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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- exports.isSymbol = isSymbol;
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- exports.isUndefined = isUndefined;
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- function isRegExp(re) {
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- return isObject(re) && objectToString(re) === '[object RegExp]';
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- }
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- exports.isRegExp = isRegExp;
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- function isObject(arg) {
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- }
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- exports.isObject = isObject;
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- function isDate(d) {
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- return isObject(d) && objectToString(d) === '[object Date]';
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- }
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- exports.isDate = isDate;
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- function isError(e) {
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- exports.isError = isError;
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- function isFunction(arg) {
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- return typeof arg === 'function';
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- }
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- exports.isFunction = isFunction;
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- module.exports = require("npm:core-util-is@1.0.1/lib/util");
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- # envify [![Build Status](https://secure.travis-ci.org/hughsk/envify.png?branch=master)](http://travis-ci.org/hughsk/envify) [![stable](http://hughsk.github.io/stability-badges/dist/stable.svg)](http://github.com/hughsk/stability-badges) #
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-
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- [Browserify](http://browserify.org) v2 transform.
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-
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- ## Installation ##
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-
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-
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- ``` bash
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- ```
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-
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- ``` bash
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- ```
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-
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- ## Usage ##
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-
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-
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- ``` javascript
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- if (process.env.NODE_ENV === "development") {
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- console.log('development only')
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- ```
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-
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- ``` javascript
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- if ("production" === "development") {
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- console.log('development only')
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- }
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- ```
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-
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- By running this through a good minifier (e.g.
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- [UglifyJS2](https://github.com/mishoo/UglifyJS)), the above code would be
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- stripped out completely.
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-
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- However, if you bundled the same script with `NODE_ENV` set to `development`:
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-
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- ``` javascript
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- if ("development" === "development") {
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- console.log('development only')
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- }
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- ```
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-
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- The `if` statement will evaluate to `true`, so the code won't be removed.
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-
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- ## CLI Usage ##
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-
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- With browserify:
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-
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- ``` bash
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- browserify index.js -t envify > bundle.js
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- ```
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-
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- Or standalone:
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-
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- ``` bash
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- envify index.js > bundle.js
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- ```
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-
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- You can also specify additional custom environment variables using
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- browserify's [subarg](http://github.com/substack/subarg) syntax, which is
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- available in versions 3.25.0 and above:
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-
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- ``` bash
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- browserify index.js -t [ envify --NODE_ENV development ] > bundle.js
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- browserify index.js -t [ envify --NODE_ENV production ] > bundle.js
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- ```
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-
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- ## Module Usage ##
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-
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- **require('envify')**
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-
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- Returns a transform stream that updates based on the Node process'
86
- `process.env` object.
87
-
88
- **require('envify/custom')([environment])**
89
-
90
- If you want to stay away from your environment variables, you can supply
91
- your own object to use in its place:
92
-
93
- ``` javascript
94
- var browserify = require('browserify')
95
- , envify = require('envify/custom')
96
- , fs = require('fs')
97
-
98
- var b = browserify('main.js')
99
- , output = fs.createWriteStream('bundle.js')
100
-
101
- b.transform(envify({
102
- NODE_ENV: 'development'
103
- }))
104
- b.bundle().pipe(output)
105
- ```
106
-
107
- ## Purging `process.env` ##
108
-
109
- By default, environment variables that are not defined will be left untouched.
110
- This is because in some cases, you might want to run an envify transform over
111
- your source more than once, and removing these values would make that
112
- impossible.
113
-
114
- However, if any references to `process.env` are remaining after transforming
115
- your source with envify, browserify will automatically insert its shim for
116
- Node's process object, which will increase the size of your bundle. This weighs
117
- in at around 2KB, so if you're trying to be conservative with your bundle size
118
- you can "purge" these remaining variables such that any missing ones are simply
119
- replaced with undefined.
120
-
121
- To do so through the command-line, simply use the subarg syntax and include
122
- `purge` after `envify`, e.g.:
123
-
124
- ``` bash
125
- browserify index.js -t [ envify purge --NODE_ENV development ]
126
- ```
127
-
128
- Or if you're using the module API, you can pass `_: "purge"` into your
129
- arguments like so:
130
-
131
- ``` javascript
132
- b.transform(envify({
133
- _: 'purge'
134
- , NODE_ENV: 'development'
135
- }))
136
- ```
137
-
138
- ## Contributors ##
139
-
140
- * [hughsk](http://github.com/hughsk)
141
- * [benjamn](http://github.com/benjamn)
142
- * [zag2art](http://github.com/zag2art)
143
- * [bjoerge](http://github.com/bjoerge)
144
- * [andreypopp](http://github.com/andreypopp)
145
- * [jupl](http://github.com/jupl)
@@ -1,17 +0,0 @@
1
- #!/usr/bin/env node
2
-
3
- var envify = require('../')
4
- , fs = require('fs')
5
-
6
- if (process.argv[2]) {
7
- fs.createReadStream(process.argv[2], { encoding: 'utf8' })
8
- .pipe(envify(process.argv[2]))
9
- .pipe(process.stdout)
10
- } else {
11
- process.stdin.resume()
12
- process.stdin
13
- .pipe(envify(__filename))
14
- .pipe(process.stdout)
15
- }
16
-
17
-
@@ -1,33 +0,0 @@
1
- /* */
2
- (function(process) {
3
- var through = require("through"),
4
- jstransform = require("jstransform"),
5
- createVisitors = require("./visitors");
6
- var processEnvPattern = /\bprocess\.env\b/;
7
- module.exports = function(rootEnv) {
8
- rootEnv = rootEnv || process.env || {};
9
- return function envify(file, argv) {
10
- if (/\.json$/.test(file))
11
- return through();
12
- var buffer = [];
13
- argv = argv || {};
14
- return through(write, flush);
15
- function write(data) {
16
- buffer.push(data);
17
- }
18
- function flush() {
19
- var source = buffer.join('');
20
- if (processEnvPattern.test(source)) {
21
- try {
22
- var visitors = createVisitors([argv, rootEnv]);
23
- source = jstransform.transform(visitors, source).code;
24
- } catch (err) {
25
- return this.emit('error', err);
26
- }
27
- }
28
- this.queue(source);
29
- this.queue(null);
30
- }
31
- };
32
- };
33
- })(require("process"));
@@ -1,4 +0,0 @@
1
- /* */
2
- (function(process) {
3
- module.exports = require("./custom")(process.env);
4
- })(require("process"));
@@ -1,35 +0,0 @@
1
- {
2
- "name": "envify",
3
- "version": "3.4.0",
4
- "description": "Selectively replace Node-style environment variables with plain strings.",
5
- "main": "index.js",
6
- "scripts": {
7
- "test": "node test.js | tap-spec"
8
- },
9
- "bin": {
10
- "envify": "bin/envify"
11
- },
12
- "repository": {
13
- "type": "git",
14
- "url": "git://github.com/hughsk/envify.git"
15
- },
16
- "author": "Hugh Kennedy <hughskennedy@gmail.com> (http://hughskennedy.com/)",
17
- "license": "MIT",
18
- "devDependencies": {
19
- "tap-spec": "^1.0.1",
20
- "tape": "~2.3.2"
21
- },
22
- "dependencies": {
23
- "through": "~2.3.4",
24
- "jstransform": "^10.0.1"
25
- },
26
- "keywords": [
27
- "environment",
28
- "variables",
29
- "browserify",
30
- "browserify-transform",
31
- "transform",
32
- "source",
33
- "configuration"
34
- ]
35
- }
@@ -1,33 +0,0 @@
1
- /* */
2
- (function(process) {
3
- var Syntax = require("jstransform").Syntax;
4
- var utils = require("jstransform/src/utils");
5
- function create(envs) {
6
- var args = [].concat(envs[0]._ || []).concat(envs[1]._ || []);
7
- var purge = args.indexOf('purge') !== -1;
8
- function visitProcessEnv(traverse, node, path, state) {
9
- var key = node.property.name || node.property.value;
10
- for (var i = 0; i < envs.length; i++) {
11
- var value = envs[i][key];
12
- if (value !== undefined) {
13
- replaceEnv(node, state, value);
14
- return false;
15
- }
16
- }
17
- if (purge) {
18
- replaceEnv(node, state, undefined);
19
- }
20
- return false;
21
- }
22
- function replaceEnv(node, state, value) {
23
- utils.catchup(node.range[0], state);
24
- utils.append(JSON.stringify(value), state);
25
- utils.move(node.range[1], state);
26
- }
27
- visitProcessEnv.test = function(node, path, state) {
28
- return (node.type === Syntax.MemberExpression && !(path[0].type === Syntax.AssignmentExpression && path[0].left === node) && node.property.type === (node.computed ? Syntax.Literal : Syntax.Identifier) && node.object.computed === false && node.object.type === Syntax.MemberExpression && node.object.object.type === Syntax.Identifier && node.object.object.name === 'process' && node.object.property.type === Syntax.Identifier && node.object.property.name === 'env');
29
- };
30
- return [visitProcessEnv];
31
- }
32
- module.exports = create;
33
- })(require("process"));
@@ -1 +0,0 @@
1
- module.exports = require("npm:envify@3.4.0/index");
@@ -1,90 +0,0 @@
1
- /* */
2
- (function(process) {
3
- var fs,
4
- esprima,
5
- fname,
6
- content,
7
- options,
8
- syntax;
9
- if (typeof require === 'function') {
10
- fs = require("fs");
11
- esprima = require("esprima");
12
- } else if (typeof load === 'function') {
13
- try {
14
- load('esprima.js');
15
- } catch (e) {
16
- load('../esprima.js');
17
- }
18
- }
19
- if (typeof console === 'undefined' && typeof process === 'undefined') {
20
- console = {log: print};
21
- fs = {readFileSync: readFile};
22
- process = {
23
- argv: arguments,
24
- exit: quit
25
- };
26
- process.argv.unshift('esparse.js');
27
- process.argv.unshift('rhino');
28
- }
29
- function showUsage() {
30
- console.log('Usage:');
31
- console.log(' esparse [options] file.js');
32
- console.log();
33
- console.log('Available options:');
34
- console.log();
35
- console.log(' --comment Gather all line and block comments in an array');
36
- console.log(' --loc Include line-column location info for each syntax node');
37
- console.log(' --range Include index-based range for each syntax node');
38
- console.log(' --raw Display the raw value of literals');
39
- console.log(' --tokens List all tokens in an array');
40
- console.log(' --tolerant Tolerate errors on a best-effort basis (experimental)');
41
- console.log(' -v, --version Shows program version');
42
- console.log();
43
- process.exit(1);
44
- }
45
- if (process.argv.length <= 2) {
46
- showUsage();
47
- }
48
- options = {};
49
- process.argv.splice(2).forEach(function(entry) {
50
- if (entry === '-h' || entry === '--help') {
51
- showUsage();
52
- } else if (entry === '-v' || entry === '--version') {
53
- console.log('ECMAScript Parser (using Esprima version', esprima.version, ')');
54
- console.log();
55
- process.exit(0);
56
- } else if (entry === '--comment') {
57
- options.comment = true;
58
- } else if (entry === '--loc') {
59
- options.loc = true;
60
- } else if (entry === '--range') {
61
- options.range = true;
62
- } else if (entry === '--raw') {
63
- options.raw = true;
64
- } else if (entry === '--tokens') {
65
- options.tokens = true;
66
- } else if (entry === '--tolerant') {
67
- options.tolerant = true;
68
- } else if (entry.slice(0, 2) === '--') {
69
- console.log('Error: unknown option ' + entry + '.');
70
- process.exit(1);
71
- } else if (typeof fname === 'string') {
72
- console.log('Error: more than one input file.');
73
- process.exit(1);
74
- } else {
75
- fname = entry;
76
- }
77
- });
78
- if (typeof fname !== 'string') {
79
- console.log('Error: no input file.');
80
- process.exit(1);
81
- }
82
- try {
83
- content = fs.readFileSync(fname, 'utf-8');
84
- syntax = esprima.parse(content, options);
85
- console.log(JSON.stringify(syntax, null, 4));
86
- } catch (e) {
87
- console.log('Error: ' + e.message);
88
- process.exit(1);
89
- }
90
- })(require("process"));
@@ -1,145 +0,0 @@
1
- /* */
2
- (function(process) {
3
- var fs,
4
- system,
5
- esprima,
6
- options,
7
- fnames,
8
- count;
9
- if (typeof esprima === 'undefined') {
10
- if (typeof phantom === 'object') {
11
- fs = require("fs");
12
- system = require("system");
13
- esprima = require("./esprima");
14
- } else if (typeof require === 'function') {
15
- fs = require("fs");
16
- esprima = require("esprima");
17
- } else if (typeof load === 'function') {
18
- try {
19
- load('esprima.js');
20
- } catch (e) {
21
- load('../esprima.js');
22
- }
23
- }
24
- }
25
- if (typeof phantom === 'object') {
26
- fs.readFileSync = fs.read;
27
- process = {
28
- argv: [].slice.call(system.args),
29
- exit: phantom.exit
30
- };
31
- process.argv.unshift('phantomjs');
32
- }
33
- if (typeof console === 'undefined' && typeof process === 'undefined') {
34
- console = {log: print};
35
- fs = {readFileSync: readFile};
36
- process = {
37
- argv: arguments,
38
- exit: quit
39
- };
40
- process.argv.unshift('esvalidate.js');
41
- process.argv.unshift('rhino');
42
- }
43
- function showUsage() {
44
- console.log('Usage:');
45
- console.log(' esvalidate [options] file.js');
46
- console.log();
47
- console.log('Available options:');
48
- console.log();
49
- console.log(' --format=type Set the report format, plain (default) or junit');
50
- console.log(' -v, --version Print program version');
51
- console.log();
52
- process.exit(1);
53
- }
54
- if (process.argv.length <= 2) {
55
- showUsage();
56
- }
57
- options = {format: 'plain'};
58
- fnames = [];
59
- process.argv.splice(2).forEach(function(entry) {
60
- if (entry === '-h' || entry === '--help') {
61
- showUsage();
62
- } else if (entry === '-v' || entry === '--version') {
63
- console.log('ECMAScript Validator (using Esprima version', esprima.version, ')');
64
- console.log();
65
- process.exit(0);
66
- } else if (entry.slice(0, 9) === '--format=') {
67
- options.format = entry.slice(9);
68
- if (options.format !== 'plain' && options.format !== 'junit') {
69
- console.log('Error: unknown report format ' + options.format + '.');
70
- process.exit(1);
71
- }
72
- } else if (entry.slice(0, 2) === '--') {
73
- console.log('Error: unknown option ' + entry + '.');
74
- process.exit(1);
75
- } else {
76
- fnames.push(entry);
77
- }
78
- });
79
- if (fnames.length === 0) {
80
- console.log('Error: no input file.');
81
- process.exit(1);
82
- }
83
- if (options.format === 'junit') {
84
- console.log('<?xml version="1.0" encoding="UTF-8"?>');
85
- console.log('<testsuites>');
86
- }
87
- count = 0;
88
- fnames.forEach(function(fname) {
89
- var content,
90
- timestamp,
91
- syntax,
92
- name;
93
- try {
94
- content = fs.readFileSync(fname, 'utf-8');
95
- if (content[0] === '#' && content[1] === '!') {
96
- content = '//' + content.substr(2, content.length);
97
- }
98
- timestamp = Date.now();
99
- syntax = esprima.parse(content, {tolerant: true});
100
- if (options.format === 'junit') {
101
- name = fname;
102
- if (name.lastIndexOf('/') >= 0) {
103
- name = name.slice(name.lastIndexOf('/') + 1);
104
- }
105
- console.log('<testsuite name="' + fname + '" errors="0" ' + ' failures="' + syntax.errors.length + '" ' + ' tests="' + syntax.errors.length + '" ' + ' time="' + Math.round((Date.now() - timestamp) / 1000) + '">');
106
- syntax.errors.forEach(function(error) {
107
- var msg = error.message;
108
- msg = msg.replace(/^Line\ [0-9]*\:\ /, '');
109
- console.log(' <testcase name="Line ' + error.lineNumber + ': ' + msg + '" ' + ' time="0">');
110
- console.log(' <error type="SyntaxError" message="' + error.message + '">' + error.message + '(' + name + ':' + error.lineNumber + ')' + '</error>');
111
- console.log(' </testcase>');
112
- });
113
- console.log('</testsuite>');
114
- } else if (options.format === 'plain') {
115
- syntax.errors.forEach(function(error) {
116
- var msg = error.message;
117
- msg = msg.replace(/^Line\ [0-9]*\:\ /, '');
118
- msg = fname + ':' + error.lineNumber + ': ' + msg;
119
- console.log(msg);
120
- ++count;
121
- });
122
- }
123
- } catch (e) {
124
- ++count;
125
- if (options.format === 'junit') {
126
- console.log('<testsuite name="' + fname + '" errors="1" failures="0" tests="1" ' + ' time="' + Math.round((Date.now() - timestamp) / 1000) + '">');
127
- console.log(' <testcase name="' + e.message + '" ' + ' time="0">');
128
- console.log(' <error type="ParseError" message="' + e.message + '">' + e.message + '(' + fname + ((e.lineNumber) ? ':' + e.lineNumber : '') + ')</error>');
129
- console.log(' </testcase>');
130
- console.log('</testsuite>');
131
- } else {
132
- console.log('Error: ' + e.message);
133
- }
134
- }
135
- });
136
- if (options.format === 'junit') {
137
- console.log('</testsuites>');
138
- }
139
- if (count > 0) {
140
- process.exit(1);
141
- }
142
- if (count === 0 && typeof phantom === 'object') {
143
- process.exit(0);
144
- }
145
- })(require("process"));