XspecT 0.1.3__py3-none-any.whl → 0.2.0__py3-none-any.whl

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.

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Files changed (58) hide show
  1. {XspecT-0.1.3.dist-info → XspecT-0.2.0.dist-info}/METADATA +23 -29
  2. XspecT-0.2.0.dist-info/RECORD +30 -0
  3. {XspecT-0.1.3.dist-info → XspecT-0.2.0.dist-info}/WHEEL +1 -1
  4. xspect/definitions.py +42 -0
  5. xspect/download_filters.py +11 -26
  6. xspect/fastapi.py +101 -0
  7. xspect/file_io.py +34 -103
  8. xspect/main.py +70 -66
  9. xspect/model_management.py +88 -0
  10. xspect/models/__init__.py +0 -0
  11. xspect/models/probabilistic_filter_model.py +277 -0
  12. xspect/models/probabilistic_filter_svm_model.py +169 -0
  13. xspect/models/probabilistic_single_filter_model.py +109 -0
  14. xspect/models/result.py +148 -0
  15. xspect/pipeline.py +201 -0
  16. xspect/run.py +38 -0
  17. xspect/train.py +304 -0
  18. xspect/train_filter/create_svm.py +6 -183
  19. xspect/train_filter/extract_and_concatenate.py +117 -121
  20. xspect/train_filter/html_scrap.py +16 -28
  21. xspect/train_filter/ncbi_api/download_assemblies.py +7 -8
  22. xspect/train_filter/ncbi_api/ncbi_assembly_metadata.py +9 -17
  23. xspect/train_filter/ncbi_api/ncbi_children_tree.py +3 -2
  24. xspect/train_filter/ncbi_api/ncbi_taxon_metadata.py +7 -5
  25. XspecT-0.1.3.dist-info/RECORD +0 -49
  26. xspect/BF_v2.py +0 -637
  27. xspect/Bootstrap.py +0 -29
  28. xspect/Classifier.py +0 -142
  29. xspect/OXA_Table.py +0 -53
  30. xspect/WebApp.py +0 -724
  31. xspect/XspecT_mini.py +0 -1363
  32. xspect/XspecT_trainer.py +0 -611
  33. xspect/map_kmers.py +0 -155
  34. xspect/search_filter.py +0 -504
  35. xspect/static/How-To.png +0 -0
  36. xspect/static/Logo.png +0 -0
  37. xspect/static/Logo2.png +0 -0
  38. xspect/static/Workflow_AspecT.png +0 -0
  39. xspect/static/Workflow_ClAssT.png +0 -0
  40. xspect/static/js.js +0 -615
  41. xspect/static/main.css +0 -280
  42. xspect/templates/400.html +0 -64
  43. xspect/templates/401.html +0 -62
  44. xspect/templates/404.html +0 -62
  45. xspect/templates/500.html +0 -62
  46. xspect/templates/about.html +0 -544
  47. xspect/templates/home.html +0 -51
  48. xspect/templates/layoutabout.html +0 -87
  49. xspect/templates/layouthome.html +0 -63
  50. xspect/templates/layoutspecies.html +0 -468
  51. xspect/templates/species.html +0 -33
  52. xspect/train_filter/README_XspecT_Erweiterung.md +0 -119
  53. xspect/train_filter/get_paths.py +0 -35
  54. xspect/train_filter/interface_XspecT.py +0 -204
  55. xspect/train_filter/k_mer_count.py +0 -162
  56. {XspecT-0.1.3.dist-info → XspecT-0.2.0.dist-info}/LICENSE +0 -0
  57. {XspecT-0.1.3.dist-info → XspecT-0.2.0.dist-info}/entry_points.txt +0 -0
  58. {XspecT-0.1.3.dist-info → XspecT-0.2.0.dist-info}/top_level.txt +0 -0
xspect/static/main.css DELETED
@@ -1,280 +0,0 @@
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- /*
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- Source:
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- https://github.com/CoreyMSchafer/code_snippets/tree/master/Python/Flask_Blog
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- */
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-
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- body {
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- background: #fafafa;
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- color: #333333;
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- margin-top: 5rem;
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- }
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-
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- html {
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- scroll-padding-top: 5rem;
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- }
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-
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- .download-btn{
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- background-color: DodgerBlue;
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- color: white;
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- padding: 0.5rem 1rem;
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- font-size: 1rem;
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- text-decoration: none;
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- border-radius:5px;
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- }
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-
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- .download-btn:hover {
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- background-color: RoyalBlue;
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- }
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-
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- .btn-default {
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- color: #000000;
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- background-color: #E4E7EA
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- }
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-
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- .arrow-left {
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- position: absolute;
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- top: 14%;
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- left: -3%;
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- width: 0;
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- height: 0;
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- border-top: 20px solid transparent;
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- border-bottom: 20px solid transparent;
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-
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- border-right:20px solid #e9ecef;
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- }
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-
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- .popup .content {
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- position: absolute;
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- top: 14%;
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- left: 42.5%;
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- transform: translate(-50%,-50%);
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- background: #e9ecef;
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- width: 390px;
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- height: 100px;
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- z-index: 2;
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- text-align: left;
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- padding: 20px;
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- box-sizing: border-box;
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- border-radius: 2%;
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- box-shadow:2px 3px 5px #BCBCBC;
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- }
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-
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- .popup .close-btn {
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- cursor: pointer;
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- position: absolute;
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- right: 15px;
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- top: 15px;
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- width: 20px;
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- height: 20px;
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- background: #0d6efd;
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- color: #fff;
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- font-size: 25px;
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- font-weight: 600;
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- line-height: 15px;
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- text-align: center;
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- border-radius: 12%;
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- }
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-
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-
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- .popup.active .content {
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- transition: all 100ms ease-in-out;
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- transform: translate(-50%,-50%) scale(0);
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- }
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-
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- .popup-2 .content-2 {
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- position: absolute;
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- top: 30%;
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- right: 5%;
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- transition: all 100ms ease-in-out;
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- transform: translate(-50%,-50%) scale(0);
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- background: #ffffff;
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- width: 200px;
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- height: 270px;
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- z-index: 2;
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- text-align: left;
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- padding: 20px;
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- box-sizing: border-box;
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- border-radius: 2%;
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- box-shadow:2px 3px 5px #BCBCBC;
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- }
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-
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- .popup-2.active .content-2 {
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- transform: translate(-50%,-50%) scale(1);
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- }
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-
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- .topnav-right {
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- float: right;
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- }
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-
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- .rightnav {
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- color: #cbd5db;
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- }
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-
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- .rightnav:hover {
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- color: #ffffff;
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- }
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-
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- .sidebar {
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- position: fixed;
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- top: 0;
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- bottom: 0;
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- left: 0;
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- padding: 58px 0 0; /* Height of navbar */
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- box-shadow: 0 2px 5px 0 rgb(0 0 0 / 5%), 0 2px 10px 0 rgb(0 0 0 / 5%);
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- width: 240px;
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- z-index: 600;
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- }
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-
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- .btn {
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- vertical-align: baseline;
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- text-align: left;
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- }
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-
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- h1, h2, h3, h4, h5, h6 {
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- color: #444444;
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- }
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-
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- .bg-steel {
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- background-color: #5f788a;
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- }
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-
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- .site-header .navbar-nav .nav-link {
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- color: #cbd5db;
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- }
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-
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- .site-header .navbar-nav .nav-link:hover {
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- color: #ffffff;
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- }
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-
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- .site-header .navbar-nav .nav-link.active {
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- font-weight: 500;
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- }
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-
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- .content-section {
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- background: #ffffff;
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- padding: 10px 20px;
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- border: 1px solid #dddddd;
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- border-radius: 3px;
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- margin-bottom: 20px;
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- }
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-
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- .article-title {
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- color: #444444;
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- }
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-
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- a, a:focus, a:active {
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- text-decoration: none;
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- color: #0071c2;
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- }
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-
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- a:hover {
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- color: #205493;
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- }
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-
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- a.article-title:hover {
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- color: #428bca;
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- text-decoration: none;
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- }
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-
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- .article-content {
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- white-space: pre-line;
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- }
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-
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- .article-img {
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- height: 65px;
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- width: 65px;
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- margin-right: 16px;
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- }
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-
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- .article-metadata {
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- padding-bottom: 1px;
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- margin-bottom: 4px;
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- border-bottom: 1px solid #e3e3e3
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- }
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-
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- .article-metadata a:hover {
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- color: #333;
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- text-decoration: none;
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- }
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- .article-svg {
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- width: 25px;
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- height: 25px;
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- vertical-align: middle;
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- }
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-
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- .account-img {
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- height: 125px;
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- width: 125px;
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- margin-right: 20px;
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- margin-bottom: 16px;
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- }
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-
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- .account-heading {
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- font-size: 2.5rem;
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- }
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-
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- .white-screen {
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- position: relative;
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- }
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-
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- /*
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- Source:
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- https://sarahleejane.github.io/learning/python/2015/08/09/simple-tables-in-webapps-using-flask-and-pandas-with-python.html
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- */
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-
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- table.dataframe, .dataframe th, .dataframe td {
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- border: none;
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- border-bottom: 1px solid #C8C8C8;
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- border-collapse: collapse;
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- text-align:left;
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- padding: 10px;
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- margin-bottom: 40px;
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- font-size: 0.9em;
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- }
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-
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- .male th {
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- background-color: #add8e6;
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- color: white;
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- }
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-
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- .female th {
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- background-color: #77dd77;
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- color: white;
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- }
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-
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- tr:nth-child(odd) { background-color:#eee; }
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- tr:nth-child(even) { background-color:#fff; }
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-
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- tr:hover { background-color: #ffff99;}
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-
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- /*
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- Source Loading Animation
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- https://www.w3schools.com/howto/howto_css_loader.asp
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- */
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- .loader {
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- border: 16px solid #4A4C4E; /* Light grey */
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- border-top: 16px solid #fa9c1d; /* Orange */
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- border-radius: 50%;
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- width: 120px;
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- height: 120px;
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- animation: spin 1.5s linear infinite;
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- justify-content: center;
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- margin: auto;
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- }
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-
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- @keyframes spin {
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- 0% { transform: rotate(0deg); }
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- 100% { transform: rotate(360deg); }
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- }
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-
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- .loader2 {
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- border: 16px solid #eaedf0; /* Light grey */
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- border-top: 16px solid #0d6efd; /* Orange */
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- border-radius: 50%;
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- width: 60px;
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- height: 60px;
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- animation: spin 2s linear infinite;
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- justify-content: center;
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- margin: auto;
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- }
xspect/templates/400.html DELETED
@@ -1,64 +0,0 @@
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- <!DOCTYPE html>
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- <html lang="en">
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- <head>
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-
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-
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- <!-- Required meta tags -->
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- <meta charset="utf-8">
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- <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
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-
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- <!-- Bootstrap CSS -->
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- <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0/css/bootstrap.min.css" integrity="sha384-Gn5384xqQ1aoWXA+058RXPxPg6fy4IWvTNh0E263XmFcJlSAwiGgFAW/dAiS6JXm" crossorigin="anonymous">
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-
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- <!-- Costum stuff from css file -->
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- <link rel="stylesheet" type="text/css" href="{{ url_for('static', filename='main.css') }}">
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-
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- <meta charset="UTF-8">
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- <title> Clonetye Assignment </title>
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- <link rel="icon" href="data:,">
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- </head>
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- <body>
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-
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- <!-- Sidebar -->
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- <header class="site-header">
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- <nav class="navbar navbar-expand-md navbar-dark bg-steel fixed-top">
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- <div class="container">
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- <a class="navbar-brand mr-4" href="/about">Home</a>
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- <button class="navbar-toggler" type="button" data-toggle="collapse" data-target="#navbarToggle" aria-controls="navbarToggle" aria-expanded="false" aria-label="Toggle navigation">
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- <span class="navbar-toggler-icon"></span>
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- </button>
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- <div class="collapse navbar-collapse" id="navbarToggle">
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- <div class="navbar-nav mr-auto">
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- <a class="nav-item nav-link" href="/species">XspecT</a>
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- <a class="nav-item nav-link" href="/about">About</a>
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- </div>
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- </div>
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- </div>
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- </nav>
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- </header>
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-
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- <!-- variable content -->
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- <main role="main" class="container">
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- <div class="row">
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- <div class="col-md-11">
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- <h4>Error 400: Bad Request</h4>
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- <h2> This Tool uses a file reader that is not supported by all browsers.</h2>
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- <h2> Find supported browsers <a href="https://caniuse.com/#feat=filereader">here</a>.</h2>
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-
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- <p> </p>
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- <p> Back to <a href="/">home</a>.</p>
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- </div>
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- </div>
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- </main>
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- <!-- Optional JavaScript -->
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- <!-- jQuery first, then Popper.js, then Bootstrap JS -->
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- <script src="https://code.jquery.com/jquery-3.2.1.slim.min.js" integrity="sha384-KJ3o2DKtIkvYIK3UENzmM7KCkRr/rE9/Qpg6aAZGJwFDMVNA/GpGFF93hXpG5KkN" crossorigin="anonymous"></script>
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- <script src="https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.12.9/umd/popper.min.js" integrity="sha384-ApNbgh9B+Y1QKtv3Rn7W3mgPxhU9K/ScQsAP7hUibX39j7fakFPskvXusvfa0b4Q" crossorigin="anonymous"></script>
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- <script src="https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0/js/bootstrap.min.js" integrity="sha384-JZR6Spejh4U02d8jOt6vLEHfe/JQGiRRSQQxSfFWpi1MquVdAyjUar5+76PVCmYl" crossorigin="anonymous"></script>
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- </body>
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xspect/templates/401.html DELETED
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- <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0/css/bootstrap.min.css" integrity="sha384-Gn5384xqQ1aoWXA+058RXPxPg6fy4IWvTNh0E263XmFcJlSAwiGgFAW/dAiS6JXm" crossorigin="anonymous">
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- <title> Clonetye Assignment </title>
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- <link rel="icon" href="data:,">
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- </head>
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- <body>
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-
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- <!-- Sidebar -->
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- <header class="site-header">
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- <nav class="navbar navbar-expand-md navbar-dark bg-steel fixed-top">
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- <div class="container">
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- <a class="navbar-brand mr-4" href="/about">Home</a>
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- <button class="navbar-toggler" type="button" data-toggle="collapse" data-target="#navbarToggle" aria-controls="navbarToggle" aria-expanded="false" aria-label="Toggle navigation">
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- <span class="navbar-toggler-icon"></span>
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- <div class="collapse navbar-collapse" id="navbarToggle">
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- <div class="navbar-nav mr-auto">
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- <a class="nav-item nav-link" href="/species">XspecT</a>
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- <a class="nav-item nav-link" href="/about">About</a>
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- </div>
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- </div>
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- </div>
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- </nav>
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- </header>
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- <h4>Error 401: Unauthorized</h4>
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- <h2> You have no access to this page.</h2>
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- <p> </p>
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- <p> Back to <a href="/">home</a>.</p>
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- </div>
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- <!-- Optional JavaScript -->
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- <script src="https://code.jquery.com/jquery-3.2.1.slim.min.js" integrity="sha384-KJ3o2DKtIkvYIK3UENzmM7KCkRr/rE9/Qpg6aAZGJwFDMVNA/GpGFF93hXpG5KkN" crossorigin="anonymous"></script>
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- <script src="https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.12.9/umd/popper.min.js" integrity="sha384-ApNbgh9B+Y1QKtv3Rn7W3mgPxhU9K/ScQsAP7hUibX39j7fakFPskvXusvfa0b4Q" crossorigin="anonymous"></script>
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- <script src="https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0/js/bootstrap.min.js" integrity="sha384-JZR6Spejh4U02d8jOt6vLEHfe/JQGiRRSQQxSfFWpi1MquVdAyjUar5+76PVCmYl" crossorigin="anonymous"></script>
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xspect/templates/404.html DELETED
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- <header class="site-header">
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- <a class="navbar-brand mr-4" href="/about">Home</a>
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- <button class="navbar-toggler" type="button" data-toggle="collapse" data-target="#navbarToggle" aria-controls="navbarToggle" aria-expanded="false" aria-label="Toggle navigation">
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- </button>
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- <div class="collapse navbar-collapse" id="navbarToggle">
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- <div class="navbar-nav mr-auto">
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- <a class="nav-item nav-link" href="/species">XspecT</a>
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- <a class="nav-item nav-link" href="/about">About</a>
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- </div>
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- </div>
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- </div>
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- </nav>
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- </header>
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- <h4>Error 404</h4>
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- <h2> This page does not exist.</h2>
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- <p> </p>
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- <p> Back to <a href="/home">home</a>.</p>
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- </div>
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- <script src="https://code.jquery.com/jquery-3.2.1.slim.min.js" integrity="sha384-KJ3o2DKtIkvYIK3UENzmM7KCkRr/rE9/Qpg6aAZGJwFDMVNA/GpGFF93hXpG5KkN" crossorigin="anonymous"></script>
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- <script src="https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.12.9/umd/popper.min.js" integrity="sha384-ApNbgh9B+Y1QKtv3Rn7W3mgPxhU9K/ScQsAP7hUibX39j7fakFPskvXusvfa0b4Q" crossorigin="anonymous"></script>
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- <script src="https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0/js/bootstrap.min.js" integrity="sha384-JZR6Spejh4U02d8jOt6vLEHfe/JQGiRRSQQxSfFWpi1MquVdAyjUar5+76PVCmYl" crossorigin="anonymous"></script>
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-
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- </body>
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- </html>
xspect/templates/500.html DELETED
@@ -1,62 +0,0 @@
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- <!DOCTYPE html>
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- <html lang="en">
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- <head>
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-
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-
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- <!-- Required meta tags -->
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- <meta charset="utf-8">
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- <meta name="viewport" content="width=device-width, initial-scale=1, shrink-to-fit=no">
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-
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- <!-- Bootstrap CSS -->
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- <link rel="stylesheet" href="https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0/css/bootstrap.min.css" integrity="sha384-Gn5384xqQ1aoWXA+058RXPxPg6fy4IWvTNh0E263XmFcJlSAwiGgFAW/dAiS6JXm" crossorigin="anonymous">
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-
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- <!-- Costum stuff from css file -->
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- <link rel="stylesheet" type="text/css" href="{{ url_for('static', filename='main.css') }}">
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-
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-
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- <meta charset="UTF-8">
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- <title> Clonetye Assignment </title>
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- <link rel="icon" href="data:,">
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- </head>
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- <body>
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-
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- <!-- Sidebar -->
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- <header class="site-header">
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- <nav class="navbar navbar-expand-md navbar-dark bg-steel fixed-top">
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- <div class="container">
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- <a class="navbar-brand mr-4" href="/about">Home</a>
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- <button class="navbar-toggler" type="button" data-toggle="collapse" data-target="#navbarToggle" aria-controls="navbarToggle" aria-expanded="false" aria-label="Toggle navigation">
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- <span class="navbar-toggler-icon"></span>
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- </button>
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- <div class="collapse navbar-collapse" id="navbarToggle">
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- <div class="navbar-nav mr-auto">
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- <a class="nav-item nav-link" href="/species">XspecT</a>
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- <a class="nav-item nav-link" href="/about">About</a>
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- </div>
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- </div>
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- </div>
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- </nav>
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- </header>
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-
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- <!-- variable content -->
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- <main role="main" class="container">
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- <div class="row">
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- <div class="col-md-11">
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- <h4>Error 500: Internal Server Error</h4>
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- <h2> The server was unable to deal with your request, data has been logged for bug fixing.</h2>
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- <p> </p>
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- <p> Back to <a href="/home">home</a>.</p>
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- </div>
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-
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- </div>
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- </main>
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-
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-
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- <!-- Optional JavaScript -->
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- <!-- jQuery first, then Popper.js, then Bootstrap JS -->
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- <script src="https://code.jquery.com/jquery-3.2.1.slim.min.js" integrity="sha384-KJ3o2DKtIkvYIK3UENzmM7KCkRr/rE9/Qpg6aAZGJwFDMVNA/GpGFF93hXpG5KkN" crossorigin="anonymous"></script>
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- <script src="https://cdnjs.cloudflare.com/ajax/libs/popper.js/1.12.9/umd/popper.min.js" integrity="sha384-ApNbgh9B+Y1QKtv3Rn7W3mgPxhU9K/ScQsAP7hUibX39j7fakFPskvXusvfa0b4Q" crossorigin="anonymous"></script>
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- <script src="https://maxcdn.bootstrapcdn.com/bootstrap/4.0.0/js/bootstrap.min.js" integrity="sha384-JZR6Spejh4U02d8jOt6vLEHfe/JQGiRRSQQxSfFWpi1MquVdAyjUar5+76PVCmYl" crossorigin="anonymous"></script>
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-
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- </body>
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- </html>