@1.0.2/tests/max-listeners.js +2 -2
  171. data/public/vendor/npm/events@1.0.2/tests/modify-in-emit.js +2 -2
  172. data/public/vendor/npm/events@1.0.2/tests/num-args.js +2 -2
  173. data/public/vendor/npm/events@1.0.2/tests/once.js +2 -2
  174. data/public/vendor/npm/events@1.0.2/tests/remove-all-listeners.js +3 -3
  175. data/public/vendor/npm/events@1.0.2/tests/remove-listeners.js +3 -3
  176. data/public/vendor/npm/events@1.0.2/tests/set-max-listeners-side-effects.js +2 -2
  177. data/public/vendor/npm/events@1.0.2/tests/subclass.js +3 -3
  178. data/public/vendor/npm/events@1.0.2.js +1 -1
  179. data/public/vendor/npm/ieee754@1.2.1/LICENSE +11 -0
  180. data/public/vendor/npm/{ieee754@1.1.6 → ieee754@1.2.1}/README.md +12 -8
  181. data/public/vendor/npm/ieee754@1.2.1/index.d.ts +10 -0
  182. data/public/vendor/npm/{ieee754@1.1.6 → ieee754@1.2.1}/index.js +6 -6
  183. data/public/vendor/npm/ieee754@1.2.1/package.json +52 -0
  184. data/public/vendor/npm/ieee754@1.2.1.js +1 -0
  185. data/public/vendor/npm/{is-array@1.0.1 → indexof@0.0.1}/Makefile +3 -3
  186. data/public/vendor/npm/indexof@0.0.1/Readme.md +15 -0
  187. data/public/vendor/npm/indexof@0.0.1/component.json +10 -0
  188. data/public/vendor/npm/indexof@0.0.1/index.js +11 -0
  189. data/public/vendor/npm/indexof@0.0.1/package.json +12 -0
  190. data/public/vendor/npm/indexof@0.0.1.js +1 -0
  191. data/public/vendor/npm/inherits@2.0.1/inherits.js +1 -1
  192. data/public/vendor/npm/inherits@2.0.1.js +1 -1
  193. data/public/vendor/npm/isarray@0.0.1.js +1 -1
  194. data/public/vendor/npm/js-tokens@4.0.0/index.js +23 -0
  195. data/public/vendor/npm/js-tokens@4.0.0/package.json +30 -0
  196. data/public/vendor/npm/js-tokens@4.0.0.js +1 -0
  197. data/public/vendor/npm/loose-envify@1.4.0/LICENSE +21 -0
  198. data/public/vendor/npm/loose-envify@1.4.0/README.md +45 -0
  199. data/public/vendor/npm/loose-envify@1.4.0/cli.js +12 -0
  200. data/public/vendor/npm/loose-envify@1.4.0/custom.js +3 -0
  201. data/public/vendor/npm/loose-envify@1.4.0/index.js +5 -0
  202. data/public/vendor/npm/loose-envify@1.4.0/loose-envify.js +33 -0
  203. data/public/vendor/npm/loose-envify@1.4.0/package.json +36 -0
  204. data/public/vendor/npm/loose-envify@1.4.0/replace.js +52 -0
  205. data/public/vendor/npm/loose-envify@1.4.0.js +1 -0
  206. data/public/vendor/npm/object-assign@4.1.1/index.js +90 -0
  207. data/public/vendor/npm/object-assign@4.1.1/package.json +42 -0
  208. data/public/vendor/npm/object-assign@4.1.1.js +1 -0
  209. data/public/vendor/npm/path-browserify@0.0.0/index.js +1 -1
  210. data/public/vendor/npm/path-browserify@0.0.0.js +1 -1
  211. data/public/vendor/npm/{process@0.10.1 → process@0.11.10}/README.md +4 -1
  212. data/public/vendor/npm/process@0.11.10/browser.js +184 -0
  213. data/public/vendor/npm/{process@0.10.1 → process@0.11.10}/package.json +10 -1
  214. data/public/vendor/npm/process@0.11.10/test.js +185 -0
  215. data/public/vendor/npm/process@0.11.10.js +1 -0
  216. data/public/vendor/npm/react-dom@18.0.0/LICENSE +21 -0
  217. data/public/vendor/npm/react-dom@18.0.0/README.md +50 -0
  218. data/public/vendor/npm/react-dom@18.0.0/cjs/react-dom-server-legacy.browser.development.js +4771 -0
  219. data/public/vendor/npm/react-dom@18.0.0/cjs/react-dom-server-legacy.browser.production.min.js +85 -0
  220. data/public/vendor/npm/react-dom@18.0.0/cjs/react-dom-server-legacy.node.development.js +4813 -0
  221. data/public/vendor/npm/react-dom@18.0.0/cjs/react-dom-server-legacy.node.production.min.js +1705 -0
  222. data/public/vendor/npm/react-dom@18.0.0/cjs/react-dom-server.browser.development.js +4746 -0
  223. data/public/vendor/npm/react-dom@18.0.0/cjs/react-dom-server.browser.production.min.js +90 -0
  224. data/public/vendor/npm/react-dom@18.0.0/cjs/react-dom-server.node.development.js +4714 -0
  225. data/public/vendor/npm/react-dom@18.0.0/cjs/react-dom-server.node.production.min.js +1746 -0
  226. data/public/vendor/npm/react-dom@18.0.0/cjs/react-dom-test-utils.development.js +1017 -0
  227. data/public/vendor/npm/react-dom@18.0.0/cjs/react-dom-test-utils.production.min.js +617 -0
  228. data/public/vendor/npm/react-dom@18.0.0/cjs/react-dom.development.js +20092 -0
  229. data/public/vendor/npm/react-dom@18.0.0/cjs/react-dom.production.min.js +322 -0
  230. data/public/vendor/npm/react-dom@18.0.0/cjs/react-dom.profiling.min.js +364 -0
  231. data/public/vendor/npm/react-dom@18.0.0/client.js +27 -0
  232. data/public/vendor/npm/react-dom@18.0.0/index.js +23 -0
  233. data/public/vendor/npm/react-dom@18.0.0/package.json +62 -0
  234. data/public/vendor/npm/react-dom@18.0.0/profiling.js +23 -0
  235. data/public/vendor/npm/react-dom@18.0.0/server.browser.js +19 -0
  236. data/public/vendor/npm/react-dom@18.0.0/server.js +3 -0
  237. data/public/vendor/npm/react-dom@18.0.0/server.node.js +19 -0
  238. data/public/vendor/npm/react-dom@18.0.0/test-utils.js +9 -0
  239. data/public/vendor/npm/react-dom@18.0.0/umd/react-dom-server-legacy.browser.development.js +4770 -0
  240. data/public/vendor/npm/react-dom@18.0.0/umd/react-dom-server-legacy.browser.production.min.js +72 -0
  241. data/public/vendor/npm/react-dom@18.0.0/umd/react-dom-server.browser.development.js +4745 -0
  242. data/public/vendor/npm/react-dom@18.0.0/umd/react-dom-server.browser.production.min.js +74 -0
  243. data/public/vendor/npm/react-dom@18.0.0/umd/react-dom-test-utils.development.js +1013 -0
  244. data/public/vendor/npm/react-dom@18.0.0/umd/react-dom-test-utils.production.min.js +625 -0
  245. data/public/vendor/npm/react-dom@18.0.0/umd/react-dom.development.js +20106 -0
  246. data/public/vendor/npm/react-dom@18.0.0/umd/react-dom.production.min.js +269 -0
  247. data/public/vendor/npm/react-dom@18.0.0/umd/react-dom.profiling.min.js +285 -0
  248. data/public/vendor/npm/react-dom@18.0.0.js +1 -0
  249. data/public/vendor/npm/react@18.0.0/LICENSE +21 -0
  250. data/public/vendor/npm/react@18.0.0/README.md +13 -0
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  729. data/public/vendor/npm/source-map@0.1.31/test/source-map/test-base64.js +0 -26
  730. data/public/vendor/npm/source-map@0.1.31/test/source-map/test-binary-search.js +0 -37
  731. data/public/vendor/npm/source-map@0.1.31/test/source-map/test-dog-fooding.js +0 -76
  732. data/public/vendor/npm/source-map@0.1.31/test/source-map/test-source-map-consumer.js +0 -426
  733. data/public/vendor/npm/source-map@0.1.31/test/source-map/test-source-map-generator.js +0 -480
  734. data/public/vendor/npm/source-map@0.1.31/test/source-map/test-source-node.js +0 -307
  735. data/public/vendor/npm/source-map@0.1.31/test/source-map/util.js +0 -84
  736. data/public/vendor/npm/source-map@0.1.31.js +0 -1
  737. data/public/vendor/npm/through@2.3.8/LICENSE.APACHE2 +0 -15
  738. data/public/vendor/npm/through@2.3.8/LICENSE.MIT +0 -24
  739. data/public/vendor/npm/through@2.3.8/index.js +0 -93
  740. data/public/vendor/npm/through@2.3.8/package.json +0 -36
  741. data/public/vendor/npm/through@2.3.8/readme.markdown +0 -64
  742. data/public/vendor/npm/through@2.3.8/test/async.js +0 -26
  743. data/public/vendor/npm/through@2.3.8/test/auto-destroy.js +0 -26
  744. data/public/vendor/npm/through@2.3.8/test/buffering.js +0 -57
  745. data/public/vendor/npm/through@2.3.8/test/end.js +0 -37
  746. data/public/vendor/npm/through@2.3.8/test/index.js +0 -98
  747. data/public/vendor/npm/through@2.3.8/test.js +0 -2
  748. data/public/vendor/npm/through@2.3.8.js +0 -1
  749. data/views/_options.erb +0 -135
  750. /data/public/vendor/github/jspm/{nodelibs-buffer@0.1.0 → nodelibs-buffer@0.1.1}/index.js +0 -0
  751. /data/public/vendor/github/jspm/{nodelibs-process@0.1.1 → nodelibs-process@0.1.2}/index.js +0 -0
  752. /data/public/vendor/npm/{readable-stream@1.1.13 → assert@1.5.0}/LICENSE +0 -0
  753. /data/public/vendor/npm/{buffer@3.4.3 → buffer@5.7.1}/LICENSE +0 -0
  754. /data/public/vendor/npm/{core-util-is@1.0.1 → core-util-is@1.0.3}/README.md +0 -0
  755. /data/public/vendor/npm/{process@0.10.1 → process@0.11.10}/LICENSE +0 -0
  756. /data/public/vendor/npm/{process@0.10.1 → process@0.11.10}/index.js +0 -0
  757. /data/public/vendor/npm/{readable-stream@1.1.13 → readable-stream@1.1.14}/README.md +0 -0
  758. /data/public/vendor/npm/{readable-stream@1.1.13 → readable-stream@1.1.14}/float.patch +0 -0
@@ -1,58 +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
- define('test/source-map/assert', ['exports'], function (exports) {
10
-
11
- let do_throw = function (msg) {
12
- throw new Error(msg);
13
- };
14
-
15
- exports.init = function (throw_fn) {
16
- do_throw = throw_fn;
17
- };
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-
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- exports.doesNotThrow = function (fn) {
20
- try {
21
- fn();
22
- }
23
- catch (e) {
24
- do_throw(e.message);
25
- }
26
- };
27
-
28
- exports.equal = function (actual, expected, msg) {
29
- msg = msg || String(actual) + ' != ' + String(expected);
30
- if (actual != expected) {
31
- do_throw(msg);
32
- }
33
- };
34
-
35
- exports.ok = function (val, msg) {
36
- msg = msg || String(val) + ' is falsey';
37
- if (!Boolean(val)) {
38
- do_throw(msg);
39
- }
40
- };
41
-
42
- exports.strictEqual = function (actual, expected, msg) {
43
- msg = msg || String(actual) + ' !== ' + String(expected);
44
- if (actual !== expected) {
45
- do_throw(msg);
46
- }
47
- };
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-
49
- exports.throws = function (fn) {
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- try {
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- fn();
52
- do_throw('Expected an error to be thrown, but it wasn\'t.');
53
- }
54
- catch (e) {
55
- }
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- };
57
-
58
- });
@@ -1,154 +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
-
10
- /**
11
- * Define a module along with a payload.
12
- * @param {string} moduleName Name for the payload
13
- * @param {ignored} deps Ignored. For compatibility with CommonJS AMD Spec
14
- * @param {function} payload Function with (require, exports, module) params
15
- */
16
- function define(moduleName, deps, payload) {
17
- if (typeof moduleName != "string") {
18
- throw new TypeError('Expected string, got: ' + moduleName);
19
- }
20
-
21
- if (arguments.length == 2) {
22
- payload = deps;
23
- }
24
-
25
- if (moduleName in define.modules) {
26
- throw new Error("Module already defined: " + moduleName);
27
- }
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- define.modules[moduleName] = payload;
29
- };
30
-
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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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-
36
-
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- /**
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- * We invoke require() in the context of a Domain so we can have multiple
39
- * sets of modules running separate from each other.
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- * This contrasts with JSMs which are singletons, Domains allows us to
41
- * optionally load a CommonJS module twice with separate data each time.
42
- * Perhaps you want 2 command lines with a different set of commands in each,
43
- * for example.
44
- */
45
- function Domain() {
46
- this.modules = {};
47
- this._currentModule = null;
48
- }
49
-
50
- (function () {
51
-
52
- /**
53
- * Lookup module names and resolve them by calling the definition function if
54
- * needed.
55
- * There are 2 ways to call this, either with an array of dependencies and a
56
- * callback to call when the dependencies are found (which can happen
57
- * asynchronously in an in-page context) or with a single string an no callback
58
- * where the dependency is resolved synchronously and returned.
59
- * The API is designed to be compatible with the CommonJS AMD spec and
60
- * RequireJS.
61
- * @param {string[]|string} deps A name, or names for the payload
62
- * @param {function|undefined} callback Function to call when the dependencies
63
- * are resolved
64
- * @return {undefined|object} The module required or undefined for
65
- * array/callback method
66
- */
67
- Domain.prototype.require = function(deps, callback) {
68
- if (Array.isArray(deps)) {
69
- var params = deps.map(function(dep) {
70
- return this.lookup(dep);
71
- }, this);
72
- if (callback) {
73
- callback.apply(null, params);
74
- }
75
- return undefined;
76
- }
77
- else {
78
- return this.lookup(deps);
79
- }
80
- };
81
-
82
- function normalize(path) {
83
- var bits = path.split('/');
84
- var i = 1;
85
- while (i < bits.length) {
86
- if (bits[i] === '..') {
87
- bits.splice(i-1, 1);
88
- } else if (bits[i] === '.') {
89
- bits.splice(i, 1);
90
- } else {
91
- i++;
92
- }
93
- }
94
- return bits.join('/');
95
- }
96
-
97
- function join(a, b) {
98
- a = a.trim();
99
- b = b.trim();
100
- if (/^\//.test(b)) {
101
- return b;
102
- } else {
103
- return a.replace(/\/*$/, '/') + b;
104
- }
105
- }
106
-
107
- function dirname(path) {
108
- var bits = path.split('/');
109
- bits.pop();
110
- return bits.join('/');
111
- }
112
-
113
- /**
114
- * Lookup module names and resolve them by calling the definition function if
115
- * needed.
116
- * @param {string} moduleName A name for the payload to lookup
117
- * @return {object} The module specified by aModuleName or null if not found.
118
- */
119
- Domain.prototype.lookup = function(moduleName) {
120
- if (/^\./.test(moduleName)) {
121
- moduleName = normalize(join(dirname(this._currentModule), moduleName));
122
- }
123
-
124
- if (moduleName in this.modules) {
125
- var module = this.modules[moduleName];
126
- return module;
127
- }
128
-
129
- if (!(moduleName in define.modules)) {
130
- throw new Error("Module not defined: " + moduleName);
131
- }
132
-
133
- var module = define.modules[moduleName];
134
-
135
- if (typeof module == "function") {
136
- var exports = {};
137
- var previousModule = this._currentModule;
138
- this._currentModule = moduleName;
139
- module(this.require.bind(this), exports, { id: moduleName, uri: "" });
140
- this._currentModule = previousModule;
141
- module = exports;
142
- }
143
-
144
- // cache the resulting module object for next time
145
- this.modules[moduleName] = module;
146
-
147
- return module;
148
- };
149
-
150
- }());
151
-
152
- define.Domain = Domain;
153
- define.globalDomain = new Domain();
154
- 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
- */
14
-
15
- ///////////////////////////////////////////////////////////////////////////////
16
-
17
-
18
- this.EXPORTED_SYMBOLS = [ "SourceMapConsumer", "SourceMapGenerator", "SourceNode" ];
19
-
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
- }
19
-
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
- });