endoreg-db 0.3.6__py3-none-any.whl → 0.8.6.1__py3-none-any.whl

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  1. endoreg_db/admin.py +92 -3
  2. endoreg_db/api_urls.py +4 -0
  3. endoreg_db/apps.py +18 -6
  4. endoreg_db/assets/dummy_model.ckpt +1 -0
  5. endoreg_db/codemods/readme.md +88 -0
  6. endoreg_db/codemods/rename_datetime_fields.py +92 -0
  7. endoreg_db/config/env.py +101 -0
  8. endoreg_db/data/__init__.py +144 -65
  9. endoreg_db/data/ai_model/data.yaml +7 -0
  10. endoreg_db/data/{label → ai_model_label}/label/data.yaml +88 -62
  11. endoreg_db/data/ai_model_label/label/polyp_classification.yaml +52 -0
  12. endoreg_db/data/ai_model_label/label-set/data.yaml +40 -0
  13. endoreg_db/data/ai_model_label/label-set/polyp_classifications.yaml +25 -0
  14. endoreg_db/data/{label → ai_model_label}/label-type/data.yaml +6 -6
  15. endoreg_db/data/ai_model_meta/default_multilabel_classification.yaml +27 -0
  16. endoreg_db/data/{model_type → ai_model_type}/data.yaml +6 -6
  17. endoreg_db/data/ai_model_video_segmentation_label/base_segmentation.yaml +176 -0
  18. endoreg_db/data/ai_model_video_segmentation_labelset/data.yaml +20 -0
  19. endoreg_db/data/case_template/rule/00_patient_lab_sample_add_default_value.yaml +167 -167
  20. endoreg_db/data/case_template/rule/01_patient-set-age.yaml +7 -7
  21. endoreg_db/data/case_template/rule/01_patient-set-gender.yaml +8 -8
  22. endoreg_db/data/case_template/rule/11_create_patient_lab_sample.yaml +22 -22
  23. endoreg_db/data/case_template/rule/12_create-patient_medication-anticoagulation.yaml +18 -18
  24. endoreg_db/data/case_template/rule/13_create-patient_medication_schedule-anticoagulation.yaml +18 -18
  25. endoreg_db/data/case_template/rule/19_create_patient.yaml +16 -16
  26. endoreg_db/data/case_template/rule_type/base_types.yaml +35 -35
  27. endoreg_db/data/case_template/rule_value_type/base_types.yaml +58 -58
  28. endoreg_db/data/case_template/template/base.yaml +7 -7
  29. endoreg_db/data/case_template/template_type/pre_endoscopy.yaml +2 -2
  30. endoreg_db/data/case_template/tmp/_rule_value +13 -13
  31. endoreg_db/data/case_template/tmp/rule/01_atrial_fibrillation.yaml +21 -21
  32. endoreg_db/data/case_template/tmp/rule/02_create_object.yaml +9 -9
  33. endoreg_db/data/case_template/tmp/template/atrial_fibrillation_low_risk.yaml +6 -6
  34. endoreg_db/data/center/data.yaml +90 -59
  35. endoreg_db/data/center_resource/green_endoscopy_dashboard_CenterResource.yaml +144 -144
  36. endoreg_db/data/center_shift/ukw.yaml +9 -0
  37. endoreg_db/data/center_waste/green_endoscopy_dashboard_CenterWaste.yaml +48 -48
  38. endoreg_db/data/contraindication/bleeding.yaml +11 -0
  39. endoreg_db/data/db_summary.csv +58 -0
  40. endoreg_db/data/db_summary.xlsx +0 -0
  41. endoreg_db/data/disease/cardiovascular.yaml +37 -37
  42. endoreg_db/data/disease/hepatology.yaml +4 -4
  43. endoreg_db/data/disease/misc.yaml +5 -6
  44. endoreg_db/data/disease/renal.yaml +4 -4
  45. endoreg_db/data/disease_classification/chronic_kidney_disease.yaml +6 -6
  46. endoreg_db/data/disease_classification/coronary_vessel_disease.yaml +5 -5
  47. endoreg_db/data/disease_classification_choice/chronic_kidney_disease.yaml +41 -41
  48. endoreg_db/data/disease_classification_choice/coronary_vessel_disease.yaml +19 -19
  49. endoreg_db/data/distribution/date/patient.yaml +6 -6
  50. endoreg_db/data/distribution/numeric/data.yaml +14 -0
  51. endoreg_db/data/distribution/single_categorical/patient.yaml +6 -6
  52. endoreg_db/data/emission_factor/green_endoscopy_dashboard_EmissionFactor.yaml +132 -132
  53. endoreg_db/data/endoscope/data.yaml +93 -0
  54. endoreg_db/data/endoscope_type/data.yaml +10 -10
  55. endoreg_db/data/endoscopy_processor/data.yaml +50 -45
  56. endoreg_db/data/event/cardiology.yaml +15 -28
  57. endoreg_db/data/event/neurology.yaml +13 -13
  58. endoreg_db/data/event/surgery.yaml +12 -12
  59. endoreg_db/data/event/thrombembolism.yaml +19 -19
  60. endoreg_db/data/examination/examinations/data.yaml +72 -66
  61. endoreg_db/data/examination/time/data.yaml +47 -47
  62. endoreg_db/data/examination/time-type/data.yaml +7 -7
  63. endoreg_db/data/examination/type/data.yaml +17 -5
  64. endoreg_db/data/examination_indication/endoscopy.yaml +424 -0
  65. endoreg_db/data/examination_indication_classification/endoscopy.yaml +160 -0
  66. endoreg_db/data/examination_indication_classification_choice/endoscopy.yaml +101 -0
  67. endoreg_db/data/examination_requirement_set/colonoscopy.yaml +15 -0
  68. endoreg_db/data/finding/anatomy_colon.yaml +128 -0
  69. endoreg_db/data/finding/colonoscopy.yaml +40 -0
  70. endoreg_db/data/finding/colonoscopy_bowel_prep.yaml +56 -0
  71. endoreg_db/data/finding/complication.yaml +16 -0
  72. endoreg_db/data/finding/data.yaml +105 -0
  73. endoreg_db/data/finding/examination_setting.yaml +16 -0
  74. endoreg_db/data/finding/medication_related.yaml +18 -0
  75. endoreg_db/data/finding/outcome.yaml +12 -0
  76. endoreg_db/data/finding_classification/colonoscopy_bowel_preparation.yaml +95 -0
  77. endoreg_db/data/finding_classification/colonoscopy_jnet.yaml +22 -0
  78. endoreg_db/data/finding_classification/colonoscopy_kudo.yaml +25 -0
  79. endoreg_db/data/finding_classification/colonoscopy_lesion_circularity.yaml +20 -0
  80. endoreg_db/data/finding_classification/colonoscopy_lesion_planarity.yaml +24 -0
  81. endoreg_db/data/finding_classification/colonoscopy_lesion_size.yaml +68 -0
  82. endoreg_db/data/finding_classification/colonoscopy_lesion_surface.yaml +20 -0
  83. endoreg_db/data/finding_classification/colonoscopy_location.yaml +80 -0
  84. endoreg_db/data/finding_classification/colonoscopy_lst.yaml +21 -0
  85. endoreg_db/data/finding_classification/colonoscopy_nice.yaml +20 -0
  86. endoreg_db/data/finding_classification/colonoscopy_paris.yaml +26 -0
  87. endoreg_db/data/finding_classification/colonoscopy_sano.yaml +22 -0
  88. endoreg_db/data/finding_classification/colonoscopy_summary.yaml +53 -0
  89. endoreg_db/data/finding_classification/complication_generic.yaml +25 -0
  90. endoreg_db/data/finding_classification/examination_setting_generic.yaml +40 -0
  91. endoreg_db/data/finding_classification/histology_colo.yaml +51 -0
  92. endoreg_db/data/finding_classification/intervention_required.yaml +26 -0
  93. endoreg_db/data/finding_classification/medication_related.yaml +23 -0
  94. endoreg_db/data/finding_classification/visualized.yaml +33 -0
  95. endoreg_db/data/finding_classification_choice/bowel_preparation.yaml +78 -0
  96. endoreg_db/data/finding_classification_choice/colon_lesion_circularity_default.yaml +32 -0
  97. endoreg_db/data/finding_classification_choice/colon_lesion_jnet.yaml +15 -0
  98. endoreg_db/data/finding_classification_choice/colon_lesion_kudo.yaml +23 -0
  99. endoreg_db/data/finding_classification_choice/colon_lesion_lst.yaml +15 -0
  100. endoreg_db/data/finding_classification_choice/colon_lesion_nice.yaml +17 -0
  101. endoreg_db/data/finding_classification_choice/colon_lesion_paris.yaml +57 -0
  102. endoreg_db/data/finding_classification_choice/colon_lesion_planarity_default.yaml +49 -0
  103. endoreg_db/data/finding_classification_choice/colon_lesion_sano.yaml +14 -0
  104. endoreg_db/data/finding_classification_choice/colon_lesion_surface_intact_default.yaml +36 -0
  105. endoreg_db/data/finding_classification_choice/colonoscopy_location.yaml +229 -0
  106. endoreg_db/data/finding_classification_choice/colonoscopy_not_complete_reason.yaml +19 -0
  107. endoreg_db/data/finding_classification_choice/colonoscopy_size.yaml +82 -0
  108. endoreg_db/data/finding_classification_choice/colonoscopy_summary_worst_finding.yaml +15 -0
  109. endoreg_db/data/finding_classification_choice/complication_generic_types.yaml +15 -0
  110. endoreg_db/data/finding_classification_choice/examination_setting_generic_types.yaml +15 -0
  111. endoreg_db/data/finding_classification_choice/histology.yaml +24 -0
  112. endoreg_db/data/finding_classification_choice/histology_polyp.yaml +20 -0
  113. endoreg_db/data/finding_classification_choice/outcome.yaml +19 -0
  114. endoreg_db/data/finding_classification_choice/yes_no_na.yaml +11 -0
  115. endoreg_db/data/finding_classification_type/colonoscopy_basic.yaml +48 -0
  116. endoreg_db/data/finding_intervention/endoscopy.yaml +43 -0
  117. endoreg_db/data/finding_intervention/endoscopy_colonoscopy.yaml +168 -0
  118. endoreg_db/data/finding_intervention/endoscopy_egd.yaml +128 -0
  119. endoreg_db/data/finding_intervention/endoscopy_ercp.yaml +32 -0
  120. endoreg_db/data/finding_intervention/endoscopy_eus_lower.yaml +9 -0
  121. endoreg_db/data/finding_intervention/endoscopy_eus_upper.yaml +36 -0
  122. endoreg_db/data/finding_intervention_type/endoscopy.yaml +15 -0
  123. endoreg_db/data/finding_morphology_classification_type/colonoscopy.yaml +79 -0
  124. endoreg_db/data/finding_type/data.yaml +43 -0
  125. endoreg_db/data/gender/data.yaml +42 -18
  126. endoreg_db/data/information_source/annotation.yaml +6 -0
  127. endoreg_db/data/information_source/data.yaml +30 -30
  128. endoreg_db/data/information_source/endoscopy_guidelines.yaml +7 -0
  129. endoreg_db/data/information_source/medication.yaml +5 -5
  130. endoreg_db/data/information_source/prediction.yaml +7 -0
  131. endoreg_db/data/information_source_type/data.yaml +8 -0
  132. endoreg_db/data/lab_value/cardiac_enzymes.yaml +37 -31
  133. endoreg_db/data/lab_value/coagulation.yaml +54 -49
  134. endoreg_db/data/lab_value/electrolytes.yaml +228 -190
  135. endoreg_db/data/lab_value/gastrointestinal_function.yaml +133 -121
  136. endoreg_db/data/lab_value/hematology.yaml +184 -169
  137. endoreg_db/data/lab_value/hormones.yaml +59 -53
  138. endoreg_db/data/lab_value/lipids.yaml +53 -44
  139. endoreg_db/data/lab_value/misc.yaml +76 -30
  140. endoreg_db/data/lab_value/renal_function.yaml +12 -11
  141. endoreg_db/data/log_type/data.yaml +57 -0
  142. endoreg_db/data/lx_client_tag/base.yaml +54 -0
  143. endoreg_db/data/lx_client_type/base.yaml +30 -0
  144. endoreg_db/data/lx_permission/base.yaml +24 -0
  145. endoreg_db/data/lx_permission/endoreg.yaml +52 -0
  146. endoreg_db/data/medication/anticoagulation.yaml +64 -64
  147. endoreg_db/data/medication/tah.yaml +69 -69
  148. endoreg_db/data/medication_indication/anticoagulation.yaml +115 -120
  149. endoreg_db/data/medication_indication_type/data.yaml +10 -10
  150. endoreg_db/data/medication_indication_type/thrombembolism.yaml +40 -40
  151. endoreg_db/data/medication_intake_time/base.yaml +30 -30
  152. endoreg_db/data/medication_schedule/apixaban.yaml +94 -94
  153. endoreg_db/data/medication_schedule/ass.yaml +12 -12
  154. endoreg_db/data/medication_schedule/enoxaparin.yaml +26 -26
  155. endoreg_db/data/names_first/first_names.yaml +54 -0
  156. endoreg_db/data/names_last/last_names.yaml +51 -0
  157. endoreg_db/data/network_device/data.yaml +59 -0
  158. endoreg_db/data/network_device_type/data.yaml +12 -0
  159. endoreg_db/data/organ/data.yaml +29 -0
  160. endoreg_db/data/patient_lab_sample_type/generic.yaml +5 -5
  161. endoreg_db/data/pdf_type/data.yaml +46 -28
  162. endoreg_db/data/product/green_endoscopy_dashboard_Product.yaml +66 -66
  163. endoreg_db/data/product_group/green_endoscopy_dashboard_ProductGroup.yaml +33 -33
  164. endoreg_db/data/product_material/green_endoscopy_dashboard_ProductMaterial.yaml +308 -308
  165. endoreg_db/data/product_weight/green_endoscopy_dashboard_ProductWeight.yaml +88 -88
  166. endoreg_db/data/profession/data.yaml +70 -70
  167. endoreg_db/data/qualification/endoscopy.yaml +36 -0
  168. endoreg_db/data/qualification/m2.yaml +39 -0
  169. endoreg_db/data/qualification/outpatient_clinic.yaml +35 -0
  170. endoreg_db/data/qualification/sonography.yaml +36 -0
  171. endoreg_db/data/qualification_type/base.yaml +29 -0
  172. endoreg_db/data/reference_product/green_endoscopy_dashboard_ReferenceProduct.yaml +55 -55
  173. endoreg_db/data/report_reader_flag/rkh-histology-generic.yaml +10 -0
  174. endoreg_db/data/report_reader_flag/ukw-examination-generic.yaml +30 -26
  175. endoreg_db/data/report_reader_flag/ukw-histology-generic.yaml +24 -19
  176. endoreg_db/data/requirement/age.yaml +26 -0
  177. endoreg_db/data/requirement/colonoscopy_baseline_austria.yaml +45 -0
  178. endoreg_db/data/requirement/disease_cardiovascular.yaml +79 -0
  179. endoreg_db/data/requirement/disease_classification_choice_cardiovascular.yaml +41 -0
  180. endoreg_db/data/requirement/disease_hepatology.yaml +12 -0
  181. endoreg_db/data/requirement/disease_misc.yaml +12 -0
  182. endoreg_db/data/requirement/disease_renal.yaml +96 -0
  183. endoreg_db/data/requirement/endoscopy_bleeding_risk.yaml +59 -0
  184. endoreg_db/data/requirement/event_cardiology.yaml +251 -0
  185. endoreg_db/data/requirement/event_requirements.yaml +145 -0
  186. endoreg_db/data/requirement/finding_colon_polyp.yaml +50 -0
  187. endoreg_db/data/requirement/gender.yaml +25 -0
  188. endoreg_db/data/requirement/lab_value.yaml +441 -0
  189. endoreg_db/data/requirement/medication.yaml +93 -0
  190. endoreg_db/data/requirement_operator/age.yaml +13 -0
  191. endoreg_db/data/requirement_operator/lab_operators.yaml +129 -0
  192. endoreg_db/data/requirement_operator/model_operators.yaml +96 -0
  193. endoreg_db/data/requirement_set/01_endoscopy_generic.yaml +48 -0
  194. endoreg_db/data/requirement_set/colonoscopy_austria_screening.yaml +57 -0
  195. endoreg_db/data/requirement_set/endoscopy_bleeding_risk.yaml +52 -0
  196. endoreg_db/data/requirement_set_type/data.yaml +20 -0
  197. endoreg_db/data/requirement_type/requirement_types.yaml +165 -0
  198. endoreg_db/data/resource/green_endoscopy_dashboard_Resource.yaml +15 -15
  199. endoreg_db/data/risk/bleeding.yaml +26 -0
  200. endoreg_db/data/risk/thrombosis.yaml +37 -0
  201. endoreg_db/data/risk_type/data.yaml +27 -0
  202. endoreg_db/data/setup_config.yaml +38 -0
  203. endoreg_db/data/shift/endoscopy.yaml +21 -0
  204. endoreg_db/data/shift/m2.yaml +0 -0
  205. endoreg_db/data/shift_type/base.yaml +35 -0
  206. endoreg_db/data/tag/requirement_set_tags.yaml +11 -0
  207. endoreg_db/data/transport_route/green_endoscopy_dashboard_TransportRoute.yaml +12 -12
  208. endoreg_db/data/unit/concentration.yaml +115 -92
  209. endoreg_db/data/unit/data.yaml +17 -17
  210. endoreg_db/data/unit/length.yaml +30 -30
  211. endoreg_db/data/unit/misc.yaml +19 -19
  212. endoreg_db/data/unit/rate.yaml +5 -5
  213. endoreg_db/data/unit/time.yaml +48 -13
  214. endoreg_db/data/unit/volume.yaml +35 -35
  215. endoreg_db/data/unit/weight.yaml +37 -37
  216. endoreg_db/data/waste/data.yaml +11 -11
  217. endoreg_db/exceptions.py +19 -0
  218. endoreg_db/factories/__init__.py +0 -0
  219. endoreg_db/forms/__init__.py +5 -3
  220. endoreg_db/forms/examination_form.py +11 -0
  221. endoreg_db/forms/patient_finding_intervention_form.py +18 -0
  222. endoreg_db/forms/patient_form.py +27 -0
  223. endoreg_db/forms/questionnaires/__init__.py +1 -1
  224. endoreg_db/forms/questionnaires/tto_questionnaire.py +23 -23
  225. endoreg_db/forms/settings/__init__.py +8 -8
  226. endoreg_db/forms/unit.py +5 -5
  227. endoreg_db/helpers/__init__.py +0 -0
  228. endoreg_db/helpers/count_db.py +45 -0
  229. endoreg_db/helpers/data_loader.py +208 -0
  230. endoreg_db/helpers/default_objects.py +378 -0
  231. endoreg_db/helpers/download_segmentation_model.py +31 -0
  232. endoreg_db/helpers/interact.py +6 -0
  233. endoreg_db/helpers/test_video_helper.py +119 -0
  234. endoreg_db/logger_conf.py +140 -0
  235. endoreg_db/management/__init__.py +1 -0
  236. endoreg_db/management/commands/__init__.py +1 -0
  237. endoreg_db/management/commands/anonymize_video.py +0 -0
  238. endoreg_db/management/commands/check_auth.py +125 -0
  239. endoreg_db/management/commands/create_model_meta_from_huggingface.py +115 -0
  240. endoreg_db/management/commands/create_multilabel_model_meta.py +214 -0
  241. endoreg_db/management/commands/fix_missing_patient_data.py +172 -0
  242. endoreg_db/management/commands/fix_video_paths.py +165 -0
  243. endoreg_db/management/commands/import_fallback_video.py +203 -0
  244. endoreg_db/management/commands/import_report.py +298 -0
  245. endoreg_db/management/commands/import_video.py +423 -0
  246. endoreg_db/management/commands/import_video_with_classification.py +367 -0
  247. endoreg_db/management/commands/init_default_ai_model.py +112 -0
  248. endoreg_db/management/commands/load_ai_model_data.py +77 -45
  249. endoreg_db/management/commands/load_ai_model_label_data.py +59 -0
  250. endoreg_db/management/commands/load_base_db_data.py +192 -128
  251. endoreg_db/management/commands/load_center_data.py +68 -43
  252. endoreg_db/management/commands/{load_medication_intake_time_data.py → load_contraindication_data.py} +40 -40
  253. endoreg_db/management/commands/load_disease_classification_choices_data.py +40 -40
  254. endoreg_db/management/commands/load_disease_classification_data.py +40 -40
  255. endoreg_db/management/commands/load_disease_data.py +61 -39
  256. endoreg_db/management/commands/load_distribution_data.py +65 -65
  257. endoreg_db/management/commands/{load_endoscope_type_data.py → load_endoscope_data.py} +67 -44
  258. endoreg_db/management/commands/load_event_data.py +40 -40
  259. endoreg_db/management/commands/load_examination_data.py +74 -74
  260. endoreg_db/management/commands/load_examination_indication_data.py +86 -0
  261. endoreg_db/management/commands/load_finding_data.py +128 -0
  262. endoreg_db/management/commands/load_gender_data.py +43 -43
  263. endoreg_db/management/commands/load_green_endoscopy_wuerzburg_data.py +131 -132
  264. endoreg_db/management/commands/load_information_source.py +50 -44
  265. endoreg_db/management/commands/load_lab_value_data.py +49 -49
  266. endoreg_db/management/commands/load_medication_data.py +103 -41
  267. endoreg_db/management/commands/load_name_data.py +37 -0
  268. endoreg_db/management/commands/{load_medication_indication_type_data.py → load_organ_data.py} +42 -40
  269. endoreg_db/management/commands/load_pdf_type_data.py +60 -60
  270. endoreg_db/management/commands/load_profession_data.py +43 -43
  271. endoreg_db/management/commands/load_qualification_data.py +59 -0
  272. endoreg_db/management/commands/{load_report_reader_flag.py → load_report_reader_flag_data.py} +45 -45
  273. endoreg_db/management/commands/load_requirement_data.py +180 -0
  274. endoreg_db/management/commands/load_risk_data.py +56 -0
  275. endoreg_db/management/commands/load_shift_data.py +60 -0
  276. endoreg_db/management/commands/load_tag_data.py +57 -0
  277. endoreg_db/management/commands/load_unit_data.py +45 -45
  278. endoreg_db/management/commands/load_user_groups.py +28 -28
  279. endoreg_db/management/commands/register_ai_model.py +64 -65
  280. endoreg_db/management/commands/reset_celery_schedule.py +9 -9
  281. endoreg_db/management/commands/setup_endoreg_db.py +381 -0
  282. endoreg_db/management/commands/start_filewatcher.py +106 -0
  283. endoreg_db/management/commands/storage_management.py +548 -0
  284. endoreg_db/management/commands/summarize_db_content.py +189 -0
  285. endoreg_db/management/commands/validate_video.py +204 -0
  286. endoreg_db/management/commands/validate_video_files.py +161 -0
  287. endoreg_db/management/commands/video_validation.py +22 -0
  288. endoreg_db/mermaid/Overall_flow_patient_finding_intervention.md +10 -0
  289. endoreg_db/mermaid/anonymized_image_annotation.md +20 -0
  290. endoreg_db/mermaid/binary_classification_annotation.md +50 -0
  291. endoreg_db/mermaid/classification.md +8 -0
  292. endoreg_db/mermaid/examination.md +8 -0
  293. endoreg_db/mermaid/findings.md +7 -0
  294. endoreg_db/mermaid/image_classification.md +28 -0
  295. endoreg_db/mermaid/interventions.md +8 -0
  296. endoreg_db/mermaid/morphology.md +8 -0
  297. endoreg_db/mermaid/patient_creation.md +14 -0
  298. endoreg_db/mermaid/video_segmentation_annotation.md +17 -0
  299. endoreg_db/migrations/0001_initial.py +1857 -582
  300. endoreg_db/migrations/0002_add_video_correction_models.py +52 -0
  301. endoreg_db/migrations/0003_add_center_display_name.py +30 -0
  302. endoreg_db/models/__init__.py +359 -74
  303. endoreg_db/models/administration/__init__.py +116 -0
  304. endoreg_db/models/administration/ai/__init__.py +9 -0
  305. endoreg_db/models/administration/ai/active_model.py +35 -0
  306. endoreg_db/models/administration/ai/ai_model.py +156 -0
  307. endoreg_db/models/{ai_model → administration/ai}/model_type.py +41 -26
  308. endoreg_db/models/administration/case/__init__.py +19 -0
  309. endoreg_db/models/administration/case/case.py +114 -0
  310. endoreg_db/models/{case_template → administration/case/case_template}/__init__.py +15 -6
  311. endoreg_db/models/{case_template → administration/case/case_template}/case_template.py +125 -81
  312. endoreg_db/models/{case_template → administration/case/case_template}/case_template_rule.py +269 -276
  313. endoreg_db/models/{case_template → administration/case/case_template}/case_template_rule_value.py +86 -73
  314. endoreg_db/models/{case_template → administration/case/case_template}/case_template_type.py +26 -28
  315. endoreg_db/models/{center → administration/center}/__init__.py +13 -4
  316. endoreg_db/models/administration/center/center.py +67 -0
  317. endoreg_db/models/administration/center/center_product.py +64 -0
  318. endoreg_db/models/administration/center/center_resource.py +49 -0
  319. endoreg_db/models/administration/center/center_shift.py +88 -0
  320. endoreg_db/models/administration/center/center_waste.py +30 -0
  321. endoreg_db/models/administration/permissions/__init__.py +44 -0
  322. endoreg_db/models/administration/person/__init__.py +24 -0
  323. endoreg_db/models/administration/person/employee/__init__.py +3 -0
  324. endoreg_db/models/administration/person/employee/employee.py +35 -0
  325. endoreg_db/models/administration/person/employee/employee_qualification.py +39 -0
  326. endoreg_db/models/administration/person/employee/employee_type.py +42 -0
  327. endoreg_db/models/administration/person/examiner/__init__.py +4 -0
  328. endoreg_db/models/administration/person/examiner/examiner.py +54 -0
  329. endoreg_db/models/administration/person/names/__init__.py +0 -0
  330. endoreg_db/models/{persons → administration/person/names}/first_name.py +18 -18
  331. endoreg_db/models/{persons → administration/person/names}/last_name.py +18 -19
  332. endoreg_db/models/administration/person/patient/__init__.py +5 -0
  333. endoreg_db/models/administration/person/patient/patient.py +460 -0
  334. endoreg_db/models/{persons → administration/person}/person.py +31 -31
  335. endoreg_db/models/administration/person/profession/__init__.py +24 -0
  336. endoreg_db/models/administration/person/user/__init__.py +5 -0
  337. endoreg_db/models/administration/person/user/portal_user_information.py +37 -0
  338. endoreg_db/models/administration/product/__init__.py +14 -0
  339. endoreg_db/models/administration/product/product.py +97 -0
  340. endoreg_db/models/administration/product/product_group.py +39 -0
  341. endoreg_db/models/administration/product/product_material.py +54 -0
  342. endoreg_db/models/{product → administration/product}/product_weight.py +47 -26
  343. endoreg_db/models/{product → administration/product}/reference_product.py +130 -99
  344. endoreg_db/models/administration/qualification/__init__.py +7 -0
  345. endoreg_db/models/administration/qualification/qualification.py +37 -0
  346. endoreg_db/models/administration/qualification/qualification_type.py +35 -0
  347. endoreg_db/models/administration/shift/__init__.py +9 -0
  348. endoreg_db/models/administration/shift/scheduled_days.py +69 -0
  349. endoreg_db/models/administration/shift/shift.py +51 -0
  350. endoreg_db/models/administration/shift/shift_type.py +108 -0
  351. endoreg_db/models/label/__init__.py +24 -1
  352. endoreg_db/models/label/annotation/__init__.py +12 -0
  353. endoreg_db/models/label/annotation/image_classification.py +84 -0
  354. endoreg_db/models/label/annotation/video_segmentation_annotation.py +66 -0
  355. endoreg_db/models/label/label.py +83 -84
  356. endoreg_db/models/label/label_set.py +53 -0
  357. endoreg_db/models/label/label_type.py +29 -0
  358. endoreg_db/models/label/label_video_segment/__init__.py +3 -0
  359. endoreg_db/models/label/label_video_segment/_create_from_video.py +41 -0
  360. endoreg_db/models/label/label_video_segment/label_video_segment.py +511 -0
  361. endoreg_db/models/label/video_segmentation_label.py +31 -0
  362. endoreg_db/models/label/video_segmentation_labelset.py +27 -0
  363. endoreg_db/models/media/__init__.py +16 -0
  364. endoreg_db/models/media/frame/__init__.py +3 -0
  365. endoreg_db/models/media/frame/frame.py +111 -0
  366. endoreg_db/models/media/pdf/__init__.py +11 -0
  367. endoreg_db/models/media/pdf/raw_pdf.py +757 -0
  368. endoreg_db/models/media/pdf/report_file.py +162 -0
  369. endoreg_db/models/media/pdf/report_reader/__init__.py +7 -0
  370. endoreg_db/models/media/pdf/report_reader/report_reader_config.py +77 -0
  371. endoreg_db/models/{report_reader → media/pdf/report_reader}/report_reader_flag.py +19 -19
  372. endoreg_db/models/media/video/__init__.py +8 -0
  373. endoreg_db/models/media/video/create_from_file.py +358 -0
  374. endoreg_db/models/media/video/pipe_1.py +213 -0
  375. endoreg_db/models/media/video/pipe_2.py +105 -0
  376. endoreg_db/models/media/video/refactor_plan.md +0 -0
  377. endoreg_db/models/media/video/video_file.py +825 -0
  378. endoreg_db/models/media/video/video_file_ai.py +443 -0
  379. endoreg_db/models/media/video/video_file_anonymize.py +349 -0
  380. endoreg_db/models/media/video/video_file_frames/__init__.py +47 -0
  381. endoreg_db/models/media/video/video_file_frames/_bulk_create_frames.py +22 -0
  382. endoreg_db/models/media/video/video_file_frames/_create_frame_object.py +23 -0
  383. endoreg_db/models/media/video/video_file_frames/_delete_frames.py +104 -0
  384. endoreg_db/models/media/video/video_file_frames/_extract_frames.py +174 -0
  385. endoreg_db/models/media/video/video_file_frames/_get_frame.py +28 -0
  386. endoreg_db/models/media/video/video_file_frames/_get_frame_number.py +27 -0
  387. endoreg_db/models/media/video/video_file_frames/_get_frame_path.py +20 -0
  388. endoreg_db/models/media/video/video_file_frames/_get_frame_paths.py +27 -0
  389. endoreg_db/models/media/video/video_file_frames/_get_frame_range.py +34 -0
  390. endoreg_db/models/media/video/video_file_frames/_get_frames.py +27 -0
  391. endoreg_db/models/media/video/video_file_frames/_initialize_frames.py +129 -0
  392. endoreg_db/models/media/video/video_file_frames/_manage_frame_range.py +141 -0
  393. endoreg_db/models/media/video/video_file_frames/_mark_frames_extracted_status.py +65 -0
  394. endoreg_db/models/media/video/video_file_frames.py +0 -0
  395. endoreg_db/models/media/video/video_file_io.py +168 -0
  396. endoreg_db/models/media/video/video_file_meta/__init__.py +22 -0
  397. endoreg_db/models/media/video/video_file_meta/get_crop_template.py +45 -0
  398. endoreg_db/models/media/video/video_file_meta/get_endo_roi.py +39 -0
  399. endoreg_db/models/media/video/video_file_meta/get_fps.py +147 -0
  400. endoreg_db/models/media/video/video_file_meta/initialize_video_specs.py +143 -0
  401. endoreg_db/models/media/video/video_file_meta/text_meta.py +134 -0
  402. endoreg_db/models/media/video/video_file_meta/video_meta.py +70 -0
  403. endoreg_db/models/media/video/video_file_segments.py +209 -0
  404. endoreg_db/models/media/video/video_metadata.py +65 -0
  405. endoreg_db/models/media/video/video_processing.py +152 -0
  406. endoreg_db/models/medical/__init__.py +146 -0
  407. endoreg_db/models/medical/contraindication/__init__.py +17 -0
  408. endoreg_db/models/medical/disease.py +156 -0
  409. endoreg_db/models/medical/event.py +137 -0
  410. endoreg_db/models/medical/examination/__init__.py +9 -0
  411. endoreg_db/models/medical/examination/examination.py +148 -0
  412. endoreg_db/models/medical/examination/examination_indication.py +278 -0
  413. endoreg_db/models/medical/examination/examination_time.py +49 -0
  414. endoreg_db/models/medical/examination/examination_time_type.py +41 -0
  415. endoreg_db/models/medical/examination/examination_type.py +48 -0
  416. endoreg_db/models/medical/finding/__init__.py +18 -0
  417. endoreg_db/models/medical/finding/finding.py +96 -0
  418. endoreg_db/models/medical/finding/finding_classification.py +142 -0
  419. endoreg_db/models/medical/finding/finding_intervention.py +52 -0
  420. endoreg_db/models/medical/finding/finding_type.py +35 -0
  421. endoreg_db/models/medical/hardware/__init__.py +8 -0
  422. endoreg_db/models/medical/hardware/endoscope.py +65 -0
  423. endoreg_db/models/{hardware → medical/hardware}/endoscopy_processor.py +182 -143
  424. endoreg_db/models/medical/laboratory/__init__.py +5 -0
  425. endoreg_db/models/medical/laboratory/lab_value.py +419 -0
  426. endoreg_db/models/medical/medication/__init__.py +19 -0
  427. endoreg_db/models/medical/medication/medication.py +31 -0
  428. endoreg_db/models/medical/medication/medication_indication.py +50 -0
  429. endoreg_db/models/medical/medication/medication_indication_type.py +39 -0
  430. endoreg_db/models/medical/medication/medication_intake_time.py +44 -0
  431. endoreg_db/models/medical/medication/medication_schedule.py +45 -0
  432. endoreg_db/models/medical/organ/__init__.py +35 -0
  433. endoreg_db/models/medical/patient/__init__.py +56 -0
  434. endoreg_db/models/medical/patient/medication_examples.py +38 -0
  435. endoreg_db/models/medical/patient/patient_disease.py +63 -0
  436. endoreg_db/models/medical/patient/patient_event.py +75 -0
  437. endoreg_db/models/medical/patient/patient_examination.py +249 -0
  438. endoreg_db/models/medical/patient/patient_examination_indication.py +44 -0
  439. endoreg_db/models/medical/patient/patient_finding.py +357 -0
  440. endoreg_db/models/medical/patient/patient_finding_classification.py +207 -0
  441. endoreg_db/models/medical/patient/patient_finding_intervention.py +40 -0
  442. endoreg_db/models/medical/patient/patient_lab_sample.py +148 -0
  443. endoreg_db/models/{persons → medical}/patient/patient_lab_value.py +222 -176
  444. endoreg_db/models/medical/patient/patient_medication.py +104 -0
  445. endoreg_db/models/medical/patient/patient_medication_schedule.py +136 -0
  446. endoreg_db/models/medical/risk/__init__.py +7 -0
  447. endoreg_db/models/medical/risk/risk.py +72 -0
  448. endoreg_db/models/medical/risk/risk_type.py +51 -0
  449. endoreg_db/models/metadata/__init__.py +19 -0
  450. endoreg_db/models/metadata/frame_ocr_result.py +0 -0
  451. endoreg_db/models/metadata/model_meta.py +206 -0
  452. endoreg_db/models/metadata/model_meta_logic.py +343 -0
  453. endoreg_db/models/{data_file/metadata → metadata}/pdf_meta.py +89 -70
  454. endoreg_db/models/metadata/sensitive_meta.py +288 -0
  455. endoreg_db/models/metadata/sensitive_meta_logic.py +1048 -0
  456. endoreg_db/models/metadata/video_meta.py +332 -0
  457. endoreg_db/models/metadata/video_prediction_logic.py +190 -0
  458. endoreg_db/models/metadata/video_prediction_meta.py +270 -0
  459. endoreg_db/models/other/__init__.py +40 -5
  460. endoreg_db/models/other/distribution/__init__.py +44 -0
  461. endoreg_db/models/other/distribution/base_value_distribution.py +20 -0
  462. endoreg_db/models/other/distribution/date_value_distribution.py +89 -0
  463. endoreg_db/models/other/distribution/multiple_categorical_value_distribution.py +32 -0
  464. endoreg_db/models/other/distribution/numeric_value_distribution.py +125 -0
  465. endoreg_db/models/other/distribution/single_categorical_value_distribution.py +22 -0
  466. endoreg_db/models/other/emission/__init__.py +5 -0
  467. endoreg_db/models/other/emission/emission_factor.py +94 -0
  468. endoreg_db/models/{persons → other}/gender.py +27 -22
  469. endoreg_db/models/other/information_source.py +159 -0
  470. endoreg_db/models/other/material.py +28 -16
  471. endoreg_db/models/other/resource.py +21 -17
  472. endoreg_db/models/other/tag.py +27 -0
  473. endoreg_db/models/other/transport_route.py +33 -21
  474. endoreg_db/models/{unit.py → other/unit.py} +32 -22
  475. endoreg_db/models/other/waste.py +27 -20
  476. endoreg_db/models/requirement/__init__.py +11 -0
  477. endoreg_db/models/requirement/requirement.py +767 -0
  478. endoreg_db/models/requirement/requirement_evaluation/__init__.py +6 -0
  479. endoreg_db/models/requirement/requirement_evaluation/get_values.py +40 -0
  480. endoreg_db/models/requirement/requirement_evaluation/operator_evaluation_models.py +9 -0
  481. endoreg_db/models/requirement/requirement_evaluation/requirement_type_parser.py +95 -0
  482. endoreg_db/models/requirement/requirement_operator.py +176 -0
  483. endoreg_db/models/requirement/requirement_set.py +287 -0
  484. endoreg_db/models/rule/__init__.py +13 -0
  485. endoreg_db/models/{rules → rule}/rule.py +27 -24
  486. endoreg_db/models/{rules → rule}/rule_applicator.py +224 -224
  487. endoreg_db/models/{rules → rule}/rule_attribute_dtype.py +16 -18
  488. endoreg_db/models/{rules → rule}/rule_type.py +19 -21
  489. endoreg_db/models/{rules → rule}/ruleset.py +17 -19
  490. endoreg_db/models/state/__init__.py +12 -0
  491. endoreg_db/models/state/abstract.py +11 -0
  492. endoreg_db/models/state/audit_ledger.py +150 -0
  493. endoreg_db/models/state/label_video_segment.py +22 -0
  494. endoreg_db/models/state/raw_pdf.py +187 -0
  495. endoreg_db/models/state/sensitive_meta.py +46 -0
  496. endoreg_db/models/state/video.py +232 -0
  497. endoreg_db/models/upload_job.py +99 -0
  498. endoreg_db/models/utils.py +135 -0
  499. endoreg_db/queries/__init__.py +4 -4
  500. endoreg_db/queries/annotations/__init__.py +2 -2
  501. endoreg_db/queries/annotations/legacy.py +158 -159
  502. endoreg_db/renames.yml +8 -0
  503. endoreg_db/root_urls.py +9 -0
  504. endoreg_db/schemas/__init__.py +0 -0
  505. endoreg_db/schemas/examination_evaluation.py +27 -0
  506. endoreg_db/serializers/Frames_NICE_and_PARIS_classifications.py +775 -0
  507. endoreg_db/serializers/__init__.py +118 -10
  508. endoreg_db/serializers/_old/raw_pdf_meta_validation.py +223 -0
  509. endoreg_db/serializers/_old/raw_video_meta_validation.py +179 -0
  510. endoreg_db/serializers/_old/video.py +71 -0
  511. endoreg_db/serializers/administration/__init__.py +14 -0
  512. endoreg_db/serializers/administration/ai/__init__.py +10 -0
  513. endoreg_db/serializers/administration/ai/active_model.py +10 -0
  514. endoreg_db/serializers/administration/ai/ai_model.py +18 -0
  515. endoreg_db/serializers/administration/ai/model_type.py +10 -0
  516. endoreg_db/serializers/administration/center.py +9 -0
  517. endoreg_db/serializers/administration/gender.py +9 -0
  518. endoreg_db/serializers/anonymization.py +69 -0
  519. endoreg_db/serializers/evaluation/examination_evaluation.py +1 -0
  520. endoreg_db/serializers/examination/__init__.py +10 -0
  521. endoreg_db/serializers/examination/base.py +46 -0
  522. endoreg_db/serializers/examination/dropdown.py +21 -0
  523. endoreg_db/serializers/examination_serializer.py +12 -0
  524. endoreg_db/serializers/finding/__init__.py +5 -0
  525. endoreg_db/serializers/finding/finding.py +54 -0
  526. endoreg_db/serializers/finding_classification/__init__.py +7 -0
  527. endoreg_db/serializers/finding_classification/choice.py +19 -0
  528. endoreg_db/serializers/finding_classification/classification.py +13 -0
  529. endoreg_db/serializers/label/__init__.py +7 -0
  530. endoreg_db/serializers/label/image_classification_annotation.py +62 -0
  531. endoreg_db/serializers/label/label.py +15 -0
  532. endoreg_db/serializers/label_video_segment/__init__.py +7 -0
  533. endoreg_db/serializers/label_video_segment/_lvs_create.py +149 -0
  534. endoreg_db/serializers/label_video_segment/_lvs_update.py +138 -0
  535. endoreg_db/serializers/label_video_segment/_lvs_validate.py +149 -0
  536. endoreg_db/serializers/label_video_segment/label_video_segment.py +344 -0
  537. endoreg_db/serializers/label_video_segment/label_video_segment_annotation.py +99 -0
  538. endoreg_db/serializers/label_video_segment/label_video_segment_update.py +163 -0
  539. endoreg_db/serializers/meta/__init__.py +19 -0
  540. endoreg_db/serializers/meta/pdf_file_meta_extraction.py +115 -0
  541. endoreg_db/serializers/meta/report_meta.py +53 -0
  542. endoreg_db/serializers/meta/sensitive_meta_detail.py +162 -0
  543. endoreg_db/serializers/meta/sensitive_meta_update.py +148 -0
  544. endoreg_db/serializers/meta/sensitive_meta_verification.py +59 -0
  545. endoreg_db/serializers/meta/video_meta.py +39 -0
  546. endoreg_db/serializers/misc/__init__.py +14 -0
  547. endoreg_db/serializers/misc/file_overview.py +182 -0
  548. endoreg_db/serializers/misc/sensitive_patient_data.py +120 -0
  549. endoreg_db/serializers/misc/stats.py +33 -0
  550. endoreg_db/serializers/misc/translatable_field_mix_in.py +44 -0
  551. endoreg_db/serializers/misc/upload_job.py +71 -0
  552. endoreg_db/serializers/patient/__init__.py +11 -0
  553. endoreg_db/serializers/patient/patient.py +86 -0
  554. endoreg_db/serializers/patient/patient_dropdown.py +27 -0
  555. endoreg_db/serializers/patient_examination/__init__.py +7 -0
  556. endoreg_db/serializers/patient_examination/patient_examination.py +141 -0
  557. endoreg_db/serializers/patient_finding/__init__.py +15 -0
  558. endoreg_db/serializers/patient_finding/patient_finding.py +31 -0
  559. endoreg_db/serializers/patient_finding/patient_finding_classification.py +39 -0
  560. endoreg_db/serializers/patient_finding/patient_finding_detail.py +53 -0
  561. endoreg_db/serializers/patient_finding/patient_finding_intervention.py +26 -0
  562. endoreg_db/serializers/patient_finding/patient_finding_list.py +41 -0
  563. endoreg_db/serializers/patient_finding/patient_finding_write.py +126 -0
  564. endoreg_db/serializers/pdf/__init__.py +5 -0
  565. endoreg_db/serializers/pdf/anony_text_validation.py +85 -0
  566. endoreg_db/serializers/report/__init__.py +9 -0
  567. endoreg_db/serializers/report/mixins.py +45 -0
  568. endoreg_db/serializers/report/report.py +105 -0
  569. endoreg_db/serializers/report/report_list.py +22 -0
  570. endoreg_db/serializers/report/secure_file_url.py +26 -0
  571. endoreg_db/serializers/requirements/requirement_schema.py +25 -0
  572. endoreg_db/serializers/requirements/requirement_sets.py +29 -0
  573. endoreg_db/serializers/sensitive_meta_serializer.py +282 -0
  574. endoreg_db/serializers/video/__init__.py +7 -0
  575. endoreg_db/serializers/video/segmentation.py +263 -0
  576. endoreg_db/serializers/video/video_file_brief.py +10 -0
  577. endoreg_db/serializers/video/video_file_detail.py +83 -0
  578. endoreg_db/serializers/video/video_file_list.py +67 -0
  579. endoreg_db/serializers/video/video_metadata.py +105 -0
  580. endoreg_db/serializers/video/video_processing_history.py +153 -0
  581. endoreg_db/serializers/video_examination.py +198 -0
  582. endoreg_db/services/__init__.py +5 -0
  583. endoreg_db/services/anonymization.py +223 -0
  584. endoreg_db/services/examination_evaluation.py +149 -0
  585. endoreg_db/services/finding_description_service.py +0 -0
  586. endoreg_db/services/lookup_service.py +411 -0
  587. endoreg_db/services/lookup_store.py +266 -0
  588. endoreg_db/services/pdf_import.py +1382 -0
  589. endoreg_db/services/polling_coordinator.py +288 -0
  590. endoreg_db/services/pseudonym_service.py +89 -0
  591. endoreg_db/services/requirements_object.py +147 -0
  592. endoreg_db/services/segment_sync.py +155 -0
  593. endoreg_db/services/storage_aware_video_processor.py +344 -0
  594. endoreg_db/services/video_import.py +1259 -0
  595. endoreg_db/tasks/upload_tasks.py +207 -0
  596. endoreg_db/tasks/video_ingest.py +157 -0
  597. endoreg_db/tasks/video_processing_tasks.py +327 -0
  598. endoreg_db/templates/admin/patient_finding_intervention.html +253 -0
  599. endoreg_db/templates/admin/start_examination.html +12 -0
  600. endoreg_db/templates/timeline.html +176 -0
  601. endoreg_db/urls/__init__.py +83 -0
  602. endoreg_db/urls/anonymization.py +32 -0
  603. endoreg_db/urls/auth.py +16 -0
  604. endoreg_db/urls/classification.py +39 -0
  605. endoreg_db/urls/examination.py +54 -0
  606. endoreg_db/urls/files.py +6 -0
  607. endoreg_db/urls/label_video_segment_validate.py +33 -0
  608. endoreg_db/urls/label_video_segments.py +46 -0
  609. endoreg_db/urls/media.py +227 -0
  610. endoreg_db/urls/patient.py +19 -0
  611. endoreg_db/urls/report.py +48 -0
  612. endoreg_db/urls/requirements.py +13 -0
  613. endoreg_db/urls/sensitive_meta.py +0 -0
  614. endoreg_db/urls/stats.py +46 -0
  615. endoreg_db/urls/upload.py +20 -0
  616. endoreg_db/urls/video.py +61 -0
  617. endoreg_db/urls.py +9 -0
  618. endoreg_db/utils/__init__.py +88 -1
  619. endoreg_db/utils/ai/__init__.py +9 -0
  620. endoreg_db/{models/ai_model/utils.py → utils/ai/get.py} +5 -8
  621. endoreg_db/utils/ai/inference_dataset.py +52 -0
  622. endoreg_db/utils/ai/multilabel_classification_net.py +159 -0
  623. endoreg_db/utils/ai/postprocess.py +63 -0
  624. endoreg_db/utils/ai/predict.py +291 -0
  625. endoreg_db/utils/ai/preprocess.py +68 -0
  626. endoreg_db/utils/calc_duration_seconds.py +24 -0
  627. endoreg_db/utils/case_generator/__init__.py +0 -0
  628. endoreg_db/utils/case_generator/case_generator.py +159 -0
  629. endoreg_db/utils/case_generator/lab_sample_factory.py +33 -0
  630. endoreg_db/utils/case_generator/utils.py +30 -0
  631. endoreg_db/utils/check_video_files.py +148 -0
  632. endoreg_db/utils/cropping.py +28 -28
  633. endoreg_db/utils/dataloader.py +175 -92
  634. endoreg_db/utils/dates.py +60 -0
  635. endoreg_db/utils/env.py +33 -0
  636. endoreg_db/utils/extract_specific_frames.py +72 -0
  637. endoreg_db/utils/file_operations.py +58 -30
  638. endoreg_db/utils/fix_video_path_direct.py +141 -0
  639. endoreg_db/utils/frame_anonymization_utils.py +463 -0
  640. endoreg_db/utils/hashs.py +153 -34
  641. endoreg_db/utils/links/__init__.py +0 -0
  642. endoreg_db/utils/links/requirement_link.py +193 -0
  643. endoreg_db/utils/mime_types.py +0 -0
  644. endoreg_db/utils/names.py +76 -0
  645. endoreg_db/utils/ocr.py +190 -197
  646. endoreg_db/utils/parse_and_generate_yaml.py +46 -0
  647. endoreg_db/utils/paths.py +95 -0
  648. endoreg_db/utils/permissions.py +143 -0
  649. endoreg_db/utils/pipelines/Readme.md +235 -0
  650. endoreg_db/utils/pipelines/__init__.py +0 -0
  651. endoreg_db/utils/pipelines/process_video_dir.py +120 -0
  652. endoreg_db/utils/product/__init__.py +0 -0
  653. endoreg_db/utils/product/sum_emissions.py +20 -0
  654. endoreg_db/utils/product/sum_weights.py +18 -0
  655. endoreg_db/utils/pydantic_models/__init__.py +6 -0
  656. endoreg_db/utils/pydantic_models/db_config.py +57 -0
  657. endoreg_db/utils/requirement_helpers.py +0 -0
  658. endoreg_db/utils/requirement_operator_logic/__init__.py +0 -0
  659. endoreg_db/utils/requirement_operator_logic/lab_value_operators.py +578 -0
  660. endoreg_db/utils/requirement_operator_logic/model_evaluators.py +368 -0
  661. endoreg_db/utils/setup_config.py +177 -0
  662. endoreg_db/utils/translation.py +27 -0
  663. endoreg_db/utils/uuid.py +4 -4
  664. endoreg_db/utils/validate_endo_roi.py +19 -0
  665. endoreg_db/utils/validate_subcategory_dict.py +91 -0
  666. endoreg_db/utils/validate_video_detailed.py +357 -0
  667. endoreg_db/utils/video/__init__.py +26 -0
  668. endoreg_db/utils/video/extract_frames.py +88 -0
  669. endoreg_db/utils/video/ffmpeg_wrapper.py +835 -0
  670. endoreg_db/utils/video/names.py +42 -0
  671. endoreg_db/utils/video/streaming_processor.py +312 -0
  672. endoreg_db/utils/video/video_splitter.py +94 -0
  673. endoreg_db/views/Frames_NICE_and_PARIS_classifications_views.py +238 -0
  674. endoreg_db/views/__init__.py +275 -0
  675. endoreg_db/views/anonymization/__init__.py +27 -0
  676. endoreg_db/views/anonymization/media_management.py +454 -0
  677. endoreg_db/views/anonymization/overview.py +216 -0
  678. endoreg_db/views/anonymization/validate.py +107 -0
  679. endoreg_db/views/auth/__init__.py +13 -0
  680. endoreg_db/views/auth/keycloak.py +113 -0
  681. endoreg_db/views/examination/__init__.py +33 -0
  682. endoreg_db/views/examination/examination.py +37 -0
  683. endoreg_db/views/examination/examination_manifest_cache.py +26 -0
  684. endoreg_db/views/examination/get_finding_classification_choices.py +59 -0
  685. endoreg_db/views/examination/get_finding_classifications.py +36 -0
  686. endoreg_db/views/examination/get_findings.py +41 -0
  687. endoreg_db/views/examination/get_instruments.py +18 -0
  688. endoreg_db/views/examination/get_interventions.py +14 -0
  689. endoreg_db/views/finding/__init__.py +9 -0
  690. endoreg_db/views/finding/finding.py +112 -0
  691. endoreg_db/views/finding/get_classifications.py +14 -0
  692. endoreg_db/views/finding/get_interventions.py +17 -0
  693. endoreg_db/views/finding_classification/__init__.py +13 -0
  694. endoreg_db/views/finding_classification/base.py +0 -0
  695. endoreg_db/views/finding_classification/finding_classification.py +42 -0
  696. endoreg_db/views/finding_classification/get_classification_choices.py +55 -0
  697. endoreg_db/views/label/__init__.py +5 -0
  698. endoreg_db/views/label/label.py +15 -0
  699. endoreg_db/views/label_video_segment/__init__.py +16 -0
  700. endoreg_db/views/label_video_segment/create_lvs_from_annotation.py +44 -0
  701. endoreg_db/views/label_video_segment/get_lvs_by_name_and_video.py +50 -0
  702. endoreg_db/views/label_video_segment/label_video_segment.py +77 -0
  703. endoreg_db/views/label_video_segment/label_video_segment_by_label.py +174 -0
  704. endoreg_db/views/label_video_segment/label_video_segment_detail.py +73 -0
  705. endoreg_db/views/label_video_segment/update_lvs_from_annotation.py +46 -0
  706. endoreg_db/views/label_video_segment/validate.py +226 -0
  707. endoreg_db/views/media/__init__.py +45 -0
  708. endoreg_db/views/media/pdf_media.py +388 -0
  709. endoreg_db/views/media/segments.py +71 -0
  710. endoreg_db/views/media/sensitive_metadata.py +314 -0
  711. endoreg_db/views/media/video_media.py +272 -0
  712. endoreg_db/views/media/video_segments.py +524 -0
  713. endoreg_db/views/meta/__init__.py +15 -0
  714. endoreg_db/views/meta/available_files_list.py +146 -0
  715. endoreg_db/views/meta/report_meta.py +53 -0
  716. endoreg_db/views/meta/sensitive_meta_detail.py +148 -0
  717. endoreg_db/views/meta/sensitive_meta_list.py +104 -0
  718. endoreg_db/views/meta/sensitive_meta_verification.py +71 -0
  719. endoreg_db/views/misc/__init__.py +63 -0
  720. endoreg_db/views/misc/center.py +13 -0
  721. endoreg_db/views/misc/csrf.py +7 -0
  722. endoreg_db/views/misc/gender.py +14 -0
  723. endoreg_db/views/misc/secure_file_serving_view.py +80 -0
  724. endoreg_db/views/misc/secure_file_url_view.py +84 -0
  725. endoreg_db/views/misc/secure_url_validate.py +79 -0
  726. endoreg_db/views/misc/stats.py +220 -0
  727. endoreg_db/views/misc/translation.py +182 -0
  728. endoreg_db/views/misc/upload_views.py +240 -0
  729. endoreg_db/views/patient/__init__.py +5 -0
  730. endoreg_db/views/patient/patient.py +210 -0
  731. endoreg_db/views/patient_examination/DEPRECATED_video_backup.py +164 -0
  732. endoreg_db/views/patient_examination/__init__.py +11 -0
  733. endoreg_db/views/patient_examination/patient_examination.py +140 -0
  734. endoreg_db/views/patient_examination/patient_examination_create.py +63 -0
  735. endoreg_db/views/patient_examination/patient_examination_detail.py +66 -0
  736. endoreg_db/views/patient_examination/patient_examination_list.py +68 -0
  737. endoreg_db/views/patient_examination/video.py +194 -0
  738. endoreg_db/views/patient_finding/__init__.py +7 -0
  739. endoreg_db/views/patient_finding/base.py +0 -0
  740. endoreg_db/views/patient_finding/patient_finding.py +64 -0
  741. endoreg_db/views/patient_finding/patient_finding_optimized.py +259 -0
  742. endoreg_db/views/patient_finding_classification/__init__.py +5 -0
  743. endoreg_db/views/patient_finding_classification/pfc_create.py +67 -0
  744. endoreg_db/views/patient_finding_location/__init__.py +5 -0
  745. endoreg_db/views/patient_finding_location/pfl_create.py +70 -0
  746. endoreg_db/views/patient_finding_morphology/__init__.py +5 -0
  747. endoreg_db/views/patient_finding_morphology/pfm_create.py +70 -0
  748. endoreg_db/views/pdf/__init__.py +8 -0
  749. endoreg_db/views/pdf/pdf_stream.py +187 -0
  750. endoreg_db/views/pdf/reimport.py +177 -0
  751. endoreg_db/views/report/__init__.py +9 -0
  752. endoreg_db/views/report/report_list.py +112 -0
  753. endoreg_db/views/report/report_with_secure_url.py +28 -0
  754. endoreg_db/views/report/start_examination.py +7 -0
  755. endoreg_db/views/requirement/__init__.py +10 -0
  756. endoreg_db/views/requirement/evaluate.py +279 -0
  757. endoreg_db/views/requirement/lookup.py +367 -0
  758. endoreg_db/views/requirement/lookup_store.py +252 -0
  759. endoreg_db/views/requirement_lookup/lookup.py +0 -0
  760. endoreg_db/views/requirement_lookup/lookup_store.py +0 -0
  761. endoreg_db/views/stats/__init__.py +13 -0
  762. endoreg_db/views/stats/stats_views.py +229 -0
  763. endoreg_db/views/video/__init__.py +59 -0
  764. endoreg_db/views/video/correction.py +530 -0
  765. endoreg_db/views/video/reimport.py +195 -0
  766. endoreg_db/views/video/segmentation.py +274 -0
  767. endoreg_db/views/video/task_status.py +49 -0
  768. endoreg_db/views/video/timeline.py +46 -0
  769. endoreg_db/views/video/video_analyze.py +52 -0
  770. endoreg_db/views/video/video_apply_mask.py +48 -0
  771. endoreg_db/views/video/video_correction.py +21 -0
  772. endoreg_db/views/video/video_download_processed.py +58 -0
  773. endoreg_db/views/video/video_examination_viewset.py +242 -0
  774. endoreg_db/views/video/video_meta.py +29 -0
  775. endoreg_db/views/video/video_processing_history.py +24 -0
  776. endoreg_db/views/video/video_remove_frames.py +48 -0
  777. endoreg_db/views/video/video_stream.py +306 -0
  778. endoreg_db/views.py +0 -3
  779. endoreg_db-0.8.6.1.dist-info/METADATA +383 -0
  780. endoreg_db-0.8.6.1.dist-info/RECORD +793 -0
  781. {endoreg_db-0.3.6.dist-info → endoreg_db-0.8.6.1.dist-info}/WHEEL +1 -1
  782. {endoreg_db-0.3.6.dist-info → endoreg_db-0.8.6.1.dist-info/licenses}/LICENSE +674 -674
  783. endoreg_db/data/active_model/data.yaml +0 -3
  784. endoreg_db/data/label/label-set/data.yaml +0 -18
  785. endoreg_db/management/commands/_load_model_template.py +0 -41
  786. endoreg_db/management/commands/delete_all.py +0 -18
  787. endoreg_db/management/commands/delete_legacy_images.py +0 -19
  788. endoreg_db/management/commands/delete_legacy_videos.py +0 -17
  789. endoreg_db/management/commands/extract_legacy_video_frames.py +0 -18
  790. endoreg_db/management/commands/fetch_legacy_image_dataset.py +0 -32
  791. endoreg_db/management/commands/fix_auth_permission.py +0 -20
  792. endoreg_db/management/commands/import_legacy_images.py +0 -94
  793. endoreg_db/management/commands/import_legacy_videos.py +0 -76
  794. endoreg_db/management/commands/load_active_model_data.py +0 -45
  795. endoreg_db/management/commands/load_endoscopy_processor_data.py +0 -45
  796. endoreg_db/management/commands/load_g_play_data.py +0 -113
  797. endoreg_db/management/commands/load_label_data.py +0 -67
  798. endoreg_db/management/commands/load_medication_indication_data.py +0 -63
  799. endoreg_db/management/commands/load_medication_schedule_data.py +0 -55
  800. endoreg_db/migrations/0002_rawvideofile.py +0 -26
  801. endoreg_db/migrations/0003_rawvideofile_frames_required.py +0 -18
  802. endoreg_db/migrations/0004_rename_hash_rawvideofile_video_hash.py +0 -18
  803. endoreg_db/migrations/0005_ffmpegmeta_remove_videoimportmeta_center_and_more.py +0 -56
  804. endoreg_db/migrations/0006_rawvideofile_center_alter_videometa_processor.py +0 -25
  805. endoreg_db/migrations/0007_rawvideofile_processor.py +0 -19
  806. endoreg_db/migrations/0008_rename_frames_required_rawvideofile_state_frames_required.py +0 -18
  807. endoreg_db/migrations/0009_sensitivemeta_rawvideofile_sensitive_meta.py +0 -31
  808. endoreg_db/migrations/0010_rename_endoscope_serial_number_sensitivemeta_endoscope_sn.py +0 -18
  809. endoreg_db/migrations/0011_rawvideofile_state_sensitive_data_retrieved.py +0 -18
  810. endoreg_db/migrations/0012_rawvideofile_prediction_dir_and_more.py +0 -109
  811. endoreg_db/migrations/0013_rawpdffile.py +0 -31
  812. endoreg_db/migrations/0014_pdftype_alter_rawpdffile_file_pdfmeta.py +0 -38
  813. endoreg_db/migrations/0015_rename_report_processed_rawpdffile_state_report_processed_and_more.py +0 -31
  814. endoreg_db/migrations/0016_rawpdffile_state_report_processing_required.py +0 -18
  815. endoreg_db/migrations/0017_firstname_lastname_center_first_names_and_more.py +0 -37
  816. endoreg_db/migrations/0018_reportreaderflag_reportreaderconfig.py +0 -37
  817. endoreg_db/migrations/0019_pdftype_cut_off_above_lines_and_more.py +0 -42
  818. endoreg_db/migrations/0020_rename_endoscopy_info_line_pdftype_endoscope_info_line.py +0 -18
  819. endoreg_db/migrations/0021_alter_pdftype_endoscope_info_line.py +0 -19
  820. endoreg_db/migrations/0022_alter_pdftype_endoscope_info_line.py +0 -19
  821. endoreg_db/migrations/0023_ttoquestionnaire_alter_pdftype_endoscope_info_line.py +0 -59
  822. endoreg_db/migrations/0024_remove_ttoquestionnaire_infections_and_more.py +0 -27
  823. endoreg_db/migrations/0025_event_alter_rawpdffile_file_patientevent.py +0 -42
  824. endoreg_db/migrations/0026_disease_diseaseclassification_and_more.py +0 -166
  825. endoreg_db/migrations/0027_labvalue_abbreviation_labvalue_default_normal_range_and_more.py +0 -38
  826. endoreg_db/migrations/0028_alter_unit_abbreviation.py +0 -18
  827. endoreg_db/migrations/0029_medicationintaketime_and_more.py +0 -75
  828. endoreg_db/migrations/0030_medicationindicationtype_and_more.py +0 -101
  829. endoreg_db/migrations/0031_rename_adapt_to_liver_function_medication_adapt_to_age_and_more.py +0 -38
  830. endoreg_db/migrations/0032_alter_medicationschedule_therapy_duration_d.py +0 -18
  831. endoreg_db/migrations/0033_medicationindication_sources.py +0 -18
  832. endoreg_db/migrations/0034_alter_rawpdffile_file.py +0 -20
  833. endoreg_db/migrations/0035_alter_medicationindication_sources.py +0 -18
  834. endoreg_db/migrations/0036_alter_rawpdffile_file.py +0 -20
  835. endoreg_db/migrations/0037_alter_medicationindication_sources.py +0 -18
  836. endoreg_db/migrations/0038_emissionfactor_material_product_productgroup_and_more.py +0 -164
  837. endoreg_db/migrations/0039_referenceproduct_name.py +0 -19
  838. endoreg_db/migrations/0040_quizanswertype_quizquestiontype_quizquestion_and_more.py +0 -50
  839. endoreg_db/migrations/0041_gender_patientmedication_medication_indication_and_more.py +0 -40
  840. endoreg_db/migrations/0042_casetemplateruletype_casetemplaterulevalue_and_more.py +0 -74
  841. endoreg_db/migrations/0043_casetemplatetype_name_de_casetemplatetype_name_en.py +0 -23
  842. endoreg_db/migrations/0044_casetemplateruletype_name_de_and_more.py +0 -23
  843. endoreg_db/migrations/0045_casetemplaterulevalue_value_type.py +0 -19
  844. endoreg_db/migrations/0046_casetemplaterulevalue_target_field.py +0 -18
  845. endoreg_db/migrations/0047_casetemplaterule_target_model.py +0 -18
  846. endoreg_db/migrations/0048_remove_casetemplaterule_chained_rules_and_more.py +0 -22
  847. endoreg_db/migrations/0049_remove_casetemplaterule_rule_values.py +0 -17
  848. endoreg_db/migrations/0050_casetemplaterule_rule_values.py +0 -18
  849. endoreg_db/migrations/0051_remove_casetemplaterule_calling_rules_and_more.py +0 -27
  850. endoreg_db/migrations/0052_rename_case_template_type_casetemplate_template_type.py +0 -18
  851. endoreg_db/migrations/0053_patientlabsampletype_patientlabsample_and_more.py +0 -38
  852. endoreg_db/migrations/0054_multiplecategoricalvaluedistribution_and_more.py +0 -69
  853. endoreg_db/migrations/0055_remove_casetemplaterule_rule_values_and_more.py +0 -59
  854. endoreg_db/migrations/0056_datevaluedistribution_and_more.py +0 -32
  855. endoreg_db/migrations/0057_remove_datevaluedistribution_max_date_and_more.py +0 -72
  856. endoreg_db/migrations/0058_datevaluedistribution_description_and_more.py +0 -28
  857. endoreg_db/migrations/0059_casetemplaterule_rule_values.py +0 -18
  858. endoreg_db/migrations/0060_labvalue__default_date_value_distribution_and_more.py +0 -44
  859. endoreg_db/migrations/0061_remove_patientlabvalue_date_patientlabvalue_datetime.py +0 -24
  860. endoreg_db/migrations/0062_labvalue_numeric_precision.py +0 -18
  861. endoreg_db/migrations/0063_alter_labvalue_numeric_precision.py +0 -18
  862. endoreg_db/migrations/0064_casetemplaterule_extra_parameters_and_more.py +0 -23
  863. endoreg_db/migrations/0065_rename__date_value_distribution_casetemplaterule_date_value_distribution_and_more.py +0 -58
  864. endoreg_db/migrations/0066_alter_patientlabvalue_patient_and_more.py +0 -29
  865. endoreg_db/migrations/0067_alter_medicationindication_indication_type.py +0 -19
  866. endoreg_db/models/ai_model/__init__.py +0 -3
  867. endoreg_db/models/ai_model/active_model.py +0 -9
  868. endoreg_db/models/ai_model/model_meta.py +0 -24
  869. endoreg_db/models/annotation/__init__.py +0 -2
  870. endoreg_db/models/annotation/binary_classification_annotation_task.py +0 -80
  871. endoreg_db/models/annotation/image_classification.py +0 -27
  872. endoreg_db/models/center/center.py +0 -25
  873. endoreg_db/models/center/center_product.py +0 -34
  874. endoreg_db/models/center/center_resource.py +0 -19
  875. endoreg_db/models/center/center_waste.py +0 -11
  876. endoreg_db/models/data_file/__init__.py +0 -6
  877. endoreg_db/models/data_file/base_classes/__init__.py +0 -2
  878. endoreg_db/models/data_file/base_classes/abstract_frame.py +0 -51
  879. endoreg_db/models/data_file/base_classes/abstract_video.py +0 -201
  880. endoreg_db/models/data_file/frame.py +0 -45
  881. endoreg_db/models/data_file/import_classes/__init__.py +0 -32
  882. endoreg_db/models/data_file/import_classes/processing_functions/__init__.py +0 -35
  883. endoreg_db/models/data_file/import_classes/processing_functions/pdf.py +0 -28
  884. endoreg_db/models/data_file/import_classes/processing_functions/video.py +0 -260
  885. endoreg_db/models/data_file/import_classes/raw_pdf.py +0 -188
  886. endoreg_db/models/data_file/import_classes/raw_video.py +0 -343
  887. endoreg_db/models/data_file/metadata/__init__.py +0 -3
  888. endoreg_db/models/data_file/metadata/sensitive_meta.py +0 -31
  889. endoreg_db/models/data_file/metadata/video_meta.py +0 -133
  890. endoreg_db/models/data_file/report_file.py +0 -89
  891. endoreg_db/models/data_file/video/__init__.py +0 -7
  892. endoreg_db/models/data_file/video/import_meta.py +0 -25
  893. endoreg_db/models/data_file/video/video.py +0 -25
  894. endoreg_db/models/data_file/video_segment.py +0 -107
  895. endoreg_db/models/disease.py +0 -56
  896. endoreg_db/models/emission/__init__.py +0 -1
  897. endoreg_db/models/emission/emission_factor.py +0 -20
  898. endoreg_db/models/event.py +0 -22
  899. endoreg_db/models/examination/__init__.py +0 -4
  900. endoreg_db/models/examination/examination.py +0 -26
  901. endoreg_db/models/examination/examination_time.py +0 -27
  902. endoreg_db/models/examination/examination_time_type.py +0 -24
  903. endoreg_db/models/examination/examination_type.py +0 -18
  904. endoreg_db/models/hardware/__init__.py +0 -2
  905. endoreg_db/models/hardware/endoscope.py +0 -44
  906. endoreg_db/models/information_source.py +0 -29
  907. endoreg_db/models/laboratory/__init__.py +0 -1
  908. endoreg_db/models/laboratory/lab_value.py +0 -102
  909. endoreg_db/models/legacy_data/__init__.py +0 -3
  910. endoreg_db/models/legacy_data/image.py +0 -34
  911. endoreg_db/models/medication/__init__.py +0 -1
  912. endoreg_db/models/medication/medication.py +0 -148
  913. endoreg_db/models/other/distribution.py +0 -215
  914. endoreg_db/models/patient_examination/__init__.py +0 -35
  915. endoreg_db/models/permissions/__init__.py +0 -44
  916. endoreg_db/models/persons/__init__.py +0 -7
  917. endoreg_db/models/persons/examiner/__init__.py +0 -2
  918. endoreg_db/models/persons/examiner/examiner.py +0 -16
  919. endoreg_db/models/persons/examiner/examiner_type.py +0 -2
  920. endoreg_db/models/persons/patient/__init__.py +0 -8
  921. endoreg_db/models/persons/patient/case/case.py +0 -30
  922. endoreg_db/models/persons/patient/patient.py +0 -216
  923. endoreg_db/models/persons/patient/patient_disease.py +0 -16
  924. endoreg_db/models/persons/patient/patient_event.py +0 -22
  925. endoreg_db/models/persons/patient/patient_lab_sample.py +0 -106
  926. endoreg_db/models/persons/patient/patient_medication.py +0 -44
  927. endoreg_db/models/persons/patient/patient_medication_schedule.py +0 -28
  928. endoreg_db/models/persons/portal_user_information.py +0 -27
  929. endoreg_db/models/prediction/__init__.py +0 -2
  930. endoreg_db/models/prediction/image_classification.py +0 -37
  931. endoreg_db/models/prediction/video_prediction_meta.py +0 -244
  932. endoreg_db/models/product/__init__.py +0 -5
  933. endoreg_db/models/product/product.py +0 -97
  934. endoreg_db/models/product/product_group.py +0 -19
  935. endoreg_db/models/product/product_material.py +0 -24
  936. endoreg_db/models/questionnaires/__init__.py +0 -114
  937. endoreg_db/models/quiz/__init__.py +0 -2
  938. endoreg_db/models/quiz/quiz_answer.py +0 -41
  939. endoreg_db/models/quiz/quiz_question.py +0 -54
  940. endoreg_db/models/report_reader/__init__.py +0 -2
  941. endoreg_db/models/report_reader/report_reader_config.py +0 -53
  942. endoreg_db/models/rules/__init__.py +0 -5
  943. endoreg_db/queries/get/__init__.py +0 -6
  944. endoreg_db/queries/get/center.py +0 -42
  945. endoreg_db/queries/get/model.py +0 -13
  946. endoreg_db/queries/get/patient.py +0 -14
  947. endoreg_db/queries/get/patient_examination.py +0 -20
  948. endoreg_db/queries/get/report_file.py +0 -33
  949. endoreg_db/queries/get/video.py +0 -31
  950. endoreg_db/serializers/ai_model.py +0 -19
  951. endoreg_db/serializers/annotation.py +0 -17
  952. endoreg_db/serializers/center.py +0 -11
  953. endoreg_db/serializers/examination.py +0 -33
  954. endoreg_db/serializers/frame.py +0 -13
  955. endoreg_db/serializers/hardware.py +0 -21
  956. endoreg_db/serializers/label.py +0 -22
  957. endoreg_db/serializers/patient.py +0 -10
  958. endoreg_db/serializers/prediction.py +0 -15
  959. endoreg_db/serializers/report_file.py +0 -7
  960. endoreg_db/serializers/video.py +0 -27
  961. endoreg_db/tests.py +0 -3
  962. endoreg_db/utils/legacy_ocr.py +0 -201
  963. endoreg_db/utils/video_metadata.py +0 -87
  964. endoreg_db-0.3.6.dist-info/METADATA +0 -33
  965. endoreg_db-0.3.6.dist-info/RECORD +0 -357
  966. /endoreg_db/{models/persons/patient/case/__init__.py → api/serializers/finding_descriptions.py} +0 -0
  967. /endoreg_db/{queries/get/annotation.py → api/views/finding_descriptions.py} +0 -0
  968. /endoreg_db/{queries/get/prediction.py → config/__init__.py} +0 -0
  969. /endoreg_db/{queries/get/video_import_meta.py → data/case_template/rule_value/.init} +0 -0
  970. /endoreg_db/{queries/get/video_prediction_meta.py → data/distribution/multiple_categorical/.init} +0 -0
@@ -0,0 +1,825 @@
1
+ """Concrete model for video files, handling both raw and processed states."""
2
+
3
+ import logging
4
+ import os
5
+ import uuid
6
+ from pathlib import Path
7
+ from typing import TYPE_CHECKING, Optional, Union, cast
8
+
9
+ from django.core.files import File
10
+ from django.core.validators import FileExtensionValidator
11
+ from django.db import models
12
+ from django.db.models import F
13
+ from django.db.models.fields.files import FieldFile
14
+
15
+ from endoreg_db.utils.calc_duration_seconds import _calc_duration_vf
16
+
17
+ from ...label import Label, LabelVideoSegment
18
+ from ...state import VideoState
19
+ from ...utils import ANONYM_VIDEO_DIR, VIDEO_DIR
20
+
21
+ # --- Import model-specific function modules ---
22
+ from .create_from_file import _create_from_file
23
+ from .pipe_1 import _pipe_1, _test_after_pipe_1
24
+ from .pipe_2 import _pipe_2
25
+ from .video_file_ai import _extract_text_from_video_frames, _predict_video_pipeline
26
+ from .video_file_anonymize import (
27
+ _anonymize,
28
+ _cleanup_raw_assets,
29
+ _create_anonymized_frame_files,
30
+ )
31
+ from .video_file_frames import (
32
+ _bulk_create_frames,
33
+ _create_frame_object,
34
+ _delete_frames,
35
+ _extract_frames,
36
+ _get_frame,
37
+ _get_frame_number,
38
+ _get_frame_path,
39
+ _get_frame_paths,
40
+ _get_frame_range,
41
+ _get_frames,
42
+ _initialize_frames,
43
+ )
44
+
45
+ # Update import aliases for clarity and to use as helpers
46
+ from .video_file_frames._manage_frame_range import (
47
+ _delete_frame_range as _delete_frame_range_helper,
48
+ )
49
+ from .video_file_frames._manage_frame_range import (
50
+ _extract_frame_range as _extract_frame_range_helper,
51
+ )
52
+ from .video_file_io import (
53
+ _delete_with_file,
54
+ _get_base_frame_dir,
55
+ _get_frame_dir_path,
56
+ _get_processed_file_path,
57
+ _get_raw_file_path,
58
+ _get_target_anonymized_video_path,
59
+ _get_temp_anonymized_frame_dir,
60
+ _set_frame_dir,
61
+ )
62
+ from .video_file_meta import (
63
+ _get_crop_template,
64
+ _get_endo_roi,
65
+ _get_fps,
66
+ _initialize_video_specs,
67
+ _update_text_metadata,
68
+ _update_video_meta,
69
+ )
70
+
71
+ # Configure logging
72
+ logger = logging.getLogger(__name__) # Changed from "video_file"
73
+
74
+ if TYPE_CHECKING:
75
+ from endoreg_db.models import (
76
+ Center,
77
+ EndoscopyProcessor,
78
+ FFMpegMeta,
79
+ Frame,
80
+ ModelMeta,
81
+ Patient,
82
+ PatientExamination,
83
+ SensitiveMeta,
84
+ VideoImportMeta,
85
+ VideoMeta,
86
+ VideoState,
87
+ )
88
+
89
+
90
+ class VideoQuerySet(models.QuerySet):
91
+ def next_after(self, last_id=None):
92
+ """
93
+ Return the next VideoFile instance with a primary key greater than the given last_id.
94
+
95
+ Parameters:
96
+ last_id (int or None): The primary key to start after. If None or invalid, returns the first instance.
97
+
98
+ Returns:
99
+ VideoFile or None: The next VideoFile instance, or None if not found.
100
+ """
101
+ if last_id is not None:
102
+ try:
103
+ last_id = int(last_id)
104
+ except (ValueError, TypeError):
105
+ return None
106
+ q = self if last_id is None else self.filter(pk__gt=last_id)
107
+ return q.order_by("pk").first()
108
+
109
+
110
+ class VideoFile(models.Model):
111
+ uuid = models.UUIDField(default=uuid.uuid4, editable=False, unique=True)
112
+
113
+ objects = VideoQuerySet.as_manager()
114
+
115
+ raw_file = models.FileField(
116
+ upload_to=VIDEO_DIR.name, # Use .name for relative path
117
+ validators=[FileExtensionValidator(allowed_extensions=["mp4"])],
118
+ null=True,
119
+ blank=True,
120
+ )
121
+ processed_file = models.FileField(
122
+ upload_to=ANONYM_VIDEO_DIR.name, # Use .name for relative path
123
+ validators=[FileExtensionValidator(allowed_extensions=["mp4"])],
124
+ null=True,
125
+ blank=True,
126
+ )
127
+
128
+ video_hash = models.CharField(
129
+ max_length=255, unique=True, help_text="Hash of the raw video file."
130
+ )
131
+ processed_video_hash = models.CharField(
132
+ max_length=255,
133
+ unique=True,
134
+ null=True,
135
+ blank=True,
136
+ help_text="Hash of the processed video file, unique if not null.",
137
+ )
138
+
139
+ sensitive_meta = models.OneToOneField(
140
+ "SensitiveMeta",
141
+ on_delete=models.SET_NULL,
142
+ null=True,
143
+ blank=True,
144
+ related_name="video_file",
145
+ ) # type: ignore
146
+ center = models.ForeignKey("Center", on_delete=models.PROTECT) # type: ignore
147
+ processor = models.ForeignKey(
148
+ "EndoscopyProcessor", on_delete=models.PROTECT, blank=True, null=True
149
+ ) # type: ignore
150
+ video_meta = models.OneToOneField(
151
+ "VideoMeta",
152
+ on_delete=models.SET_NULL,
153
+ null=True,
154
+ blank=True,
155
+ related_name="video_file",
156
+ ) # type: ignore
157
+ examination = models.ForeignKey(
158
+ "PatientExamination",
159
+ on_delete=models.SET_NULL,
160
+ blank=True,
161
+ null=True,
162
+ related_name="video_files",
163
+ ) # type: ignore
164
+ patient = models.ForeignKey(
165
+ "Patient",
166
+ on_delete=models.SET_NULL,
167
+ blank=True,
168
+ null=True,
169
+ related_name="video_files",
170
+ ) # type: ignore
171
+ ai_model_meta = models.ForeignKey(
172
+ "ModelMeta", on_delete=models.SET_NULL, blank=True, null=True
173
+ ) # type: ignore
174
+ state = models.OneToOneField(
175
+ "VideoState",
176
+ on_delete=models.SET_NULL,
177
+ null=True,
178
+ blank=True,
179
+ related_name="video_file",
180
+ ) # type: ignore
181
+ import_meta = models.OneToOneField(
182
+ "VideoImportMeta", on_delete=models.CASCADE, blank=True, null=True
183
+ ) # type: ignore
184
+
185
+ original_file_name = models.CharField(max_length=255, blank=True, null=True)
186
+ uploaded_at = models.DateTimeField(auto_now_add=True)
187
+ frame_dir = models.CharField(
188
+ max_length=512,
189
+ blank=True,
190
+ help_text="Path to frames extracted from the raw video.",
191
+ )
192
+ fps = models.FloatField(blank=True, null=True)
193
+ duration = models.FloatField(blank=True, null=True)
194
+ frame_count = models.IntegerField(blank=True, null=True)
195
+ width = models.IntegerField(blank=True, null=True)
196
+ height = models.IntegerField(blank=True, null=True)
197
+ suffix = models.CharField(max_length=10, blank=True, null=True)
198
+ sequences = models.JSONField(
199
+ default=dict,
200
+ blank=True,
201
+ help_text="AI prediction sequences based on raw frames.",
202
+ )
203
+ date = models.DateField(blank=True, null=True)
204
+ meta = models.JSONField(blank=True, null=True)
205
+ date_created = models.DateTimeField(auto_now_add=True)
206
+ date_modified = models.DateTimeField(auto_now=True)
207
+
208
+ if TYPE_CHECKING:
209
+ label_video_segments: "models.QuerySet[LabelVideoSegment]"
210
+ frames: "models.QuerySet[Frame]"
211
+ center: "Center"
212
+ processor: "EndoscopyProcessor"
213
+ video_meta: "VideoMeta"
214
+ examination: "PatientExamination"
215
+ patient: "Patient"
216
+ sensitive_meta: "SensitiveMeta"
217
+ state: "VideoState"
218
+ ai_model_meta: "ModelMeta"
219
+ import_meta: "VideoImportMeta"
220
+
221
+ @property
222
+ def ffmpeg_meta(self) -> "FFMpegMeta":
223
+ """
224
+ Return the associated FFMpegMeta instance for this video, initializing video specs if necessary.
225
+
226
+ Returns:
227
+ FFMpegMeta: The FFMpegMeta object containing metadata for this video.
228
+ """
229
+ from endoreg_db.models import FFMpegMeta
230
+
231
+ if self.video_meta is not None:
232
+ if self.video_meta.ffmpeg_meta is not None:
233
+ return self.video_meta.ffmpeg_meta
234
+ raise AssertionError("Expected FFMpegMeta instance.")
235
+ else:
236
+ self.initialize_video_specs()
237
+ ffmpeg_meta = self.video_meta.ffmpeg_meta if self.video_meta else None
238
+ assert isinstance(ffmpeg_meta, FFMpegMeta), "Expected FFMpegMeta instance."
239
+ return ffmpeg_meta
240
+
241
+ # Exception message constants
242
+
243
+ NO_ACTIVE_FILE = "Has no raw file"
244
+ NO_FILE_ASSOCIATED = "Active file has no associated file."
245
+
246
+ @property
247
+ def active_raw_file(self) -> File:
248
+ """Return the raw file if available, otherwise raise ValueError."""
249
+ if self.has_raw:
250
+ return self.raw_file
251
+ raise ValueError(self.NO_ACTIVE_FILE)
252
+
253
+ @property
254
+ def active_raw_file_url(self) -> str:
255
+ """Return the URL of the active raw file, or raise ValueError if unavailable."""
256
+ _file = self.active_raw_file
257
+ assert _file is not None, self.NO_ACTIVE_FILE
258
+ if not _file or not _file.name:
259
+ raise ValueError(self.NO_FILE_ASSOCIATED)
260
+ return _file.url
261
+
262
+ # Pipeline Functions
263
+ pipe_1 = _pipe_1
264
+ test_after_pipe_1 = _test_after_pipe_1
265
+ pipe_2 = _pipe_2
266
+
267
+ # Metadata Funtions
268
+ update_video_meta = _update_video_meta
269
+ initialize_video_specs = _initialize_video_specs
270
+ get_fps = _get_fps
271
+ get_endo_roi = _get_endo_roi
272
+ get_crop_template = _get_crop_template
273
+ update_text_metadata = _update_text_metadata
274
+
275
+ extract_frames = _extract_frames
276
+ initialize_frames = _initialize_frames
277
+ delete_frames = _delete_frames
278
+ get_frame_path = _get_frame_path
279
+ get_frame_paths = _get_frame_paths
280
+ get_frame_number = _get_frame_number
281
+ get_frames = _get_frames
282
+ get_frame = _get_frame
283
+ get_frame_range = _get_frame_range
284
+ get_duration = _calc_duration_vf
285
+ create_frame_object = _create_frame_object
286
+ bulk_create_frames = _bulk_create_frames
287
+
288
+ # Define new methods that call the helper functions
289
+ def extract_specific_frame_range(
290
+ self, start_frame: int, end_frame: int, overwrite: bool = False, **kwargs
291
+ ) -> bool:
292
+ """
293
+ Extract frames from the video within the specified frame range.
294
+
295
+ Parameters:
296
+ start_frame (int): The starting frame number (inclusive).
297
+ end_frame (int): The ending frame number (exclusive).
298
+ overwrite (bool): Whether to overwrite existing frames in the range.
299
+
300
+ Returns:
301
+ bool: True if frame extraction was successful, False otherwise.
302
+
303
+ Additional keyword arguments:
304
+ quality (int, optional): Quality setting for extracted frames.
305
+ ext (str, optional): File extension for extracted frames.
306
+ verbose (bool, optional): Whether to enable verbose output.
307
+ """
308
+ quality = kwargs.get("quality", 2)
309
+ ext = kwargs.get("ext", "jpg")
310
+ verbose = kwargs.get("verbose", False)
311
+
312
+ # Log if unexpected kwargs are passed, beyond those used by the helper
313
+ expected_helper_kwargs = {"quality", "ext", "verbose"}
314
+ unexpected_kwargs = {
315
+ k: v for k, v in kwargs.items() if k not in expected_helper_kwargs
316
+ }
317
+ if unexpected_kwargs:
318
+ logger.warning(
319
+ f"Unexpected keyword arguments for extract_specific_frame_range, will be ignored by helper: {unexpected_kwargs}"
320
+ )
321
+
322
+ return _extract_frame_range_helper(
323
+ video=self,
324
+ start_frame=start_frame,
325
+ end_frame=end_frame,
326
+ quality=quality,
327
+ overwrite=overwrite,
328
+ ext=ext,
329
+ verbose=verbose,
330
+ )
331
+
332
+ def delete_specific_frame_range(self, start_frame: int, end_frame: int) -> None:
333
+ """
334
+ Deletes frame files for a specific range [start_frame, end_frame).
335
+ """
336
+ _delete_frame_range_helper(
337
+ video=self, start_frame=start_frame, end_frame=end_frame
338
+ )
339
+
340
+ delete_with_file = _delete_with_file
341
+ get_base_frame_dir = _get_base_frame_dir
342
+ set_frame_dir = _set_frame_dir
343
+ get_frame_dir_path = _get_frame_dir_path
344
+ get_temp_anonymized_frame_dir = _get_temp_anonymized_frame_dir
345
+ get_target_anonymized_video_path = _get_target_anonymized_video_path
346
+ get_raw_file_path = _get_raw_file_path
347
+ get_processed_file_path = _get_processed_file_path
348
+
349
+ anonymize = _anonymize
350
+ _create_anonymized_frame_files = _create_anonymized_frame_files
351
+ _cleanup_raw_assets = _cleanup_raw_assets
352
+
353
+ predict_video = _predict_video_pipeline
354
+ extract_text_from_frames = _extract_text_from_video_frames
355
+
356
+ @classmethod
357
+ def check_hash_exists(cls, video_hash: str) -> bool:
358
+ """
359
+ Checks if a VideoFile with the given raw video hash already exists.
360
+ """
361
+ return cls.objects.filter(video_hash=video_hash).exists()
362
+
363
+ @property
364
+ def is_processed(self) -> bool:
365
+ return bool(self.processed_file and self.processed_file.name)
366
+
367
+ @property
368
+ def has_raw(self) -> bool:
369
+ """
370
+ Return True if a raw video file is associated with this instance.
371
+ """
372
+ return bool(self.raw_file and self.raw_file.name)
373
+
374
+ @property
375
+ def active_file(self) -> FieldFile:
376
+ """
377
+ Return the active video file, preferring the processed file if available.
378
+
379
+ Returns:
380
+ File: The processed file if present; otherwise, the raw file.
381
+
382
+ Raises:
383
+ ValueError: If neither a processed nor a raw file is available.
384
+ """
385
+ processed = self.processed_file
386
+ if isinstance(processed, FieldFile) and processed.name:
387
+ return processed
388
+
389
+ raw = self.raw_file
390
+ if isinstance(raw, FieldFile) and raw.name:
391
+ return raw
392
+
393
+ raise ValueError(
394
+ "No active file available. VideoFile has neither raw nor processed file."
395
+ )
396
+
397
+ @property
398
+ def active_file_path(self) -> Path:
399
+ """
400
+ Return the filesystem path of the active video file.
401
+
402
+ Returns:
403
+ Path: The path to the processed file if available, otherwise the raw file.
404
+
405
+ Raises:
406
+ ValueError: If neither a processed nor raw file is present.
407
+ """
408
+ active = self.active_file
409
+ if active is self.processed_file:
410
+ path = _get_processed_file_path(self)
411
+ elif active is self.raw_file:
412
+ path = _get_raw_file_path(self)
413
+ else:
414
+ raise ValueError(
415
+ "No active file path available. VideoFile has neither raw nor processed file."
416
+ )
417
+
418
+ if path is None:
419
+ raise ValueError("Active file path could not be resolved.")
420
+ return path
421
+
422
+ @classmethod
423
+ def create_from_file(
424
+ cls, file_path: Union[str, Path], center_name: str, **kwargs
425
+ ) -> Optional["VideoFile"]:
426
+ # Ensure file_path is a Path object
427
+ if isinstance(file_path, str):
428
+ file_path = Path(file_path)
429
+ # Pass center_name and other kwargs to the helper function
430
+ if not center_name:
431
+ try:
432
+ center_name = os.environ["CENTER_NAME"]
433
+ except KeyError:
434
+ logger.error(
435
+ "Center name must be provided to create VideoFile from file. You can set CENTER_NAME in environment variables."
436
+ )
437
+ return None
438
+ return _create_from_file(cls, file_path, center_name=center_name, **kwargs)
439
+
440
+ @classmethod
441
+ def create_from_file_initialized(
442
+ cls,
443
+ file_path: Union[str, Path],
444
+ center_name: str,
445
+ processor_name: Optional[str] = None,
446
+ delete_source: bool = False,
447
+ save_video_file: bool = True, # Add this line
448
+ ):
449
+ """
450
+ Creates a VideoFile instance from a given video file path.
451
+ Handles transcoding (if necessary), hashing, file storage, and database record creation.
452
+ Raises exceptions on failure.
453
+ """
454
+ # Ensure file_path is a Path object
455
+ if isinstance(file_path, str):
456
+ file_path = Path(file_path)
457
+
458
+ # Call the helper function to create the VideoFile instance
459
+ video_file = _create_from_file(
460
+ cls_model=VideoFile,
461
+ file_path=file_path,
462
+ center_name=center_name,
463
+ processor_name=processor_name,
464
+ delete_source=delete_source,
465
+ save=save_video_file, # Add this line
466
+ )
467
+
468
+ video_file = video_file.initialize()
469
+ return video_file
470
+
471
+ def delete(self, using=None, keep_parents=False) -> tuple[int, dict[str, int]]:
472
+ """
473
+ Delete the VideoFile instance, including associated files and frames.
474
+
475
+ Overrides the default delete method to ensure proper cleanup of related resources.
476
+ """
477
+ # Ensure frames are deleted before the main instance
478
+ _delete_frames(self)
479
+
480
+ # Call the original delete method to remove the instance from the database
481
+ active_path = self.active_file_path
482
+ logger.info(f"Deleting VideoFile: {self.uuid} - {active_path}")
483
+
484
+ # Delete associated files if they exist
485
+ if active_path.exists():
486
+ active_path.unlink(missing_ok=True)
487
+
488
+ # Delete file storage
489
+ if self.raw_file and self.raw_file.storage.exists(self.raw_file.name):
490
+ self.raw_file.storage.delete(self.raw_file.name)
491
+ if self.processed_file and self.processed_file.storage.exists(
492
+ self.processed_file.name
493
+ ):
494
+ self.processed_file.storage.delete(self.processed_file.name)
495
+
496
+ # Use proper database connection
497
+ if using is None:
498
+ using = "default"
499
+
500
+ raw_file_path = self.get_raw_file_path()
501
+ if raw_file_path:
502
+ raw_file_path = Path(raw_file_path)
503
+ lock_path = raw_file_path.with_suffix(raw_file_path.suffix + ".lock")
504
+ if lock_path.exists():
505
+ try:
506
+ lock_path.unlink()
507
+ logger.info(f"Removed processing lock: {lock_path}")
508
+ except Exception as e:
509
+ logger.warning(f"Could not remove processing lock {lock_path}: {e}")
510
+
511
+ try:
512
+ # Call parent delete with proper parameters
513
+ result = super().delete(using=using, keep_parents=keep_parents)
514
+ logger.info(f"VideoFile {self.uuid} deleted successfully.")
515
+ return result
516
+ except Exception as e:
517
+ logger.error(f"Error deleting VideoFile {self.uuid}: {e}")
518
+ raise
519
+
520
+ def validate_metadata_annotation(
521
+ self, extracted_data_dict: Optional[dict] = None
522
+ ) -> bool:
523
+ """
524
+ Validate the metadata of the VideoFile instance.
525
+
526
+ Called after annotation in the frontend, this method:
527
+ 1. Updates sensitive metadata with user-annotated data
528
+ 2. Deletes the RAW video file (keeping only the anonymized version)
529
+ 3. Marks the video as validated
530
+
531
+ **IMPORTANT:** Only the raw video is deleted. The processed (anonymized)
532
+ video is preserved as the final validated output.
533
+ """
534
+ from datetime import date as dt_date
535
+
536
+ from endoreg_db.models import SensitiveMeta
537
+
538
+ if not self.sensitive_meta:
539
+ # CRITICAL FIX: Use create_from_dict with default patient data
540
+ default_data = {
541
+ "patient_first_name": "Patient",
542
+ "patient_last_name": "Unknown",
543
+ "patient_dob": dt_date(1990, 1, 1),
544
+ "examination_date": dt_date.today(),
545
+ "center": self.center,
546
+ }
547
+ self.sensitive_meta = SensitiveMeta.create_from_dict(default_data)
548
+
549
+ # CRITICAL FIX: Delete RAW video file, not the processed (anonymized) one
550
+ # CRITICAL: Update metadata BEFORE deleting raw video
551
+ # Metadata update may trigger frame extraction, which needs raw video
552
+ sensitive_meta = _update_text_metadata(
553
+ self, extracted_data_dict, overwrite=True
554
+ )
555
+
556
+ # After validation and metadata update, only the anonymized video should remain
557
+ from .video_file_io import _get_raw_file_path
558
+
559
+ raw_path = _get_raw_file_path(self)
560
+ if raw_path and raw_path.exists():
561
+ logger.info(f"Deleting raw video file after validation: {raw_path}")
562
+ raw_path.unlink(missing_ok=True)
563
+ # Clear the raw_file field in database (use delete() to avoid save issues)
564
+ if self.raw_file:
565
+ self.raw_file.delete(save=False)
566
+ logger.info(
567
+ f"Raw video deleted for {self.uuid}. Anonymized video preserved."
568
+ )
569
+ else:
570
+ logger.warning(f"Raw video file not found for deletion: {self.uuid}")
571
+
572
+ if sensitive_meta:
573
+ # Mark as processed after validation
574
+ self.get_or_create_state().mark_sensitive_meta_processed(save=True)
575
+ # Save the VideoFile instance to persist changes
576
+ self.save()
577
+ logger.info(
578
+ f"Metadata annotation validated and saved for video {self.uuid}."
579
+ )
580
+ return True
581
+ else:
582
+ logger.error(
583
+ f"Failed to validate metadata annotation for video {self.uuid}."
584
+ )
585
+ return False
586
+
587
+ def initialize(self):
588
+ """
589
+ Initialize the VideoFile instance by updating metadata, setting up video specs, assigning frame directory, ensuring related state and sensitive metadata exist, saving the instance, and initializing frames.
590
+
591
+ Returns:
592
+ VideoFile: The initialized VideoFile instance.
593
+ """
594
+
595
+ self.update_video_meta()
596
+ # Initialize video specs
597
+ self.initialize_video_specs(use_raw=True)
598
+
599
+ # Set the frame directory
600
+ self.set_frame_dir()
601
+
602
+ # Create a new state if it doesn't exist
603
+ self.state = self.get_or_create_state()
604
+
605
+ self.sensitive_meta = self.get_or_create_sensitive_meta()
606
+ self.save()
607
+ # Initialize frames based on the video specs
608
+ self.initialize_frames()
609
+
610
+ return self
611
+
612
+ def __str__(self):
613
+ """
614
+ Return a human-readable string summarizing the video's state, active file name, and UUID.
615
+ """
616
+ active_path = self.active_file_path
617
+ file_name = active_path.name if active_path else "No file"
618
+ state = (
619
+ "Processed" if self.is_processed else ("Raw" if self.has_raw else "No File")
620
+ )
621
+ return f"VideoFile ({state}): {file_name} (UUID: {self.uuid})"
622
+
623
+ # --- Convenience state/meta helpers used in tests and admin workflows ---
624
+ def mark_sensitive_meta_processed(self, *, save: bool = True) -> "VideoFile":
625
+ """
626
+ Mark this video's processing state as having its sensitive meta fully processed.
627
+ This proxies to the related VideoState and persists by default.
628
+ """
629
+ state = self.get_or_create_state()
630
+ state.mark_sensitive_meta_processed(save=save)
631
+ return self
632
+
633
+ def mark_sensitive_meta_verified(self) -> "VideoFile":
634
+ """
635
+ Mark the associated SensitiveMeta as verified by setting both DOB and names as verified.
636
+ Ensures the SensitiveMeta and its state exist.
637
+ """
638
+ sm = self.get_or_create_sensitive_meta()
639
+ # Use SensitiveMeta methods to update underlying SensitiveMetaState
640
+ sm.mark_dob_verified()
641
+ sm.mark_names_verified()
642
+ return self
643
+
644
+ def save(self, *args, **kwargs):
645
+ # Ensure state exists or is created before the main save operation
646
+ # Now call the original save method
647
+ """
648
+ Saves the VideoFile instance to the database.
649
+
650
+ Overrides the default save method to persist changes to the VideoFile model.
651
+ """
652
+ super().save(*args, **kwargs)
653
+
654
+ def get_or_create_state(self) -> "VideoState":
655
+ """Ensure this video has a persisted ``VideoState`` and return it."""
656
+
657
+ state = self.state
658
+
659
+ # When tests reuse cached instances across database flushes, ``state`` may reference
660
+ # a row that no longer exists. Guard against that by validating persistence.
661
+ state_pk = getattr(state, "pk", None)
662
+ if state is not None and state_pk is not None:
663
+ if not VideoState.objects.filter(pk=state_pk).exists():
664
+ state = None
665
+
666
+ if state is None:
667
+ # Create a fresh state to avoid refresh_from_db() failures on unsaved instances.
668
+ state = VideoState.objects.create()
669
+ self.state = state
670
+
671
+ # Persist the relation immediately if the VideoFile already exists in the DB so
672
+ # later refreshes see the association without requiring additional saves.
673
+ if self.pk:
674
+ self.save(update_fields=["state"])
675
+
676
+ return state
677
+
678
+ def get_or_create_sensitive_meta(self) -> "SensitiveMeta":
679
+ """
680
+ Retrieve the associated SensitiveMeta instance for this video, creating and assigning one if it does not exist.
681
+
682
+ **Two-Phase Patient Data Pattern:**
683
+ This method implements a two-phase approach to handle incomplete patient data:
684
+
685
+ **Phase 1: Initial Creation (with defaults)**
686
+ - Creates SensitiveMeta with default patient data to prevent hash calculation errors
687
+ - Default values: patient_first_name="Patient", patient_last_name="Unknown", patient_dob=1990-01-01
688
+ - Allows video import to proceed even without extracted patient data
689
+ - Temporary hash and pseudo-entities are created
690
+
691
+ **Phase 2: Update (with extracted data)**
692
+ - Real patient data is extracted later (e.g., from video OCR via lx_anonymizer)
693
+ - update_from_dict() is called with actual patient information
694
+ - Hash is recalculated automatically using real data
695
+ - Correct pseudo-entities are created/linked based on new hash
696
+
697
+ **Example workflow:**
698
+ ```python
699
+ # Phase 1: Video creation
700
+ video = VideoFile.create_from_file_initialized(...)
701
+ video.initialize() # Calls this method
702
+ # → SensitiveMeta created with defaults
703
+ # → Hash: sha256("Patient Unknown 1990-01-01...")
704
+
705
+ # Phase 2: Frame cleaning extracts real data
706
+ extracted = {"patient_first_name": "Max", "patient_last_name": "Mustermann", ...}
707
+ video.sensitive_meta.update_from_dict(extracted)
708
+ # → Hash: sha256("Max Mustermann 1985-03-15...") (RECALCULATED)
709
+ ```
710
+
711
+ Returns:
712
+ SensitiveMeta: The related SensitiveMeta instance.
713
+
714
+ See Also:
715
+ - sensitive_meta_logic.perform_save_logic() for hash calculation details
716
+ - sensitive_meta_logic.update_sensitive_meta_from_dict() for update mechanism
717
+ """
718
+ from datetime import date as dt_date
719
+
720
+ from endoreg_db.models import SensitiveMeta
721
+
722
+ if self.sensitive_meta is None:
723
+ # Use create_from_dict with default patient data
724
+ # to prevent "First name is required to calculate patient hash" error
725
+ default_data = {
726
+ "patient_first_name": "Patient",
727
+ "patient_last_name": "Unknown",
728
+ "patient_dob": dt_date(1990, 1, 1),
729
+ "examination_date": dt_date.today(),
730
+ "center": self.center,
731
+ }
732
+ self.sensitive_meta = SensitiveMeta.create_from_dict(default_data)
733
+ self.save(update_fields=["sensitive_meta"])
734
+ # Do not mark state as processed here; it will be set after extraction/validation steps
735
+ return self.sensitive_meta
736
+
737
+ def get_outside_segments(
738
+ self, only_validated: bool = False
739
+ ) -> models.QuerySet["LabelVideoSegment"]:
740
+ """
741
+ Return all video segments labeled as "outside" for this video.
742
+
743
+ Parameters:
744
+ only_validated (bool): If True, only segments with a validated state are included.
745
+
746
+ Returns:
747
+ QuerySet: A queryset of LabelVideoSegment instances labeled as "outside". Returns an empty queryset if the label does not exist or an error occurs.
748
+ """
749
+ try:
750
+ outside_label = Label.objects.get(name__iexact="outside")
751
+ segments = self.label_video_segments.filter(label=outside_label)
752
+
753
+ if only_validated:
754
+ # Filter based on the is_validated field in the related state object
755
+ segments = segments.filter(state__is_validated=True)
756
+
757
+ return segments
758
+ except Label.DoesNotExist:
759
+ logger.warning("Outside label not found in the database.")
760
+ return self.label_video_segments.none()
761
+ except Exception as e:
762
+ logger.error(
763
+ "Error getting outside segments for video %s: %s",
764
+ self.uuid,
765
+ e,
766
+ exc_info=True,
767
+ )
768
+ return self.label_video_segments.none()
769
+
770
+ @classmethod
771
+ def get_all_videos(cls) -> models.QuerySet["VideoFile"]:
772
+ """
773
+ Returns a queryset containing all VideoFile records.
774
+
775
+ This class method retrieves every VideoFile instance in the database without filtering.
776
+ """
777
+ return cast(models.QuerySet["VideoFile"], cls.objects.all())
778
+
779
+ def count_unmodified_others(self) -> int:
780
+ """
781
+ Count the number of other VideoFile instances that have not been modified since creation.
782
+
783
+ Returns:
784
+ int: The count of VideoFile records, excluding this instance, where the modification timestamp matches the creation timestamp.
785
+ """
786
+ return (
787
+ VideoFile.objects.filter(
788
+ date_modified=F("date_created")
789
+ ) # compare the two fields in SQL
790
+ .exclude(pk=self.pk) # exclude this instance
791
+ .count() # run a fast COUNT(*) on the filtered set
792
+ )
793
+
794
+ def frame_number_to_s(self, frame_number: int) -> float:
795
+ """
796
+ Convert a frame number to its corresponding time in seconds based on the video's frames per second (FPS).
797
+
798
+ Parameters:
799
+ frame_number (int): The frame number to convert.
800
+
801
+ Returns:
802
+ float: The time in seconds corresponding to the given frame number.
803
+
804
+ Raises:
805
+ ValueError: If the video's FPS is not set or is less than or equal to zero.
806
+ """
807
+ fps = self.get_fps()
808
+ if fps is None or fps <= 0:
809
+ raise ValueError("FPS must be set and greater than zero.")
810
+ return frame_number / fps
811
+
812
+ def get_video_by_id(self, video_id: int) -> "VideoFile":
813
+ """
814
+ Retrieve a VideoFile instance by its primary key (ID).
815
+
816
+ Parameters:
817
+ video_id (int): The primary key of the VideoFile to retrieve.
818
+
819
+ Returns:
820
+ VideoFile: The VideoFile instance with the specified ID.
821
+
822
+ Raises:
823
+ VideoFile.DoesNotExist: If no VideoFile with the given ID exists.
824
+ """
825
+ return self.objects.get(pk=video_id)