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 +1,1048 @@
1
+ import logging
2
+ import os
3
+ import random
4
+ import re # Neu hinzugefügt für Regex-Pattern
5
+ from datetime import date, datetime, timedelta
6
+ from hashlib import sha256
7
+ from typing import TYPE_CHECKING, Any, Dict, Optional, Type
8
+
9
+ from django.db import transaction
10
+ from django.utils import timezone
11
+
12
+ from endoreg_db.utils import guess_name_gender
13
+
14
+ # Assuming these utils are correctly located
15
+ from endoreg_db.utils.hashs import get_patient_examination_hash, get_patient_hash
16
+
17
+ # Import models needed for logic, use local imports inside functions if needed to break cycles
18
+ from ..administration import Center, Examiner, FirstName, LastName, Patient
19
+ from ..medical import PatientExamination
20
+ from ..other import Gender
21
+ from ..state import SensitiveMetaState
22
+
23
+ if TYPE_CHECKING:
24
+ from .sensitive_meta import SensitiveMeta # Import model for type hinting
25
+
26
+ logger = logging.getLogger(__name__)
27
+ SECRET_SALT = os.getenv("DJANGO_SALT", "default_salt")
28
+ DEFAULT_UNKNOWN_NAME = "unknown"
29
+
30
+ # Regex-Pattern für verschiedene Datumsformate
31
+ ISO_RX = re.compile(r"^\d{4}-\d{2}-\d{2}$")
32
+ DE_RX = re.compile(r"^\d{2}\.\d{2}\.\d{4}$")
33
+
34
+
35
+ def parse_any_date(s: str) -> Optional[date]:
36
+ """
37
+ Parst Datumsstring mit Priorität auf deutsches Format (DD.MM.YYYY).
38
+
39
+ Unterstützte Formate:
40
+ 1. DD.MM.YYYY (Priorität) - deutsches Format
41
+ 2. YYYY-MM-DD (Fallback) - ISO-Format
42
+ 3. Erweiterte Fallbacks über dateparser
43
+
44
+ Args:
45
+ s: Datumsstring zum Parsen
46
+
47
+ Returns:
48
+ date-Objekt oder None bei ungültigem/fehlendem Input
49
+ """
50
+ if not s:
51
+ return None
52
+
53
+ s = s.strip()
54
+
55
+ # 1. German dd.mm.yyyy (PRIORITÄT)
56
+ if DE_RX.match(s):
57
+ try:
58
+ dd, mm, yyyy = s.split(".")
59
+ return date(int(yyyy), int(mm), int(dd))
60
+ except ValueError as e:
61
+ logger.warning(f"Invalid German date format '{s}': {e}")
62
+ return None
63
+
64
+ # 2. ISO yyyy-mm-dd (Fallback für Rückwärtskompatibilität)
65
+ if ISO_RX.match(s):
66
+ try:
67
+ return date.fromisoformat(s)
68
+ except ValueError as e:
69
+ logger.warning(f"Invalid ISO date format '{s}': {e}")
70
+ return None
71
+
72
+ # 3. Extended fallbacks
73
+ try:
74
+ # Try standard datetime parsing
75
+ return datetime.fromisoformat(s).date()
76
+ except Exception:
77
+ pass
78
+
79
+ try:
80
+ # Try dateparser with German locale preference
81
+ import dateparser
82
+
83
+ dt = dateparser.parse(
84
+ s, settings={"DATE_ORDER": "DMY", "PREFER_DAY_OF_MONTH": "first"}
85
+ )
86
+ return dt.date() if dt else None
87
+ except Exception as e:
88
+ logger.debug(f"Dateparser fallback failed for '{s}': {e}")
89
+ return None
90
+
91
+
92
+ def format_date_german(d: Optional[date]) -> str:
93
+ """
94
+ Formatiert date-Objekt als deutsches Datumsformat (DD.MM.YYYY).
95
+
96
+ Args:
97
+ d: date-Objekt oder None
98
+
99
+ Returns:
100
+ Formatiertes Datum als String oder leerer String bei None
101
+ """
102
+ if not d:
103
+ return ""
104
+ return d.strftime("%d.%m.%Y")
105
+
106
+
107
+ def format_date_iso(d: Optional[date]) -> str:
108
+ """
109
+ Formatiert date-Objekt als ISO-Format (YYYY-MM-DD).
110
+
111
+ Args:
112
+ d: date-Objekt oder None
113
+
114
+ Returns:
115
+ Formatiertes Datum als String oder leerer String bei None
116
+ """
117
+ if not d:
118
+ return ""
119
+ return d.isoformat()
120
+
121
+
122
+ def generate_random_dob() -> datetime:
123
+ """Generates a random timezone-aware datetime between 1920-01-01 and 2000-12-31."""
124
+ start_date = date(1920, 1, 1)
125
+ end_date = date(2000, 12, 31)
126
+ time_between_dates = end_date - start_date
127
+ days_between_dates = time_between_dates.days
128
+ random_number_of_days = random.randrange(days_between_dates)
129
+ random_date = start_date + timedelta(days=random_number_of_days)
130
+ random_datetime = datetime.combine(random_date, datetime.min.time())
131
+ return timezone.make_aware(random_datetime)
132
+
133
+
134
+ def generate_random_examination_date() -> date:
135
+ """Generates a random date within the last 20 years."""
136
+ today = date.today()
137
+ start_date = today - timedelta(days=20 * 365) # Approximate 20 years back
138
+ time_between_dates = today - start_date
139
+ days_between_dates = time_between_dates.days
140
+ random_number_of_days = random.randrange(days_between_dates)
141
+ random_date = start_date + timedelta(days=random_number_of_days)
142
+ return random_date
143
+
144
+
145
+ def update_name_db(first_name: Optional[str], last_name: Optional[str]):
146
+ """Adds first and last names to the respective lookup tables if they don't exist."""
147
+ if first_name:
148
+ FirstName.objects.get_or_create(name=first_name)
149
+ if last_name:
150
+ LastName.objects.get_or_create(name=last_name)
151
+
152
+
153
+ def calculate_patient_hash(instance: "SensitiveMeta", salt: str = SECRET_SALT) -> str:
154
+ """Calculates the patient hash for the instance."""
155
+ dob = instance.patient_dob
156
+ first_name = instance.patient_first_name
157
+ last_name = instance.patient_last_name
158
+ center = instance.center
159
+
160
+ if not dob:
161
+ raise ValueError("Patient DOB is required to calculate patient hash.")
162
+ if not center:
163
+ raise ValueError("Center is required to calculate patient hash.")
164
+
165
+ assert first_name is not None, "First name is required to calculate patient hash."
166
+ assert last_name is not None, "Last name is required to calculate patient hash."
167
+
168
+ hash_str = get_patient_hash(
169
+ first_name=first_name,
170
+ last_name=last_name,
171
+ dob=dob,
172
+ center=center.name, # Use center name
173
+ salt=salt,
174
+ )
175
+ return sha256(hash_str.encode()).hexdigest()
176
+
177
+
178
+ def calculate_examination_hash(
179
+ instance: "SensitiveMeta", salt: str = SECRET_SALT
180
+ ) -> str:
181
+ """Calculates the examination hash for the instance."""
182
+ dob = instance.patient_dob
183
+ first_name = instance.patient_first_name
184
+ last_name = instance.patient_last_name
185
+ examination_date = instance.examination_date
186
+ center = instance.center
187
+
188
+ if not dob:
189
+ raise ValueError("Patient DOB is required to calculate examination hash.")
190
+ if not examination_date:
191
+ raise ValueError("Examination date is required to calculate examination hash.")
192
+ if not center:
193
+ raise ValueError("Center is required to calculate examination hash.")
194
+
195
+ hash_str = get_patient_examination_hash(
196
+ first_name=first_name,
197
+ last_name=last_name,
198
+ dob=dob,
199
+ examination_date=examination_date,
200
+ center=center.name, # Use center name
201
+ salt=salt,
202
+ )
203
+ return sha256(hash_str.encode()).hexdigest()
204
+
205
+
206
+ def create_pseudo_examiner_logic(instance: "SensitiveMeta") -> "Examiner":
207
+ """Creates or retrieves the pseudo examiner based on instance data."""
208
+ first_name = instance.examiner_first_name
209
+ last_name = instance.examiner_last_name
210
+ center = instance.center # Should be set before calling save
211
+
212
+ if not first_name or not last_name or not center:
213
+ logger.warning(
214
+ f"Incomplete examiner info for SensitiveMeta (pk={instance.pk or 'new'}). Using default examiner."
215
+ )
216
+ # Ensure default center exists or handle appropriately
217
+ try:
218
+ default_center = Center.objects.get(name="endoreg_db_demo")
219
+ except Center.DoesNotExist:
220
+ logger.error(
221
+ "Default center 'endoreg_db_demo' not found. Cannot create default examiner."
222
+ )
223
+ raise ValueError("Default center 'endoreg_db_demo' not found.")
224
+
225
+ examiner, _created = Examiner.custom_get_or_create(
226
+ first_name="Unknown", last_name="Unknown", center=default_center
227
+ )
228
+ else:
229
+ examiner, _created = Examiner.custom_get_or_create(
230
+ first_name=first_name, last_name=last_name, center=center
231
+ )
232
+
233
+ return examiner
234
+
235
+
236
+ def get_or_create_pseudo_patient_logic(instance: "SensitiveMeta") -> "Patient":
237
+ """Gets or creates the pseudo patient based on instance data."""
238
+ # Ensure necessary fields are set
239
+ if not instance.patient_hash:
240
+ instance.patient_hash = calculate_patient_hash(instance)
241
+ if not instance.center:
242
+ raise ValueError("Center must be set before creating pseudo patient.")
243
+ if not instance.patient_gender:
244
+ raise ValueError("Patient gender must be set before creating pseudo patient.")
245
+ if not instance.patient_dob:
246
+ raise ValueError("Patient DOB must be set before creating pseudo patient.")
247
+
248
+ dob = instance.patient_dob
249
+ year = dob.year
250
+ month = dob.month
251
+
252
+ patient, _created = Patient.get_or_create_pseudo_patient_by_hash(
253
+ patient_hash=instance.patient_hash,
254
+ center=instance.center,
255
+ gender=instance.patient_gender,
256
+ birth_year=year,
257
+ birth_month=month,
258
+ )
259
+ return patient
260
+
261
+
262
+ def get_or_create_pseudo_patient_examination_logic(
263
+ instance: "SensitiveMeta",
264
+ ) -> "PatientExamination":
265
+ """Gets or creates the pseudo patient examination based on instance data."""
266
+ # Ensure necessary fields are set
267
+ if not instance.patient_hash:
268
+ instance.patient_hash = calculate_patient_hash(instance)
269
+ if not instance.examination_hash:
270
+ instance.examination_hash = calculate_examination_hash(instance)
271
+
272
+ # Ensure the pseudo patient exists first, as PatientExamination might depend on it
273
+ if not instance.pseudo_patient_id:
274
+ pseudo_patient = get_or_create_pseudo_patient_logic(instance)
275
+ instance.pseudo_patient_id = pseudo_patient.pk # Assign FK directly
276
+
277
+ patient_examination, _created = (
278
+ PatientExamination.get_or_create_pseudo_patient_examination_by_hash(
279
+ patient_hash=instance.patient_hash,
280
+ examination_hash=instance.examination_hash,
281
+ # Optionally pass pseudo_patient if the method requires it
282
+ # pseudo_patient=instance.pseudo_patient
283
+ )
284
+ )
285
+ return patient_examination
286
+
287
+
288
+ @transaction.atomic # Ensure all operations within save succeed or fail together
289
+ def perform_save_logic(instance: "SensitiveMeta") -> "Examiner":
290
+ """
291
+ Contains the core logic for preparing a SensitiveMeta instance for saving.
292
+ Handles data generation (dates), hash calculation, and linking pseudo-entities.
293
+
294
+ This function is called on every save() operation and implements a two-phase approach:
295
+
296
+ **Phase 1: Initial Creation (with defaults)**
297
+ - When a SensitiveMeta is first created (e.g., via get_or_create_sensitive_meta()),
298
+ it may have missing patient data (names, DOB, etc.)
299
+ - Default values are set to prevent hash calculation errors:
300
+ * patient_first_name: "unknown"
301
+ * patient_last_name: "unknown"
302
+ * patient_dob: random date (1920-2000)
303
+ - A temporary hash is calculated using these defaults
304
+ - Temporary pseudo-entities (Patient, Examination) are created
305
+
306
+ **Phase 2: Update (with extracted data)**
307
+ - When real patient data is extracted (e.g., from video OCR via lx_anonymizer),
308
+ update_from_dict() is called with actual values
309
+ - The instance fields are updated with real data (names, DOB, etc.)
310
+ - save() is called again, triggering this function
311
+ - Default-setting logic is skipped (fields are no longer empty)
312
+ - Hash is RECALCULATED with real data
313
+ - New pseudo-entities are created/retrieved based on new hash
314
+
315
+ **Example Flow:**
316
+ ```
317
+ # Initial creation
318
+ sm = SensitiveMeta.create_from_dict({"center": center})
319
+ # → patient_first_name = "unknown", patient_last_name = "unknown"
320
+ # → hash = sha256("unknown unknown 1990-01-01 ...")
321
+ # → pseudo_patient_temp created
322
+
323
+ # Later update with extracted data
324
+ sm.update_from_dict({"patient_first_name": "Max", "patient_last_name": "Mustermann"})
325
+ # → patient_first_name = "Max", patient_last_name = "Mustermann" (overwrites)
326
+ # → save() triggered → perform_save_logic() called again
327
+ # → Default-setting skipped (names already exist)
328
+ # → hash = sha256("Max Mustermann 1985-03-15 ...") (RECALCULATED)
329
+ # → pseudo_patient_real created/retrieved with new hash
330
+ ```
331
+
332
+ Args:
333
+ instance: The SensitiveMeta instance being saved
334
+
335
+ Returns:
336
+ Examiner: The pseudo examiner instance to be linked via M2M after save
337
+
338
+ Raises:
339
+ ValueError: If required fields (center, gender) cannot be determined
340
+ """
341
+
342
+ # --- Pre-Save Checks and Data Generation ---
343
+
344
+ # 1. Ensure DOB and Examination Date exist
345
+ if not instance.patient_dob:
346
+ logger.debug(
347
+ f"SensitiveMeta (pk={instance.pk or 'new'}): Patient DOB missing, generating random."
348
+ )
349
+ instance.patient_dob = generate_random_dob()
350
+ if not instance.examination_date:
351
+ logger.debug(
352
+ f"SensitiveMeta (pk={instance.pk or 'new'}): Examination date missing, generating random."
353
+ )
354
+ instance.examination_date = generate_random_examination_date()
355
+
356
+ # 2. Ensure Center exists (should be set before calling save)
357
+ if not instance.center:
358
+ raise ValueError("Center must be set before saving SensitiveMeta.")
359
+
360
+ # 2.5 CRITICAL: Set default patient names BEFORE hash calculation
361
+ #
362
+ # **Why this is necessary:**
363
+ # Hash calculation (step 4) requires first_name and last_name to be non-None.
364
+ # However, on initial creation (e.g., via get_or_create_sensitive_meta()), these
365
+ # fields may be empty because real patient data hasn't been extracted yet.
366
+ #
367
+ # **Two-phase approach:**
368
+ # - Phase 1 (Initial): Set defaults if names are missing
369
+ # → Allows hash calculation to succeed without errors
370
+ # → Creates temporary pseudo-entities with default hash
371
+ #
372
+ # - Phase 2 (Update): Real data extraction (OCR, manual input)
373
+ # → update_from_dict() sets real names ("Max", "Mustermann")
374
+ # → save() is called again
375
+ # → This block is SKIPPED (names already exist)
376
+ # → Hash is recalculated with real data (step 4)
377
+ # → New pseudo-entities created with correct hash
378
+ #
379
+ # **Example:**
380
+ # Initial: patient_first_name = "unknown" → hash = sha256("unknown unknown...")
381
+ # Updated: patient_first_name = "Max" → hash = sha256("Max Mustermann...")
382
+ #
383
+ if not instance.patient_first_name:
384
+ instance.patient_first_name = DEFAULT_UNKNOWN_NAME
385
+ logger.debug(
386
+ "SensitiveMeta (pk=%s): Patient first name missing, set to default '%s'.",
387
+ instance.pk or "new",
388
+ DEFAULT_UNKNOWN_NAME,
389
+ )
390
+
391
+ if not instance.patient_last_name:
392
+ instance.patient_last_name = DEFAULT_UNKNOWN_NAME
393
+ logger.debug(
394
+ "SensitiveMeta (pk=%s): Patient last name missing, set to default '%s'.",
395
+ instance.pk or "new",
396
+ DEFAULT_UNKNOWN_NAME,
397
+ )
398
+
399
+ # 3. Ensure Gender exists (should be set before calling save, e.g., during creation/update)
400
+ if not instance.patient_gender:
401
+ # Use the now-guaranteed first_name for gender guessing
402
+ first_name = instance.patient_first_name
403
+ gender_str = guess_name_gender(first_name)
404
+ if not gender_str:
405
+ raise ValueError(
406
+ "Patient gender could not be determined and must be set before saving."
407
+ )
408
+ # Convert string to Gender object
409
+ try:
410
+ gender_obj = Gender.objects.get(name=gender_str)
411
+ instance.patient_gender = gender_obj
412
+ except Gender.DoesNotExist:
413
+ raise ValueError(f"Gender '{gender_str}' not found in database.")
414
+
415
+ # 4. Calculate Hashes (depends on DOB, Exam Date, Center, Names)
416
+ #
417
+ # **IMPORTANT: Hashes are RECALCULATED on every save!**
418
+ # This enables the two-phase update pattern:
419
+ # - Initial save: Hash based on default "unknown unknown" names
420
+ # - Updated save: Hash based on real extracted names ("Max Mustermann")
421
+ #
422
+ # The new hash will link to different pseudo-entities, ensuring proper
423
+ # anonymization while maintaining referential integrity.
424
+ instance.patient_hash = calculate_patient_hash(instance)
425
+ instance.examination_hash = calculate_examination_hash(instance)
426
+
427
+ # 5. Get or Create Pseudo Patient (depends on hash, center, gender, dob)
428
+ # Assign directly to the FK field to avoid premature saving issues
429
+ pseudo_patient = get_or_create_pseudo_patient_logic(instance)
430
+ instance.pseudo_patient_id = pseudo_patient.pk
431
+
432
+ # 6. Get or Create Pseudo Examination (depends on hashes)
433
+ # Assign directly to the FK field
434
+ pseudo_examination = get_or_create_pseudo_patient_examination_logic(instance)
435
+ instance.pseudo_examination_id = pseudo_examination.pk
436
+
437
+ # 7. Get or Create Pseudo Examiner (depends on names, center)
438
+ # This needs to happen *after* the main instance has a PK for M2M linking.
439
+ # We create/get it here and return it to the main save method.
440
+ examiner_instance = create_pseudo_examiner_logic(instance)
441
+
442
+ # 8. Ensure SensitiveMetaState exists (will be checked/created *after* main save)
443
+
444
+ # Return the examiner instance so the model's save method can handle M2M linking
445
+ return examiner_instance
446
+
447
+
448
+ def create_sensitive_meta_from_dict(
449
+ cls: Type["SensitiveMeta"], data: Dict[str, Any]
450
+ ) -> "SensitiveMeta":
451
+ """
452
+ Create a SensitiveMeta instance from a dictionary.
453
+
454
+ **Center handling:**
455
+ This function accepts TWO ways to specify the center:
456
+ 1. `center` (Center object) - Directly pass a Center instance
457
+ 2. `center_name` (string) - Pass the center name as a string (will be resolved to Center object)
458
+
459
+ At least ONE of these must be provided.
460
+
461
+ **Example usage:**
462
+ ```python
463
+ # Option 1: With Center object
464
+ data = {
465
+ "patient_first_name": "Patient",
466
+ "patient_last_name": "Unknown",
467
+ "patient_dob": date(1990, 1, 1),
468
+ "examination_date": date.today(),
469
+ "center": center_obj, # ← Center object
470
+ }
471
+ sm = SensitiveMeta.create_from_dict(data)
472
+
473
+ # Option 2: With center name string
474
+ data = {
475
+ "patient_first_name": "Patient",
476
+ "patient_last_name": "Unknown",
477
+ "patient_dob": date(1990, 1, 1),
478
+ "examination_date": date.today(),
479
+ "center_name": "university_hospital_wuerzburg", # ← String
480
+ }
481
+ sm = SensitiveMeta.create_from_dict(data)
482
+ ```
483
+
484
+ Args:
485
+ cls: The SensitiveMeta class
486
+ data: Dictionary containing field values
487
+
488
+ Returns:
489
+ SensitiveMeta: The created instance
490
+
491
+ Raises:
492
+ ValueError: If neither center nor center_name is provided
493
+ ValueError: If center_name does not match any Center in database
494
+ """
495
+
496
+ field_names = {
497
+ f.name
498
+ for f in cls._meta.get_fields()
499
+ if not f.is_relation or f.one_to_one or (f.many_to_one and f.related_model)
500
+ }
501
+ selected_data = {k: v for k, v in data.items() if k in field_names}
502
+
503
+ # --- Convert patient_dob if it's a date object ---
504
+ dob = selected_data.get("patient_dob")
505
+ if isinstance(dob, date) and not isinstance(dob, datetime):
506
+ # Convert date to datetime at the start of the day and make it timezone-aware
507
+ aware_dob = timezone.make_aware(datetime.combine(dob, datetime.min.time()))
508
+ selected_data["patient_dob"] = aware_dob
509
+ logger.debug("Converted patient_dob from date to aware datetime: %s", aware_dob)
510
+ elif isinstance(dob, str):
511
+ # Handle string DOB - check if it's a field name or actual date
512
+ if dob == "patient_dob" or dob in [
513
+ "patient_first_name",
514
+ "patient_last_name",
515
+ "examination_date",
516
+ ]:
517
+ logger.warning(
518
+ "Skipping invalid patient_dob value '%s' - appears to be field name",
519
+ dob,
520
+ )
521
+ selected_data.pop("patient_dob", None) # Remove invalid value
522
+ else:
523
+ # Try to parse as date string
524
+ try:
525
+ import dateparser
526
+
527
+ parsed_dob = dateparser.parse(
528
+ dob, languages=["de"], settings={"DATE_ORDER": "DMY"}
529
+ )
530
+ if parsed_dob:
531
+ aware_dob = timezone.make_aware(
532
+ parsed_dob.replace(hour=0, minute=0, second=0, microsecond=0)
533
+ )
534
+ selected_data["patient_dob"] = aware_dob
535
+ logger.debug(
536
+ "Parsed string patient_dob '%s' to aware datetime: %s",
537
+ dob,
538
+ aware_dob,
539
+ )
540
+ else:
541
+ logger.warning(
542
+ "Could not parse patient_dob string '%s', removing from data",
543
+ dob,
544
+ )
545
+ selected_data.pop("patient_dob", None)
546
+ except Exception as e:
547
+ logger.warning(
548
+ "Error parsing patient_dob string '%s': %s, removing from data",
549
+ dob,
550
+ e,
551
+ )
552
+ selected_data.pop("patient_dob", None)
553
+ # --- End Conversion ---
554
+
555
+ # Similar validation for examination_date
556
+ exam_date = selected_data.get("examination_date")
557
+ if isinstance(exam_date, str):
558
+ if exam_date == "examination_date" or exam_date in [
559
+ "patient_first_name",
560
+ "patient_last_name",
561
+ "patient_dob",
562
+ ]:
563
+ logger.warning(
564
+ "Skipping invalid examination_date value '%s' - appears to be field name",
565
+ exam_date,
566
+ )
567
+ selected_data.pop("examination_date", None)
568
+ else:
569
+ # Try to parse as date string
570
+ try:
571
+ # First try simple ISO format for YYYY-MM-DD
572
+ if len(exam_date) == 10 and exam_date.count("-") == 2:
573
+ try:
574
+ from datetime import datetime as dt
575
+
576
+ parsed_date = dt.strptime(exam_date, "%Y-%m-%d").date()
577
+ selected_data["examination_date"] = parsed_date
578
+ logger.debug(
579
+ "Parsed ISO examination_date '%s' to date: %s",
580
+ exam_date,
581
+ parsed_date,
582
+ )
583
+ except ValueError:
584
+ # Fall back to dateparser for complex formats
585
+ import dateparser
586
+
587
+ parsed_date = dateparser.parse(
588
+ exam_date, languages=["de"], settings={"DATE_ORDER": "DMY"}
589
+ )
590
+ if parsed_date:
591
+ selected_data["examination_date"] = parsed_date.date()
592
+ logger.debug(
593
+ "Parsed string examination_date '%s' to date: %s",
594
+ exam_date,
595
+ parsed_date.date(),
596
+ )
597
+ else:
598
+ logger.warning(
599
+ "Could not parse examination_date string '%s', removing from data",
600
+ exam_date,
601
+ )
602
+ selected_data.pop("examination_date", None)
603
+ else:
604
+ # Use dateparser for non-ISO formats
605
+ import dateparser
606
+
607
+ parsed_date = dateparser.parse(
608
+ exam_date, languages=["de"], settings={"DATE_ORDER": "DMY"}
609
+ )
610
+ if parsed_date:
611
+ selected_data["examination_date"] = parsed_date.date()
612
+ logger.debug(
613
+ "Parsed string examination_date '%s' to date: %s",
614
+ exam_date,
615
+ parsed_date.date(),
616
+ )
617
+ else:
618
+ logger.warning(
619
+ "Could not parse examination_date string '%s', removing from data",
620
+ exam_date,
621
+ )
622
+ selected_data.pop("examination_date", None)
623
+ except Exception as e:
624
+ logger.warning(
625
+ "Error parsing examination_date string '%s': %s, removing from data",
626
+ exam_date,
627
+ e,
628
+ )
629
+ selected_data.pop("examination_date", None)
630
+
631
+ # Handle Center - accept both center_name (string) and center (object)
632
+ from ..administration import Center
633
+
634
+ center = data.get("center") # First try direct Center object
635
+ center_name = data.get("center_name")
636
+
637
+ if center is not None:
638
+ # Center object provided directly - validate it's a Center instance
639
+ if not isinstance(center, Center):
640
+ raise ValueError(f"'center' must be a Center instance, got {type(center)}")
641
+ selected_data["center"] = center
642
+ elif center_name:
643
+ # center_name string provided - resolve to Center object
644
+ try:
645
+ center = Center.objects.get(name=center_name)
646
+ selected_data["center"] = center
647
+ except Center.DoesNotExist:
648
+ raise ValueError(f"Center with name '{center_name}' does not exist.")
649
+ else:
650
+ # Neither center nor center_name provided
651
+ raise ValueError(
652
+ "Either 'center' (Center object) or 'center_name' (string) is required in data dictionary."
653
+ )
654
+
655
+ # Handle Names and Gender
656
+ first_name = selected_data.get("patient_first_name") or DEFAULT_UNKNOWN_NAME
657
+ last_name = selected_data.get("patient_last_name") or DEFAULT_UNKNOWN_NAME
658
+ selected_data["patient_first_name"] = first_name # Ensure defaults are set
659
+ selected_data["patient_last_name"] = last_name
660
+
661
+ patient_gender_input = selected_data.get("patient_gender")
662
+
663
+ if isinstance(patient_gender_input, Gender):
664
+ # Already a Gender object, nothing to do
665
+ pass
666
+ elif isinstance(patient_gender_input, str):
667
+ # Input is a string (gender name)
668
+ try:
669
+ selected_data["patient_gender"] = Gender.objects.get(
670
+ name=patient_gender_input
671
+ )
672
+ except Gender.DoesNotExist:
673
+ logger.warning(
674
+ f"Gender with name '{patient_gender_input}' provided but not found. Attempting to guess or use default."
675
+ )
676
+ # Fall through to guessing logic if provided string name is invalid
677
+ patient_gender_input = None # Reset to trigger guessing
678
+
679
+ if not isinstance(
680
+ selected_data.get("patient_gender"), Gender
681
+ ): # If not already a Gender object (e.g. was None, or string lookup failed)
682
+ gender_name_to_use = guess_name_gender(first_name)
683
+ if not gender_name_to_use:
684
+ logger.warning(
685
+ f"Could not guess gender for name '{first_name}'. Setting Gender to unknown."
686
+ )
687
+ gender_name_to_use = "unknown"
688
+ try:
689
+ selected_data["patient_gender"] = Gender.objects.get(
690
+ name=gender_name_to_use
691
+ )
692
+ except Gender.DoesNotExist:
693
+ # This should ideally not happen if "unknown" gender is guaranteed to exist
694
+ raise ValueError(
695
+ f"Default or guessed gender '{gender_name_to_use}' does not exist in Gender table."
696
+ )
697
+
698
+ # Update name DB
699
+ update_name_db(first_name, last_name)
700
+
701
+ # Instantiate without saving yet
702
+ sensitive_meta = cls(**selected_data)
703
+
704
+ # Call save once at the end. This triggers the custom save logic.
705
+ sensitive_meta.save() # This will call perform_save_logic internally
706
+
707
+ return sensitive_meta
708
+
709
+
710
+ def update_sensitive_meta_from_dict(
711
+ instance: "SensitiveMeta", data: Dict[str, Any]
712
+ ) -> "SensitiveMeta":
713
+ """
714
+ Updates a SensitiveMeta instance from a dictionary of new values.
715
+
716
+ **Integration with two-phase save pattern:**
717
+ This function is typically called after initial SensitiveMeta creation when real
718
+ patient data becomes available (e.g., extracted from video OCR, PDF parsing, or
719
+ manual annotation).
720
+
721
+ **Example workflow:**
722
+ ```python
723
+ # Phase 1: Initial creation with defaults
724
+ sm = SensitiveMeta.create_from_dict({"center": center})
725
+ # → patient_first_name = "unknown", hash = sha256("unknown...")
726
+
727
+ # Phase 2: Update with extracted data
728
+ extracted = {
729
+ "patient_first_name": "Max",
730
+ "patient_last_name": "Mustermann",
731
+ "patient_dob": date(1985, 3, 15)
732
+ }
733
+ update_sensitive_meta_from_dict(sm, extracted)
734
+ # → Sets: sm.patient_first_name = "Max", sm.patient_last_name = "Mustermann"
735
+ # → Calls: sm.save()
736
+ # → Triggers: perform_save_logic() again
737
+ # → Result: Hash recalculated with real data, new pseudo-entities created
738
+ ```
739
+
740
+ **Key behaviors:**
741
+ - Updates instance attributes from provided dictionary
742
+ - Handles type conversions (date strings → date objects, gender strings → Gender objects)
743
+ - Tracks patient name changes to update name database
744
+ - Calls save() at the end, triggering full save logic including hash recalculation
745
+ - Default-setting in perform_save_logic() is skipped (fields already populated)
746
+
747
+ Args:
748
+ instance: The existing SensitiveMeta instance to update
749
+ data: Dictionary of field names and new values
750
+
751
+ Returns:
752
+ The updated SensitiveMeta instance
753
+
754
+ Raises:
755
+ Exception: If save fails or required conversions fail
756
+ """
757
+ field_names = {
758
+ f.name
759
+ for f in instance._meta.get_fields()
760
+ if not f.is_relation or f.one_to_one or (f.many_to_one and f.related_model)
761
+ }
762
+ # Exclude FKs that should not be updated directly from dict keys (handled separately or via save logic)
763
+ excluded_fields = {"pseudo_patient", "pseudo_examination"}
764
+ selected_data = {
765
+ k: v for k, v in data.items() if k in field_names and k not in excluded_fields
766
+ }
767
+
768
+ # Handle potential Center update - accept both center_name (string) and center (object)
769
+ from ..administration import Center
770
+
771
+ center = data.get("center") # First try direct Center object
772
+ center_name = data.get("center_name")
773
+
774
+ if center is not None:
775
+ # Center object provided directly - validate and update
776
+ if isinstance(center, Center):
777
+ instance.center = center
778
+ logger.debug(f"Updated center from Center object: {center.name}")
779
+ else:
780
+ logger.warning(
781
+ f"Invalid center type {type(center)}, expected Center instance. Ignoring."
782
+ )
783
+ # Remove from selected_data to prevent override
784
+ selected_data.pop("center", None)
785
+ elif center_name:
786
+ # center_name string provided - resolve to Center object
787
+ try:
788
+ center_obj = Center.objects.get(name=center_name)
789
+ instance.center = center_obj
790
+ logger.debug(f"Updated center from center_name string: {center_name}")
791
+ except Center.DoesNotExist:
792
+ logger.warning(
793
+ f"Center '{center_name}' not found during update. Keeping existing center."
794
+ )
795
+ else:
796
+ # Both are None/missing - remove 'center' from selected_data to preserve existing value
797
+ selected_data.pop("center", None)
798
+ # If both are None/missing, keep existing center (no update needed)
799
+
800
+ # Set examiner names if provided, before calling save
801
+ examiner_first_name = data.get("examiner_first_name")
802
+ examiner_last_name = data.get("examiner_last_name")
803
+ if examiner_first_name is not None: # Allow setting empty strings
804
+ instance.examiner_first_name = examiner_first_name
805
+ if examiner_last_name is not None:
806
+ instance.examiner_last_name = examiner_last_name
807
+
808
+ # Handle patient_gender specially with graceful error handling
809
+ patient_gender_input = data.get("patient_gender")
810
+ if patient_gender_input is not None:
811
+ try:
812
+ if isinstance(patient_gender_input, Gender):
813
+ selected_data["patient_gender"] = patient_gender_input
814
+ elif isinstance(patient_gender_input, str):
815
+ gender_input_clean = patient_gender_input.strip()
816
+ # Try direct case-insensitive DB lookup first
817
+ gender_obj = Gender.objects.filter(
818
+ name__iexact=gender_input_clean
819
+ ).first()
820
+ if gender_obj:
821
+ selected_data["patient_gender"] = gender_obj
822
+ logger.debug(
823
+ f"Successfully matched gender string '{patient_gender_input}' to Gender object via iexact lookup"
824
+ )
825
+ else:
826
+ # Use mapping helper for fallback
827
+ mapped = _map_gender_string_to_standard(gender_input_clean)
828
+ if mapped:
829
+ gender_obj = Gender.objects.filter(name__iexact=mapped).first()
830
+ if gender_obj:
831
+ selected_data["patient_gender"] = gender_obj
832
+ logger.info(
833
+ f"Mapped gender '{patient_gender_input}' to '{mapped}' via fallback mapping"
834
+ )
835
+ else:
836
+ logger.warning(
837
+ f"Mapped gender '{patient_gender_input}' to '{mapped}', but no such Gender in DB. Trying 'unknown'."
838
+ )
839
+ unknown_gender = Gender.objects.filter(
840
+ name__iexact="unknown"
841
+ ).first()
842
+ if unknown_gender:
843
+ selected_data["patient_gender"] = unknown_gender
844
+ logger.warning(
845
+ f"Using 'unknown' gender as fallback for '{patient_gender_input}'"
846
+ )
847
+ else:
848
+ logger.error(
849
+ f"No 'unknown' gender found in database. Cannot handle gender '{patient_gender_input}'. Skipping gender update."
850
+ )
851
+ selected_data.pop("patient_gender", None)
852
+ else:
853
+ # Last resort: try to get 'unknown' gender
854
+ unknown_gender = Gender.objects.filter(
855
+ name__iexact="unknown"
856
+ ).first()
857
+ if unknown_gender:
858
+ selected_data["patient_gender"] = unknown_gender
859
+ logger.warning(
860
+ f"Using 'unknown' gender as fallback for '{patient_gender_input}' (no mapping)"
861
+ )
862
+ else:
863
+ logger.error(
864
+ f"No 'unknown' gender found in database. Cannot handle gender '{patient_gender_input}'. Skipping gender update."
865
+ )
866
+ selected_data.pop("patient_gender", None)
867
+ else:
868
+ logger.warning(
869
+ f"Unexpected patient_gender type {type(patient_gender_input)}: {patient_gender_input}. Skipping gender update."
870
+ )
871
+ selected_data.pop("patient_gender", None)
872
+ except Exception as e:
873
+ logger.exception(
874
+ f"Error handling patient_gender '{patient_gender_input}': {e}. Skipping gender update."
875
+ )
876
+ selected_data.pop("patient_gender", None)
877
+
878
+ # Update other attributes from selected_data
879
+ patient_name_changed = False
880
+ for k, v in selected_data.items():
881
+ # Skip None values to avoid overwriting existing data
882
+ if v is None:
883
+ logger.debug(f"Skipping field '{k}' during update because value is None")
884
+ continue
885
+
886
+ # Avoid overwriting examiner names if they were just explicitly set
887
+ if (
888
+ k not in ["examiner_first_name", "examiner_last_name"]
889
+ or (k == "examiner_first_name" and examiner_first_name is None)
890
+ or (k == "examiner_last_name" and examiner_last_name is None)
891
+ ):
892
+ try:
893
+ # --- Convert patient_dob if it's a date object ---
894
+ value_to_set = v
895
+ if k == "patient_dob":
896
+ if isinstance(v, date) and not isinstance(v, datetime):
897
+ aware_dob = timezone.make_aware(
898
+ datetime.combine(v, datetime.min.time())
899
+ )
900
+ value_to_set = aware_dob
901
+ logger.debug(
902
+ "Converted patient_dob from date to aware datetime during update: %s",
903
+ aware_dob,
904
+ )
905
+ elif isinstance(v, str):
906
+ # Handle string DOB - check if it's a field name or actual date
907
+ if v == "patient_dob" or v in [
908
+ "patient_first_name",
909
+ "patient_last_name",
910
+ "examination_date",
911
+ ]:
912
+ logger.warning(
913
+ "Skipping invalid patient_dob value '%s' during update - appears to be field name",
914
+ v,
915
+ )
916
+ continue # Skip this field
917
+ else:
918
+ # Try to parse as date string
919
+ try:
920
+ import dateparser
921
+
922
+ parsed_dob = dateparser.parse(
923
+ v, languages=["de"], settings={"DATE_ORDER": "DMY"}
924
+ )
925
+ if parsed_dob:
926
+ value_to_set = timezone.make_aware(
927
+ parsed_dob.replace(
928
+ hour=0, minute=0, second=0, microsecond=0
929
+ )
930
+ )
931
+ logger.debug(
932
+ "Parsed string patient_dob '%s' during update to aware datetime: %s",
933
+ v,
934
+ value_to_set,
935
+ )
936
+ else:
937
+ logger.warning(
938
+ "Could not parse patient_dob string '%s' during update, skipping",
939
+ v,
940
+ )
941
+ continue
942
+ except Exception as e:
943
+ logger.warning(
944
+ "Error parsing patient_dob string '%s' during update: %s, skipping",
945
+ v,
946
+ e,
947
+ )
948
+ continue
949
+ elif k == "examination_date" and isinstance(v, str):
950
+ if v == "examination_date" or v in [
951
+ "patient_first_name",
952
+ "patient_last_name",
953
+ "patient_dob",
954
+ ]:
955
+ logger.warning(
956
+ "Skipping invalid examination_date value '%s' during update - appears to be field name",
957
+ v,
958
+ )
959
+ continue
960
+ else:
961
+ # Try to parse as date string
962
+ try:
963
+ import dateparser
964
+
965
+ parsed_date = dateparser.parse(
966
+ v, languages=["de"], settings={"DATE_ORDER": "DMY"}
967
+ )
968
+ if parsed_date:
969
+ value_to_set = parsed_date.date()
970
+ logger.debug(
971
+ "Parsed string examination_date '%s' during update to date: %s",
972
+ v,
973
+ value_to_set,
974
+ )
975
+ else:
976
+ logger.warning(
977
+ "Could not parse examination_date string '%s' during update, skipping",
978
+ v,
979
+ )
980
+ continue
981
+ except Exception as e:
982
+ logger.warning(
983
+ "Error parsing examination_date string '%s' during update: %s, skipping",
984
+ v,
985
+ e,
986
+ )
987
+ continue
988
+ # --- End Conversion ---
989
+
990
+ # Check if patient name is changing
991
+ if (
992
+ k in ["patient_first_name", "patient_last_name"]
993
+ and getattr(instance, k) != value_to_set
994
+ ):
995
+ patient_name_changed = True
996
+
997
+ setattr(instance, k, value_to_set) # Use value_to_set
998
+
999
+ except Exception as e:
1000
+ logger.error(
1001
+ f"Error setting attribute '{k}' to '{v}': {e}. Skipping this field."
1002
+ )
1003
+ continue
1004
+
1005
+ # Update name DB if patient names changed
1006
+ if patient_name_changed:
1007
+ try:
1008
+ update_name_db(instance.patient_first_name, instance.patient_last_name)
1009
+ except Exception as e:
1010
+ logger.warning(f"Error updating name database: {e}")
1011
+
1012
+ # Call save - this will trigger the full save logic including hash recalculation etc.
1013
+ try:
1014
+ instance.save()
1015
+ except Exception as e:
1016
+ logger.error(f"Error saving SensitiveMeta instance: {e}")
1017
+ raise
1018
+
1019
+ return instance
1020
+
1021
+
1022
+ def update_or_create_sensitive_meta_from_dict(
1023
+ cls: Type["SensitiveMeta"],
1024
+ data: Dict[str, Any],
1025
+ instance: Optional["SensitiveMeta"] = None,
1026
+ ) -> "SensitiveMeta":
1027
+ """Logic to update or create a SensitiveMeta instance from a dictionary."""
1028
+ # Check if the instance already exists based on unique fields
1029
+ if instance:
1030
+ # Update the existing instance
1031
+ return update_sensitive_meta_from_dict(instance, data), False
1032
+ else:
1033
+ # Create a new instance
1034
+ return create_sensitive_meta_from_dict(cls, data), True
1035
+
1036
+
1037
+ def _map_gender_string_to_standard(gender_str: str) -> Optional[str]:
1038
+ """Maps various gender string inputs to standard gender names used in the DB."""
1039
+ mapping = {
1040
+ "male": ["male", "m", "männlich", "man"],
1041
+ "female": ["female", "f", "weiblich", "woman"],
1042
+ "unknown": ["unknown", "unbekannt", "other", "diverse", ""],
1043
+ }
1044
+ gender_lower = gender_str.strip().lower()
1045
+ for standard, variants in mapping.items():
1046
+ if gender_lower in variants:
1047
+ return standard
1048
+ return None