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
@@ -1,37 +1,39 @@
1
- # buffer [![travis][travis-image]][travis-url] [![npm][npm-image]][npm-url] [![downloads][downloads-image]][npm-url]
1
+ # buffer [![travis][travis-image]][travis-url] [![npm][npm-image]][npm-url] [![downloads][downloads-image]][downloads-url] [![javascript style guide][standard-image]][standard-url]
2
2
 
3
- #### The buffer module from [node.js](http://nodejs.org/), for the browser.
3
+ [travis-image]: https://img.shields.io/travis/feross/buffer/master.svg
4
+ [travis-url]: https://travis-ci.org/feross/buffer
5
+ [npm-image]: https://img.shields.io/npm/v/buffer.svg
6
+ [npm-url]: https://npmjs.org/package/buffer
7
+ [downloads-image]: https://img.shields.io/npm/dm/buffer.svg
8
+ [downloads-url]: https://npmjs.org/package/buffer
9
+ [standard-image]: https://img.shields.io/badge/code_style-standard-brightgreen.svg
10
+ [standard-url]: https://standardjs.com
11
+
12
+ #### The buffer module from [node.js](https://nodejs.org/), for the browser.
4
13
 
5
14
  [![saucelabs][saucelabs-image]][saucelabs-url]
6
15
 
7
- [travis-image]: https://img.shields.io/travis/feross/buffer.svg?style=flat
8
- [travis-url]: https://travis-ci.org/feross/buffer
9
- [npm-image]: https://img.shields.io/npm/v/buffer.svg?style=flat
10
- [npm-url]: https://npmjs.org/package/buffer
11
- [downloads-image]: https://img.shields.io/npm/dm/buffer.svg?style=flat
12
16
  [saucelabs-image]: https://saucelabs.com/browser-matrix/buffer.svg
13
17
  [saucelabs-url]: https://saucelabs.com/u/buffer
14
18
 
15
19
  With [browserify](http://browserify.org), simply `require('buffer')` or use the `Buffer` global and you will get this module.
16
20
 
17
21
  The goal is to provide an API that is 100% identical to
18
- [node's Buffer API](http://iojs.org/api/buffer.html). Read the
19
- [official docs](http://iojs.org/api/buffer.html) for the full list of properties,
22
+ [node's Buffer API](https://nodejs.org/api/buffer.html). Read the
23
+ [official docs](https://nodejs.org/api/buffer.html) for the full list of properties,
20
24
  instance methods, and class methods that are supported.
21
25
 
22
26
  ## features
23
27
 
24
- - Manipulate binary data like a boss, in all browsers -- even IE6!
28
+ - Manipulate binary data like a boss, in all browsers!
25
29
  - Super fast. Backed by Typed Arrays (`Uint8Array`/`ArrayBuffer`, not `Object`)
26
- - Extremely small bundle size (**5.04KB minified + gzipped**, 35.5KB with comments)
27
- - Excellent browser support (IE 6+, Chrome 4+, Firefox 3+, Safari 5.1+, Opera 11+, iOS, etc.)
28
- - Preserves Node API exactly, with one important difference (see below)
29
- - `.slice()` returns instances of the same type (Buffer)
30
- - Square-bracket `buf[4]` notation works, even in old browsers like IE6!
30
+ - Extremely small bundle size (**6.75KB minified + gzipped**, 51.9KB with comments)
31
+ - Excellent browser support (Chrome, Firefox, Edge, Safari 9+, IE 11, iOS 9+, Android, etc.)
32
+ - Preserves Node API exactly, with one minor difference (see below)
33
+ - Square-bracket `buf[4]` notation works!
31
34
  - Does not modify any browser prototypes or put anything on `window`
32
35
  - Comprehensive test suite (including all buffer tests from node.js core)
33
36
 
34
-
35
37
  ## install
36
38
 
37
39
  To use this module directly (without browserify), install it:
@@ -43,11 +45,12 @@ npm install buffer
43
45
  This module was previously called **native-buffer-browserify**, but please use **buffer**
44
46
  from now on.
45
47
 
48
+ If you do not use a bundler, you can use the [standalone script](https://bundle.run/buffer).
46
49
 
47
50
  ## usage
48
51
 
49
52
  The module's API is identical to node's `Buffer` API. Read the
50
- [official docs](http://iojs.org/api/buffer.html) for the full list of properties,
53
+ [official docs](https://nodejs.org/api/buffer.html) for the full list of properties,
51
54
  instance methods, and class methods that are supported.
52
55
 
53
56
  As mentioned above, `require('buffer')` or use the `Buffer` global with
@@ -68,41 +71,77 @@ instead of the **node.js core** module named `buffer`!
68
71
 
69
72
  ## how does it work?
70
73
 
71
- The `Buffer` constructor returns instances of `Uint8Array` that are augmented with function properties for all the `Buffer` API functions. We use `Uint8Array` so that square bracket notation works as expected -- it returns a single octet. By augmenting the instances, we can avoid modifying the `Uint8Array` prototype.
74
+ The Buffer constructor returns instances of `Uint8Array` that have their prototype
75
+ changed to `Buffer.prototype`. Furthermore, `Buffer` is a subclass of `Uint8Array`,
76
+ so the returned instances will have all the node `Buffer` methods and the
77
+ `Uint8Array` methods. Square bracket notation works as expected -- it returns a
78
+ single octet.
72
79
 
80
+ The `Uint8Array` prototype remains unmodified.
73
81
 
74
- ## differences
75
82
 
76
- #### IMPORTANT: always use `Buffer.isBuffer` instead of `instanceof Buffer`
83
+ ## tracking the latest node api
77
84
 
78
- The Buffer constructor returns a `Uint8Array` (with all the Buffer methods added as
79
- properties on the instance) for performance reasons, so `instanceof Buffer` won't work. In
80
- node, you can use either `Buffer.isBuffer` or `instanceof Buffer` to check if an object
81
- is a `Buffer`. But, in the browser you must use `Buffer.isBuffer` to detect the special
82
- `Uint8Array`-based Buffers.
85
+ This module tracks the Buffer API in the latest (unstable) version of node.js. The Buffer
86
+ API is considered **stable** in the
87
+ [node stability index](https://nodejs.org/docs/latest/api/documentation.html#documentation_stability_index),
88
+ so it is unlikely that there will ever be breaking changes.
89
+ Nonetheless, when/if the Buffer API changes in node, this module's API will change
90
+ accordingly.
83
91
 
84
- #### Minor: `buf.slice()` does not modify parent buffer's memory in old browsers
92
+ ## related packages
85
93
 
86
- If you only support modern browsers (specifically, those with typed array support), then
87
- this issue does not affect you.
94
+ - [`buffer-reverse`](https://www.npmjs.com/package/buffer-reverse) - Reverse a buffer
95
+ - [`buffer-xor`](https://www.npmjs.com/package/buffer-xor) - Bitwise xor a buffer
96
+ - [`is-buffer`](https://www.npmjs.com/package/is-buffer) - Determine if an object is a Buffer without including the whole `Buffer` package
88
97
 
89
- In node, the `slice()` method returns a new `Buffer` that shares underlying memory with
90
- the original Buffer. When you modify one buffer, you modify the other. [Read more.](http://iojs.org/api/buffer.html#buffer_buf_slice_start_end)
98
+ ## conversion packages
91
99
 
92
- This works correctly in browsers with typed array support (\* with the exception of Firefox older than version 30). Browsers that lack typed arrays get an alternate buffer implementation based on `Object` which has no mechanism to point separate `Buffer`s to the same underlying slab of memory.
100
+ ### convert typed array to buffer
93
101
 
94
- \* *Firefox older than version 30 gets the `Object` implementation -- not the typed arrays one -- because of [this
95
- bug](https://bugzilla.mozilla.org/show_bug.cgi?id=952403) (now fixed!) that made it impossible to add properties to a typed array.*
102
+ Use [`typedarray-to-buffer`](https://www.npmjs.com/package/typedarray-to-buffer) to convert any kind of typed array to a `Buffer`. Does not perform a copy, so it's super fast.
96
103
 
104
+ ### convert buffer to typed array
97
105
 
98
- ## tracking the latest node api
106
+ `Buffer` is a subclass of `Uint8Array` (which is a typed array). So there is no need to explicitly convert to typed array. Just use the buffer as a `Uint8Array`.
99
107
 
100
- This module tracks the Buffer API in the latest (unstable) version of node.js. The Buffer
101
- API is considered **stable** in the
102
- [node stability index](http://nodejs.org/docs/latest/api/documentation.html#documentation_stability_index),
103
- so it is unlikely that there will ever be breaking changes.
104
- Nonetheless, when/if the Buffer API changes in node, this module's API will change
105
- accordingly.
108
+ ### convert blob to buffer
109
+
110
+ Use [`blob-to-buffer`](https://www.npmjs.com/package/blob-to-buffer) to convert a `Blob` to a `Buffer`.
111
+
112
+ ### convert buffer to blob
113
+
114
+ To convert a `Buffer` to a `Blob`, use the `Blob` constructor:
115
+
116
+ ```js
117
+ var blob = new Blob([ buffer ])
118
+ ```
119
+
120
+ Optionally, specify a mimetype:
121
+
122
+ ```js
123
+ var blob = new Blob([ buffer ], { type: 'text/html' })
124
+ ```
125
+
126
+ ### convert arraybuffer to buffer
127
+
128
+ To convert an `ArrayBuffer` to a `Buffer`, use the `Buffer.from` function. Does not perform a copy, so it's super fast.
129
+
130
+ ```js
131
+ var buffer = Buffer.from(arrayBuffer)
132
+ ```
133
+
134
+ ### convert buffer to arraybuffer
135
+
136
+ To convert a `Buffer` to an `ArrayBuffer`, use the `.buffer` property (which is present on all `Uint8Array` objects):
137
+
138
+ ```js
139
+ var arrayBuffer = buffer.buffer.slice(
140
+ buffer.byteOffset, buffer.byteOffset + buffer.byteLength
141
+ )
142
+ ```
143
+
144
+ Alternatively, use the [`to-arraybuffer`](https://www.npmjs.com/package/to-arraybuffer) module.
106
145
 
107
146
  ## performance
108
147
 
@@ -113,6 +152,8 @@ sanity check (since `BrowserBuffer` uses `Uint8Array` under the hood, `Uint8Arra
113
152
  always be at least a bit faster). Finally, `NodeBuffer` is the node.js buffer module,
114
153
  which is included to compare against.
115
154
 
155
+ NOTE: Performance has improved since these benchmarks were taken. PR welcome to update the README.
156
+
116
157
  ### Chrome 38
117
158
 
118
159
  | Method | Operations | Accuracy | Sampled | Fastest |
@@ -323,17 +364,46 @@ which is included to compare against.
323
364
  | NodeBuffer#writeFloatBE | 135,763 ops/sec | ±0.65% | 96 | |
324
365
  | | | | |
325
366
 
367
+ ## Testing the project
368
+
369
+ First, install the project:
370
+
371
+ npm install
372
+
373
+ Then, to run tests in Node.js, run:
374
+
375
+ npm run test-node
376
+
377
+ To test locally in a browser, you can run:
378
+
379
+ npm run test-browser-es5-local # For ES5 browsers that don't support ES6
380
+ npm run test-browser-es6-local # For ES6 compliant browsers
381
+
382
+ This will print out a URL that you can then open in a browser to run the tests, using [airtap](https://www.npmjs.com/package/airtap).
383
+
384
+ To run automated browser tests using Saucelabs, ensure that your `SAUCE_USERNAME` and `SAUCE_ACCESS_KEY` environment variables are set, then run:
385
+
386
+ npm test
387
+
388
+ This is what's run in Travis, to check against various browsers. The list of browsers is kept in the `bin/airtap-es5.yml` and `bin/airtap-es6.yml` files.
389
+
326
390
  ## JavaScript Standard Style
327
391
 
328
392
  This module uses [JavaScript Standard Style](https://github.com/feross/standard).
329
393
 
330
- [![js-standard-style](https://raw.githubusercontent.com/feross/standard/master/badge.png)](https://github.com/feross/standard)
394
+ [![JavaScript Style Guide](https://cdn.rawgit.com/feross/standard/master/badge.svg)](https://github.com/feross/standard)
395
+
396
+ To test that the code conforms to the style, `npm install` and run:
331
397
 
398
+ ./node_modules/.bin/standard
332
399
 
333
400
  ## credit
334
401
 
335
402
  This was originally forked from [buffer-browserify](https://github.com/toots/buffer-browserify).
336
403
 
404
+ ## Security Policies and Procedures
405
+
406
+ The `buffer` team and community take all security bugs in `buffer` seriously. Please see our [security policies and procedures](https://github.com/feross/security) document to learn how to report issues.
337
407
 
338
408
  ## license
339
409
 
@@ -0,0 +1,186 @@
1
+ export class Buffer extends Uint8Array {
2
+ length: number
3
+ write(string: string, offset?: number, length?: number, encoding?: string): number;
4
+ toString(encoding?: string, start?: number, end?: number): string;
5
+ toJSON(): { type: 'Buffer', data: any[] };
6
+ equals(otherBuffer: Buffer): boolean;
7
+ compare(otherBuffer: Buffer, targetStart?: number, targetEnd?: number, sourceStart?: number, sourceEnd?: number): number;
8
+ copy(targetBuffer: Buffer, targetStart?: number, sourceStart?: number, sourceEnd?: number): number;
9
+ slice(start?: number, end?: number): Buffer;
10
+ writeUIntLE(value: number, offset: number, byteLength: number, noAssert?: boolean): number;
11
+ writeUIntBE(value: number, offset: number, byteLength: number, noAssert?: boolean): number;
12
+ writeIntLE(value: number, offset: number, byteLength: number, noAssert?: boolean): number;
13
+ writeIntBE(value: number, offset: number, byteLength: number, noAssert?: boolean): number;
14
+ readUIntLE(offset: number, byteLength: number, noAssert?: boolean): number;
15
+ readUIntBE(offset: number, byteLength: number, noAssert?: boolean): number;
16
+ readIntLE(offset: number, byteLength: number, noAssert?: boolean): number;
17
+ readIntBE(offset: number, byteLength: number, noAssert?: boolean): number;
18
+ readUInt8(offset: number, noAssert?: boolean): number;
19
+ readUInt16LE(offset: number, noAssert?: boolean): number;
20
+ readUInt16BE(offset: number, noAssert?: boolean): number;
21
+ readUInt32LE(offset: number, noAssert?: boolean): number;
22
+ readUInt32BE(offset: number, noAssert?: boolean): number;
23
+ readInt8(offset: number, noAssert?: boolean): number;
24
+ readInt16LE(offset: number, noAssert?: boolean): number;
25
+ readInt16BE(offset: number, noAssert?: boolean): number;
26
+ readInt32LE(offset: number, noAssert?: boolean): number;
27
+ readInt32BE(offset: number, noAssert?: boolean): number;
28
+ readFloatLE(offset: number, noAssert?: boolean): number;
29
+ readFloatBE(offset: number, noAssert?: boolean): number;
30
+ readDoubleLE(offset: number, noAssert?: boolean): number;
31
+ readDoubleBE(offset: number, noAssert?: boolean): number;
32
+ reverse(): this;
33
+ swap16(): Buffer;
34
+ swap32(): Buffer;
35
+ swap64(): Buffer;
36
+ writeUInt8(value: number, offset: number, noAssert?: boolean): number;
37
+ writeUInt16LE(value: number, offset: number, noAssert?: boolean): number;
38
+ writeUInt16BE(value: number, offset: number, noAssert?: boolean): number;
39
+ writeUInt32LE(value: number, offset: number, noAssert?: boolean): number;
40
+ writeUInt32BE(value: number, offset: number, noAssert?: boolean): number;
41
+ writeInt8(value: number, offset: number, noAssert?: boolean): number;
42
+ writeInt16LE(value: number, offset: number, noAssert?: boolean): number;
43
+ writeInt16BE(value: number, offset: number, noAssert?: boolean): number;
44
+ writeInt32LE(value: number, offset: number, noAssert?: boolean): number;
45
+ writeInt32BE(value: number, offset: number, noAssert?: boolean): number;
46
+ writeFloatLE(value: number, offset: number, noAssert?: boolean): number;
47
+ writeFloatBE(value: number, offset: number, noAssert?: boolean): number;
48
+ writeDoubleLE(value: number, offset: number, noAssert?: boolean): number;
49
+ writeDoubleBE(value: number, offset: number, noAssert?: boolean): number;
50
+ fill(value: any, offset?: number, end?: number): this;
51
+ indexOf(value: string | number | Buffer, byteOffset?: number, encoding?: string): number;
52
+ lastIndexOf(value: string | number | Buffer, byteOffset?: number, encoding?: string): number;
53
+ includes(value: string | number | Buffer, byteOffset?: number, encoding?: string): boolean;
54
+
55
+ /**
56
+ * Allocates a new buffer containing the given {str}.
57
+ *
58
+ * @param str String to store in buffer.
59
+ * @param encoding encoding to use, optional. Default is 'utf8'
60
+ */
61
+ constructor (str: string, encoding?: string);
62
+ /**
63
+ * Allocates a new buffer of {size} octets.
64
+ *
65
+ * @param size count of octets to allocate.
66
+ */
67
+ constructor (size: number);
68
+ /**
69
+ * Allocates a new buffer containing the given {array} of octets.
70
+ *
71
+ * @param array The octets to store.
72
+ */
73
+ constructor (array: Uint8Array);
74
+ /**
75
+ * Produces a Buffer backed by the same allocated memory as
76
+ * the given {ArrayBuffer}.
77
+ *
78
+ *
79
+ * @param arrayBuffer The ArrayBuffer with which to share memory.
80
+ */
81
+ constructor (arrayBuffer: ArrayBuffer);
82
+ /**
83
+ * Allocates a new buffer containing the given {array} of octets.
84
+ *
85
+ * @param array The octets to store.
86
+ */
87
+ constructor (array: any[]);
88
+ /**
89
+ * Copies the passed {buffer} data onto a new {Buffer} instance.
90
+ *
91
+ * @param buffer The buffer to copy.
92
+ */
93
+ constructor (buffer: Buffer);
94
+ prototype: Buffer;
95
+ /**
96
+ * Allocates a new Buffer using an {array} of octets.
97
+ *
98
+ * @param array
99
+ */
100
+ static from(array: any[]): Buffer;
101
+ /**
102
+ * When passed a reference to the .buffer property of a TypedArray instance,
103
+ * the newly created Buffer will share the same allocated memory as the TypedArray.
104
+ * The optional {byteOffset} and {length} arguments specify a memory range
105
+ * within the {arrayBuffer} that will be shared by the Buffer.
106
+ *
107
+ * @param arrayBuffer The .buffer property of a TypedArray or a new ArrayBuffer()
108
+ * @param byteOffset
109
+ * @param length
110
+ */
111
+ static from(arrayBuffer: ArrayBuffer, byteOffset?: number, length?: number): Buffer;
112
+ /**
113
+ * Copies the passed {buffer} data onto a new Buffer instance.
114
+ *
115
+ * @param buffer
116
+ */
117
+ static from(buffer: Buffer | Uint8Array): Buffer;
118
+ /**
119
+ * Creates a new Buffer containing the given JavaScript string {str}.
120
+ * If provided, the {encoding} parameter identifies the character encoding.
121
+ * If not provided, {encoding} defaults to 'utf8'.
122
+ *
123
+ * @param str
124
+ */
125
+ static from(str: string, encoding?: string): Buffer;
126
+ /**
127
+ * Returns true if {obj} is a Buffer
128
+ *
129
+ * @param obj object to test.
130
+ */
131
+ static isBuffer(obj: any): obj is Buffer;
132
+ /**
133
+ * Returns true if {encoding} is a valid encoding argument.
134
+ * Valid string encodings in Node 0.12: 'ascii'|'utf8'|'utf16le'|'ucs2'(alias of 'utf16le')|'base64'|'binary'(deprecated)|'hex'
135
+ *
136
+ * @param encoding string to test.
137
+ */
138
+ static isEncoding(encoding: string): boolean;
139
+ /**
140
+ * Gives the actual byte length of a string. encoding defaults to 'utf8'.
141
+ * This is not the same as String.prototype.length since that returns the number of characters in a string.
142
+ *
143
+ * @param string string to test.
144
+ * @param encoding encoding used to evaluate (defaults to 'utf8')
145
+ */
146
+ static byteLength(string: string, encoding?: string): number;
147
+ /**
148
+ * Returns a buffer which is the result of concatenating all the buffers in the list together.
149
+ *
150
+ * If the list has no items, or if the totalLength is 0, then it returns a zero-length buffer.
151
+ * If the list has exactly one item, then the first item of the list is returned.
152
+ * If the list has more than one item, then a new Buffer is created.
153
+ *
154
+ * @param list An array of Buffer objects to concatenate
155
+ * @param totalLength Total length of the buffers when concatenated.
156
+ * If totalLength is not provided, it is read from the buffers in the list. However, this adds an additional loop to the function, so it is faster to provide the length explicitly.
157
+ */
158
+ static concat(list: Buffer[], totalLength?: number): Buffer;
159
+ /**
160
+ * The same as buf1.compare(buf2).
161
+ */
162
+ static compare(buf1: Buffer, buf2: Buffer): number;
163
+ /**
164
+ * Allocates a new buffer of {size} octets.
165
+ *
166
+ * @param size count of octets to allocate.
167
+ * @param fill if specified, buffer will be initialized by calling buf.fill(fill).
168
+ * If parameter is omitted, buffer will be filled with zeros.
169
+ * @param encoding encoding used for call to buf.fill while initializing
170
+ */
171
+ static alloc(size: number, fill?: string | Buffer | number, encoding?: string): Buffer;
172
+ /**
173
+ * Allocates a new buffer of {size} octets, leaving memory not initialized, so the contents
174
+ * of the newly created Buffer are unknown and may contain sensitive data.
175
+ *
176
+ * @param size count of octets to allocate
177
+ */
178
+ static allocUnsafe(size: number): Buffer;
179
+ /**
180
+ * Allocates a new non-pooled buffer of {size} octets, leaving memory not initialized, so the contents
181
+ * of the newly created Buffer are unknown and may contain sensitive data.
182
+ *
183
+ * @param size count of octets to allocate
184
+ */
185
+ static allocUnsafeSlow(size: number): Buffer;
186
+ }