scout-browser 4.81__py3-none-any.whl → 4.82.2__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 (58) hide show
  1. scout/__version__.py +1 -1
  2. scout/adapter/mongo/disease_terms.py +5 -2
  3. scout/adapter/mongo/query.py +23 -11
  4. scout/build/managed_variant.py +12 -1
  5. scout/build/variant/genotype.py +2 -0
  6. scout/build/variant/variant.py +5 -0
  7. scout/constants/clinvar.py +1 -1
  8. scout/constants/query_terms.py +3 -1
  9. scout/models/variant/variant.py +1 -0
  10. scout/parse/variant/frequency.py +56 -54
  11. scout/parse/variant/genotype.py +89 -15
  12. scout/parse/variant/transcript.py +17 -9
  13. scout/parse/variant/variant.py +12 -0
  14. scout/server/app.py +6 -3
  15. scout/server/blueprints/alignviewers/templates/alignviewers/utils.html +1 -1
  16. scout/server/blueprints/cases/controllers.py +2 -57
  17. scout/server/blueprints/cases/templates/cases/case_bionano.html +3 -24
  18. scout/server/blueprints/cases/templates/cases/case_report.html +87 -69
  19. scout/server/blueprints/cases/templates/cases/case_sma.html +2 -13
  20. scout/server/blueprints/cases/templates/cases/chanjo2_form.html +47 -0
  21. scout/server/blueprints/cases/templates/cases/collapsible_actionbar.html +4 -4
  22. scout/server/blueprints/cases/templates/cases/gene_panel.html +4 -11
  23. scout/server/blueprints/cases/templates/cases/individuals_table.html +2 -12
  24. scout/server/blueprints/cases/templates/cases/utils.html +20 -1
  25. scout/server/blueprints/cases/views.py +0 -22
  26. scout/server/blueprints/clinvar/controllers.py +3 -3
  27. scout/server/blueprints/clinvar/templates/clinvar/clinvar_submissions.html +29 -2
  28. scout/server/blueprints/clinvar/templates/clinvar/multistep_add_variant.html +36 -18
  29. scout/server/blueprints/clinvar/views.py +13 -1
  30. scout/server/blueprints/diagnoses/controllers.py +2 -0
  31. scout/server/blueprints/institutes/controllers.py +76 -38
  32. scout/server/blueprints/institutes/templates/overview/cases.html +54 -42
  33. scout/server/blueprints/managed_variants/templates/managed_variants/managed_variants.html +1 -1
  34. scout/server/blueprints/managed_variants/views.py +2 -4
  35. scout/server/blueprints/panels/templates/panels/panel.html +8 -7
  36. scout/server/blueprints/panels/views.py +2 -11
  37. scout/server/blueprints/phenotypes/templates/phenotypes/hpo_terms.html +3 -2
  38. scout/server/blueprints/variant/controllers.py +3 -2
  39. scout/server/blueprints/variant/templates/variant/components.html +1 -1
  40. scout/server/blueprints/variant/templates/variant/utils.html +3 -1
  41. scout/server/blueprints/variant/templates/variant/variant.html +20 -15
  42. scout/server/blueprints/variant/templates/variant/variant_details.html +78 -26
  43. scout/server/blueprints/variant/utils.py +9 -13
  44. scout/server/blueprints/variants/controllers.py +30 -3
  45. scout/server/blueprints/variants/forms.py +15 -1
  46. scout/server/blueprints/variants/templates/variants/components.html +55 -0
  47. scout/server/blueprints/variants/templates/variants/fusion-variants.html +3 -50
  48. scout/server/blueprints/variants/templates/variants/str-variants.html +8 -5
  49. scout/server/blueprints/variants/templates/variants/utils.html +57 -31
  50. scout/server/blueprints/variants/templates/variants/variants.html +1 -1
  51. scout/server/blueprints/variants/utils.py +7 -10
  52. scout/server/extensions/clinvar_extension.py +10 -2
  53. {scout_browser-4.81.dist-info → scout_browser-4.82.2.dist-info}/METADATA +6 -5
  54. {scout_browser-4.81.dist-info → scout_browser-4.82.2.dist-info}/RECORD +58 -57
  55. {scout_browser-4.81.dist-info → scout_browser-4.82.2.dist-info}/LICENSE +0 -0
  56. {scout_browser-4.81.dist-info → scout_browser-4.82.2.dist-info}/WHEEL +0 -0
  57. {scout_browser-4.81.dist-info → scout_browser-4.82.2.dist-info}/entry_points.txt +0 -0
  58. {scout_browser-4.81.dist-info → scout_browser-4.82.2.dist-info}/top_level.txt +0 -0