sequenceserver 2.0.0.rc8 → 2.0.0

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Files changed (116) hide show
  1. checksums.yaml +4 -4
  2. data/bin/sequenceserver +22 -30
  3. data/lib/sequenceserver/api_errors.rb +5 -1
  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 +9 -18
  7. data/lib/sequenceserver/blast/report.rb +5 -3
  8. data/lib/sequenceserver/config.rb +4 -1
  9. data/lib/sequenceserver/database.rb +69 -9
  10. data/lib/sequenceserver/job.rb +1 -1
  11. data/lib/sequenceserver/makeblastdb.rb +40 -45
  12. data/lib/sequenceserver/routes.rb +4 -0
  13. data/lib/sequenceserver/version.rb +1 -1
  14. data/lib/sequenceserver.rb +15 -11
  15. data/public/config.js +143 -142
  16. data/public/css/fonts.css +23 -22
  17. data/public/css/grapher.css +598 -594
  18. data/public/css/sequenceserver.css +86 -24
  19. data/public/css/sequenceserver.min.css +2 -2
  20. data/public/js/alignment_exporter.js +14 -14
  21. data/public/js/databases_tree.js +215 -0
  22. data/public/js/download_fasta.js +1 -1
  23. data/public/js/hit.js +6 -2
  24. data/public/js/hits_overview.js +1 -1
  25. data/public/js/length_distribution.js +5 -5
  26. data/public/js/query.js +4 -7
  27. data/public/js/report.js +12 -24
  28. data/public/js/search.js +21 -2
  29. data/public/js/sidebar.js +4 -4
  30. data/public/js/svgExporter.js +12 -12
  31. data/public/js/visualisation_helpers.js +4 -5
  32. data/public/sequenceserver-report.min.js +11 -11
  33. data/public/sequenceserver-search.min.js +15 -11
  34. data/public/vendor/github/vakata/jstree@3.3.8/LICENSE-MIT +22 -0
  35. data/public/vendor/github/vakata/jstree@3.3.8/README.md +663 -0
  36. data/public/vendor/github/vakata/jstree@3.3.8/bower.json +33 -0
  37. data/public/vendor/github/vakata/jstree@3.3.8/component.json +28 -0
  38. data/public/vendor/github/vakata/jstree@3.3.8/composer.json +46 -0
  39. data/public/vendor/github/vakata/jstree@3.3.8/demo/README.md +2 -0
  40. data/public/vendor/github/vakata/jstree@3.3.8/demo/basic/index.html +146 -0
  41. data/public/vendor/github/vakata/jstree@3.3.8/demo/basic/root.json +1 -0
  42. data/public/vendor/github/vakata/jstree@3.3.8/dist/jstree.js +8612 -0
  43. data/public/vendor/github/vakata/jstree@3.3.8/dist/jstree.min.js +6 -0
  44. data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default/32px.png +0 -0
  45. data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default/40px.png +0 -0
  46. data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default/style.css +1102 -0
  47. data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default/style.min.css +1 -0
  48. data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default/throbber.gif +0 -0
  49. data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default-dark/32px.png +0 -0
  50. data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default-dark/40px.png +0 -0
  51. data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default-dark/style.css +1146 -0
  52. data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default-dark/style.min.css +1 -0
  53. data/public/vendor/github/vakata/jstree@3.3.8/dist/themes/default-dark/throbber.gif +0 -0
  54. data/public/vendor/github/vakata/jstree@3.3.8/gruntfile.js +242 -0
  55. data/public/vendor/github/vakata/jstree@3.3.8/jstree.jquery.json +28 -0
  56. data/public/vendor/github/vakata/jstree@3.3.8/package.json +58 -0
  57. data/public/vendor/github/vakata/jstree@3.3.8/src/intro.js +14 -0
  58. data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.changed.js +69 -0
  59. data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.checkbox.js +976 -0
  60. data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.conditionalselect.js +38 -0
  61. data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.contextmenu.js +661 -0
  62. data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.dnd.js +669 -0
  63. data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.js +4931 -0
  64. data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.massload.js +137 -0
  65. data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.search.js +421 -0
  66. data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.sort.js +74 -0
  67. data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.state.js +138 -0
  68. data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.types.js +372 -0
  69. data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.unique.js +164 -0
  70. data/public/vendor/github/vakata/jstree@3.3.8/src/jstree.wholerow.js +122 -0
  71. data/public/vendor/github/vakata/jstree@3.3.8/src/misc.js +656 -0
  72. data/public/vendor/github/vakata/jstree@3.3.8/src/outro.js +1 -0
  73. data/public/vendor/github/vakata/jstree@3.3.8/src/sample.js +93 -0
  74. data/public/vendor/github/vakata/jstree@3.3.8/src/themes/base.less +93 -0
  75. data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default/32px.png +0 -0
  76. data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default/40px.png +0 -0
  77. data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default/style.css +1102 -0
  78. data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default/style.less +22 -0
  79. data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default/throbber.gif +0 -0
  80. data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default-dark/32px.png +0 -0
  81. data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default-dark/40px.png +0 -0
  82. data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default-dark/style.css +1146 -0
  83. data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default-dark/style.less +50 -0
  84. data/public/vendor/github/vakata/jstree@3.3.8/src/themes/default-dark/throbber.gif +0 -0
  85. data/public/vendor/github/vakata/jstree@3.3.8/src/themes/main.less +77 -0
  86. data/public/vendor/github/vakata/jstree@3.3.8/src/themes/mixins.less +104 -0
  87. data/public/vendor/github/vakata/jstree@3.3.8/src/themes/responsive.less +67 -0
  88. data/public/vendor/github/vakata/jstree@3.3.8/src/vakata-jstree.js +38 -0
  89. data/public/vendor/github/vakata/jstree@3.3.8/test/unit/index.html +16 -0
  90. data/public/vendor/github/vakata/jstree@3.3.8/test/unit/libs/qunit.css +244 -0
  91. data/public/vendor/github/vakata/jstree@3.3.8/test/unit/libs/qunit.js +2212 -0
  92. data/public/vendor/github/vakata/jstree@3.3.8/test/unit/test.js +11 -0
  93. data/public/vendor/github/vakata/jstree@3.3.8/test/visual/desktop/index.html +44 -0
  94. data/public/vendor/github/vakata/jstree@3.3.8/test/visual/mobile/index.html +42 -0
  95. data/public/vendor/github/vakata/jstree@3.3.8/test/visual/screenshots/desktop/desktop.png +0 -0
  96. data/public/vendor/github/vakata/jstree@3.3.8/test/visual/screenshots/desktop/home.png +0 -0
  97. data/public/vendor/github/vakata/jstree@3.3.8/test/visual/screenshots/mobile/home.png +0 -0
  98. data/public/vendor/github/vakata/jstree@3.3.8/test/visual/screenshots/mobile/mobile.png +0 -0
  99. data/public/vendor/github/vakata/jstree@3.3.8.js +3 -0
  100. data/public/vendor/system-csp-production.js +3 -3
  101. data/public/vendor/system-csp-production.js.map +1 -1
  102. data/public/vendor/system-csp-production.src.js +146 -140
  103. data/public/vendor/system-polyfills.js.map +1 -1
  104. data/public/vendor/system-polyfills.src.js +1 -0
  105. data/public/vendor/system.js +3 -3
  106. data/public/vendor/system.js.map +1 -1
  107. data/public/vendor/system.src.js +4771 -2383
  108. data/views/_options.erb +21 -0
  109. data/views/layout.erb +17 -18
  110. metadata +102 -43
  111. data/bin/chromedriver +0 -0
  112. data/bin/geckodriver +0 -0
  113. data/public/shims/form-core.js +0 -3
  114. data/public/shims/form-validation.js +0 -3
  115. data/public/shims/plugins/jquery.ui.position.js +0 -13
  116. data/public/shims/styles/shim.css +0 -1
@@ -0,0 +1,33 @@
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+ {
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+ "name": "jstree",
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+ "license": "MIT",
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+ "version": "3.3.8",
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+ "main" : [
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+ "./dist/jstree.js",
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+ "./dist/themes/default/style.css"
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+ ],
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+ "ignore": [
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+ "**/.*",
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+ "docs",
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+ "demo",
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+ "libs",
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+ "node_modules",
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+ "test",
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+ "libs",
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+ "jstree.jquery.json",
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+ "gruntfile.js",
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+ "package.json",
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+ "bower.json",
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+ "component.json",
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+ "LICENCE-MIT",
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+ "README.md"
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+ ],
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+ "dependencies": {
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+ "jquery": ">=1.9.1"
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+ },
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+ "keywords": [
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+ "ui",
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+ "tree",
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+ "jstree"
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+ ]
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+ }
@@ -0,0 +1,28 @@
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+ {
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+ "name": "jstree",
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+ "repo": "vakata/jstree",
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+ "description": "jsTree is jquery plugin, that provides interactive trees.",
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+ "version": "3.3.8",
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+ "license": "MIT",
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+ "keywords": [
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+ "ui",
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+ "tree",
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+ "jstree"
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+ ],
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+ "scripts": [
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+ "dist/jstree.js",
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+ "dist/jstree.min.js"
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+ ],
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+ "images": [
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+ "dist/themes/default/32px.png",
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+ "dist/themes/default/40px.png",
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+ "dist/themes/default/throbber.gif"
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+ ],
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+ "styles": [
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+ "dist/themes/default/style.css",
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+ "dist/themes/default/style.min.css"
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+ ],
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+ "dependencies": {
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+ "components/jquery": ">=1.9.1"
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+ }
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+ }
@@ -0,0 +1,46 @@
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+ {
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+ "name": "vakata/jstree",
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+ "description": "jsTree is jquery plugin, that provides interactive trees.",
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+ "type": "component",
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+ "homepage": "http://jstree.com",
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+ "license": "MIT",
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+ "support": {
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+ "issues": "https://github.com/vakata/jstree/issues",
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+ "forum": "https://groups.google.com/forum/#!forum/jstree",
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+ "source": "https://github.com/vakata/jstree"
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+ },
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+ "authors": [
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+ {
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+ "name": "Ivan Bozhanov",
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+ "email": "jstree@jstree.com"
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+ }
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+ ],
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+ "require": {
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+ "components/jquery": ">=1.9.1"
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+ },
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+ "suggest": {
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+ "robloach/component-installer": "Allows installation of Components via Composer"
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+ },
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+ "extra": {
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+ "component": {
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+ "scripts": [
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+ "dist/jstree.js"
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+ ],
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+ "styles": [
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+ "dist/themes/default/style.css"
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+ ],
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+ "images": [
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+ "dist/themes/default/32px.png",
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+ "dist/themes/default/40px.png",
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+ "dist/themes/default/throbber.gif"
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+ ],
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+ "files": [
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+ "dist/jstree.min.js",
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+ "dist/themes/default/style.min.css",
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+ "dist/themes/default/32px.png",
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+ "dist/themes/default/40px.png",
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+ "dist/themes/default/throbber.gif"
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+ ]
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+ }
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+ }
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+ }
@@ -0,0 +1,2 @@
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+ ## PHP demos moved to new repository
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+ https://github.com/vakata/jstree-php-demos
@@ -0,0 +1,146 @@
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+ <!DOCTYPE html>
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+ <html lang="en">
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+ <head>
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+ <meta charset="UTF-8">
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+ <title>jstree basic demos</title>
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+ <style>
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+ html { margin:0; padding:0; font-size:62.5%; }
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+ body { max-width:800px; min-width:300px; margin:0 auto; padding:20px 10px; font-size:14px; font-size:1.4em; }
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+ h1 { font-size:1.8em; }
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+ .demo { overflow:auto; border:1px solid silver; min-height:100px; }
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+ </style>
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+ <link rel="stylesheet" href="./../../dist/themes/default/style.min.css" />
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+ </head>
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+ <body>
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+ <h1>HTML demo</h1>
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+ <div id="html" class="demo">
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+ <ul>
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+ <li data-jstree='{ "opened" : true }'>Root node
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+ <ul>
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+ <li data-jstree='{ "selected" : true }'>Child node 1</li>
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+ <li>Child node 2</li>
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+ </ul>
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+ </li>
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+ </ul>
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+ </div>
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+
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+ <h1>Inline data demo</h1>
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+ <div id="data" class="demo"></div>
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+
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+ <h1>Data format demo</h1>
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+ <div id="frmt" class="demo"></div>
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+
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+ <h1>AJAX demo</h1>
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+ <div id="ajax" class="demo"></div>
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+
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+ <h1>Lazy loading demo</h1>
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+ <div id="lazy" class="demo"></div>
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+
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+ <h1>Callback function data demo</h1>
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+ <div id="clbk" class="demo"></div>
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+
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+ <h1>Interaction and events demo</h1>
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+ <button id="evts_button">select node with id 1</button> <em>either click the button or a node in the tree</em>
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+ <div id="evts" class="demo"></div>
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+
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+ <script src="https://ajax.googleapis.com/ajax/libs/jquery/3.3.1/jquery.min.js"></script>
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+ <script src="./../../dist/jstree.min.js"></script>
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+
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+ <script>
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+ // html demo
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+ $('#html').jstree();
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+
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+ // inline data demo
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+ $('#data').jstree({
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+ 'core' : {
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+ 'data' : [
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+ { "text" : "Root node", "children" : [
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+ { "text" : "Child node 1" },
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+ { "text" : "Child node 2" }
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+ ]}
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+ ]
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+ }
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+ });
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+
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+ // data format demo
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+ $('#frmt').jstree({
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+ 'core' : {
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+ 'data' : [
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+ {
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+ "text" : "Root node",
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+ "state" : { "opened" : true },
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+ "children" : [
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+ {
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+ "text" : "Child node 1",
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+ "state" : { "selected" : true },
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+ "icon" : "jstree-file"
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+ },
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+ { "text" : "Child node 2", "state" : { "disabled" : true } }
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+ ]
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+ }
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+ ]
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+ }
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+ });
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+
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+ // ajax demo
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+ $('#ajax').jstree({
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+ 'core' : {
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+ 'data' : {
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+ "url" : "./root.json",
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+ "dataType" : "json" // needed only if you do not supply JSON headers
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+ }
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+ }
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+ });
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+
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+ // lazy demo
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+ $('#lazy').jstree({
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+ 'core' : {
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+ 'data' : {
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+ "url" : "//www.jstree.com/fiddle/?lazy",
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+ "data" : function (node) {
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+ return { "id" : node.id };
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+ }
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+ }
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+ }
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+ });
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+
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+ // data from callback
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+ $('#clbk').jstree({
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+ 'core' : {
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+ 'data' : function (node, cb) {
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+ if(node.id === "#") {
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+ cb([{"text" : "Root", "id" : "1", "children" : true}]);
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+ }
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+ else {
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+ cb(["Child"]);
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+ }
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+ }
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+ }
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+ });
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+
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+ // interaction and events
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+ $('#evts_button').on("click", function () {
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+ var instance = $('#evts').jstree(true);
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+ instance.deselect_all();
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+ instance.select_node('1');
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+ });
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+ $('#evts')
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+ .on("changed.jstree", function (e, data) {
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+ if(data.selected.length) {
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+ alert('The selected node is: ' + data.instance.get_node(data.selected[0]).text);
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+ }
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+ })
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+ .jstree({
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+ 'core' : {
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+ 'multiple' : false,
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+ 'data' : [
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+ { "text" : "Root node", "children" : [
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+ { "text" : "Child node 1", "id" : 1 },
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+ { "text" : "Child node 2" }
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+ ]}
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+ ]
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+ }
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+ });
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+ </script>
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+ </body>
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+ </html>
@@ -0,0 +1 @@
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+ [{"id":1,"text":"Root node","children":[{"id":2,"text":"Child node 1"},{"id":3,"text":"Child node 2"}]}]