endoreg-db 0.8.9.32__py3-none-any.whl

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  1. endoreg_db/__init__.py +0 -0
  2. endoreg_db/_version.py +34 -0
  3. endoreg_db/admin.py +97 -0
  4. endoreg_db/api/serializers/finding_descriptions.py +0 -0
  5. endoreg_db/api/views/finding_descriptions.py +0 -0
  6. endoreg_db/api_urls.py +4 -0
  7. endoreg_db/apps.py +17 -0
  8. endoreg_db/assets/dummy_model.ckpt +1 -0
  9. endoreg_db/authz/auth.py +78 -0
  10. endoreg_db/authz/backends.py +168 -0
  11. endoreg_db/authz/management/commands/list_routes.py +20 -0
  12. endoreg_db/authz/middleware.py +84 -0
  13. endoreg_db/authz/permissions.py +138 -0
  14. endoreg_db/authz/policy.py +224 -0
  15. endoreg_db/authz/settings.py +64 -0
  16. endoreg_db/authz/views_auth.py +70 -0
  17. endoreg_db/codemods/readme.md +88 -0
  18. endoreg_db/codemods/rename_datetime_fields.py +99 -0
  19. endoreg_db/config/__init__.py +0 -0
  20. endoreg_db/config/env.py +106 -0
  21. endoreg_db/config/settings/__init__.py +6 -0
  22. endoreg_db/config/settings/base.py +148 -0
  23. endoreg_db/config/settings/case_gen.py +32 -0
  24. endoreg_db/config/settings/dev.py +108 -0
  25. endoreg_db/config/settings/keycloak.py +177 -0
  26. endoreg_db/config/settings/prod.py +66 -0
  27. endoreg_db/config/settings/test.py +72 -0
  28. endoreg_db/data/__init__.py +135 -0
  29. endoreg_db/data/ai_model/data.yaml +7 -0
  30. endoreg_db/data/ai_model_label/label/data.yaml +88 -0
  31. endoreg_db/data/ai_model_label/label/polyp_classification.yaml +52 -0
  32. endoreg_db/data/ai_model_label/label-set/data.yaml +40 -0
  33. endoreg_db/data/ai_model_label/label-set/polyp_classifications.yaml +25 -0
  34. endoreg_db/data/ai_model_label/label-type/data.yaml +7 -0
  35. endoreg_db/data/ai_model_meta/default_multilabel_classification.yaml +27 -0
  36. endoreg_db/data/ai_model_type/data.yaml +7 -0
  37. endoreg_db/data/ai_model_video_segmentation_label/base_segmentation.yaml +176 -0
  38. endoreg_db/data/ai_model_video_segmentation_labelset/data.yaml +20 -0
  39. endoreg_db/data/case_template/rule/00_patient_lab_sample_add_default_value.yaml +167 -0
  40. endoreg_db/data/case_template/rule/01_patient-set-age.yaml +8 -0
  41. endoreg_db/data/case_template/rule/01_patient-set-gender.yaml +9 -0
  42. endoreg_db/data/case_template/rule/11_create_patient_lab_sample.yaml +23 -0
  43. endoreg_db/data/case_template/rule/12_create-patient_medication-anticoagulation.yaml +19 -0
  44. endoreg_db/data/case_template/rule/13_create-patient_medication_schedule-anticoagulation.yaml +19 -0
  45. endoreg_db/data/case_template/rule/19_create_patient.yaml +17 -0
  46. endoreg_db/data/case_template/rule_type/base_types.yaml +35 -0
  47. endoreg_db/data/case_template/rule_value/.init +0 -0
  48. endoreg_db/data/case_template/rule_value_type/base_types.yaml +59 -0
  49. endoreg_db/data/case_template/template/base.yaml +8 -0
  50. endoreg_db/data/case_template/template_type/pre_endoscopy.yaml +3 -0
  51. endoreg_db/data/case_template/tmp/_rule_value +13 -0
  52. endoreg_db/data/case_template/tmp/rule/01_atrial_fibrillation.yaml +21 -0
  53. endoreg_db/data/case_template/tmp/rule/02_create_object.yaml +10 -0
  54. endoreg_db/data/case_template/tmp/template/atrial_fibrillation_low_risk.yaml +7 -0
  55. endoreg_db/data/center/data.yaml +99 -0
  56. endoreg_db/data/center_resource/green_endoscopy_dashboard_CenterResource.yaml +144 -0
  57. endoreg_db/data/center_shift/ukw.yaml +9 -0
  58. endoreg_db/data/center_waste/green_endoscopy_dashboard_CenterWaste.yaml +48 -0
  59. endoreg_db/data/contraindication/bleeding.yaml +11 -0
  60. endoreg_db/data/db_summary.csv +58 -0
  61. endoreg_db/data/db_summary.xlsx +0 -0
  62. endoreg_db/data/disease/cardiovascular.yaml +37 -0
  63. endoreg_db/data/disease/hepatology.yaml +5 -0
  64. endoreg_db/data/disease/misc.yaml +5 -0
  65. endoreg_db/data/disease/renal.yaml +5 -0
  66. endoreg_db/data/disease_classification/chronic_kidney_disease.yaml +6 -0
  67. endoreg_db/data/disease_classification/coronary_vessel_disease.yaml +6 -0
  68. endoreg_db/data/disease_classification_choice/chronic_kidney_disease.yaml +41 -0
  69. endoreg_db/data/disease_classification_choice/coronary_vessel_disease.yaml +20 -0
  70. endoreg_db/data/distribution/date/patient.yaml +7 -0
  71. endoreg_db/data/distribution/multiple_categorical/.init +0 -0
  72. endoreg_db/data/distribution/numeric/data.yaml +14 -0
  73. endoreg_db/data/distribution/single_categorical/patient.yaml +7 -0
  74. endoreg_db/data/emission_factor/green_endoscopy_dashboard_EmissionFactor.yaml +132 -0
  75. endoreg_db/data/endoscope/data.yaml +93 -0
  76. endoreg_db/data/endoscope_type/data.yaml +11 -0
  77. endoreg_db/data/endoscopy_processor/data.yaml +50 -0
  78. endoreg_db/data/event/cardiology.yaml +15 -0
  79. endoreg_db/data/event/neurology.yaml +14 -0
  80. endoreg_db/data/event/surgery.yaml +13 -0
  81. endoreg_db/data/event/thrombembolism.yaml +20 -0
  82. endoreg_db/data/event_classification/data.yaml +4 -0
  83. endoreg_db/data/event_classification_choice/data.yaml +9 -0
  84. endoreg_db/data/examination/examinations/data.yaml +172 -0
  85. endoreg_db/data/examination/time/data.yaml +48 -0
  86. endoreg_db/data/examination/time-type/data.yaml +5 -0
  87. endoreg_db/data/examination/type/data.yaml +17 -0
  88. endoreg_db/data/examination_indication/endoscopy.yaml +359 -0
  89. endoreg_db/data/examination_indication_classification/endoscopy.yaml +90 -0
  90. endoreg_db/data/examination_indication_classification_choice/endoscopy.yaml +97 -0
  91. endoreg_db/data/examination_requirement_set/colonoscopy.yaml +15 -0
  92. endoreg_db/data/finding/00_generic.yaml +35 -0
  93. endoreg_db/data/finding/00_generic_complication.yaml +9 -0
  94. endoreg_db/data/finding/01_gastroscopy_baseline.yaml +88 -0
  95. endoreg_db/data/finding/01_gastroscopy_observation.yaml +113 -0
  96. endoreg_db/data/finding/02_colonoscopy_baseline.yaml +53 -0
  97. endoreg_db/data/finding/02_colonoscopy_hidden.yaml +119 -0
  98. endoreg_db/data/finding/02_colonoscopy_observation.yaml +152 -0
  99. endoreg_db/data/finding_classification/00_generic.yaml +44 -0
  100. endoreg_db/data/finding_classification/00_generic_histology.yaml +28 -0
  101. endoreg_db/data/finding_classification/00_generic_lesion.yaml +52 -0
  102. endoreg_db/data/finding_classification/02_colonoscopy_baseline.yaml +83 -0
  103. endoreg_db/data/finding_classification/02_colonoscopy_histology.yaml +13 -0
  104. endoreg_db/data/finding_classification/02_colonoscopy_other.yaml +12 -0
  105. endoreg_db/data/finding_classification/02_colonoscopy_polyp.yaml +101 -0
  106. endoreg_db/data/finding_classification_choice/00_generic.yaml +15 -0
  107. endoreg_db/data/finding_classification_choice/00_generic_baseline.yaml +23 -0
  108. endoreg_db/data/finding_classification_choice/00_generic_complication.yaml +15 -0
  109. endoreg_db/data/finding_classification_choice/00_generic_histology.yaml +21 -0
  110. endoreg_db/data/finding_classification_choice/00_generic_lesion.yaml +158 -0
  111. endoreg_db/data/finding_classification_choice/02_colonoscopy_bowel_preparation.yaml +49 -0
  112. endoreg_db/data/finding_classification_choice/02_colonoscopy_generic.yaml +19 -0
  113. endoreg_db/data/finding_classification_choice/02_colonoscopy_histology.yaml +20 -0
  114. endoreg_db/data/finding_classification_choice/02_colonoscopy_location.yaml +248 -0
  115. endoreg_db/data/finding_classification_choice/02_colonoscopy_other.yaml +34 -0
  116. endoreg_db/data/finding_classification_choice/02_colonoscopy_polyp_advanced_imaging.yaml +76 -0
  117. endoreg_db/data/finding_classification_choice/02_colonoscopy_polyp_morphology.yaml +75 -0
  118. endoreg_db/data/finding_classification_choice/02_colonoscopy_size.yaml +27 -0
  119. endoreg_db/data/finding_classification_type/00_generic.yaml +53 -0
  120. endoreg_db/data/finding_classification_type/02_colonoscopy.yaml +9 -0
  121. endoreg_db/data/finding_intervention/00_generic_endoscopy.yaml +59 -0
  122. endoreg_db/data/finding_intervention/00_generic_endoscopy_ablation.yaml +44 -0
  123. endoreg_db/data/finding_intervention/00_generic_endoscopy_bleeding.yaml +55 -0
  124. endoreg_db/data/finding_intervention/00_generic_endoscopy_resection.yaml +85 -0
  125. endoreg_db/data/finding_intervention/00_generic_endoscopy_stenosis.yaml +17 -0
  126. endoreg_db/data/finding_intervention/00_generic_endoscopy_stent.yaml +9 -0
  127. endoreg_db/data/finding_intervention/01_gastroscopy.yaml +19 -0
  128. endoreg_db/data/finding_intervention/04_eus.yaml +39 -0
  129. endoreg_db/data/finding_intervention/05_ercp.yaml +3 -0
  130. endoreg_db/data/finding_intervention_type/endoscopy.yaml +15 -0
  131. endoreg_db/data/finding_type/data.yaml +39 -0
  132. endoreg_db/data/gender/data.yaml +42 -0
  133. endoreg_db/data/information_source/annotation.yaml +6 -0
  134. endoreg_db/data/information_source/data.yaml +30 -0
  135. endoreg_db/data/information_source/endoscopy_guidelines.yaml +7 -0
  136. endoreg_db/data/information_source/medication.yaml +6 -0
  137. endoreg_db/data/information_source/prediction.yaml +7 -0
  138. endoreg_db/data/information_source_type/data.yaml +8 -0
  139. endoreg_db/data/lab_value/cardiac_enzymes.yaml +37 -0
  140. endoreg_db/data/lab_value/coagulation.yaml +54 -0
  141. endoreg_db/data/lab_value/electrolytes.yaml +228 -0
  142. endoreg_db/data/lab_value/gastrointestinal_function.yaml +133 -0
  143. endoreg_db/data/lab_value/hematology.yaml +184 -0
  144. endoreg_db/data/lab_value/hormones.yaml +59 -0
  145. endoreg_db/data/lab_value/lipids.yaml +53 -0
  146. endoreg_db/data/lab_value/misc.yaml +76 -0
  147. endoreg_db/data/lab_value/renal_function.yaml +12 -0
  148. endoreg_db/data/log_type/data.yaml +57 -0
  149. endoreg_db/data/lx_client_tag/base.yaml +54 -0
  150. endoreg_db/data/lx_client_type/base.yaml +30 -0
  151. endoreg_db/data/lx_permission/base.yaml +24 -0
  152. endoreg_db/data/lx_permission/endoreg.yaml +52 -0
  153. endoreg_db/data/material/material.yaml +91 -0
  154. endoreg_db/data/medication/anticoagulation.yaml +65 -0
  155. endoreg_db/data/medication/tah.yaml +70 -0
  156. endoreg_db/data/medication_indication/anticoagulation.yaml +115 -0
  157. endoreg_db/data/medication_indication_type/data.yaml +11 -0
  158. endoreg_db/data/medication_indication_type/thrombembolism.yaml +41 -0
  159. endoreg_db/data/medication_intake_time/base.yaml +31 -0
  160. endoreg_db/data/medication_schedule/apixaban.yaml +95 -0
  161. endoreg_db/data/medication_schedule/ass.yaml +12 -0
  162. endoreg_db/data/medication_schedule/enoxaparin.yaml +26 -0
  163. endoreg_db/data/names_first/first_names.yaml +54 -0
  164. endoreg_db/data/names_last/last_names.yaml +51 -0
  165. endoreg_db/data/network_device/data.yaml +59 -0
  166. endoreg_db/data/network_device_type/data.yaml +12 -0
  167. endoreg_db/data/organ/data.yaml +29 -0
  168. endoreg_db/data/patient_lab_sample_type/generic.yaml +6 -0
  169. endoreg_db/data/pdf_type/data.yaml +46 -0
  170. endoreg_db/data/product/green_endoscopy_dashboard_Product.yaml +66 -0
  171. endoreg_db/data/product_group/green_endoscopy_dashboard_ProductGroup.yaml +33 -0
  172. endoreg_db/data/product_material/green_endoscopy_dashboard_ProductMaterial.yaml +308 -0
  173. endoreg_db/data/product_weight/green_endoscopy_dashboard_ProductWeight.yaml +88 -0
  174. endoreg_db/data/profession/data.yaml +70 -0
  175. endoreg_db/data/qualification/endoscopy.yaml +36 -0
  176. endoreg_db/data/qualification/m2.yaml +39 -0
  177. endoreg_db/data/qualification/outpatient_clinic.yaml +35 -0
  178. endoreg_db/data/qualification/sonography.yaml +36 -0
  179. endoreg_db/data/qualification_type/base.yaml +29 -0
  180. endoreg_db/data/reference_product/green_endoscopy_dashboard_ReferenceProduct.yaml +55 -0
  181. endoreg_db/data/report_reader_flag/rkh-histology-generic.yaml +10 -0
  182. endoreg_db/data/report_reader_flag/ukw-examination-generic.yaml +30 -0
  183. endoreg_db/data/report_reader_flag/ukw-histology-generic.yaml +24 -0
  184. endoreg_db/data/requirement/01_patient_data.yaml +93 -0
  185. endoreg_db/data/requirement/old/colon_polyp_intervention.yaml +49 -0
  186. endoreg_db/data/requirement/old/colonoscopy_baseline_austria.yaml +45 -0
  187. endoreg_db/data/requirement/old/coloreg_colon_polyp.yaml +49 -0
  188. endoreg_db/data/requirement/old/disease_cardiovascular.yaml +79 -0
  189. endoreg_db/data/requirement/old/disease_classification_choice_cardiovascular.yaml +41 -0
  190. endoreg_db/data/requirement/old/disease_hepatology.yaml +12 -0
  191. endoreg_db/data/requirement/old/disease_misc.yaml +12 -0
  192. endoreg_db/data/requirement/old/disease_renal.yaml +96 -0
  193. endoreg_db/data/requirement/old/endoscopy_bleeding_risk.yaml +59 -0
  194. endoreg_db/data/requirement/old/event_cardiology.yaml +251 -0
  195. endoreg_db/data/requirement/old/event_requirements.yaml +145 -0
  196. endoreg_db/data/requirement/old/finding_colon_polyp.yaml +50 -0
  197. endoreg_db/data/requirement/old/gender.yaml +0 -0
  198. endoreg_db/data/requirement/old/lab_value.yaml +441 -0
  199. endoreg_db/data/requirement/old/medication.yaml +93 -0
  200. endoreg_db/data/requirement_operator/_old/age.yaml +13 -0
  201. endoreg_db/data/requirement_operator/_old/lab_operators.yaml +129 -0
  202. endoreg_db/data/requirement_operator/_old/model_operators.yaml +96 -0
  203. endoreg_db/data/requirement_operator/new_operators.yaml +36 -0
  204. endoreg_db/data/requirement_set/01_endoscopy_generic.yaml +65 -0
  205. endoreg_db/data/requirement_set/01_laboratory.yaml +13 -0
  206. endoreg_db/data/requirement_set/02_endoscopy_bleeding_risk.yaml +46 -0
  207. endoreg_db/data/requirement_set/90_coloreg.yaml +190 -0
  208. endoreg_db/data/requirement_set/_old_ +109 -0
  209. endoreg_db/data/requirement_set/colonoscopy_austria_screening.yaml +57 -0
  210. endoreg_db/data/requirement_set_type/data.yaml +41 -0
  211. endoreg_db/data/requirement_type/requirement_types.yaml +165 -0
  212. endoreg_db/data/resource/green_endoscopy_dashboard_Resource.yaml +15 -0
  213. endoreg_db/data/risk/bleeding.yaml +26 -0
  214. endoreg_db/data/risk/thrombosis.yaml +37 -0
  215. endoreg_db/data/risk_type/data.yaml +27 -0
  216. endoreg_db/data/setup_config.yaml +38 -0
  217. endoreg_db/data/shift/endoscopy.yaml +21 -0
  218. endoreg_db/data/shift/m2.yaml +0 -0
  219. endoreg_db/data/shift_type/base.yaml +35 -0
  220. endoreg_db/data/tag/requirement_set_tags.yaml +32 -0
  221. endoreg_db/data/tmp/chronic_kidney_disease.yaml +0 -0
  222. endoreg_db/data/tmp/congestive_heart_failure.yaml +0 -0
  223. endoreg_db/data/transport_route/green_endoscopy_dashboard_TransportRoute.yaml +12 -0
  224. endoreg_db/data/unit/concentration.yaml +115 -0
  225. endoreg_db/data/unit/data.yaml +17 -0
  226. endoreg_db/data/unit/length.yaml +31 -0
  227. endoreg_db/data/unit/misc.yaml +20 -0
  228. endoreg_db/data/unit/rate.yaml +6 -0
  229. endoreg_db/data/unit/time.yaml +48 -0
  230. endoreg_db/data/unit/volume.yaml +35 -0
  231. endoreg_db/data/unit/weight.yaml +38 -0
  232. endoreg_db/data/waste/data.yaml +12 -0
  233. endoreg_db/exceptions.py +24 -0
  234. endoreg_db/export/frames/export.py +6 -0
  235. endoreg_db/export/frames/export_frames_with_labels.py +616 -0
  236. endoreg_db/factories/__init__.py +0 -0
  237. endoreg_db/forms/__init__.py +4 -0
  238. endoreg_db/forms/examination_form.py +12 -0
  239. endoreg_db/forms/patient_finding_intervention_form.py +40 -0
  240. endoreg_db/forms/patient_form.py +23 -0
  241. endoreg_db/forms/questionnaires/__init__.py +1 -0
  242. endoreg_db/forms/questionnaires/tto_questionnaire.py +23 -0
  243. endoreg_db/forms/settings/__init__.py +11 -0
  244. endoreg_db/forms/unit.py +7 -0
  245. endoreg_db/helpers/__init__.py +0 -0
  246. endoreg_db/helpers/count_db.py +48 -0
  247. endoreg_db/helpers/data_loader.py +280 -0
  248. endoreg_db/helpers/default_objects.py +414 -0
  249. endoreg_db/helpers/download_segmentation_model.py +32 -0
  250. endoreg_db/helpers/interact.py +1 -0
  251. endoreg_db/helpers/test_video_helper.py +127 -0
  252. endoreg_db/import_files/__init__.py +27 -0
  253. endoreg_db/import_files/context/__init__.py +7 -0
  254. endoreg_db/import_files/context/default_sensitive_meta.py +83 -0
  255. endoreg_db/import_files/context/ensure_center.py +17 -0
  256. endoreg_db/import_files/context/file_lock.py +66 -0
  257. endoreg_db/import_files/context/import_context.py +42 -0
  258. endoreg_db/import_files/context/validate_directories.py +57 -0
  259. endoreg_db/import_files/file_storage/__init__.py +15 -0
  260. endoreg_db/import_files/file_storage/create_report_file.py +99 -0
  261. endoreg_db/import_files/file_storage/create_video_file.py +104 -0
  262. endoreg_db/import_files/file_storage/sensitive_meta_storage.py +42 -0
  263. endoreg_db/import_files/file_storage/state_management.py +463 -0
  264. endoreg_db/import_files/file_storage/storage.py +42 -0
  265. endoreg_db/import_files/import_service.md +26 -0
  266. endoreg_db/import_files/processing/__init__.py +11 -0
  267. endoreg_db/import_files/processing/report_processing/report_anonymization.py +99 -0
  268. endoreg_db/import_files/processing/sensitive_meta_adapter.py +51 -0
  269. endoreg_db/import_files/processing/video_processing/video_anonymization.py +107 -0
  270. endoreg_db/import_files/pseudonymization/__init__.py +0 -0
  271. endoreg_db/import_files/pseudonymization/fake.py +52 -0
  272. endoreg_db/import_files/pseudonymization/k_anonymity.py +181 -0
  273. endoreg_db/import_files/pseudonymization/k_pseudonymity.py +139 -0
  274. endoreg_db/import_files/pseudonymization/pseudonymize.py +0 -0
  275. endoreg_db/import_files/report_import_service.py +147 -0
  276. endoreg_db/import_files/video_import_service.py +154 -0
  277. endoreg_db/logger_conf.py +156 -0
  278. endoreg_db/management/__init__.py +1 -0
  279. endoreg_db/management/commands/__init__.py +1 -0
  280. endoreg_db/management/commands/anonymize_video.py +0 -0
  281. endoreg_db/management/commands/check_auth.py +132 -0
  282. endoreg_db/management/commands/create_model_meta_from_huggingface.py +177 -0
  283. endoreg_db/management/commands/create_multilabel_model_meta.py +419 -0
  284. endoreg_db/management/commands/export_frame_annot.py +196 -0
  285. endoreg_db/management/commands/fix_missing_patient_data.py +206 -0
  286. endoreg_db/management/commands/fix_video_paths.py +186 -0
  287. endoreg_db/management/commands/import_report.py +361 -0
  288. endoreg_db/management/commands/list_routes.py +20 -0
  289. endoreg_db/management/commands/load_ai_model_data.py +83 -0
  290. endoreg_db/management/commands/load_ai_model_label_data.py +60 -0
  291. endoreg_db/management/commands/load_base_db_data.py +63 -0
  292. endoreg_db/management/commands/load_center_data.py +68 -0
  293. endoreg_db/management/commands/load_contraindication_data.py +39 -0
  294. endoreg_db/management/commands/load_disease_classification_choices_data.py +38 -0
  295. endoreg_db/management/commands/load_disease_classification_data.py +38 -0
  296. endoreg_db/management/commands/load_disease_data.py +59 -0
  297. endoreg_db/management/commands/load_distribution_data.py +63 -0
  298. endoreg_db/management/commands/load_endoscope_data.py +58 -0
  299. endoreg_db/management/commands/load_event_data.py +39 -0
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  604. endoreg_db/serializers/video/__init__.py +7 -0
  605. endoreg_db/serializers/video/video_file.py +283 -0
  606. endoreg_db/serializers/video/video_file_brief.py +14 -0
  607. endoreg_db/serializers/video/video_file_detail.py +96 -0
  608. endoreg_db/serializers/video/video_file_list.py +100 -0
  609. endoreg_db/serializers/video/video_processing_history.py +172 -0
  610. endoreg_db/serializers/video_examination.py +198 -0
  611. endoreg_db/services/__init__.py +5 -0
  612. endoreg_db/services/anonymization.py +274 -0
  613. endoreg_db/services/examination_evaluation.py +172 -0
  614. endoreg_db/services/finding_description_service.py +0 -0
  615. endoreg_db/services/lookup_service.py +424 -0
  616. endoreg_db/services/lookup_store.py +266 -0
  617. endoreg_db/services/model_meta_from_hf.py +76 -0
  618. endoreg_db/services/pdf_import.py +0 -0
  619. endoreg_db/services/polling_coordinator.py +319 -0
  620. endoreg_db/services/pseudonym_service.py +94 -0
  621. endoreg_db/services/report_import.py +13 -0
  622. endoreg_db/services/segment_sync.py +171 -0
  623. endoreg_db/services/video_import.py +9 -0
  624. endoreg_db/templates/admin/patient_finding_intervention.html +253 -0
  625. endoreg_db/templates/admin/start_examination.html +12 -0
  626. endoreg_db/templates/timeline.html +176 -0
  627. endoreg_db/urls/__init__.py +56 -0
  628. endoreg_db/urls/ai.py +14 -0
  629. endoreg_db/urls/anonymization.py +78 -0
  630. endoreg_db/urls/auth.py +16 -0
  631. endoreg_db/urls/classification.py +34 -0
  632. endoreg_db/urls/examination.py +63 -0
  633. endoreg_db/urls/media.py +251 -0
  634. endoreg_db/urls/patient.py +23 -0
  635. endoreg_db/urls/requirements.py +15 -0
  636. endoreg_db/urls/root_urls.py +28 -0
  637. endoreg_db/urls/stats.py +54 -0
  638. endoreg_db/urls/upload.py +12 -0
  639. endoreg_db/urls.py +9 -0
  640. endoreg_db/utils/__init__.py +97 -0
  641. endoreg_db/utils/ai/__init__.py +9 -0
  642. endoreg_db/utils/ai/data_loader_for_model_input.py +262 -0
  643. endoreg_db/utils/ai/data_loader_for_model_training.py +262 -0
  644. endoreg_db/utils/ai/get.py +6 -0
  645. endoreg_db/utils/ai/inference_dataset.py +51 -0
  646. endoreg_db/utils/ai/model_training/config.py +117 -0
  647. endoreg_db/utils/ai/model_training/dataset.py +74 -0
  648. endoreg_db/utils/ai/model_training/losses.py +68 -0
  649. endoreg_db/utils/ai/model_training/metrics.py +78 -0
  650. endoreg_db/utils/ai/model_training/model_backbones.py +155 -0
  651. endoreg_db/utils/ai/model_training/model_gastronet_resnet.py +118 -0
  652. endoreg_db/utils/ai/model_training/trainer_gastronet_multilabel.py +771 -0
  653. endoreg_db/utils/ai/multilabel_classification_net.py +270 -0
  654. endoreg_db/utils/ai/postprocess.py +63 -0
  655. endoreg_db/utils/ai/predict.py +293 -0
  656. endoreg_db/utils/ai/preprocess.py +76 -0
  657. endoreg_db/utils/calc_duration_seconds.py +24 -0
  658. endoreg_db/utils/case_generator/__init__.py +3 -0
  659. endoreg_db/utils/case_generator/lab_sample_factory.py +32 -0
  660. endoreg_db/utils/check_video_files.py +175 -0
  661. endoreg_db/utils/cropping.py +30 -0
  662. endoreg_db/utils/dataloader.py +285 -0
  663. endoreg_db/utils/dates.py +59 -0
  664. endoreg_db/utils/defaults/set_default_center.py +33 -0
  665. endoreg_db/utils/env.py +37 -0
  666. endoreg_db/utils/extract_specific_frames.py +87 -0
  667. endoreg_db/utils/file_operations.py +70 -0
  668. endoreg_db/utils/fix_video_path_direct.py +157 -0
  669. endoreg_db/utils/frame_anonymization_utils.py +463 -0
  670. endoreg_db/utils/hashs.py +138 -0
  671. endoreg_db/utils/links/__init__.py +0 -0
  672. endoreg_db/utils/links/requirement_link.py +237 -0
  673. endoreg_db/utils/mime_types.py +0 -0
  674. endoreg_db/utils/names.py +82 -0
  675. endoreg_db/utils/ocr.py +195 -0
  676. endoreg_db/utils/operation_log.py +87 -0
  677. endoreg_db/utils/parse_and_generate_yaml.py +45 -0
  678. endoreg_db/utils/paths.py +159 -0
  679. endoreg_db/utils/permissions.py +160 -0
  680. endoreg_db/utils/pipelines/Readme.md +235 -0
  681. endoreg_db/utils/pipelines/__init__.py +0 -0
  682. endoreg_db/utils/pipelines/process_video_dir.py +144 -0
  683. endoreg_db/utils/product/__init__.py +0 -0
  684. endoreg_db/utils/product/sum_emissions.py +22 -0
  685. endoreg_db/utils/product/sum_weights.py +20 -0
  686. endoreg_db/utils/pydantic_models/__init__.py +5 -0
  687. endoreg_db/utils/pydantic_models/db_config.py +57 -0
  688. endoreg_db/utils/requirement_helpers.py +0 -0
  689. endoreg_db/utils/requirement_operator_logic/__init__.py +0 -0
  690. endoreg_db/utils/requirement_operator_logic/_old/lab_value_operators.py +678 -0
  691. endoreg_db/utils/requirement_operator_logic/_old/model_evaluators.py +842 -0
  692. endoreg_db/utils/requirement_operator_logic/new_operator_logic.py +114 -0
  693. endoreg_db/utils/setup_config.py +196 -0
  694. endoreg_db/utils/storage.py +117 -0
  695. endoreg_db/utils/translation.py +31 -0
  696. endoreg_db/utils/uuid.py +5 -0
  697. endoreg_db/utils/validate_endo_roi.py +33 -0
  698. endoreg_db/utils/validate_subcategory_dict.py +93 -0
  699. endoreg_db/utils/validate_video_detailed.py +415 -0
  700. endoreg_db/utils/video/__init__.py +30 -0
  701. endoreg_db/utils/video/extract_frames.py +100 -0
  702. endoreg_db/utils/video/ffmpeg_wrapper.py +996 -0
  703. endoreg_db/utils/video/names.py +47 -0
  704. endoreg_db/utils/video/streaming_processor.py +386 -0
  705. endoreg_db/utils/video/video_splitter.py +105 -0
  706. endoreg_db/versioning.md +79 -0
  707. endoreg_db/views/Frames_NICE_and_PARIS_classifications_views.py +247 -0
  708. endoreg_db/views/__init__.py +157 -0
  709. endoreg_db/views/anonymization/__init__.py +31 -0
  710. endoreg_db/views/anonymization/media_management.py +486 -0
  711. endoreg_db/views/anonymization/overview.py +307 -0
  712. endoreg_db/views/anonymization/validate.py +310 -0
  713. endoreg_db/views/auth/__init__.py +13 -0
  714. endoreg_db/views/auth/keycloak.py +146 -0
  715. endoreg_db/views/examination/__init__.py +30 -0
  716. endoreg_db/views/examination/examination.py +37 -0
  717. endoreg_db/views/examination/examination_manifest_cache.py +26 -0
  718. endoreg_db/views/examination/get_finding_classification_choices.py +62 -0
  719. endoreg_db/views/examination/get_finding_classifications.py +38 -0
  720. endoreg_db/views/examination/get_findings.py +39 -0
  721. endoreg_db/views/examination/get_instruments.py +19 -0
  722. endoreg_db/views/examination/get_interventions.py +14 -0
  723. endoreg_db/views/finding/__init__.py +9 -0
  724. endoreg_db/views/finding/finding.py +116 -0
  725. endoreg_db/views/finding/get_classifications.py +14 -0
  726. endoreg_db/views/finding/get_interventions.py +17 -0
  727. endoreg_db/views/finding_classification/__init__.py +13 -0
  728. endoreg_db/views/finding_classification/base.py +0 -0
  729. endoreg_db/views/finding_classification/finding_classification.py +41 -0
  730. endoreg_db/views/finding_classification/get_classification_choices.py +54 -0
  731. endoreg_db/views/media/__init__.py +32 -0
  732. endoreg_db/views/media/pdf_media.py +411 -0
  733. endoreg_db/views/media/sensitive_metadata.py +372 -0
  734. endoreg_db/views/media/video_media.py +275 -0
  735. endoreg_db/views/meta/__init__.py +7 -0
  736. endoreg_db/views/meta/sensitive_meta_list.py +102 -0
  737. endoreg_db/views/meta/sensitive_meta_verification.py +74 -0
  738. endoreg_db/views/misc/__init__.py +29 -0
  739. endoreg_db/views/misc/center.py +14 -0
  740. endoreg_db/views/misc/csrf.py +8 -0
  741. endoreg_db/views/misc/gender.py +15 -0
  742. endoreg_db/views/misc/stats.py +255 -0
  743. endoreg_db/views/misc/upload_views.py +241 -0
  744. endoreg_db/views/patient/__init__.py +3 -0
  745. endoreg_db/views/patient/patient.py +253 -0
  746. endoreg_db/views/patient_examination/__init__.py +11 -0
  747. endoreg_db/views/patient_examination/patient_examination.py +141 -0
  748. endoreg_db/views/patient_examination/patient_examination_create.py +58 -0
  749. endoreg_db/views/patient_examination/patient_examination_detail.py +63 -0
  750. endoreg_db/views/patient_examination/patient_examination_list.py +72 -0
  751. endoreg_db/views/patient_examination/video.py +228 -0
  752. endoreg_db/views/patient_finding/__init__.py +7 -0
  753. endoreg_db/views/patient_finding/base.py +0 -0
  754. endoreg_db/views/patient_finding/patient_finding.py +71 -0
  755. endoreg_db/views/patient_finding/patient_finding_optimized.py +291 -0
  756. endoreg_db/views/patient_finding_classification/__init__.py +5 -0
  757. endoreg_db/views/patient_finding_classification/pfc_create.py +75 -0
  758. endoreg_db/views/report/__init__.py +7 -0
  759. endoreg_db/views/report/reimport.py +177 -0
  760. endoreg_db/views/report/report_stream.py +191 -0
  761. endoreg_db/views/requirement/__init__.py +11 -0
  762. endoreg_db/views/requirement/evaluate.py +278 -0
  763. endoreg_db/views/requirement/lookup.py +380 -0
  764. endoreg_db/views/requirement/lookup_store.py +183 -0
  765. endoreg_db/views/requirement/requirement_utils.py +87 -0
  766. endoreg_db/views/requirement_lookup/lookup.py +0 -0
  767. endoreg_db/views/requirement_lookup/lookup_store.py +0 -0
  768. endoreg_db/views/stats/__init__.py +13 -0
  769. endoreg_db/views/stats/stats_views.py +266 -0
  770. endoreg_db/views/video/__init__.py +49 -0
  771. endoreg_db/views/video/ai/__init__.py +8 -0
  772. endoreg_db/views/video/ai/label.py +159 -0
  773. endoreg_db/views/video/correction.py +529 -0
  774. endoreg_db/views/video/reimport.py +230 -0
  775. endoreg_db/views/video/segments_crud.py +709 -0
  776. endoreg_db/views/video/video_apply_mask.py +49 -0
  777. endoreg_db/views/video/video_correction.py +22 -0
  778. endoreg_db/views/video/video_download_processed.py +58 -0
  779. endoreg_db/views/video/video_examination_viewset.py +242 -0
  780. endoreg_db/views/video/video_metadata.py +101 -0
  781. endoreg_db/views/video/video_processing_history.py +25 -0
  782. endoreg_db/views/video/video_remove_frames.py +49 -0
  783. endoreg_db/views/video/video_stream.py +334 -0
  784. endoreg_db-0.8.9.32.dist-info/METADATA +404 -0
  785. endoreg_db-0.8.9.32.dist-info/RECORD +787 -0
  786. endoreg_db-0.8.9.32.dist-info/WHEEL +4 -0
  787. endoreg_db-0.8.9.32.dist-info/licenses/LICENSE +674 -0
@@ -0,0 +1,205 @@
1
+ import logging
2
+ import time
3
+ from pathlib import Path
4
+ from typing import TYPE_CHECKING, List, Optional
5
+
6
+ from django.db import OperationalError
7
+ from tqdm import tqdm
8
+
9
+ if TYPE_CHECKING:
10
+ from endoreg_db.models import VideoFile
11
+
12
+ logger = logging.getLogger(__name__)
13
+
14
+
15
+ def _initialize_frames(video: "VideoFile", frame_paths: Optional[List[Path]] = None):
16
+ """
17
+ Initializes Frame objects in the database based on either provided existing
18
+ frame paths or the expected frame count from the video metadata.
19
+
20
+ If `frame_paths` is provided, Frame objects are created/updated and marked
21
+ as `is_extracted=True`.
22
+ If `frame_paths` is None, Frame objects are created based on `video.frame_count`
23
+ and marked as `is_extracted=False`.
24
+
25
+ Updates state.frames_initialized and state.frame_count.
26
+ Uses bulk_create with ignore_conflicts=True, so it won't fail if frames already exist.
27
+
28
+ Raises RuntimeError on failure to create/update frames or update state.
29
+
30
+ State Transitions:
31
+ - On Success: Sets state.frames_initialized=True, state.frame_count=N.
32
+ - On Failure: Does not change state (error is raised).
33
+ """
34
+ from endoreg_db.models import Frame
35
+ from endoreg_db.models.media.video.video_file_frames._bulk_create_frames import (
36
+ _bulk_create_frames,
37
+ )
38
+ from endoreg_db.models.media.video.video_file_frames._create_frame_object import (
39
+ _create_frame_object,
40
+ )
41
+
42
+ frames_to_create = []
43
+ num_expected_or_provided = 0
44
+ mark_as_extracted = False
45
+
46
+ if frame_paths:
47
+ logger.info(
48
+ "Initializing Frame objects based on %d provided paths for video %s.",
49
+ len(frame_paths),
50
+ video.video_hash,
51
+ )
52
+ mark_as_extracted = True
53
+ num_expected_or_provided = len(frame_paths)
54
+ for frame_path in tqdm(
55
+ frame_paths,
56
+ desc=f"Initializing Frames from Paths {video.video_hash}",
57
+ unit="frame",
58
+ ):
59
+ try:
60
+ frame_number = int(frame_path.stem.split("_")[-1])
61
+ relative_path_str = frame_path.name
62
+ frames_to_create.append(
63
+ _create_frame_object(
64
+ video,
65
+ frame_number,
66
+ relative_path_str,
67
+ extracted=mark_as_extracted,
68
+ )
69
+ )
70
+ except (ValueError, IndexError) as e:
71
+ logger.warning(
72
+ "Could not parse frame number from %s: %s", frame_path.name, e
73
+ )
74
+ continue
75
+ else:
76
+ expected_frame_count = video.frame_count
77
+ if expected_frame_count is None or expected_frame_count <= 0:
78
+ logger.warning(
79
+ "Cannot initialize frames for video %s: Frame count is %s.",
80
+ video.video_hash,
81
+ expected_frame_count,
82
+ )
83
+ try:
84
+ state = video.get_or_create_state()
85
+ if state.frames_initialized or state.frame_count is not None:
86
+ state.frames_initialized = False
87
+ state.frame_count = None
88
+ state.save(update_fields=["frames_initialized", "frame_count"])
89
+ except Exception as state_e:
90
+ logger.error(
91
+ "Failed to reset state during empty initialization for video %s: %s",
92
+ video.video_hash,
93
+ state_e,
94
+ exc_info=True,
95
+ )
96
+ return
97
+
98
+ logger.info(
99
+ "Initializing %d expected Frame objects for video %s (is_extracted=False).",
100
+ expected_frame_count,
101
+ video.video_hash,
102
+ )
103
+ mark_as_extracted = False
104
+ num_expected_or_provided = expected_frame_count
105
+ for frame_number in tqdm(
106
+ range(expected_frame_count),
107
+ desc=f"Initializing Expected Frames {video.video_hash}",
108
+ unit="frame",
109
+ ):
110
+ relative_path_str = f"frame_{frame_number:07d}.jpg"
111
+ frames_to_create.append(
112
+ _create_frame_object(
113
+ video, frame_number, relative_path_str, extracted=mark_as_extracted
114
+ )
115
+ )
116
+
117
+ if frames_to_create:
118
+ for attempt in range(5):
119
+ try:
120
+ _bulk_create_frames(video, frames_to_create)
121
+ num_created_or_ignored = len(frames_to_create)
122
+ logger.info(
123
+ "Bulk create attempted for %d Frame objects for video %s (ignore_conflicts=True).",
124
+ num_created_or_ignored,
125
+ video.video_hash,
126
+ )
127
+
128
+ if mark_as_extracted:
129
+ frame_numbers_to_update = [f.frame_number for f in frames_to_create]
130
+ if frame_numbers_to_update:
131
+ update_count = Frame.objects.filter(
132
+ video=video,
133
+ frame_number__in=frame_numbers_to_update,
134
+ is_extracted=False,
135
+ ).update(is_extracted=True)
136
+ if update_count > 0:
137
+ logger.info(
138
+ "Marked %d existing Frame objects as is_extracted=True for video %s.",
139
+ update_count,
140
+ video.video_hash,
141
+ )
142
+
143
+ try:
144
+ state = video.get_or_create_state()
145
+ state.frames_initialized = True
146
+ state.frame_count = num_expected_or_provided
147
+ state.save(update_fields=["frames_initialized", "frame_count"])
148
+ logger.info(
149
+ "Set frames_initialized=True and frame_count=%d for video %s.",
150
+ num_expected_or_provided,
151
+ video.video_hash,
152
+ )
153
+ except Exception as state_e:
154
+ logger.error(
155
+ "Failed to update state after frame initialization for video %s: %s",
156
+ video.video_hash,
157
+ state_e,
158
+ exc_info=True,
159
+ )
160
+ raise RuntimeError(
161
+ f"Failed to update state after frame initialization for video {video.video_hash}"
162
+ ) from state_e
163
+
164
+ except OperationalError as e:
165
+ if "database is locked" in str(e):
166
+ logger.warning(
167
+ "Database is locked, retrying frame initialization for video %s (attempt %d/5).",
168
+ video.video_hash,
169
+ attempt + 1,
170
+ )
171
+ time.sleep(2**attempt)
172
+ if attempt < 4:
173
+ continue
174
+ else:
175
+ raise RuntimeError(
176
+ f"Failed to initialize frames for video {video.video_hash}."
177
+ ) from e
178
+ logger.error(
179
+ "Error initializing frames for video %s: %s",
180
+ video.video_hash,
181
+ e,
182
+ exc_info=True,
183
+ )
184
+ raise RuntimeError(
185
+ f"Failed to initialize frames for video {video.video_hash}."
186
+ ) from e
187
+
188
+ else:
189
+ logger.warning(
190
+ "No valid frames found/generated to initialize for video %s.",
191
+ video.video_hash,
192
+ )
193
+ try:
194
+ state = video.get_or_create_state()
195
+ if state.frames_initialized or state.frame_count is not None:
196
+ state.frames_initialized = False
197
+ state.frame_count = None
198
+ state.save(update_fields=["frames_initialized", "frame_count"])
199
+ except Exception as state_e:
200
+ logger.error(
201
+ "Failed to reset state during empty initialization for video %s: %s",
202
+ video.video_hash,
203
+ state_e,
204
+ exc_info=True,
205
+ )
@@ -0,0 +1,228 @@
1
+ import logging
2
+ import os
3
+ from typing import TYPE_CHECKING
4
+
5
+ from django.db import transaction
6
+
7
+ from endoreg_db.models.media.video.video_file_io import _get_frame_dir_path
8
+
9
+ # Assuming ffmpeg_wrapper has or will have this function
10
+ from endoreg_db.utils.video.ffmpeg_wrapper import (
11
+ extract_frame_range as ffmpeg_extract_frame_range,
12
+ )
13
+
14
+ if TYPE_CHECKING:
15
+ from endoreg_db.models import VideoFile
16
+
17
+ logger = logging.getLogger(__name__)
18
+
19
+
20
+ def _delete_frame_range(video: "VideoFile", start_frame: int, end_frame: int):
21
+ """
22
+ Deletes frame image files within the specified range [start_frame, end_frame)
23
+ and updates their is_extracted status to False. Runs within the caller's transaction.
24
+ """
25
+
26
+ logger.info(
27
+ "Deleting frame files for video %s in range [%d, %d)",
28
+ video.video_hash,
29
+ start_frame,
30
+ end_frame,
31
+ )
32
+ frames_to_delete = video.frames.filter(
33
+ frame_number__gte=start_frame, frame_number__lt=end_frame, is_extracted=True
34
+ )
35
+
36
+ deleted_count = 0
37
+ paths_to_delete = [
38
+ frame.file_path for frame in frames_to_delete
39
+ ] # Get paths before potential DB changes
40
+
41
+ # Update DB first
42
+ update_count = frames_to_delete.update(is_extracted=False)
43
+ logger.info(
44
+ "Marked %d Frame objects as is_extracted=False for video %s range [%d, %d).",
45
+ update_count,
46
+ video.video_hash,
47
+ start_frame,
48
+ end_frame,
49
+ )
50
+
51
+ # Then delete files
52
+ for frame_path in paths_to_delete:
53
+ try:
54
+ if frame_path.exists():
55
+ os.remove(frame_path)
56
+ deleted_count += 1
57
+ except Exception as e:
58
+ # Log warning but continue; DB state is already updated.
59
+ logger.warning(
60
+ "Could not delete frame file %s for video %s: %s",
61
+ frame_path,
62
+ video.video_hash,
63
+ e,
64
+ )
65
+
66
+ logger.info(
67
+ "Attempted deletion of %d files for video %s range [%d, %d). Actual deleted: %d.",
68
+ len(paths_to_delete),
69
+ video.video_hash,
70
+ start_frame,
71
+ end_frame,
72
+ deleted_count,
73
+ )
74
+
75
+
76
+ @transaction.atomic
77
+ def _extract_frame_range(
78
+ video: "VideoFile",
79
+ start_frame: int,
80
+ end_frame: int,
81
+ quality: int = 2,
82
+ overwrite: bool = False,
83
+ ext="jpg",
84
+ verbose=False,
85
+ ) -> bool:
86
+ """
87
+ Extracts frames within the range [start_frame, end_frame) using ffmpeg.
88
+ Updates corresponding Frame objects' is_extracted flag.
89
+ Runs within the caller's transaction.
90
+ Does NOT update VideoState.frames_extracted.
91
+ """
92
+
93
+ if not video.has_raw:
94
+ raise FileNotFoundError(
95
+ f"Raw video file not available for {video.video_hash}. Cannot extract frame range."
96
+ )
97
+
98
+ raw_file_path = video.get_raw_file_path()
99
+ if not raw_file_path or not raw_file_path.exists():
100
+ raise FileNotFoundError(
101
+ f"Raw video file not found at {raw_file_path} for video {video.video_hash}. Cannot extract frame range."
102
+ )
103
+
104
+ frame_dir = _get_frame_dir_path(video)
105
+ if not frame_dir:
106
+ raise ValueError(
107
+ f"Cannot determine frame directory path for video {video.video_hash}."
108
+ )
109
+
110
+ # Check frames within the range that might already exist
111
+ frames_in_range = video.frames.filter(
112
+ frame_number__gte=start_frame, frame_number__lt=end_frame
113
+ )
114
+ existing_extracted_in_range = frames_in_range.filter(is_extracted=True)
115
+
116
+ if existing_extracted_in_range.exists():
117
+ if overwrite:
118
+ logger.info(
119
+ "Overwrite=True, deleting existing frame files in range [%d, %d) for video %s before extraction.",
120
+ start_frame,
121
+ end_frame,
122
+ video.video_hash,
123
+ )
124
+ _delete_frame_range(video, start_frame, end_frame)
125
+ else:
126
+ logger.info(
127
+ "Frames already exist in range [%d, %d) for video %s and overwrite=False. Skipping extraction for this range.",
128
+ start_frame,
129
+ end_frame,
130
+ video.video_hash,
131
+ )
132
+ updated_count = frames_in_range.filter(is_extracted=False).update(
133
+ is_extracted=True
134
+ )
135
+ if updated_count > 0:
136
+ logger.info(
137
+ "Marked %d existing Frame objects in range [%d, %d) as extracted for video %s.",
138
+ updated_count,
139
+ start_frame,
140
+ end_frame,
141
+ video.video_hash,
142
+ )
143
+ return True # Indicate success as frames are considered present
144
+
145
+ frame_dir.mkdir(parents=True, exist_ok=True)
146
+ extracted_paths = []
147
+
148
+ try:
149
+ logger.info(
150
+ "Starting frame range extraction [%d, %d) for video %s to %s",
151
+ start_frame,
152
+ end_frame,
153
+ video.video_hash,
154
+ frame_dir,
155
+ )
156
+ extracted_paths = ffmpeg_extract_frame_range(
157
+ raw_file_path, frame_dir, start_frame, end_frame, quality=quality, ext=ext
158
+ )
159
+
160
+ logger.info(
161
+ "ffmpeg extraction process completed for video %s range [%d, %d). Found %d files.",
162
+ video.video_hash,
163
+ start_frame,
164
+ end_frame,
165
+ len(extracted_paths),
166
+ )
167
+
168
+ update_count = frames_in_range.update(is_extracted=True)
169
+ logger.info(
170
+ "Marked %d Frame objects in range [%d, %d) as is_extracted=True for video %s.",
171
+ update_count,
172
+ start_frame,
173
+ end_frame,
174
+ video.video_hash,
175
+ )
176
+
177
+ return True
178
+
179
+ except FileNotFoundError as err:
180
+ logger.error(
181
+ "Frame range extraction [%d, %d) failed for video %s: %s",
182
+ start_frame,
183
+ end_frame,
184
+ video.video_hash,
185
+ err,
186
+ exc_info=True,
187
+ )
188
+ raise
189
+
190
+ except Exception as e:
191
+ logger.error(
192
+ "Frame range extraction [%d, %d) or DB update failed for video %s: %s",
193
+ start_frame,
194
+ end_frame,
195
+ video.video_hash,
196
+ e,
197
+ exc_info=True,
198
+ )
199
+
200
+ logger.warning(
201
+ "Attempting file cleanup in range [%d, %d) for video %s due to extraction error.",
202
+ start_frame,
203
+ end_frame,
204
+ video.video_hash,
205
+ )
206
+ files_to_check = (
207
+ extracted_paths if "extracted_paths" in locals() and extracted_paths else []
208
+ )
209
+ if not files_to_check:
210
+ files_to_check = [
211
+ frame_dir / f"frame_{i:07d}.{ext}"
212
+ for i in range(start_frame, end_frame)
213
+ ]
214
+
215
+ for potential_file in files_to_check:
216
+ if potential_file.exists():
217
+ try:
218
+ os.remove(potential_file)
219
+ except OSError as unlink_err:
220
+ logger.error(
221
+ "Failed to delete potential frame %s during cleanup: %s",
222
+ potential_file,
223
+ unlink_err,
224
+ )
225
+
226
+ raise RuntimeError(
227
+ f"Frame range extraction or update failed for video {video.video_hash} range [{start_frame}, {end_frame})."
228
+ ) from e
@@ -0,0 +1,107 @@
1
+ import logging
2
+ from typing import TYPE_CHECKING, Set
3
+
4
+ from django.db import transaction
5
+
6
+ if TYPE_CHECKING:
7
+ from endoreg_db.models import VideoFile
8
+
9
+ logger = logging.getLogger(__name__)
10
+
11
+
12
+ @transaction.atomic
13
+ def _mark_frames_extracted_status(
14
+ video: "VideoFile", extracted_frame_numbers: Set[int], status: bool
15
+ ):
16
+ """
17
+ Bulk updates the is_extracted status for a set of frame numbers.
18
+ """
19
+ from endoreg_db.models.media.frame import Frame
20
+
21
+ if not extracted_frame_numbers:
22
+ logger.warning(
23
+ "No frame numbers provided to update status for video %s.", video.video_hash
24
+ )
25
+ return 0
26
+
27
+ # --- Enhanced Logging ---
28
+ min_frame = min(extracted_frame_numbers) if extracted_frame_numbers else "N/A"
29
+ max_frame = max(extracted_frame_numbers) if extracted_frame_numbers else "N/A"
30
+ contains_zero = 0 in extracted_frame_numbers
31
+ logger.info(
32
+ "Attempting to mark %d Frame objects as is_extracted=%s for video %s. Frame numbers range: [%s-%s]. Contains frame 0: %s",
33
+ len(extracted_frame_numbers),
34
+ status,
35
+ video.video_hash,
36
+ min_frame,
37
+ max_frame,
38
+ contains_zero,
39
+ )
40
+ # --- End Enhanced Logging ---
41
+
42
+ try:
43
+ # Update Frame objects based on frame_number
44
+ # Convert set to list for potentially better compatibility with some DB backends
45
+ updated_count = Frame.objects.filter(
46
+ video=video, frame_number__in=list(extracted_frame_numbers)
47
+ ).update(is_extracted=status)
48
+
49
+ logger.info(
50
+ "Database reported updating %d Frame objects to is_extracted=%s for video %s.",
51
+ updated_count,
52
+ status,
53
+ video.video_hash,
54
+ )
55
+
56
+ # Verification step
57
+ if updated_count != len(extracted_frame_numbers):
58
+ logger.warning(
59
+ "Mismatch during status update for video %s. Expected to update %d frames, but DB reported updating %d.",
60
+ video.video_hash,
61
+ len(extracted_frame_numbers),
62
+ updated_count,
63
+ )
64
+ # --- Add detailed check for frame 0 if status is True and it should have been updated ---
65
+ if (
66
+ status is True
67
+ and contains_zero
68
+ and updated_count < len(extracted_frame_numbers)
69
+ ):
70
+ try:
71
+ # Check the status of frame 0 directly after the update attempt
72
+ frame_zero = Frame.objects.get(video=video, frame_number=0)
73
+ if not frame_zero.is_extracted:
74
+ logger.error(
75
+ "Verification check: Frame 0 (PK: %s) was NOT updated to is_extracted=True for video %s.",
76
+ frame_zero.pk,
77
+ video.video_hash,
78
+ )
79
+ else:
80
+ # This case should ideally not happen if updated_count < expected count, but log just in case
81
+ logger.info(
82
+ "Verification check: Frame 0 (PK: %s) IS is_extracted=True for video %s, despite count mismatch.",
83
+ frame_zero.pk,
84
+ video.video_hash,
85
+ )
86
+ except Frame.DoesNotExist:
87
+ logger.error(
88
+ "Verification check: Frame 0 does not exist for video %s during status check.",
89
+ video.video_hash,
90
+ )
91
+ except Exception as verify_e:
92
+ logger.error(
93
+ "Verification check: Error checking frame 0 status for video %s: %s",
94
+ video.video_hash,
95
+ verify_e,
96
+ )
97
+ # --- End detailed check ---
98
+
99
+ return updated_count
100
+ except Exception as e:
101
+ logger.error(
102
+ "Failed to bulk update is_extracted status for video %s: %s",
103
+ video.video_hash,
104
+ e,
105
+ exc_info=True,
106
+ )
107
+ raise # Re-raise to ensure transaction rollback if needed