endoreg-db 0.8.6.1__py3-none-any.whl → 0.8.8.9__py3-none-any.whl

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  1. endoreg_db/authz/auth.py +74 -0
  2. endoreg_db/authz/backends.py +168 -0
  3. endoreg_db/authz/management/commands/list_routes.py +18 -0
  4. endoreg_db/authz/middleware.py +83 -0
  5. endoreg_db/authz/permissions.py +127 -0
  6. endoreg_db/authz/policy.py +218 -0
  7. endoreg_db/authz/views_auth.py +66 -0
  8. endoreg_db/config/env.py +13 -8
  9. endoreg_db/data/__init__.py +2 -11
  10. endoreg_db/data/ai_model_meta/default_multilabel_classification.yaml +3 -3
  11. endoreg_db/data/event_classification/data.yaml +4 -0
  12. endoreg_db/data/event_classification_choice/data.yaml +9 -0
  13. endoreg_db/data/examination/examinations/data.yaml +114 -14
  14. endoreg_db/data/examination/time-type/data.yaml +0 -3
  15. endoreg_db/data/examination_indication/endoscopy.yaml +108 -173
  16. endoreg_db/data/examination_indication_classification/endoscopy.yaml +0 -70
  17. endoreg_db/data/examination_indication_classification_choice/endoscopy.yaml +33 -37
  18. endoreg_db/data/finding/00_generic.yaml +35 -0
  19. endoreg_db/data/finding/00_generic_complication.yaml +9 -0
  20. endoreg_db/data/finding/01_gastroscopy_baseline.yaml +88 -0
  21. endoreg_db/data/finding/01_gastroscopy_observation.yaml +113 -0
  22. endoreg_db/data/finding/02_colonoscopy_baseline.yaml +53 -0
  23. endoreg_db/data/finding/02_colonoscopy_hidden.yaml +119 -0
  24. endoreg_db/data/finding/02_colonoscopy_observation.yaml +152 -0
  25. endoreg_db/data/finding_classification/00_generic.yaml +44 -0
  26. endoreg_db/data/finding_classification/00_generic_histology.yaml +28 -0
  27. endoreg_db/data/finding_classification/00_generic_lesion.yaml +52 -0
  28. endoreg_db/data/finding_classification/02_colonoscopy_baseline.yaml +83 -0
  29. endoreg_db/data/finding_classification/02_colonoscopy_histology.yaml +13 -0
  30. endoreg_db/data/finding_classification/02_colonoscopy_other.yaml +12 -0
  31. endoreg_db/data/finding_classification/02_colonoscopy_polyp.yaml +101 -0
  32. endoreg_db/data/finding_classification_choice/{yes_no_na.yaml → 00_generic.yaml} +5 -1
  33. endoreg_db/data/finding_classification_choice/{examination_setting_generic_types.yaml → 00_generic_baseline.yaml} +10 -2
  34. endoreg_db/data/finding_classification_choice/{complication_generic_types.yaml → 00_generic_complication.yaml} +1 -1
  35. endoreg_db/data/finding_classification_choice/{histology.yaml → 00_generic_histology.yaml} +1 -4
  36. endoreg_db/data/finding_classification_choice/00_generic_lesion.yaml +158 -0
  37. endoreg_db/data/finding_classification_choice/{bowel_preparation.yaml → 02_colonoscopy_bowel_preparation.yaml} +1 -30
  38. endoreg_db/data/finding_classification_choice/{colonoscopy_not_complete_reason.yaml → 02_colonoscopy_generic.yaml} +1 -1
  39. endoreg_db/data/finding_classification_choice/{histology_polyp.yaml → 02_colonoscopy_histology.yaml} +1 -1
  40. endoreg_db/data/finding_classification_choice/{colonoscopy_location.yaml → 02_colonoscopy_location.yaml} +23 -4
  41. endoreg_db/data/finding_classification_choice/02_colonoscopy_other.yaml +34 -0
  42. endoreg_db/data/finding_classification_choice/02_colonoscopy_polyp_advanced_imaging.yaml +76 -0
  43. endoreg_db/data/finding_classification_choice/{colon_lesion_paris.yaml → 02_colonoscopy_polyp_morphology.yaml} +26 -8
  44. endoreg_db/data/finding_classification_choice/02_colonoscopy_size.yaml +27 -0
  45. endoreg_db/data/finding_classification_type/{colonoscopy_basic.yaml → 00_generic.yaml} +18 -13
  46. endoreg_db/data/finding_classification_type/02_colonoscopy.yaml +9 -0
  47. endoreg_db/data/finding_intervention/00_generic_endoscopy.yaml +59 -0
  48. endoreg_db/data/finding_intervention/00_generic_endoscopy_ablation.yaml +44 -0
  49. endoreg_db/data/finding_intervention/00_generic_endoscopy_bleeding.yaml +55 -0
  50. endoreg_db/data/finding_intervention/00_generic_endoscopy_resection.yaml +85 -0
  51. endoreg_db/data/finding_intervention/00_generic_endoscopy_stenosis.yaml +17 -0
  52. endoreg_db/data/finding_intervention/00_generic_endoscopy_stent.yaml +9 -0
  53. endoreg_db/data/finding_intervention/01_gastroscopy.yaml +19 -0
  54. endoreg_db/data/finding_intervention/04_eus.yaml +39 -0
  55. endoreg_db/data/finding_intervention/05_ercp.yaml +3 -0
  56. endoreg_db/data/finding_type/data.yaml +8 -12
  57. endoreg_db/data/requirement/01_patient_data.yaml +93 -0
  58. endoreg_db/data/requirement/old/colon_polyp_intervention.yaml +49 -0
  59. endoreg_db/data/requirement/old/coloreg_colon_polyp.yaml +49 -0
  60. endoreg_db/data/requirement_operator/new_operators.yaml +36 -0
  61. endoreg_db/data/requirement_set/01_endoscopy_generic.yaml +29 -12
  62. endoreg_db/data/requirement_set/01_laboratory.yaml +13 -0
  63. endoreg_db/data/requirement_set/{endoscopy_bleeding_risk.yaml → 02_endoscopy_bleeding_risk.yaml} +0 -6
  64. endoreg_db/data/requirement_set/90_coloreg.yaml +190 -0
  65. endoreg_db/data/requirement_set/_old_ +109 -0
  66. endoreg_db/data/requirement_set_type/data.yaml +21 -0
  67. endoreg_db/data/setup_config.yaml +4 -4
  68. endoreg_db/data/tag/requirement_set_tags.yaml +21 -0
  69. endoreg_db/exceptions.py +4 -2
  70. endoreg_db/forms/examination_form.py +1 -1
  71. endoreg_db/helpers/data_loader.py +125 -53
  72. endoreg_db/helpers/default_objects.py +116 -81
  73. endoreg_db/import_files/__init__.py +27 -0
  74. endoreg_db/import_files/context/__init__.py +7 -0
  75. endoreg_db/import_files/context/default_sensitive_meta.py +81 -0
  76. endoreg_db/import_files/context/ensure_center.py +17 -0
  77. endoreg_db/import_files/context/file_lock.py +66 -0
  78. endoreg_db/import_files/context/import_context.py +43 -0
  79. endoreg_db/import_files/context/validate_directories.py +56 -0
  80. endoreg_db/import_files/file_storage/__init__.py +15 -0
  81. endoreg_db/import_files/file_storage/create_report_file.py +76 -0
  82. endoreg_db/import_files/file_storage/create_video_file.py +75 -0
  83. endoreg_db/import_files/file_storage/sensitive_meta_storage.py +39 -0
  84. endoreg_db/import_files/file_storage/state_management.py +400 -0
  85. endoreg_db/import_files/file_storage/storage.py +36 -0
  86. endoreg_db/import_files/import_service.md +26 -0
  87. endoreg_db/import_files/processing/__init__.py +11 -0
  88. endoreg_db/import_files/processing/report_processing/report_anonymization.py +94 -0
  89. endoreg_db/import_files/processing/sensitive_meta_adapter.py +51 -0
  90. endoreg_db/import_files/processing/video_processing/video_anonymization.py +107 -0
  91. endoreg_db/import_files/processing/video_processing/video_cleanup_on_error.py +119 -0
  92. endoreg_db/import_files/pseudonymization/fake.py +52 -0
  93. endoreg_db/import_files/pseudonymization/k_anonymity.py +182 -0
  94. endoreg_db/import_files/pseudonymization/k_pseudonymity.py +128 -0
  95. endoreg_db/import_files/report_import_service.py +141 -0
  96. endoreg_db/import_files/video_import_service.py +150 -0
  97. endoreg_db/management/commands/create_model_meta_from_huggingface.py +21 -10
  98. endoreg_db/management/commands/create_multilabel_model_meta.py +299 -129
  99. endoreg_db/management/commands/import_report.py +130 -65
  100. endoreg_db/management/commands/import_video.py +9 -10
  101. endoreg_db/management/commands/import_video_with_classification.py +2 -2
  102. endoreg_db/management/commands/list_routes.py +18 -0
  103. endoreg_db/management/commands/load_ai_model_data.py +5 -5
  104. endoreg_db/management/commands/load_ai_model_label_data.py +9 -7
  105. endoreg_db/management/commands/load_base_db_data.py +5 -134
  106. endoreg_db/management/commands/load_center_data.py +12 -12
  107. endoreg_db/management/commands/load_contraindication_data.py +14 -16
  108. endoreg_db/management/commands/load_disease_classification_choices_data.py +15 -18
  109. endoreg_db/management/commands/load_disease_classification_data.py +15 -18
  110. endoreg_db/management/commands/load_disease_data.py +25 -28
  111. endoreg_db/management/commands/load_endoscope_data.py +20 -27
  112. endoreg_db/management/commands/load_event_data.py +14 -16
  113. endoreg_db/management/commands/load_examination_data.py +31 -44
  114. endoreg_db/management/commands/load_examination_indication_data.py +20 -21
  115. endoreg_db/management/commands/load_finding_data.py +52 -80
  116. endoreg_db/management/commands/load_information_source.py +21 -23
  117. endoreg_db/management/commands/load_lab_value_data.py +17 -26
  118. endoreg_db/management/commands/load_medication_data.py +13 -12
  119. endoreg_db/management/commands/load_organ_data.py +15 -19
  120. endoreg_db/management/commands/load_pdf_type_data.py +19 -18
  121. endoreg_db/management/commands/load_profession_data.py +14 -17
  122. endoreg_db/management/commands/load_qualification_data.py +20 -23
  123. endoreg_db/management/commands/load_report_reader_flag_data.py +17 -19
  124. endoreg_db/management/commands/load_requirement_data.py +62 -39
  125. endoreg_db/management/commands/load_requirement_set_tags.py +95 -0
  126. endoreg_db/management/commands/load_risk_data.py +7 -6
  127. endoreg_db/management/commands/load_shift_data.py +20 -23
  128. endoreg_db/management/commands/load_tag_data.py +8 -11
  129. endoreg_db/management/commands/load_unit_data.py +17 -19
  130. endoreg_db/management/commands/setup_endoreg_db.py +3 -3
  131. endoreg_db/management/commands/start_filewatcher.py +46 -37
  132. endoreg_db/management/commands/storage_management.py +271 -203
  133. endoreg_db/management/commands/validate_video_files.py +1 -5
  134. endoreg_db/migrations/0001_initial.py +297 -250
  135. endoreg_db/models/__init__.py +78 -123
  136. endoreg_db/models/administration/__init__.py +21 -42
  137. endoreg_db/models/administration/ai/active_model.py +2 -2
  138. endoreg_db/models/administration/ai/ai_model.py +7 -6
  139. endoreg_db/models/administration/case/__init__.py +1 -15
  140. endoreg_db/models/administration/case/case.py +3 -3
  141. endoreg_db/models/administration/case/case_template/__init__.py +2 -14
  142. endoreg_db/models/administration/case/case_template/case_template.py +2 -124
  143. endoreg_db/models/administration/case/case_template/case_template_rule.py +2 -268
  144. endoreg_db/models/administration/case/case_template/case_template_rule_value.py +2 -85
  145. endoreg_db/models/administration/case/case_template/case_template_type.py +2 -25
  146. endoreg_db/models/administration/center/center.py +33 -19
  147. endoreg_db/models/administration/center/center_product.py +12 -9
  148. endoreg_db/models/administration/center/center_resource.py +25 -19
  149. endoreg_db/models/administration/center/center_shift.py +21 -17
  150. endoreg_db/models/administration/center/center_waste.py +16 -8
  151. endoreg_db/models/administration/person/__init__.py +2 -0
  152. endoreg_db/models/administration/person/employee/employee.py +10 -5
  153. endoreg_db/models/administration/person/employee/employee_qualification.py +9 -4
  154. endoreg_db/models/administration/person/employee/employee_type.py +12 -6
  155. endoreg_db/models/administration/person/examiner/examiner.py +13 -11
  156. endoreg_db/models/administration/person/patient/__init__.py +2 -0
  157. endoreg_db/models/administration/person/patient/patient.py +129 -100
  158. endoreg_db/models/administration/person/patient/patient_external_id.py +37 -0
  159. endoreg_db/models/administration/person/person.py +4 -0
  160. endoreg_db/models/administration/person/profession/__init__.py +8 -4
  161. endoreg_db/models/administration/person/user/portal_user_information.py +11 -7
  162. endoreg_db/models/administration/product/product.py +20 -15
  163. endoreg_db/models/administration/product/product_material.py +17 -18
  164. endoreg_db/models/administration/product/product_weight.py +12 -8
  165. endoreg_db/models/administration/product/reference_product.py +23 -55
  166. endoreg_db/models/administration/qualification/qualification.py +7 -3
  167. endoreg_db/models/administration/qualification/qualification_type.py +7 -3
  168. endoreg_db/models/administration/shift/scheduled_days.py +8 -5
  169. endoreg_db/models/administration/shift/shift.py +16 -12
  170. endoreg_db/models/administration/shift/shift_type.py +23 -31
  171. endoreg_db/models/label/__init__.py +8 -9
  172. endoreg_db/models/label/annotation/image_classification.py +10 -9
  173. endoreg_db/models/label/annotation/video_segmentation_annotation.py +23 -28
  174. endoreg_db/models/label/label.py +15 -15
  175. endoreg_db/models/label/label_set.py +19 -6
  176. endoreg_db/models/label/label_type.py +1 -1
  177. endoreg_db/models/label/label_video_segment/_create_from_video.py +5 -8
  178. endoreg_db/models/label/label_video_segment/label_video_segment.py +98 -102
  179. endoreg_db/models/label/video_segmentation_label.py +4 -0
  180. endoreg_db/models/label/video_segmentation_labelset.py +4 -3
  181. endoreg_db/models/media/frame/frame.py +22 -22
  182. endoreg_db/models/media/pdf/raw_pdf.py +194 -194
  183. endoreg_db/models/media/pdf/report_file.py +25 -29
  184. endoreg_db/models/media/pdf/report_reader/report_reader_config.py +55 -47
  185. endoreg_db/models/media/pdf/report_reader/report_reader_flag.py +23 -7
  186. endoreg_db/models/media/processing_history/__init__.py +5 -0
  187. endoreg_db/models/media/processing_history/processing_history.py +96 -0
  188. endoreg_db/models/media/video/__init__.py +1 -0
  189. endoreg_db/models/media/video/create_from_file.py +139 -77
  190. endoreg_db/models/media/video/pipe_2.py +8 -9
  191. endoreg_db/models/media/video/video_file.py +174 -112
  192. endoreg_db/models/media/video/video_file_ai.py +288 -74
  193. endoreg_db/models/media/video/video_file_anonymize.py +38 -38
  194. endoreg_db/models/media/video/video_file_frames/__init__.py +3 -1
  195. endoreg_db/models/media/video/video_file_frames/_bulk_create_frames.py +6 -8
  196. endoreg_db/models/media/video/video_file_frames/_create_frame_object.py +7 -9
  197. endoreg_db/models/media/video/video_file_frames/_delete_frames.py +9 -8
  198. endoreg_db/models/media/video/video_file_frames/_extract_frames.py +38 -45
  199. endoreg_db/models/media/video/video_file_frames/_get_frame.py +6 -8
  200. endoreg_db/models/media/video/video_file_frames/_get_frame_number.py +4 -18
  201. endoreg_db/models/media/video/video_file_frames/_get_frame_path.py +4 -3
  202. endoreg_db/models/media/video/video_file_frames/_get_frame_paths.py +7 -6
  203. endoreg_db/models/media/video/video_file_frames/_get_frame_range.py +6 -8
  204. endoreg_db/models/media/video/video_file_frames/_get_frames.py +6 -8
  205. endoreg_db/models/media/video/video_file_frames/_initialize_frames.py +15 -25
  206. endoreg_db/models/media/video/video_file_frames/_manage_frame_range.py +26 -23
  207. endoreg_db/models/media/video/video_file_frames/_mark_frames_extracted_status.py +23 -14
  208. endoreg_db/models/media/video/video_file_io.py +113 -61
  209. endoreg_db/models/media/video/video_file_meta/get_crop_template.py +3 -3
  210. endoreg_db/models/media/video/video_file_meta/get_endo_roi.py +5 -3
  211. endoreg_db/models/media/video/video_file_meta/get_fps.py +37 -34
  212. endoreg_db/models/media/video/video_file_meta/initialize_video_specs.py +19 -25
  213. endoreg_db/models/media/video/video_file_meta/text_meta.py +41 -38
  214. endoreg_db/models/media/video/video_file_meta/video_meta.py +14 -7
  215. endoreg_db/models/media/video/video_file_segments.py +24 -17
  216. endoreg_db/models/media/video/video_metadata.py +19 -35
  217. endoreg_db/models/media/video/video_processing.py +96 -95
  218. endoreg_db/models/medical/contraindication/README.md +1 -0
  219. endoreg_db/models/medical/contraindication/__init__.py +13 -3
  220. endoreg_db/models/medical/disease.py +22 -16
  221. endoreg_db/models/medical/event.py +31 -18
  222. endoreg_db/models/medical/examination/__init__.py +13 -6
  223. endoreg_db/models/medical/examination/examination.py +39 -20
  224. endoreg_db/models/medical/examination/examination_indication.py +30 -95
  225. endoreg_db/models/medical/examination/examination_time.py +23 -8
  226. endoreg_db/models/medical/examination/examination_time_type.py +9 -6
  227. endoreg_db/models/medical/examination/examination_type.py +3 -4
  228. endoreg_db/models/medical/finding/finding.py +32 -40
  229. endoreg_db/models/medical/finding/finding_classification.py +42 -72
  230. endoreg_db/models/medical/finding/finding_intervention.py +25 -22
  231. endoreg_db/models/medical/finding/finding_type.py +13 -12
  232. endoreg_db/models/medical/hardware/endoscope.py +26 -26
  233. endoreg_db/models/medical/hardware/endoscopy_processor.py +2 -2
  234. endoreg_db/models/medical/laboratory/lab_value.py +62 -91
  235. endoreg_db/models/medical/medication/medication.py +22 -10
  236. endoreg_db/models/medical/medication/medication_indication.py +29 -3
  237. endoreg_db/models/medical/medication/medication_indication_type.py +25 -14
  238. endoreg_db/models/medical/medication/medication_intake_time.py +31 -19
  239. endoreg_db/models/medical/medication/medication_schedule.py +27 -16
  240. endoreg_db/models/medical/organ/__init__.py +15 -12
  241. endoreg_db/models/medical/patient/medication_examples.py +6 -6
  242. endoreg_db/models/medical/patient/patient_disease.py +20 -23
  243. endoreg_db/models/medical/patient/patient_event.py +19 -22
  244. endoreg_db/models/medical/patient/patient_examination.py +48 -54
  245. endoreg_db/models/medical/patient/patient_examination_indication.py +16 -14
  246. endoreg_db/models/medical/patient/patient_finding.py +122 -139
  247. endoreg_db/models/medical/patient/patient_finding_classification.py +44 -49
  248. endoreg_db/models/medical/patient/patient_finding_intervention.py +8 -19
  249. endoreg_db/models/medical/patient/patient_lab_sample.py +28 -23
  250. endoreg_db/models/medical/patient/patient_lab_value.py +82 -89
  251. endoreg_db/models/medical/patient/patient_medication.py +27 -38
  252. endoreg_db/models/medical/patient/patient_medication_schedule.py +28 -36
  253. endoreg_db/models/medical/risk/risk.py +7 -6
  254. endoreg_db/models/medical/risk/risk_type.py +8 -5
  255. endoreg_db/models/metadata/model_meta.py +60 -29
  256. endoreg_db/models/metadata/model_meta_logic.py +125 -18
  257. endoreg_db/models/metadata/pdf_meta.py +31 -24
  258. endoreg_db/models/metadata/sensitive_meta.py +105 -85
  259. endoreg_db/models/metadata/sensitive_meta_logic.py +198 -103
  260. endoreg_db/models/metadata/video_meta.py +51 -31
  261. endoreg_db/models/metadata/video_prediction_logic.py +16 -23
  262. endoreg_db/models/metadata/video_prediction_meta.py +29 -33
  263. endoreg_db/models/other/distribution/date_value_distribution.py +89 -29
  264. endoreg_db/models/other/distribution/multiple_categorical_value_distribution.py +21 -5
  265. endoreg_db/models/other/distribution/numeric_value_distribution.py +114 -53
  266. endoreg_db/models/other/distribution/single_categorical_value_distribution.py +4 -3
  267. endoreg_db/models/other/emission/emission_factor.py +18 -8
  268. endoreg_db/models/other/gender.py +10 -5
  269. endoreg_db/models/other/information_source.py +50 -29
  270. endoreg_db/models/other/material.py +9 -5
  271. endoreg_db/models/other/resource.py +6 -4
  272. endoreg_db/models/other/tag.py +10 -5
  273. endoreg_db/models/other/transport_route.py +13 -8
  274. endoreg_db/models/other/unit.py +10 -6
  275. endoreg_db/models/other/waste.py +6 -5
  276. endoreg_db/models/report/report.py +6 -0
  277. endoreg_db/models/requirement/requirement.py +329 -361
  278. endoreg_db/models/requirement/requirement_error.py +85 -0
  279. endoreg_db/models/requirement/requirement_evaluation/evaluate_with_dependencies.py +268 -0
  280. endoreg_db/models/requirement/requirement_evaluation/operator_evaluation_models.py +3 -6
  281. endoreg_db/models/requirement/requirement_evaluation/requirement_type_parser.py +90 -64
  282. endoreg_db/models/requirement/requirement_operator.py +103 -112
  283. endoreg_db/models/requirement/requirement_set.py +74 -57
  284. endoreg_db/models/state/__init__.py +4 -4
  285. endoreg_db/models/state/abstract.py +2 -2
  286. endoreg_db/models/state/anonymization.py +12 -0
  287. endoreg_db/models/state/audit_ledger.py +49 -51
  288. endoreg_db/models/state/label_video_segment.py +9 -0
  289. endoreg_db/models/state/raw_pdf.py +101 -68
  290. endoreg_db/models/state/sensitive_meta.py +6 -2
  291. endoreg_db/models/state/video.py +110 -90
  292. endoreg_db/models/upload_job.py +35 -34
  293. endoreg_db/models/utils.py +28 -25
  294. endoreg_db/queries/__init__.py +3 -1
  295. endoreg_db/root_urls.py +21 -2
  296. endoreg_db/schemas/examination_evaluation.py +1 -1
  297. endoreg_db/serializers/__init__.py +2 -10
  298. endoreg_db/serializers/anonymization.py +18 -10
  299. endoreg_db/serializers/label_video_segment/label_video_segment.py +2 -29
  300. endoreg_db/serializers/meta/__init__.py +1 -6
  301. endoreg_db/serializers/meta/sensitive_meta_detail.py +63 -118
  302. endoreg_db/serializers/misc/file_overview.py +11 -99
  303. endoreg_db/serializers/misc/sensitive_patient_data.py +50 -26
  304. endoreg_db/serializers/patient_examination/patient_examination.py +3 -3
  305. endoreg_db/serializers/pdf/anony_text_validation.py +39 -23
  306. endoreg_db/serializers/requirements/requirement_sets.py +92 -22
  307. endoreg_db/serializers/video/segmentation.py +2 -1
  308. endoreg_db/serializers/video/video_file_list.py +65 -34
  309. endoreg_db/serializers/video/video_processing_history.py +20 -5
  310. endoreg_db/services/__old/pdf_import.py +1487 -0
  311. endoreg_db/services/__old/video_import.py +1306 -0
  312. endoreg_db/services/anonymization.py +128 -89
  313. endoreg_db/services/lookup_service.py +65 -52
  314. endoreg_db/services/lookup_store.py +2 -2
  315. endoreg_db/services/pdf_import.py +0 -1382
  316. endoreg_db/services/report_import.py +10 -0
  317. endoreg_db/services/video_import.py +6 -1255
  318. endoreg_db/tasks/upload_tasks.py +79 -70
  319. endoreg_db/tasks/video_ingest.py +8 -4
  320. endoreg_db/urls/__init__.py +5 -32
  321. endoreg_db/urls/ai.py +32 -0
  322. endoreg_db/urls/media.py +121 -83
  323. endoreg_db/urls/root_urls.py +29 -0
  324. endoreg_db/utils/__init__.py +15 -5
  325. endoreg_db/utils/ai/multilabel_classification_net.py +116 -20
  326. endoreg_db/utils/case_generator/__init__.py +3 -0
  327. endoreg_db/utils/dataloader.py +142 -40
  328. endoreg_db/utils/defaults/set_default_center.py +32 -0
  329. endoreg_db/utils/names.py +22 -16
  330. endoreg_db/utils/paths.py +110 -46
  331. endoreg_db/utils/permissions.py +2 -1
  332. endoreg_db/utils/pipelines/Readme.md +1 -1
  333. endoreg_db/utils/pipelines/process_video_dir.py +1 -1
  334. endoreg_db/utils/requirement_operator_logic/_old/model_evaluators.py +655 -0
  335. endoreg_db/utils/requirement_operator_logic/new_operator_logic.py +97 -0
  336. endoreg_db/utils/setup_config.py +8 -5
  337. endoreg_db/utils/storage.py +115 -0
  338. endoreg_db/utils/validate_endo_roi.py +8 -2
  339. endoreg_db/utils/video/ffmpeg_wrapper.py +184 -188
  340. endoreg_db/views/__init__.py +85 -183
  341. endoreg_db/views/ai/__init__.py +8 -0
  342. endoreg_db/views/ai/label.py +155 -0
  343. endoreg_db/views/anonymization/media_management.py +202 -166
  344. endoreg_db/views/anonymization/overview.py +99 -67
  345. endoreg_db/views/anonymization/validate.py +182 -44
  346. endoreg_db/views/media/__init__.py +7 -20
  347. endoreg_db/views/media/pdf_media.py +197 -174
  348. endoreg_db/views/media/sensitive_metadata.py +193 -138
  349. endoreg_db/views/media/video_media.py +89 -82
  350. endoreg_db/views/meta/__init__.py +0 -8
  351. endoreg_db/views/misc/__init__.py +1 -7
  352. endoreg_db/views/misc/upload_views.py +94 -93
  353. endoreg_db/views/patient/patient.py +5 -4
  354. endoreg_db/views/report/__init__.py +5 -7
  355. endoreg_db/views/{pdf → report}/reimport.py +22 -22
  356. endoreg_db/views/{pdf/pdf_stream.py → report/report_stream.py} +46 -39
  357. endoreg_db/views/requirement/evaluate.py +188 -187
  358. endoreg_db/views/requirement/lookup.py +17 -3
  359. endoreg_db/views/requirement/lookup_store.py +22 -90
  360. endoreg_db/views/requirement/requirement_utils.py +89 -0
  361. endoreg_db/views/video/__init__.py +23 -24
  362. endoreg_db/views/video/correction.py +201 -172
  363. endoreg_db/views/video/reimport.py +1 -1
  364. endoreg_db/views/{media/video_segments.py → video/segments_crud.py} +77 -40
  365. endoreg_db/views/video/{video_meta.py → video_meta_stats.py} +2 -2
  366. endoreg_db/views/video/video_stream.py +7 -8
  367. {endoreg_db-0.8.6.1.dist-info → endoreg_db-0.8.8.9.dist-info}/METADATA +7 -3
  368. {endoreg_db-0.8.6.1.dist-info → endoreg_db-0.8.8.9.dist-info}/RECORD +391 -413
  369. {endoreg_db-0.8.6.1.dist-info → endoreg_db-0.8.8.9.dist-info}/WHEEL +1 -1
  370. endoreg_db/data/finding/anatomy_colon.yaml +0 -128
  371. endoreg_db/data/finding/colonoscopy.yaml +0 -40
  372. endoreg_db/data/finding/colonoscopy_bowel_prep.yaml +0 -56
  373. endoreg_db/data/finding/complication.yaml +0 -16
  374. endoreg_db/data/finding/data.yaml +0 -105
  375. endoreg_db/data/finding/examination_setting.yaml +0 -16
  376. endoreg_db/data/finding/medication_related.yaml +0 -18
  377. endoreg_db/data/finding/outcome.yaml +0 -12
  378. endoreg_db/data/finding_classification/colonoscopy_bowel_preparation.yaml +0 -95
  379. endoreg_db/data/finding_classification/colonoscopy_jnet.yaml +0 -22
  380. endoreg_db/data/finding_classification/colonoscopy_kudo.yaml +0 -25
  381. endoreg_db/data/finding_classification/colonoscopy_lesion_circularity.yaml +0 -20
  382. endoreg_db/data/finding_classification/colonoscopy_lesion_planarity.yaml +0 -24
  383. endoreg_db/data/finding_classification/colonoscopy_lesion_size.yaml +0 -68
  384. endoreg_db/data/finding_classification/colonoscopy_lesion_surface.yaml +0 -20
  385. endoreg_db/data/finding_classification/colonoscopy_location.yaml +0 -80
  386. endoreg_db/data/finding_classification/colonoscopy_lst.yaml +0 -21
  387. endoreg_db/data/finding_classification/colonoscopy_nice.yaml +0 -20
  388. endoreg_db/data/finding_classification/colonoscopy_paris.yaml +0 -26
  389. endoreg_db/data/finding_classification/colonoscopy_sano.yaml +0 -22
  390. endoreg_db/data/finding_classification/colonoscopy_summary.yaml +0 -53
  391. endoreg_db/data/finding_classification/complication_generic.yaml +0 -25
  392. endoreg_db/data/finding_classification/examination_setting_generic.yaml +0 -40
  393. endoreg_db/data/finding_classification/histology_colo.yaml +0 -51
  394. endoreg_db/data/finding_classification/intervention_required.yaml +0 -26
  395. endoreg_db/data/finding_classification/medication_related.yaml +0 -23
  396. endoreg_db/data/finding_classification/visualized.yaml +0 -33
  397. endoreg_db/data/finding_classification_choice/colon_lesion_circularity_default.yaml +0 -32
  398. endoreg_db/data/finding_classification_choice/colon_lesion_jnet.yaml +0 -15
  399. endoreg_db/data/finding_classification_choice/colon_lesion_kudo.yaml +0 -23
  400. endoreg_db/data/finding_classification_choice/colon_lesion_lst.yaml +0 -15
  401. endoreg_db/data/finding_classification_choice/colon_lesion_nice.yaml +0 -17
  402. endoreg_db/data/finding_classification_choice/colon_lesion_planarity_default.yaml +0 -49
  403. endoreg_db/data/finding_classification_choice/colon_lesion_sano.yaml +0 -14
  404. endoreg_db/data/finding_classification_choice/colon_lesion_surface_intact_default.yaml +0 -36
  405. endoreg_db/data/finding_classification_choice/colonoscopy_size.yaml +0 -82
  406. endoreg_db/data/finding_classification_choice/colonoscopy_summary_worst_finding.yaml +0 -15
  407. endoreg_db/data/finding_classification_choice/outcome.yaml +0 -19
  408. endoreg_db/data/finding_intervention/endoscopy.yaml +0 -43
  409. endoreg_db/data/finding_intervention/endoscopy_colonoscopy.yaml +0 -168
  410. endoreg_db/data/finding_intervention/endoscopy_egd.yaml +0 -128
  411. endoreg_db/data/finding_intervention/endoscopy_ercp.yaml +0 -32
  412. endoreg_db/data/finding_intervention/endoscopy_eus_lower.yaml +0 -9
  413. endoreg_db/data/finding_intervention/endoscopy_eus_upper.yaml +0 -36
  414. endoreg_db/data/finding_morphology_classification_type/colonoscopy.yaml +0 -79
  415. endoreg_db/data/requirement/age.yaml +0 -26
  416. endoreg_db/data/requirement/gender.yaml +0 -25
  417. endoreg_db/management/commands/init_default_ai_model.py +0 -112
  418. endoreg_db/management/commands/reset_celery_schedule.py +0 -9
  419. endoreg_db/management/commands/validate_video.py +0 -204
  420. endoreg_db/migrations/0002_add_video_correction_models.py +0 -52
  421. endoreg_db/migrations/0003_add_center_display_name.py +0 -30
  422. endoreg_db/models/administration/permissions/__init__.py +0 -44
  423. endoreg_db/models/rule/__init__.py +0 -13
  424. endoreg_db/models/rule/rule.py +0 -27
  425. endoreg_db/models/rule/rule_applicator.py +0 -224
  426. endoreg_db/models/rule/rule_attribute_dtype.py +0 -17
  427. endoreg_db/models/rule/rule_type.py +0 -20
  428. endoreg_db/models/rule/ruleset.py +0 -17
  429. endoreg_db/renames.yml +0 -8
  430. endoreg_db/serializers/_old/raw_pdf_meta_validation.py +0 -223
  431. endoreg_db/serializers/_old/raw_video_meta_validation.py +0 -179
  432. endoreg_db/serializers/_old/video.py +0 -71
  433. endoreg_db/serializers/meta/pdf_file_meta_extraction.py +0 -115
  434. endoreg_db/serializers/meta/report_meta.py +0 -53
  435. endoreg_db/serializers/report/__init__.py +0 -9
  436. endoreg_db/serializers/report/mixins.py +0 -45
  437. endoreg_db/serializers/report/report.py +0 -105
  438. endoreg_db/serializers/report/report_list.py +0 -22
  439. endoreg_db/serializers/report/secure_file_url.py +0 -26
  440. endoreg_db/serializers/video/video_metadata.py +0 -105
  441. endoreg_db/services/requirements_object.py +0 -147
  442. endoreg_db/services/storage_aware_video_processor.py +0 -344
  443. endoreg_db/urls/files.py +0 -6
  444. endoreg_db/urls/label_video_segment_validate.py +0 -33
  445. endoreg_db/urls/label_video_segments.py +0 -46
  446. endoreg_db/urls/report.py +0 -48
  447. endoreg_db/urls/video.py +0 -61
  448. endoreg_db/utils/case_generator/case_generator.py +0 -159
  449. endoreg_db/utils/case_generator/utils.py +0 -30
  450. endoreg_db/utils/requirement_operator_logic/model_evaluators.py +0 -368
  451. endoreg_db/views/label/__init__.py +0 -5
  452. endoreg_db/views/label/label.py +0 -15
  453. endoreg_db/views/label_video_segment/__init__.py +0 -16
  454. endoreg_db/views/label_video_segment/create_lvs_from_annotation.py +0 -44
  455. endoreg_db/views/label_video_segment/get_lvs_by_name_and_video.py +0 -50
  456. endoreg_db/views/label_video_segment/label_video_segment.py +0 -77
  457. endoreg_db/views/label_video_segment/label_video_segment_by_label.py +0 -174
  458. endoreg_db/views/label_video_segment/label_video_segment_detail.py +0 -73
  459. endoreg_db/views/label_video_segment/update_lvs_from_annotation.py +0 -46
  460. endoreg_db/views/label_video_segment/validate.py +0 -226
  461. endoreg_db/views/media/segments.py +0 -71
  462. endoreg_db/views/meta/available_files_list.py +0 -146
  463. endoreg_db/views/meta/report_meta.py +0 -53
  464. endoreg_db/views/meta/sensitive_meta_detail.py +0 -148
  465. endoreg_db/views/misc/secure_file_serving_view.py +0 -80
  466. endoreg_db/views/misc/secure_file_url_view.py +0 -84
  467. endoreg_db/views/misc/secure_url_validate.py +0 -79
  468. endoreg_db/views/patient_examination/DEPRECATED_video_backup.py +0 -164
  469. endoreg_db/views/patient_finding_location/__init__.py +0 -5
  470. endoreg_db/views/patient_finding_location/pfl_create.py +0 -70
  471. endoreg_db/views/patient_finding_morphology/__init__.py +0 -5
  472. endoreg_db/views/patient_finding_morphology/pfm_create.py +0 -70
  473. endoreg_db/views/pdf/__init__.py +0 -8
  474. endoreg_db/views/report/report_list.py +0 -112
  475. endoreg_db/views/report/report_with_secure_url.py +0 -28
  476. endoreg_db/views/report/start_examination.py +0 -7
  477. endoreg_db/views/video/segmentation.py +0 -274
  478. endoreg_db/views/video/task_status.py +0 -49
  479. endoreg_db/views/video/timeline.py +0 -46
  480. endoreg_db/views/video/video_analyze.py +0 -52
  481. endoreg_db/views.py +0 -0
  482. /endoreg_db/data/requirement/{colonoscopy_baseline_austria.yaml → old/colonoscopy_baseline_austria.yaml} +0 -0
  483. /endoreg_db/data/requirement/{disease_cardiovascular.yaml → old/disease_cardiovascular.yaml} +0 -0
  484. /endoreg_db/data/requirement/{disease_classification_choice_cardiovascular.yaml → old/disease_classification_choice_cardiovascular.yaml} +0 -0
  485. /endoreg_db/data/requirement/{disease_hepatology.yaml → old/disease_hepatology.yaml} +0 -0
  486. /endoreg_db/data/requirement/{disease_misc.yaml → old/disease_misc.yaml} +0 -0
  487. /endoreg_db/data/requirement/{disease_renal.yaml → old/disease_renal.yaml} +0 -0
  488. /endoreg_db/data/requirement/{endoscopy_bleeding_risk.yaml → old/endoscopy_bleeding_risk.yaml} +0 -0
  489. /endoreg_db/data/requirement/{event_cardiology.yaml → old/event_cardiology.yaml} +0 -0
  490. /endoreg_db/data/requirement/{event_requirements.yaml → old/event_requirements.yaml} +0 -0
  491. /endoreg_db/data/requirement/{finding_colon_polyp.yaml → old/finding_colon_polyp.yaml} +0 -0
  492. /endoreg_db/{migrations/__init__.py → data/requirement/old/gender.yaml} +0 -0
  493. /endoreg_db/data/requirement/{lab_value.yaml → old/lab_value.yaml} +0 -0
  494. /endoreg_db/data/requirement/{medication.yaml → old/medication.yaml} +0 -0
  495. /endoreg_db/data/requirement_operator/{age.yaml → _old/age.yaml} +0 -0
  496. /endoreg_db/data/requirement_operator/{lab_operators.yaml → _old/lab_operators.yaml} +0 -0
  497. /endoreg_db/data/requirement_operator/{model_operators.yaml → _old/model_operators.yaml} +0 -0
  498. /endoreg_db/{models/media/video/refactor_plan.md → import_files/pseudonymization/__init__.py} +0 -0
  499. /endoreg_db/{models/media/video/video_file_frames.py → import_files/pseudonymization/pseudonymize.py} +0 -0
  500. /endoreg_db/models/{metadata/frame_ocr_result.py → report/__init__.py} +0 -0
  501. /endoreg_db/{urls/sensitive_meta.py → models/report/images.py} +0 -0
  502. /endoreg_db/utils/requirement_operator_logic/{lab_value_operators.py → _old/lab_value_operators.py} +0 -0
  503. {endoreg_db-0.8.6.1.dist-info → endoreg_db-0.8.8.9.dist-info}/licenses/LICENSE +0 -0
@@ -0,0 +1,655 @@
1
+ import calendar
2
+ import datetime
3
+ from datetime import timedelta
4
+ from typing import TYPE_CHECKING
5
+
6
+ if TYPE_CHECKING:
7
+ from endoreg_db.models.requirement.requirement import Requirement
8
+ from endoreg_db.utils.links.requirement_link import RequirementLinks
9
+ # from endoreg_db.models import Unit # Potentially needed for dynamic unit handling
10
+
11
+
12
+ # Helper function to check if a date is within the timeframe specified by a Requirement
13
+ def _normalize_timeframe_unit(requirement: "Requirement") -> str | None:
14
+ """Derives a canonical timeframe unit string from the requirement."""
15
+ if not requirement.unit:
16
+ return None
17
+
18
+ name = (requirement.unit.name or "").strip().lower()
19
+ abbreviation = (requirement.unit.abbreviation or "").strip().lower()
20
+
21
+ unit_aliases = {
22
+ "hour": "hours",
23
+ "hours": "hours",
24
+ "h": "hours",
25
+ "day": "days",
26
+ "days": "days",
27
+ "d": "days",
28
+ "week": "weeks",
29
+ "weeks": "weeks",
30
+ "w": "weeks",
31
+ "month": "months",
32
+ "months": "months",
33
+ "m": "months",
34
+ "year": "years",
35
+ "years": "years",
36
+ "y": "years",
37
+ }
38
+
39
+ if name in unit_aliases:
40
+ return unit_aliases[name]
41
+ if abbreviation in unit_aliases:
42
+ return unit_aliases[abbreviation]
43
+ return None
44
+
45
+
46
+ def _add_months(base_date: datetime.date, months: int) -> datetime.date:
47
+ """Shifts ``base_date`` by the given number of months, clamping the day when needed."""
48
+ if months == 0:
49
+ return base_date
50
+
51
+ total_months = base_date.month - 1 + months
52
+ year = base_date.year + total_months // 12
53
+ month = total_months % 12 + 1
54
+ day = min(base_date.day, calendar.monthrange(year, month)[1])
55
+ return base_date.replace(year=year, month=month, day=day)
56
+
57
+
58
+ def _shift_date_by_unit(base_date: datetime.date, value: int, unit: str) -> datetime.date:
59
+ """Returns ``base_date`` shifted by ``value`` units using the supported unit set.
60
+
61
+ Hour-level offsets are not supported because ``base_date`` is a ``date``
62
+ object without time information; callers must switch to datetime-aware
63
+ handling before requesting hourly shifts.
64
+ """
65
+ if unit == "days":
66
+ return base_date + timedelta(days=value)
67
+ if unit == "hours":
68
+ raise NotImplementedError("Hour-level timeframe comparisons require datetime-aware inputs; _shift_date_by_unit only operates on date objects.")
69
+ if unit == "weeks":
70
+ return base_date + timedelta(weeks=value)
71
+ if unit == "months":
72
+ return _add_months(base_date, value)
73
+ if unit == "years":
74
+ return _add_months(base_date, value * 12)
75
+ raise NotImplementedError(f"Timeframe unit '{unit}' is not supported.")
76
+
77
+
78
+ def _is_date_in_timeframe(date_to_check: datetime.date | None, requirement: "Requirement") -> bool:
79
+ """
80
+ Checks if a given date falls within the timeframe specified by a Requirement.
81
+
82
+ The timeframe is defined by `numeric_value_min` and `numeric_value_max` on the
83
+ Requirement, interpreted relative to the current date.
84
+
85
+ Currently supports day/week/month/year windows. Hour-level units are
86
+ explicitly rejected because the timeframe calculations operate on dates
87
+ rather than datetimes.
88
+
89
+ Args:
90
+ date_to_check: The date to evaluate. If None, returns False.
91
+ requirement: The Requirement instance containing timeframe definitions
92
+ (unit, numeric_value_min, numeric_value_max).
93
+
94
+ Returns:
95
+ True if the date_to_check is within the defined timeframe, False otherwise.
96
+ Returns False if date_to_check is None or if the requirement lacks
97
+ necessary timeframe information (unit, min/max values).
98
+
99
+ Raises:
100
+ NotImplementedError: If the requirement.unit resolves to an unsupported
101
+ unit (e.g. hours) or cannot be normalised.
102
+ """
103
+ if date_to_check is None:
104
+ return False
105
+ if requirement.numeric_value_min is None or requirement.numeric_value_max is None:
106
+ return False # Not enough information for timeframe evaluation
107
+
108
+ unit = _normalize_timeframe_unit(requirement)
109
+ if not unit:
110
+ raise NotImplementedError("Timeframe unit could not be resolved from requirement's Unit name/abbreviation.")
111
+
112
+ today = datetime.date.today()
113
+ timeframe_start_delta = int(requirement.numeric_value_min)
114
+ timeframe_end_delta = int(requirement.numeric_value_max)
115
+
116
+ start_date_bound = _shift_date_by_unit(today, timeframe_start_delta, unit)
117
+ end_date_bound = _shift_date_by_unit(today, timeframe_end_delta, unit)
118
+
119
+ if start_date_bound > end_date_bound:
120
+ start_date_bound, end_date_bound = end_date_bound, start_date_bound
121
+
122
+ return start_date_bound <= date_to_check <= end_date_bound
123
+
124
+
125
+ def _evaluate_models_match_any(requirement_links: "RequirementLinks", input_links: "RequirementLinks", **kwargs) -> bool:
126
+ """
127
+ Checks if the requirement_links matches any of the input_links.
128
+
129
+ Args:
130
+ requirement_links: The reference set of requirement links to compare against.
131
+ input_links: The aggregated requirement links from the input objects.
132
+
133
+ Returns:
134
+ True if the input set of requirement links matches according to requirement_links.match_any; otherwise, False.
135
+ """
136
+ return requirement_links.match_any(input_links)
137
+
138
+
139
+ def _evaluate_models_match_any_in_timeframe(
140
+ requirement_links: "RequirementLinks",
141
+ input_links: "RequirementLinks",
142
+ requirement: "Requirement", # Explicitly pass Requirement
143
+ **kwargs, # Keep for consistency, though 'requirement' is the main one used here
144
+ ) -> bool:
145
+ """
146
+ Checks if any relevant model in input_links matches a model specified in
147
+ requirement_links AND falls within the timeframe defined on the Requirement.
148
+
149
+ Currently focuses on PatientEvent instances and their dates.
150
+ """
151
+ if not _has_timeframe_configuration(requirement):
152
+ return False
153
+
154
+ active_req_links_dict = requirement_links.active()
155
+ if not active_req_links_dict:
156
+ # If the Requirement itself doesn't specify any models to match (e.g., requirement.events is empty),
157
+ # then it's vacuously true that "any" of these (non-existent) required models are matched.
158
+ # The timeframe aspect becomes irrelevant if no specific models are being checked.
159
+ return True
160
+
161
+ # --- Handle PatientEvents ---
162
+ # Check if the requirement is concerned with events
163
+ if requirement_links.events: # This list contains Event model instances
164
+ required_event_models = set(requirement_links.events) # Target Event models from the Requirement
165
+
166
+ # input_links.patient_events contains PatientEvent instances provided as input
167
+ for patient_event_instance in input_links.patient_events:
168
+ # Check if the event of the current PatientEvent instance is one of the target events
169
+ if patient_event_instance.event in required_event_models:
170
+ # If it is, check if this PatientEvent's date is within the timeframe
171
+ if _is_date_in_timeframe(patient_event_instance.date, requirement):
172
+ return True # Found a matching event within the timeframe
173
+
174
+ # --- Handle Other Model Types (Example: PatientLabValue) ---
175
+ # if requirement_links.lab_values:
176
+ # required_lab_value_models = set(requirement_links.lab_values)
177
+ # for plv_instance in input_links.patient_lab_values:
178
+ # if plv_instance.lab_value in required_lab_value_models:
179
+ # date_to_check = None
180
+ # if hasattr(plv_instance, 'date_time_value') and plv_instance.date_time_value:
181
+ # date_to_check = plv_instance.date_time_value.date()
182
+ # elif hasattr(plv_instance, 'date') and plv_instance.date: # If it had a simple date field
183
+ # date_to_check = plv_instance.date
184
+ #
185
+ # if _is_date_in_timeframe(date_to_check, requirement):
186
+ # return True
187
+
188
+ # If the code reaches here, no matching model within the timeframe was found
189
+ # for any of the categories specified in requirement_links.
190
+ return False
191
+
192
+
193
+ def _evaluate_models_match_all_in_timeframe(
194
+ requirement_links: "RequirementLinks", input_links: "RequirementLinks", requirement: "Requirement", **kwargs
195
+ ) -> bool:
196
+ if not _evaluate_models_match_all(requirement_links, input_links, **kwargs):
197
+ return False
198
+
199
+ if not requirement_links.events:
200
+ return True
201
+
202
+ if not _has_timeframe_configuration(requirement):
203
+ return False
204
+
205
+ required_events = set(requirement_links.events)
206
+ patient_events = getattr(input_links, "patient_events", [])
207
+ if not patient_events:
208
+ return False
209
+
210
+ for event in required_events:
211
+ found_in_timeframe = False
212
+ for patient_event in patient_events:
213
+ if getattr(patient_event, "event", None) == event:
214
+ if _is_date_in_timeframe(getattr(patient_event, "date", None), requirement):
215
+ found_in_timeframe = True
216
+ break
217
+ if not found_in_timeframe:
218
+ return False
219
+ return True
220
+
221
+ if requirement.unit is None:
222
+ return False
223
+
224
+
225
+ def _evaluate_models_match_none_in_timeframe(
226
+ requirement_links: "RequirementLinks", input_links: "RequirementLinks", requirement: "Requirement", **kwargs
227
+ ) -> bool:
228
+ if not requirement_links.events:
229
+ return True
230
+
231
+ if not _has_timeframe_configuration(requirement):
232
+ return False
233
+
234
+ required_events = set(requirement_links.events)
235
+ for patient_event in getattr(input_links, "patient_events", []):
236
+ if getattr(patient_event, "event", None) in required_events:
237
+ if _is_date_in_timeframe(getattr(patient_event, "date", None), requirement):
238
+ return False
239
+ return True
240
+
241
+
242
+ def _evaluate_models_match_all(requirement_links: "RequirementLinks", input_links: "RequirementLinks", **kwargs) -> bool:
243
+ """
244
+ Evaluates if all active links in requirement_links are present in input_links.
245
+
246
+ For each category of links in requirement_links (e.g., diseases, examinations),
247
+ all items specified in that category in requirement_links must be present in the
248
+ corresponding category in input_links.
249
+
250
+ Args:
251
+ requirement_links: The RequirementLinks object from the Requirement model.
252
+ input_links: The aggregated RequirementLinks object from the input arguments.
253
+ **kwargs: Additional keyword arguments (currently unused).
254
+
255
+ Returns:
256
+ True if all specified items in requirement_links are found in input_links,
257
+ False otherwise.
258
+ """
259
+ active_req_links = requirement_links.active() # Get dict of non-empty lists from requirement
260
+
261
+ if not active_req_links: # If the requirement specifies no actual items to link
262
+ return True # Vacuously true, as there are no conditions to fail
263
+
264
+ for link_category_name, req_items_list in active_req_links.items():
265
+ input_items_list = getattr(input_links, link_category_name, [])
266
+
267
+ try:
268
+ set_input_items = set(input_items_list)
269
+ set_req_items = set(req_items_list)
270
+ except TypeError:
271
+ for req_item in req_items_list:
272
+ if req_item not in input_items_list:
273
+ return False
274
+ continue
275
+
276
+ if not set_req_items.issubset(set_input_items):
277
+ return False
278
+
279
+ return True
280
+
281
+
282
+ def _evaluate_models_match_none(requirement_links: "RequirementLinks", input_links: "RequirementLinks", **kwargs) -> bool:
283
+ """Returns True when no required models are present in the input links."""
284
+ active_req_links = requirement_links.active()
285
+ if not active_req_links:
286
+ return True
287
+
288
+ for link_category_name, req_items_list in active_req_links.items():
289
+ input_items_list = getattr(input_links, link_category_name, [])
290
+ if not input_items_list:
291
+ continue
292
+ try:
293
+ if set(req_items_list) & set(input_items_list):
294
+ return False
295
+ except TypeError:
296
+ for req_item in req_items_list:
297
+ if req_item in input_items_list:
298
+ return False
299
+ return True
300
+
301
+
302
+ def _count_matching_models(
303
+ requirement_links: "RequirementLinks",
304
+ input_links: "RequirementLinks",
305
+ ) -> int:
306
+ """Counts how many required models are present in the input links."""
307
+ active_req_links = requirement_links.active()
308
+ if not active_req_links:
309
+ return 0
310
+
311
+ match_count = 0
312
+ for link_category_name, req_items_list in active_req_links.items():
313
+ input_items_list = getattr(input_links, link_category_name, [])
314
+ if not input_items_list:
315
+ continue
316
+ try:
317
+ match_count += len(set(req_items_list) & set(input_items_list))
318
+ except TypeError:
319
+ for req_item in req_items_list:
320
+ if req_item in input_items_list:
321
+ match_count += 1
322
+ return match_count
323
+
324
+
325
+ def _resolve_expected_count(requirement: "Requirement") -> int | None:
326
+ """Extracts the expected count from numeric fields on the requirement."""
327
+ if requirement.numeric_value is not None:
328
+ return int(requirement.numeric_value)
329
+ if requirement.numeric_value_min is not None:
330
+ return int(requirement.numeric_value_min)
331
+ return None
332
+
333
+
334
+ def _has_timeframe_configuration(requirement: "Requirement") -> bool:
335
+ """Checks whether timeframe boundaries and unit are configured."""
336
+ return (
337
+ requirement.unit is not None
338
+ and requirement.numeric_value_min is not None
339
+ and requirement.numeric_value_max is not None
340
+ and _normalize_timeframe_unit(requirement) is not None
341
+ )
342
+
343
+
344
+ def _count_matching_events_in_timeframe(
345
+ requirement_links: "RequirementLinks",
346
+ input_links: "RequirementLinks",
347
+ requirement: "Requirement",
348
+ ) -> int:
349
+ """Counts required events that have a matching patient event within the timeframe."""
350
+ required_events = set(requirement_links.events)
351
+ if not required_events:
352
+ return 0
353
+
354
+ patient_events = getattr(input_links, "patient_events", [])
355
+ if not patient_events:
356
+ return 0
357
+
358
+ matched_events = 0
359
+ for event in required_events:
360
+ for patient_event in patient_events:
361
+ if getattr(patient_event, "event", None) != event:
362
+ continue
363
+ if _is_date_in_timeframe(getattr(patient_event, "date", None), requirement):
364
+ matched_events += 1
365
+ break
366
+ return matched_events
367
+
368
+
369
+ def _evaluate_models_match_n(requirement_links: "RequirementLinks", input_links: "RequirementLinks", requirement: "Requirement", **kwargs) -> bool:
370
+ expected = _resolve_expected_count(requirement)
371
+ if expected is None:
372
+ return False
373
+ return _count_matching_models(requirement_links, input_links) == expected
374
+
375
+
376
+ def _evaluate_models_match_n_or_more(requirement_links: "RequirementLinks", input_links: "RequirementLinks", requirement: "Requirement", **kwargs) -> bool:
377
+ threshold = _resolve_expected_count(requirement)
378
+ if threshold is None:
379
+ return False
380
+ return _count_matching_models(requirement_links, input_links) >= max(threshold, 0)
381
+
382
+
383
+ def _evaluate_models_match_n_or_less(requirement_links: "RequirementLinks", input_links: "RequirementLinks", requirement: "Requirement", **kwargs) -> bool:
384
+ limit = _resolve_expected_count(requirement)
385
+ if limit is None:
386
+ return False
387
+ return _count_matching_models(requirement_links, input_links) <= limit
388
+
389
+
390
+ def _evaluate_models_match_count_in_range(requirement_links: "RequirementLinks", input_links: "RequirementLinks", requirement: "Requirement", **kwargs) -> bool:
391
+ if requirement.numeric_value_min is None or requirement.numeric_value_max is None:
392
+ return False
393
+
394
+ lower = int(requirement.numeric_value_min)
395
+ upper = int(requirement.numeric_value_max)
396
+ if lower > upper:
397
+ lower, upper = upper, lower
398
+
399
+ match_count = _count_matching_models(requirement_links, input_links)
400
+ return lower <= match_count <= upper
401
+
402
+
403
+ def _evaluate_models_match_n_in_timeframe(requirement_links: "RequirementLinks", input_links: "RequirementLinks", requirement: "Requirement", **kwargs) -> bool:
404
+ if not _has_timeframe_configuration(requirement):
405
+ return False
406
+
407
+ expected = _resolve_expected_count(requirement)
408
+ if expected is None:
409
+ return False
410
+
411
+ return _count_matching_events_in_timeframe(requirement_links, input_links, requirement) == expected
412
+
413
+
414
+ def _evaluate_models_match_n_or_more_in_timeframe(
415
+ requirement_links: "RequirementLinks", input_links: "RequirementLinks", requirement: "Requirement", **kwargs
416
+ ) -> bool:
417
+ if not _has_timeframe_configuration(requirement):
418
+ return False
419
+
420
+ threshold = _resolve_expected_count(requirement)
421
+ if threshold is None:
422
+ return False
423
+
424
+ return _count_matching_events_in_timeframe(requirement_links, input_links, requirement) >= max(threshold, 0)
425
+
426
+
427
+ def _evaluate_models_match_n_or_less_in_timeframe(
428
+ requirement_links: "RequirementLinks", input_links: "RequirementLinks", requirement: "Requirement", **kwargs
429
+ ) -> bool:
430
+ if not _has_timeframe_configuration(requirement):
431
+ return False
432
+
433
+ limit = _resolve_expected_count(requirement)
434
+ if limit is None:
435
+ return False
436
+
437
+ return _count_matching_events_in_timeframe(requirement_links, input_links, requirement) <= limit
438
+
439
+
440
+ def _evaluate_age_gte(requirement_links: "RequirementLinks", input_links: "RequirementLinks", requirement: "Requirement", **kwargs) -> bool:
441
+ """
442
+ Checks if any patient in the input has an age greater than or equal to the requirement's numeric_value.
443
+
444
+ Args:
445
+ requirement_links: The RequirementLinks object from the Requirement model (not used for age checks).
446
+ input_links: The aggregated RequirementLinks object from the input arguments.
447
+ requirement: The Requirement instance containing the minimum age in numeric_value.
448
+ **kwargs: Additional keyword arguments, should contain 'original_input_args' with the original Patient instances.
449
+
450
+ Returns:
451
+ True if any patient in the input has an age >= requirement.numeric_value, False otherwise.
452
+ """
453
+ import logging
454
+
455
+ from endoreg_db.models.administration.person.patient import Patient
456
+
457
+ logger = logging.getLogger(__name__)
458
+
459
+ if requirement.numeric_value is None:
460
+ logger.debug("age_gte: requirement.numeric_value is None, returning False")
461
+ return False # Cannot evaluate without a minimum age requirement
462
+
463
+ min_age = requirement.numeric_value
464
+ logger.debug(f"age_gte: Checking if any patient has age >= {min_age}")
465
+
466
+ # Check if we have Patient instances in the original_input_args
467
+ original_args = kwargs.get("original_input_args", [])
468
+ logger.debug(f"age_gte: Found {len(original_args)} original input arguments: {[type(arg).__name__ for arg in original_args]}")
469
+
470
+ for i, arg in enumerate(original_args):
471
+ logger.debug(f"age_gte: Checking argument {i}: {type(arg).__name__}")
472
+ if isinstance(arg, Patient):
473
+ patient_age = arg.age()
474
+ logger.debug(f"age_gte: Patient {arg} has age {patient_age}, comparing with min_age {min_age}")
475
+ if patient_age is not None and patient_age >= min_age:
476
+ logger.debug(f"age_gte: Patient age {patient_age} >= {min_age}, returning True")
477
+ return True
478
+ else:
479
+ logger.debug(f"age_gte: Patient age {patient_age} < {min_age} or is None")
480
+ # Handle QuerySets of patients
481
+ elif hasattr(arg, "model") and issubclass(arg.model, Patient):
482
+ logger.debug(f"age_gte: Found Patient QuerySet with {arg.count()} patients")
483
+ for patient in arg:
484
+ patient_age = patient.age()
485
+ logger.debug(f"age_gte: Patient {patient} has age {patient_age}, comparing with min_age {min_age}")
486
+ if patient_age is not None and patient_age >= min_age:
487
+ logger.debug(f"age_gte: Patient age {patient_age} >= {min_age}, returning True")
488
+ return True
489
+ else:
490
+ logger.debug(f"age_gte: Argument {i} is not a Patient or Patient QuerySet: {type(arg)}")
491
+
492
+ logger.debug(f"age_gte: No patient found with age >= {min_age}, returning False")
493
+ return False
494
+
495
+
496
+ def _evaluate_age_lte(requirement_links: "RequirementLinks", input_links: "RequirementLinks", requirement: "Requirement", **kwargs) -> bool:
497
+ """
498
+ Checks if any patient in the input has an age less than or equal to the requirement's numeric_value.
499
+
500
+ Args:
501
+ requirement_links: The RequirementLinks object from the Requirement model (not used for age checks).
502
+ input_links: The aggregated RequirementLinks object from the input arguments.
503
+ requirement: The Requirement instance containing the maximum age in numeric_value.
504
+ **kwargs: Additional keyword arguments, should contain 'original_input_args' with the original Patient instances.
505
+
506
+ Returns:
507
+ True if any patient in the input has an age <= requirement.numeric_value, False otherwise.
508
+ """
509
+ from endoreg_db.models.administration.person.patient import Patient
510
+
511
+ if requirement.numeric_value is None:
512
+ return False # Cannot evaluate without a maximum age requirement
513
+
514
+ max_age = requirement.numeric_value
515
+
516
+ # Check if we have Patient instances in the original_input_args
517
+ original_args = kwargs.get("original_input_args", [])
518
+ for arg in original_args:
519
+ if isinstance(arg, Patient):
520
+ patient_age = arg.age()
521
+ if patient_age is not None and patient_age <= max_age:
522
+ return True
523
+ # Handle QuerySets of patients
524
+ elif hasattr(arg, "model") and issubclass(arg.model, Patient):
525
+ for patient in arg:
526
+ patient_age = patient.age()
527
+ if patient_age is not None and patient_age <= max_age:
528
+ return True
529
+
530
+ return False
531
+
532
+
533
+ def dispatch_operator_evaluation(operator_name: str, requirement_links: "RequirementLinks", input_links: "RequirementLinks", **kwargs) -> bool:
534
+ """
535
+ Dispatches the evaluation to the appropriate function based on the operator name.
536
+
537
+ Args:
538
+ operator_name: The name of the operator to evaluate.
539
+ requirement_links: The RequirementLinks object from the Requirement model.
540
+ input_links: The aggregated RequirementLinks object from the input arguments.
541
+ **kwargs: Additional keyword arguments for specific operator logic.
542
+ For lab value operators, this includes 'requirement' (the Requirement model instance).
543
+
544
+ Returns:
545
+ True if the condition defined by the operator is met, False otherwise.
546
+
547
+ Raises:
548
+ NotImplementedError: If the evaluation logic for the operator's name is not implemented.
549
+ """
550
+ from endoreg_db.models.requirement.requirement import Requirement # Runtime import for isinstance
551
+
552
+ from .lab_value_operators import LAB_VALUE_OPERATOR_FUNCTIONS
553
+
554
+ eval_func = None
555
+ requirement = kwargs.get("requirement") # Get requirement for operators that need it
556
+
557
+ def _kwargs_without_requirement() -> dict:
558
+ return {k: v for k, v in kwargs.items() if k != "requirement"}
559
+
560
+ if operator_name == "models_match_any":
561
+ eval_func = _evaluate_models_match_any
562
+ return eval_func(requirement_links=requirement_links, input_links=input_links, **kwargs)
563
+ elif operator_name == "models_match_all":
564
+ eval_func = _evaluate_models_match_all
565
+ return eval_func(requirement_links=requirement_links, input_links=input_links, **kwargs)
566
+ elif operator_name == "models_match_none":
567
+ eval_func = _evaluate_models_match_none
568
+ return eval_func(requirement_links=requirement_links, input_links=input_links, **kwargs)
569
+ elif operator_name == "models_match_any_in_timeframe":
570
+ # 'requirement' is already extracted from kwargs via requirement = kwargs.get("requirement")
571
+ if not isinstance(requirement, Requirement): # Ensure requirement is present and correct type
572
+ raise ValueError("models_match_any_in_timeframe operator requires a valid 'requirement' instance in kwargs.")
573
+ kwargs_for_eval = _kwargs_without_requirement()
574
+ eval_func = _evaluate_models_match_any_in_timeframe
575
+ return eval_func(
576
+ requirement_links=requirement_links,
577
+ input_links=input_links,
578
+ requirement=requirement, # Pass the requirement instance explicitly
579
+ **kwargs_for_eval, # Pass the remaining kwargs
580
+ )
581
+ elif operator_name == "models_match_all_in_timeframe":
582
+ if not isinstance(requirement, Requirement):
583
+ raise ValueError("models_match_all_in_timeframe operator requires a valid 'requirement' instance in kwargs.")
584
+ kwargs_for_eval = _kwargs_without_requirement()
585
+ return _evaluate_models_match_all_in_timeframe(requirement_links=requirement_links, input_links=input_links, requirement=requirement, **kwargs_for_eval)
586
+ elif operator_name == "models_match_none_in_timeframe":
587
+ if not isinstance(requirement, Requirement):
588
+ raise ValueError("models_match_none_in_timeframe operator requires a valid 'requirement' instance in kwargs.")
589
+ kwargs_for_eval = _kwargs_without_requirement()
590
+ return _evaluate_models_match_none_in_timeframe(
591
+ requirement_links=requirement_links, input_links=input_links, requirement=requirement, **kwargs_for_eval
592
+ )
593
+ elif operator_name == "models_match_n":
594
+ if not isinstance(requirement, Requirement):
595
+ raise ValueError("models_match_n operator requires a valid 'requirement' instance in kwargs.")
596
+ kwargs_for_eval = _kwargs_without_requirement()
597
+ return _evaluate_models_match_n(requirement_links=requirement_links, input_links=input_links, requirement=requirement, **kwargs_for_eval)
598
+ elif operator_name == "models_match_n_or_more":
599
+ if not isinstance(requirement, Requirement):
600
+ raise ValueError("models_match_n_or_more operator requires a valid 'requirement' instance in kwargs.")
601
+ kwargs_for_eval = _kwargs_without_requirement()
602
+ return _evaluate_models_match_n_or_more(requirement_links=requirement_links, input_links=input_links, requirement=requirement, **kwargs_for_eval)
603
+ elif operator_name == "models_match_n_or_less":
604
+ if not isinstance(requirement, Requirement):
605
+ raise ValueError("models_match_n_or_less operator requires a valid 'requirement' instance in kwargs.")
606
+ kwargs_for_eval = _kwargs_without_requirement()
607
+ return _evaluate_models_match_n_or_less(requirement_links=requirement_links, input_links=input_links, requirement=requirement, **kwargs_for_eval)
608
+ elif operator_name == "models_match_count_in_range":
609
+ if not isinstance(requirement, Requirement):
610
+ raise ValueError("models_match_count_in_range operator requires a valid 'requirement' instance in kwargs.")
611
+ kwargs_for_eval = _kwargs_without_requirement()
612
+ return _evaluate_models_match_count_in_range(requirement_links=requirement_links, input_links=input_links, requirement=requirement, **kwargs_for_eval)
613
+ elif operator_name == "models_match_n_in_timeframe":
614
+ if not isinstance(requirement, Requirement):
615
+ raise ValueError("models_match_n_in_timeframe operator requires a valid 'requirement' instance in kwargs.")
616
+ kwargs_for_eval = _kwargs_without_requirement()
617
+ return _evaluate_models_match_n_in_timeframe(requirement_links=requirement_links, input_links=input_links, requirement=requirement, **kwargs_for_eval)
618
+ elif operator_name == "models_match_n_or_more_in_timeframe":
619
+ if not isinstance(requirement, Requirement):
620
+ raise ValueError("models_match_n_or_more_in_timeframe operator requires a valid 'requirement' instance in kwargs.")
621
+ kwargs_for_eval = _kwargs_without_requirement()
622
+ return _evaluate_models_match_n_or_more_in_timeframe(
623
+ requirement_links=requirement_links, input_links=input_links, requirement=requirement, **kwargs_for_eval
624
+ )
625
+ elif operator_name == "models_match_n_or_less_in_timeframe":
626
+ if not isinstance(requirement, Requirement):
627
+ raise ValueError("models_match_n_or_less_in_timeframe operator requires a valid 'requirement' instance in kwargs.")
628
+ kwargs_for_eval = _kwargs_without_requirement()
629
+ return _evaluate_models_match_n_or_less_in_timeframe(
630
+ requirement_links=requirement_links, input_links=input_links, requirement=requirement, **kwargs_for_eval
631
+ )
632
+ elif operator_name in LAB_VALUE_OPERATOR_FUNCTIONS:
633
+ if not isinstance(requirement, Requirement): # Ensure requirement is present and correct type
634
+ raise ValueError(f"Lab value operator '{operator_name}' requires a valid 'requirement' instance in kwargs.")
635
+
636
+ eval_func = LAB_VALUE_OPERATOR_FUNCTIONS[operator_name]
637
+ return eval_func(input_links=input_links, requirement=requirement, operator_kwargs=kwargs)
638
+ elif operator_name == "age_gte":
639
+ if not isinstance(requirement, Requirement):
640
+ raise ValueError("age_gte operator requires a valid 'requirement' instance in kwargs.")
641
+
642
+ # Create a new kwargs dict for the call, excluding 'requirement' to avoid passing it twice
643
+ kwargs_for_eval = {k: v for k, v in kwargs.items() if k != "requirement"}
644
+
645
+ return _evaluate_age_gte(requirement_links=requirement_links, input_links=input_links, requirement=requirement, **kwargs_for_eval)
646
+ elif operator_name == "age_lte":
647
+ if not isinstance(requirement, Requirement):
648
+ raise ValueError("age_lte operator requires a valid 'requirement' instance in kwargs.")
649
+
650
+ # Create a new kwargs dict for the call, excluding 'requirement' to avoid passing it twice
651
+ kwargs_for_eval = {k: v for k, v in kwargs.items() if k != "requirement"}
652
+
653
+ return _evaluate_age_lte(requirement_links=requirement_links, input_links=input_links, requirement=requirement, **kwargs_for_eval)
654
+ else:
655
+ raise NotImplementedError(f"Evaluation logic for operator '{operator_name}' is not implemented.")