scout-browser 4.95.0__py3-none-any.whl → 4.97.0__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.
Files changed (99) hide show
  1. scout/adapter/mongo/case.py +75 -70
  2. scout/adapter/mongo/filter.py +28 -11
  3. scout/adapter/mongo/institute.py +2 -0
  4. scout/adapter/mongo/omics_variant.py +20 -5
  5. scout/adapter/mongo/query.py +104 -95
  6. scout/adapter/mongo/variant.py +0 -5
  7. scout/adapter/mongo/variant_loader.py +10 -12
  8. scout/build/case.py +3 -1
  9. scout/build/individual.py +3 -11
  10. scout/commands/delete/delete_command.py +87 -49
  11. scout/commands/load/research.py +4 -4
  12. scout/commands/load/variants.py +25 -8
  13. scout/commands/setup/setup_scout.py +1 -1
  14. scout/commands/update/case.py +12 -0
  15. scout/commands/update/individual.py +1 -2
  16. scout/constants/__init__.py +7 -2
  17. scout/constants/acmg.py +25 -18
  18. scout/constants/file_types.py +68 -119
  19. scout/constants/filters.py +2 -1
  20. scout/constants/gene_tags.py +3 -3
  21. scout/constants/igv_tracks.py +7 -11
  22. scout/constants/query_terms.py +2 -2
  23. scout/demo/643594.config.yaml +6 -0
  24. scout/demo/643594.peddy.ped +1 -1
  25. scout/demo/643594.somalier.ancestry.tsv +4 -0
  26. scout/demo/643594.somalier.pairs.tsv +4 -0
  27. scout/demo/643594.somalier.samples.tsv +4 -0
  28. scout/demo/cancer.load_config.yaml +2 -3
  29. scout/demo/resources/__init__.py +1 -1
  30. scout/demo/resources/gnomad.v4.1.constraint_metrics_reduced.tsv +3755 -0
  31. scout/demo/rnafusion.load_config.yaml +1 -0
  32. scout/exceptions/database.py +1 -1
  33. scout/load/all.py +8 -16
  34. scout/models/case/case.py +1 -0
  35. scout/models/case/case_loading_models.py +15 -5
  36. scout/models/managed_variant.py +3 -3
  37. scout/models/omics_variant.py +3 -3
  38. scout/parse/case.py +113 -5
  39. scout/parse/pedqc.py +127 -0
  40. scout/parse/variant/frequency.py +9 -6
  41. scout/parse/variant/variant.py +71 -39
  42. scout/server/app.py +14 -0
  43. scout/server/blueprints/alignviewers/controllers.py +2 -0
  44. scout/server/blueprints/alignviewers/templates/alignviewers/igv_viewer.html +3 -0
  45. scout/server/blueprints/alignviewers/templates/alignviewers/utils.html +1 -1
  46. scout/server/blueprints/cases/controllers.py +25 -3
  47. scout/server/blueprints/cases/templates/cases/case.html +3 -0
  48. scout/server/blueprints/cases/templates/cases/case_report.html +28 -2
  49. scout/server/blueprints/cases/templates/cases/chanjo2_form.html +2 -2
  50. scout/server/blueprints/cases/templates/cases/collapsible_actionbar.html +12 -0
  51. scout/server/blueprints/cases/templates/cases/gene_panel.html +9 -3
  52. scout/server/blueprints/cases/templates/cases/individuals_table.html +4 -1
  53. scout/server/blueprints/cases/templates/cases/utils.html +23 -19
  54. scout/server/blueprints/cases/views.py +5 -9
  55. scout/server/blueprints/clinvar/controllers.py +12 -11
  56. scout/server/blueprints/clinvar/templates/clinvar/clinvar_submissions.html +10 -14
  57. scout/server/blueprints/clinvar/templates/clinvar/multistep_add_variant.html +15 -7
  58. scout/server/blueprints/clinvar/views.py +18 -31
  59. scout/server/blueprints/institutes/controllers.py +20 -1
  60. scout/server/blueprints/institutes/forms.py +5 -1
  61. scout/server/blueprints/institutes/templates/overview/institute_settings.html +7 -0
  62. scout/server/blueprints/institutes/templates/overview/utils.html +20 -1
  63. scout/server/blueprints/omics_variants/templates/omics_variants/outliers.html +9 -2
  64. scout/server/blueprints/omics_variants/views.py +8 -10
  65. scout/server/blueprints/variant/controllers.py +30 -1
  66. scout/server/blueprints/variant/templates/variant/cancer-variant.html +21 -5
  67. scout/server/blueprints/variant/templates/variant/components.html +26 -9
  68. scout/server/blueprints/variant/templates/variant/variant.html +4 -2
  69. scout/server/blueprints/variant/templates/variant/variant_details.html +1 -1
  70. scout/server/blueprints/variant/utils.py +2 -0
  71. scout/server/blueprints/variant/views.py +10 -3
  72. scout/server/blueprints/variants/controllers.py +29 -3
  73. scout/server/blueprints/variants/forms.py +37 -10
  74. scout/server/blueprints/variants/templates/variants/cancer-variants.html +5 -4
  75. scout/server/blueprints/variants/templates/variants/components.html +12 -10
  76. scout/server/blueprints/variants/templates/variants/str-variants.html +13 -9
  77. scout/server/blueprints/variants/templates/variants/utils.html +59 -36
  78. scout/server/blueprints/variants/views.py +45 -60
  79. scout/server/extensions/beacon_extension.py +1 -1
  80. scout/server/extensions/bionano_extension.py +5 -5
  81. scout/server/extensions/chanjo2_extension.py +40 -1
  82. scout/server/extensions/chanjo_extension.py +1 -1
  83. scout/server/extensions/clinvar_extension.py +56 -2
  84. scout/server/extensions/matchmaker_extension.py +1 -1
  85. scout/server/links.py +0 -14
  86. scout/server/static/bs_styles.css +2 -0
  87. scout/server/templates/layout.html +1 -0
  88. scout/server/utils.py +5 -0
  89. scout/utils/acmg.py +5 -5
  90. scout/utils/ensembl_biomart_clients.py +2 -11
  91. scout/utils/scout_requests.py +1 -1
  92. {scout_browser-4.95.0.dist-info → scout_browser-4.97.0.dist-info}/METADATA +1 -1
  93. {scout_browser-4.95.0.dist-info → scout_browser-4.97.0.dist-info}/RECORD +96 -94
  94. scout/demo/resources/gnomad.v4.0.constraint_metrics_reduced.tsv +0 -3755
  95. scout/parse/peddy.py +0 -149
  96. scout/utils/sort.py +0 -21
  97. {scout_browser-4.95.0.dist-info → scout_browser-4.97.0.dist-info}/WHEEL +0 -0
  98. {scout_browser-4.95.0.dist-info → scout_browser-4.97.0.dist-info}/entry_points.txt +0 -0
  99. {scout_browser-4.95.0.dist-info → scout_browser-4.97.0.dist-info}/licenses/LICENSE +0 -0

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