sequenceserver 3.1.2 → 3.2.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
Files changed (78) hide show
  1. checksums.yaml +4 -4
  2. data/lib/sequenceserver/api_errors.rb +18 -0
  3. data/lib/sequenceserver/blast/hit.rb +1 -2
  4. data/lib/sequenceserver/blast/job.rb +15 -5
  5. data/lib/sequenceserver/blast/report.rb +5 -1
  6. data/lib/sequenceserver/blast/tasks.rb +1 -1
  7. data/lib/sequenceserver/database.rb +5 -1
  8. data/lib/sequenceserver/job.rb +26 -10
  9. data/lib/sequenceserver/makeblastdb.rb +2 -1
  10. data/lib/sequenceserver/routes.rb +38 -13
  11. data/lib/sequenceserver/version.rb +1 -1
  12. data/lib/sequenceserver/zip_file_generator.rb +1 -1
  13. data/lib/sequenceserver.rb +1 -1
  14. data/public/404.html +8 -16
  15. data/public/css/app.css +794 -111
  16. data/public/css/app.min.css +1 -1
  17. data/public/css/sequenceserver.min.css +1 -8
  18. data/public/js/alignment_exporter.js +16 -28
  19. data/public/js/circos.js +103 -96
  20. data/public/{packages/circosJS@1.7.0.js → js/circosjs.js} +156 -778
  21. data/public/js/cloud_share_modal.js +95 -98
  22. data/public/js/collapse_preferences.js +13 -15
  23. data/public/js/databases.js +4 -3
  24. data/public/js/databases_tree.js +51 -30
  25. data/public/js/error_modal.js +35 -22
  26. data/public/js/exporter.js +2 -0
  27. data/public/js/form.js +55 -17
  28. data/public/js/grapher.js +94 -92
  29. data/public/js/hit.js +24 -22
  30. data/public/js/hits.js +283 -0
  31. data/public/js/hits_overview.js +8 -27
  32. data/public/js/hsp.js +140 -144
  33. data/public/js/jquery_world.js +25 -16
  34. data/public/js/kablammo.js +14 -10
  35. data/public/js/length_distribution.js +23 -37
  36. data/public/js/mailto.js +1 -3
  37. data/public/js/null_plugins/report_plugins.js +4 -5
  38. data/public/js/options.js +19 -25
  39. data/public/js/query.js +36 -35
  40. data/public/js/report/alignment_results.js +18 -0
  41. data/public/js/report/graphical_overview.js +38 -0
  42. data/public/js/report/report_header.js +28 -0
  43. data/public/js/report/run_summary.js +43 -0
  44. data/public/js/report.js +124 -348
  45. data/public/js/report_root.js +10 -8
  46. data/public/js/search.js +31 -11
  47. data/public/js/search_button.js +85 -78
  48. data/public/js/sequence.js +169 -180
  49. data/public/js/sequence_modal.js +58 -65
  50. data/public/js/share_url.js +5 -5
  51. data/public/js/sidebar.js +152 -89
  52. data/public/js/svgExporter.js +8 -3
  53. data/public/js/tests/alignment_exporter.spec.js +38 -0
  54. data/public/js/tests/cloud_share_modal.spec.js +75 -0
  55. data/public/js/tests/form.spec.js +1 -1
  56. data/public/js/tests/report.spec.js +37 -15
  57. data/public/js/tests/visualisation_helpers.spec.js +28 -0
  58. data/public/js/visualisation_helpers.js +24 -27
  59. data/public/packages/jquery-ui@1.13.3.js +19070 -0
  60. data/public/sequenceserver-report.min.js +3 -2481
  61. data/public/sequenceserver-report.min.js.LICENSE.txt +213 -0
  62. data/public/sequenceserver-report.min.js.map +1 -0
  63. data/public/sequenceserver-search.min.js +3 -2382
  64. data/public/sequenceserver-search.min.js.LICENSE.txt +262 -0
  65. data/public/sequenceserver-search.min.js.map +1 -0
  66. data/views/error.erb +1 -1
  67. data/views/layout.erb +122 -133
  68. data/views/report.erb +3 -2
  69. data/views/search.erb +10 -14
  70. metadata +21 -28
  71. data/public/config.js +0 -147
  72. data/public/css/fonts.css +0 -31
  73. data/public/css/grapher.css +0 -670
  74. data/public/css/sequenceserver.css +0 -527
  75. data/public/packages/jquery-ui@1.11.4.js +0 -16624
  76. data/public/vendor/github/mbostock/d3@3.5.6/d3.js +0 -9506
  77. data/public/vendor/github/mbostock/d3@3.5.6.js +0 -1
  78. data/views/search_layout.erb +0 -153
data/public/sequenceserver-report.min.js.LICENSE.txt ADDED
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+ * https://github.com/gabceb/jquery-browser-plugin
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+ *
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+ * http://jquery.org/license
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+ * Modifications Copyright 2013 Gabriel Cebrian
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+ * https://github.com/gabceb
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+ *
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+ * Released under the MIT license
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+ *
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+ * Date: 2013-07-29T17:23:27-07:00
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+ * jQuery JavaScript Library v3.7.1
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+ * https://jquery.com/
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+ *
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+ */
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