sequenceserver 3.1.3 → 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 (68) 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/database.rb +5 -1
  7. data/lib/sequenceserver/job.rb +26 -10
  8. data/lib/sequenceserver/makeblastdb.rb +2 -1
  9. data/lib/sequenceserver/routes.rb +37 -12
  10. data/lib/sequenceserver/version.rb +1 -1
  11. data/lib/sequenceserver/zip_file_generator.rb +1 -1
  12. data/public/404.html +8 -16
  13. data/public/css/app.css +794 -111
  14. data/public/css/app.min.css +1 -1
  15. data/public/css/sequenceserver.min.css +1 -8
  16. data/public/js/circos.js +103 -96
  17. data/public/{packages/circosJS@1.7.0.js → js/circosjs.js} +156 -778
  18. data/public/js/cloud_share_modal.js +55 -58
  19. data/public/js/collapse_preferences.js +13 -15
  20. data/public/js/databases.js +4 -3
  21. data/public/js/databases_tree.js +51 -30
  22. data/public/js/error_modal.js +35 -22
  23. data/public/js/exporter.js +2 -0
  24. data/public/js/form.js +43 -7
  25. data/public/js/grapher.js +94 -92
  26. data/public/js/hit.js +21 -19
  27. data/public/js/hits.js +45 -38
  28. data/public/js/hits_overview.js +8 -27
  29. data/public/js/hsp.js +140 -144
  30. data/public/js/jquery_world.js +24 -15
  31. data/public/js/kablammo.js +14 -10
  32. data/public/js/length_distribution.js +23 -37
  33. data/public/js/null_plugins/report_plugins.js +3 -5
  34. data/public/js/options.js +17 -19
  35. data/public/js/query.js +36 -35
  36. data/public/js/report/alignment_results.js +18 -0
  37. data/public/js/report/graphical_overview.js +38 -0
  38. data/public/js/report/report_header.js +28 -0
  39. data/public/js/report/run_summary.js +43 -0
  40. data/public/js/report.js +62 -102
  41. data/public/js/report_root.js +3 -3
  42. data/public/js/search.js +5 -2
  43. data/public/js/search_button.js +85 -78
  44. data/public/js/sequence.js +11 -22
  45. data/public/js/sequence_modal.js +38 -37
  46. data/public/js/share_url.js +5 -5
  47. data/public/js/sidebar.js +148 -86
  48. data/public/js/svgExporter.js +8 -3
  49. data/public/js/tests/form.spec.js +1 -1
  50. data/public/js/tests/visualisation_helpers.spec.js +28 -0
  51. data/public/js/visualisation_helpers.js +24 -27
  52. data/public/sequenceserver-report.min.js +1 -1
  53. data/public/sequenceserver-report.min.js.LICENSE.txt +1 -88
  54. data/public/sequenceserver-report.min.js.map +1 -1
  55. data/public/sequenceserver-search.min.js +1 -1
  56. data/public/sequenceserver-search.min.js.LICENSE.txt +0 -30
  57. data/public/sequenceserver-search.min.js.map +1 -1
  58. data/views/error.erb +1 -1
  59. data/views/layout.erb +123 -130
  60. data/views/report.erb +3 -2
  61. data/views/search.erb +10 -14
  62. metadata +13 -26
  63. data/public/css/fonts.css +0 -31
  64. data/public/css/grapher.css +0 -670
  65. data/public/css/sequenceserver.css +0 -509
  66. data/public/vendor/github/mbostock/d3@3.5.6/d3.js +0 -9506
  67. data/public/vendor/github/mbostock/d3@3.5.6.js +0 -1
  68. data/views/search_layout.erb +0 -153
data/public/sequenceserver-search.min.js.LICENSE.txt CHANGED
@@ -247,36 +247,6 @@
247
247
  * Includes: widget.js, position.js, data.js, disable-selection.js, effect.js, effects/effect-blind.js, effects/effect-bounce.js, effects/effect-clip.js, effects/effect-drop.js, effects/effect-explode.js, effects/effect-fade.js, effects/effect-fold.js, effects/effect-highlight.js, effects/effect-puff.js, effects/effect-pulsate.js, effects/effect-scale.js, effects/effect-shake.js, effects/effect-size.js, effects/effect-slide.js, effects/effect-transfer.js, focusable.js, form-reset-mixin.js, jquery-patch.js, keycode.js, labels.js, scroll-parent.js, tabbable.js, unique-id.js, widgets/accordion.js, widgets/autocomplete.js, widgets/button.js, widgets/checkboxradio.js, widgets/controlgroup.js, widgets/datepicker.js, widgets/dialog.js, widgets/draggable.js, widgets/droppable.js, widgets/menu.js, widgets/mouse.js, widgets/progressbar.js, widgets/resizable.js, widgets/selectable.js, widgets/selectmenu.js, widgets/slider.js, widgets/sortable.js, widgets/spinner.js, widgets/tabs.js, widgets/tooltip.js
248
248
  * Copyright OpenJS Foundation and other contributors; Licensed MIT */
249
249
 
250
- /**
251
- * @license React
252
- * react-dom.development.js
253
- *
254
- * Copyright (c) Facebook, Inc. and its affiliates.
255
- *
256
- * This source code is licensed under the MIT license found in the
257
- * LICENSE file in the root directory of this source tree.
258
- */
259
-
260
- /**
261
- * @license React
262
- * react-jsx-runtime.development.js
263
- *
264
- * Copyright (c) Facebook, Inc. and its affiliates.
265
- *
266
- * This source code is licensed under the MIT license found in the
267
- * LICENSE file in the root directory of this source tree.
268
- */
269
-
270
- /**
271
- * @license React
272
- * scheduler.development.js
273
- *
274
- * Copyright (c) Facebook, Inc. and its affiliates.
275
- *
276
- * This source code is licensed under the MIT license found in the
277
- * LICENSE file in the root directory of this source tree.
278
- */
279
-
280
250
  /**
281
251
  * Checks if an event is supported in the current execution environment.
282
252
  *