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
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  * 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
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  * Copyright OpenJS Foundation and other contributors; Licensed MIT */
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- /*! regenerator-runtime -- Copyright (c) 2014-present, Facebook, Inc. -- license (MIT): https://github.com/facebook/regenerator/blob/main/LICENSE */
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-
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- /**
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- * @license React
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- * react-dom.development.js
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- *
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- * Copyright (c) Facebook, Inc. and its affiliates.
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- *
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- * This source code is licensed under the MIT license found in the
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- * LICENSE file in the root directory of this source tree.
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- */
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-
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- /**
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- * @license React
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- * react-jsx-runtime.development.js
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- *
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- * Copyright (c) Facebook, Inc. and its affiliates.
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- *
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- * This source code is licensed under the MIT license found in the
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- * LICENSE file in the root directory of this source tree.
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- */
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-
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- /**
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- * @license React
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- * scheduler.development.js
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- *
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- * Copyright (c) Facebook, Inc. and its affiliates.
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- *
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- * This source code is licensed under the MIT license found in the
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- * LICENSE file in the root directory of this source tree.
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- */
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+ /*! regenerator-runtime -- Copyright (c) 2014-present, Facebook, Inc. -- license (MIT): https://github.com/babel/babel/blob/main/packages/babel-helpers/LICENSE */
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  /**
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  * Checks if an event is supported in the current execution environment.
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  * @license Modernizr 3.0.0pre (Custom Build) | MIT
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  */
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- /**
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- * chroma.js - JavaScript library for color conversions
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- *
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- * Copyright (c) 2011-2019, Gregor Aisch
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- * All rights reserved.
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- *
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- * Redistribution and use in source and binary forms, with or without
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- * modification, are permitted provided that the following conditions are met:
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- *
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- * 1. Redistributions of source code must retain the above copyright notice, this
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- * list of conditions and the following disclaimer.
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- *
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- * 2. Redistributions in binary form must reproduce the above copyright notice,
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- * this list of conditions and the following disclaimer in the documentation
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- * and/or other materials provided with the distribution.
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- *
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- * 3. The name Gregor Aisch may not be used to endorse or promote products
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- * derived from this software without specific prior written permission.
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- *
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- * THIS SOFTWARE IS PROVIDED BY THE COPYRIGHT HOLDERS AND CONTRIBUTORS "AS IS"
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- * AND ANY EXPRESS OR IMPLIED WARRANTIES, INCLUDING, BUT NOT LIMITED TO, THE
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- * IMPLIED WARRANTIES OF MERCHANTABILITY AND FITNESS FOR A PARTICULAR PURPOSE ARE
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- * DISCLAIMED. IN NO EVENT SHALL GREGOR AISCH OR CONTRIBUTORS BE LIABLE FOR ANY DIRECT,
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- * INDIRECT, INCIDENTAL, SPECIAL, EXEMPLARY, OR CONSEQUENTIAL DAMAGES (INCLUDING,
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- * BUT NOT LIMITED TO, PROCUREMENT OF SUBSTITUTE GOODS OR SERVICES; LOSS OF USE,
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- * DATA, OR PROFITS; OR BUSINESS INTERRUPTION) HOWEVER CAUSED AND ON ANY THEORY
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- * OF LIABILITY, WHETHER IN CONTRACT, STRICT LIABILITY, OR TORT (INCLUDING
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- * NEGLIGENCE OR OTHERWISE) ARISING IN ANY WAY OUT OF THE USE OF THIS SOFTWARE,
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- * EVEN IF ADVISED OF THE POSSIBILITY OF SUCH DAMAGE.
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- *
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- * -------------------------------------------------------
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- *
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- * chroma.js includes colors from colorbrewer2.org, which are released under
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- * the following license:
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- *
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- * Copyright (c) 2002 Cynthia Brewer, Mark Harrower,
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- * and The Pennsylvania State University.
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- *
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- * Licensed under the Apache License, Version 2.0 (the "License");
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- * you may not use this file except in compliance with the License.
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- * You may obtain a copy of the License at
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- * http://www.apache.org/licenses/LICENSE-2.0
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- *
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- * Unless required by applicable law or agreed to in writing,
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- * software distributed under the License is distributed on an
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- * "AS IS" BASIS, WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND,
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- * either express or implied. See the License for the specific
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- * language governing permissions and limitations under the License.
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- *
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- * ------------------------------------------------------
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- *
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- * Named colors are taken from X11 Color Names.
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- *
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