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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  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
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  757. /data/public/vendor/npm/{readable-stream@1.1.13 → readable-stream@1.1.14}/README.md +0 -0
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@@ -0,0 +1,242 @@
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+ /*global module:false, require:false, __dirname:false*/
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+ var _ = require('lodash');
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+
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+ module.exports = function(grunt) {
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+ grunt.util.linefeed = "\n";
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+
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+ // Project configuration.
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+ grunt.initConfig({
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+ pkg: grunt.file.readJSON('package.json'),
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+ concat: {
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+ options : {
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+ separator : "\n"
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+ },
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+ dist: {
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+ src: ['src/<%= pkg.name %>.js', 'src/<%= pkg.name %>.*.js', 'src/vakata-jstree.js'],
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+ dest: 'dist/<%= pkg.name %>.js'
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+ }
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+ },
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+ copy: {
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+ libs : {
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+ files : [
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+ { expand: true, cwd : 'libs/', src: ['*'], dest: 'dist/libs/' }
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+ ]
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+ },
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+ docs : {
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+ files : [
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+ { expand: true, cwd : 'dist/', src: ['**/*'], dest: 'docs/assets/dist/' }
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+ ]
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+ }
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+ },
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+ uglify: {
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+ options: {
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+ banner: '/*! <%= pkg.title || pkg.name %> - v<%= pkg.version %> - <%= grunt.template.today("yyyy-mm-dd") %> - (<%= _.map(pkg.licenses, "type").join(", ") %>) */\n',
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+ preserveComments: false,
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+ //sourceMap: "dist/jstree.min.map",
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+ //sourceMappingURL: "jstree.min.map",
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+ report: "min",
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+ output: {
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+ ascii_only: true
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+ },
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+ compress: {
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+ hoist_funs: false,
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+ loops: false,
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+ unused: false
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+ }
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+ },
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+ dist: {
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+ src: ['<%= concat.dist.dest %>'],
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+ dest: 'dist/<%= pkg.name %>.min.js'
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+ }
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+ },
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+ qunit: {
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+ files: ['test/unit/**/*.html']
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+ },
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+ jshint: {
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+ options: {
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+ 'curly' : true,
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+ 'eqeqeq' : true,
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+ 'latedef' : true,
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+ 'newcap' : true,
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+ 'noarg' : true,
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+ 'sub' : true,
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+ 'undef' : true,
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+ 'boss' : true,
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+ 'eqnull' : true,
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+ 'browser' : true,
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+ 'trailing' : true,
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+ 'globals' : {
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+ 'console' : true,
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+ 'jQuery' : true,
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+ 'browser' : true,
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+ 'XSLTProcessor' : true,
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+ 'ActiveXObject' : true
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+ }
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+ },
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+ beforeconcat: ['src/<%= pkg.name %>.js', 'src/<%= pkg.name %>.*.js'],
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+ afterconcat: ['dist/<%= pkg.name %>.js']
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+ },
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+ dox: {
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+ files: {
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+ src: ['src/*.js'],
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+ dest: 'docs'
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+ }
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+ },
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+ amd : {
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+ files: {
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+ src: ['dist/jstree.js'],
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+ dest: 'dist/jstree.js'
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+ }
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+ },
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+ less: {
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+ production: {
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+ options : {
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+ cleancss : true,
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+ compress : true
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+ },
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+ files: {
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+ "dist/themes/default/style.min.css" : "src/themes/default/style.less",
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+ "dist/themes/default-dark/style.min.css" : "src/themes/default-dark/style.less"
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+ }
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+ },
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+ development: {
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+ files: {
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+ "src/themes/default/style.css" : "src/themes/default/style.less",
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+ "dist/themes/default/style.css" : "src/themes/default/style.less",
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+ "src/themes/default-dark/style.css" : "src/themes/default-dark/style.less",
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+ "dist/themes/default-dark/style.css" : "src/themes/default-dark/style.less"
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+ }
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+ }
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+ },
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+ watch: {
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+ js : {
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+ files: ['src/**/*.js'],
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+ tasks: ['js'],
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+ options : {
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+ atBegin : true
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+ }
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+ },
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+ css : {
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+ files: ['src/**/*.less','src/**/*.png','src/**/*.gif'],
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+ tasks: ['css'],
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+ options : {
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+ atBegin : true
124
+ }
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+ },
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+ },
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+ resemble: {
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+ options: {
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+ screenshotRoot: 'test/visual/screenshots/',
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+ url: 'http://127.0.0.1/jstree/test/visual/',
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+ gm: false
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+ },
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+ desktop: {
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+ options: {
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+ width: 1280,
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+ },
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+ src: ['desktop'],
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+ dest: 'desktop',
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+ },
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+ mobile: {
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+ options: {
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+ width: 360,
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+ },
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+ src: ['mobile'],
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+ dest: 'mobile'
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+ }
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+ },
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+ imagemin: {
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+ dynamic: {
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+ options: { // Target options
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+ optimizationLevel: 7,
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+ pngquant : true
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+ },
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+ files: [{
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+ expand: true, // Enable dynamic expansion
156
+ cwd: 'src/themes/default/', // Src matches are relative to this path
157
+ src: ['**/*.{png,jpg,gif}'], // Actual patterns to match
158
+ dest: 'dist/themes/default/' // Destination path prefix
159
+ },{
160
+ expand: true, // Enable dynamic expansion
161
+ cwd: 'src/themes/default-dark/', // Src matches are relative to this path
162
+ src: ['**/*.{png,jpg,gif}'], // Actual patterns to match
163
+ dest: 'dist/themes/default-dark/' // Destination path prefix
164
+ }]
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+ }
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+ },
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+ replace: {
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+ files: {
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+ src: ['dist/*.js', 'bower.json', 'component.json', 'jstree.jquery.json'],
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+ overwrite: true,
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+ replacements: [
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+ {
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+ from: '{{VERSION}}',
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+ to: "<%= pkg.version %>"
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+ },
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+ {
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+ from: /"version": "[^"]+"/g,
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+ to: "\"version\": \"<%= pkg.version %>\""
179
+ },
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+ ]
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+ }
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+ }
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+ });
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+
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+ grunt.loadNpmTasks('grunt-contrib-jshint');
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+ grunt.loadNpmTasks('grunt-contrib-concat');
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+ grunt.loadNpmTasks('grunt-contrib-copy');
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+ grunt.loadNpmTasks('grunt-contrib-uglify');
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+ grunt.loadNpmTasks('grunt-contrib-less');
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+ grunt.loadNpmTasks('grunt-contrib-qunit');
191
+ grunt.loadNpmTasks('grunt-resemble-cli');
192
+ grunt.loadNpmTasks('grunt-contrib-watch');
193
+ grunt.loadNpmTasks('grunt-contrib-imagemin');
194
+ grunt.loadNpmTasks('grunt-text-replace');
195
+
196
+ grunt.registerMultiTask('amd', 'Clean up AMD', function () {
197
+ var s, d;
198
+ this.files.forEach(function (f) {
199
+ s = f.src[0];
200
+ d = f.dest;
201
+ });
202
+ grunt.file.copy(s, d, {
203
+ process: function (contents) {
204
+ contents = contents.replace(/\s*if\(\$\.jstree\.plugins\.[a-z]+\)\s*\{\s*return;\s*\}/ig, '');
205
+ contents = contents.replace(/\/\*globals[^\/]+\//ig, '');
206
+ //contents = contents.replace(/\(function \(factory[\s\S]*?undefined/mig, '(function ($, undefined');
207
+ //contents = contents.replace(/\}\)\);/g, '}(jQuery));');
208
+ contents = contents.replace(/\(function \(factory[\s\S]*?undefined\s*\)[^\n]+/mig, '');
209
+ contents = contents.replace(/\}\)\);/g, '');
210
+ contents = contents.replace(/\s*("|')use strict("|');/g, '');
211
+ contents = contents.replace(/\s*return \$\.fn\.jstree;/g, '');
212
+ return grunt.file.read('src/intro.js') + contents + grunt.file.read('src/outro.js');
213
+ }
214
+ });
215
+ });
216
+
217
+ grunt.registerMultiTask('dox', 'Generate dox output ', function() {
218
+ var exec = require('child_process').exec,
219
+ path = require('path'),
220
+ done = this.async(),
221
+ doxPath = path.resolve(__dirname),
222
+ formatter = [doxPath, 'node_modules', '.bin', 'dox'].join(path.sep);
223
+ exec(formatter + ' < "dist/jstree.js" > "docs/jstree.json"', {maxBuffer: 5000*1024}, function(error, stout, sterr){
224
+ if (error) {
225
+ grunt.log.error(formatter);
226
+ grunt.log.error("WARN: "+ error);
227
+ }
228
+ if (!error) {
229
+ grunt.log.writeln('dist/jstree.js doxxed.');
230
+ done();
231
+ }
232
+ });
233
+ });
234
+
235
+ grunt.util.linefeed = "\n";
236
+
237
+ // Default task.
238
+ grunt.registerTask('default', ['jshint:beforeconcat','concat','amd','jshint:afterconcat','copy:libs','uglify','less','imagemin','replace','copy:docs','qunit','resemble','dox']);
239
+ grunt.registerTask('js', ['concat','amd','uglify']);
240
+ grunt.registerTask('css', ['copy','less']);
241
+
242
+ };
@@ -0,0 +1,28 @@
1
+ {
2
+ "name": "jstree",
3
+ "title": "jsTree",
4
+ "description": "Tree view for jQuery",
5
+ "version": "3.3.8",
6
+ "homepage": "http://jstree.com",
7
+ "keywords": [
8
+ "ui",
9
+ "tree",
10
+ "jstree"
11
+ ],
12
+ "author": {
13
+ "name": "Ivan Bozhanov",
14
+ "email": "jstree@jstree.com",
15
+ "url": "http://vakata.com"
16
+ },
17
+ "licenses": [
18
+ {
19
+ "type": "MIT",
20
+ "url": "https://github.com/vakata/jstree/blob/master/LICENSE-MIT"
21
+ }
22
+ ],
23
+ "bugs": "https://github.com/vakata/jstree/issues",
24
+ "demo": "http://jstree.com/demo",
25
+ "dependencies": {
26
+ "jquery": ">=1.9.1"
27
+ }
28
+ }
@@ -0,0 +1,58 @@
1
+ {
2
+ "name": "jstree",
3
+ "title": "jsTree",
4
+ "description": "jQuery tree plugin",
5
+ "version": "3.3.8",
6
+ "homepage": "http://jstree.com",
7
+ "main": "./dist/jstree.js",
8
+ "author": {
9
+ "name": "Ivan Bozhanov",
10
+ "email": "jstree@jstree.com",
11
+ "url": "http://vakata.com"
12
+ },
13
+ "repository": {
14
+ "type": "git",
15
+ "url": "git://github.com/vakata/jstree.git"
16
+ },
17
+ "bugs": {
18
+ "url": "https://github.com/vakata/jstree/issues"
19
+ },
20
+ "license": "MIT",
21
+ "licenses": [
22
+ {
23
+ "type": "MIT",
24
+ "url": "https://github.com/vakata/jstree/blob/master/LICENSE-MIT"
25
+ }
26
+ ],
27
+ "keywords": [],
28
+ "devDependencies": {
29
+ "dox": "~0.9.0",
30
+ "grunt": "~1.0.0",
31
+ "grunt-contrib-concat": "*",
32
+ "grunt-contrib-copy": "*",
33
+ "grunt-contrib-imagemin": "~2.0.1",
34
+ "grunt-contrib-jshint": "*",
35
+ "grunt-contrib-less": "~1.4.1",
36
+ "grunt-contrib-qunit": "~2.0.0",
37
+ "grunt-contrib-uglify": "*",
38
+ "grunt-contrib-watch": "~1.1.0",
39
+ "grunt-resemble-cli": "0.0.8",
40
+ "grunt-text-replace": "~0.4.0",
41
+ "lodash": "^4.17.10"
42
+ },
43
+ "dependencies": {
44
+ "jquery": ">=1.9.1"
45
+ },
46
+ "npmName": "jstree",
47
+ "npmFileMap": [
48
+ {
49
+ "basePath": "/dist/",
50
+ "files": [
51
+ "jstree.min.js",
52
+ "themes/**/*.png",
53
+ "themes/**/*.gif",
54
+ "themes/**/*.min.css"
55
+ ]
56
+ }
57
+ ]
58
+ }
@@ -0,0 +1,14 @@
1
+ /*globals jQuery, define, module, exports, require, window, document, postMessage */
2
+ (function (factory) {
3
+ "use strict";
4
+ if (typeof define === 'function' && define.amd) {
5
+ define(['jquery'], factory);
6
+ }
7
+ else if(typeof module !== 'undefined' && module.exports) {
8
+ module.exports = factory(require('jquery'));
9
+ }
10
+ else {
11
+ factory(jQuery);
12
+ }
13
+ }(function ($, undefined) {
14
+ "use strict";
@@ -0,0 +1,69 @@
1
+ /**
2
+ * ### Changed plugin
3
+ *
4
+ * This plugin adds more information to the `changed.jstree` event. The new data is contained in the `changed` event data property, and contains a lists of `selected` and `deselected` nodes.
5
+ */
6
+ /*globals jQuery, define, exports, require, document */
7
+ (function (factory) {
8
+ "use strict";
9
+ if (typeof define === 'function' && define.amd) {
10
+ define('jstree.changed', ['jquery','jstree'], factory);
11
+ }
12
+ else if(typeof exports === 'object') {
13
+ factory(require('jquery'), require('jstree'));
14
+ }
15
+ else {
16
+ factory(jQuery, jQuery.jstree);
17
+ }
18
+ }(function ($, jstree, undefined) {
19
+ "use strict";
20
+
21
+ if($.jstree.plugins.changed) { return; }
22
+
23
+ $.jstree.plugins.changed = function (options, parent) {
24
+ var last = [];
25
+ this.trigger = function (ev, data) {
26
+ var i, j;
27
+ if(!data) {
28
+ data = {};
29
+ }
30
+ if(ev.replace('.jstree','') === 'changed') {
31
+ data.changed = { selected : [], deselected : [] };
32
+ var tmp = {};
33
+ for(i = 0, j = last.length; i < j; i++) {
34
+ tmp[last[i]] = 1;
35
+ }
36
+ for(i = 0, j = data.selected.length; i < j; i++) {
37
+ if(!tmp[data.selected[i]]) {
38
+ data.changed.selected.push(data.selected[i]);
39
+ }
40
+ else {
41
+ tmp[data.selected[i]] = 2;
42
+ }
43
+ }
44
+ for(i = 0, j = last.length; i < j; i++) {
45
+ if(tmp[last[i]] === 1) {
46
+ data.changed.deselected.push(last[i]);
47
+ }
48
+ }
49
+ last = data.selected.slice();
50
+ }
51
+ /**
52
+ * triggered when selection changes (the "changed" plugin enhances the original event with more data)
53
+ * @event
54
+ * @name changed.jstree
55
+ * @param {Object} node
56
+ * @param {Object} action the action that caused the selection to change
57
+ * @param {Array} selected the current selection
58
+ * @param {Object} changed an object containing two properties `selected` and `deselected` - both arrays of node IDs, which were selected or deselected since the last changed event
59
+ * @param {Object} event the event (if any) that triggered this changed event
60
+ * @plugin changed
61
+ */
62
+ parent.trigger.call(this, ev, data);
63
+ };
64
+ this.refresh = function (skip_loading, forget_state) {
65
+ last = [];
66
+ return parent.refresh.apply(this, arguments);
67
+ };
68
+ };
69
+ }));