endoreg-db 0.8.5.1__py3-none-any.whl

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  1. endoreg_db/__init__.py +0 -0
  2. endoreg_db/admin.py +92 -0
  3. endoreg_db/api/serializers/finding_descriptions.py +0 -0
  4. endoreg_db/api/views/finding_descriptions.py +0 -0
  5. endoreg_db/api_urls.py +4 -0
  6. endoreg_db/apps.py +18 -0
  7. endoreg_db/assets/dummy_model.ckpt +1 -0
  8. endoreg_db/codemods/readme.md +88 -0
  9. endoreg_db/codemods/rename_datetime_fields.py +92 -0
  10. endoreg_db/config/__init__.py +0 -0
  11. endoreg_db/config/env.py +101 -0
  12. endoreg_db/data/__init__.py +144 -0
  13. endoreg_db/data/ai_model/data.yaml +7 -0
  14. endoreg_db/data/ai_model_label/label/data.yaml +88 -0
  15. endoreg_db/data/ai_model_label/label/polyp_classification.yaml +52 -0
  16. endoreg_db/data/ai_model_label/label-set/data.yaml +40 -0
  17. endoreg_db/data/ai_model_label/label-set/polyp_classifications.yaml +25 -0
  18. endoreg_db/data/ai_model_label/label-type/data.yaml +7 -0
  19. endoreg_db/data/ai_model_meta/default_multilabel_classification.yaml +27 -0
  20. endoreg_db/data/ai_model_type/data.yaml +7 -0
  21. endoreg_db/data/ai_model_video_segmentation_label/base_segmentation.yaml +176 -0
  22. endoreg_db/data/ai_model_video_segmentation_labelset/data.yaml +20 -0
  23. endoreg_db/data/case_template/rule/00_patient_lab_sample_add_default_value.yaml +167 -0
  24. endoreg_db/data/case_template/rule/01_patient-set-age.yaml +8 -0
  25. endoreg_db/data/case_template/rule/01_patient-set-gender.yaml +9 -0
  26. endoreg_db/data/case_template/rule/11_create_patient_lab_sample.yaml +23 -0
  27. endoreg_db/data/case_template/rule/12_create-patient_medication-anticoagulation.yaml +19 -0
  28. endoreg_db/data/case_template/rule/13_create-patient_medication_schedule-anticoagulation.yaml +19 -0
  29. endoreg_db/data/case_template/rule/19_create_patient.yaml +17 -0
  30. endoreg_db/data/case_template/rule_type/base_types.yaml +35 -0
  31. endoreg_db/data/case_template/rule_value/.init +0 -0
  32. endoreg_db/data/case_template/rule_value_type/base_types.yaml +59 -0
  33. endoreg_db/data/case_template/template/base.yaml +8 -0
  34. endoreg_db/data/case_template/template_type/pre_endoscopy.yaml +3 -0
  35. endoreg_db/data/case_template/tmp/_rule_value +13 -0
  36. endoreg_db/data/case_template/tmp/rule/01_atrial_fibrillation.yaml +21 -0
  37. endoreg_db/data/case_template/tmp/rule/02_create_object.yaml +10 -0
  38. endoreg_db/data/case_template/tmp/template/atrial_fibrillation_low_risk.yaml +7 -0
  39. endoreg_db/data/center/data.yaml +91 -0
  40. endoreg_db/data/center_resource/green_endoscopy_dashboard_CenterResource.yaml +144 -0
  41. endoreg_db/data/center_shift/ukw.yaml +9 -0
  42. endoreg_db/data/center_waste/green_endoscopy_dashboard_CenterWaste.yaml +48 -0
  43. endoreg_db/data/contraindication/bleeding.yaml +11 -0
  44. endoreg_db/data/db_summary.csv +58 -0
  45. endoreg_db/data/db_summary.xlsx +0 -0
  46. endoreg_db/data/disease/cardiovascular.yaml +37 -0
  47. endoreg_db/data/disease/hepatology.yaml +5 -0
  48. endoreg_db/data/disease/misc.yaml +5 -0
  49. endoreg_db/data/disease/renal.yaml +5 -0
  50. endoreg_db/data/disease_classification/chronic_kidney_disease.yaml +6 -0
  51. endoreg_db/data/disease_classification/coronary_vessel_disease.yaml +6 -0
  52. endoreg_db/data/disease_classification_choice/chronic_kidney_disease.yaml +41 -0
  53. endoreg_db/data/disease_classification_choice/coronary_vessel_disease.yaml +20 -0
  54. endoreg_db/data/distribution/date/patient.yaml +7 -0
  55. endoreg_db/data/distribution/multiple_categorical/.init +0 -0
  56. endoreg_db/data/distribution/numeric/data.yaml +14 -0
  57. endoreg_db/data/distribution/single_categorical/patient.yaml +7 -0
  58. endoreg_db/data/emission_factor/green_endoscopy_dashboard_EmissionFactor.yaml +132 -0
  59. endoreg_db/data/endoscope/data.yaml +93 -0
  60. endoreg_db/data/endoscope_type/data.yaml +11 -0
  61. endoreg_db/data/endoscopy_processor/data.yaml +50 -0
  62. endoreg_db/data/event/cardiology.yaml +15 -0
  63. endoreg_db/data/event/neurology.yaml +14 -0
  64. endoreg_db/data/event/surgery.yaml +13 -0
  65. endoreg_db/data/event/thrombembolism.yaml +20 -0
  66. endoreg_db/data/examination/examinations/data.yaml +72 -0
  67. endoreg_db/data/examination/time/data.yaml +48 -0
  68. endoreg_db/data/examination/time-type/data.yaml +8 -0
  69. endoreg_db/data/examination/type/data.yaml +17 -0
  70. endoreg_db/data/examination_indication/endoscopy.yaml +424 -0
  71. endoreg_db/data/examination_indication_classification/endoscopy.yaml +160 -0
  72. endoreg_db/data/examination_indication_classification_choice/endoscopy.yaml +101 -0
  73. endoreg_db/data/examination_requirement_set/colonoscopy.yaml +15 -0
  74. endoreg_db/data/finding/anatomy_colon.yaml +128 -0
  75. endoreg_db/data/finding/colonoscopy.yaml +40 -0
  76. endoreg_db/data/finding/colonoscopy_bowel_prep.yaml +56 -0
  77. endoreg_db/data/finding/complication.yaml +16 -0
  78. endoreg_db/data/finding/data.yaml +105 -0
  79. endoreg_db/data/finding/examination_setting.yaml +16 -0
  80. endoreg_db/data/finding/medication_related.yaml +18 -0
  81. endoreg_db/data/finding/outcome.yaml +12 -0
  82. endoreg_db/data/finding_classification/colonoscopy_bowel_preparation.yaml +95 -0
  83. endoreg_db/data/finding_classification/colonoscopy_jnet.yaml +22 -0
  84. endoreg_db/data/finding_classification/colonoscopy_kudo.yaml +25 -0
  85. endoreg_db/data/finding_classification/colonoscopy_lesion_circularity.yaml +20 -0
  86. endoreg_db/data/finding_classification/colonoscopy_lesion_planarity.yaml +24 -0
  87. endoreg_db/data/finding_classification/colonoscopy_lesion_size.yaml +68 -0
  88. endoreg_db/data/finding_classification/colonoscopy_lesion_surface.yaml +20 -0
  89. endoreg_db/data/finding_classification/colonoscopy_location.yaml +80 -0
  90. endoreg_db/data/finding_classification/colonoscopy_lst.yaml +21 -0
  91. endoreg_db/data/finding_classification/colonoscopy_nice.yaml +20 -0
  92. endoreg_db/data/finding_classification/colonoscopy_paris.yaml +26 -0
  93. endoreg_db/data/finding_classification/colonoscopy_sano.yaml +22 -0
  94. endoreg_db/data/finding_classification/colonoscopy_summary.yaml +53 -0
  95. endoreg_db/data/finding_classification/complication_generic.yaml +25 -0
  96. endoreg_db/data/finding_classification/examination_setting_generic.yaml +40 -0
  97. endoreg_db/data/finding_classification/histology_colo.yaml +51 -0
  98. endoreg_db/data/finding_classification/intervention_required.yaml +26 -0
  99. endoreg_db/data/finding_classification/medication_related.yaml +23 -0
  100. endoreg_db/data/finding_classification/visualized.yaml +33 -0
  101. endoreg_db/data/finding_classification_choice/bowel_preparation.yaml +78 -0
  102. endoreg_db/data/finding_classification_choice/colon_lesion_circularity_default.yaml +32 -0
  103. endoreg_db/data/finding_classification_choice/colon_lesion_jnet.yaml +15 -0
  104. endoreg_db/data/finding_classification_choice/colon_lesion_kudo.yaml +23 -0
  105. endoreg_db/data/finding_classification_choice/colon_lesion_lst.yaml +15 -0
  106. endoreg_db/data/finding_classification_choice/colon_lesion_nice.yaml +17 -0
  107. endoreg_db/data/finding_classification_choice/colon_lesion_paris.yaml +57 -0
  108. endoreg_db/data/finding_classification_choice/colon_lesion_planarity_default.yaml +49 -0
  109. endoreg_db/data/finding_classification_choice/colon_lesion_sano.yaml +14 -0
  110. endoreg_db/data/finding_classification_choice/colon_lesion_surface_intact_default.yaml +36 -0
  111. endoreg_db/data/finding_classification_choice/colonoscopy_location.yaml +229 -0
  112. endoreg_db/data/finding_classification_choice/colonoscopy_not_complete_reason.yaml +19 -0
  113. endoreg_db/data/finding_classification_choice/colonoscopy_size.yaml +82 -0
  114. endoreg_db/data/finding_classification_choice/colonoscopy_summary_worst_finding.yaml +15 -0
  115. endoreg_db/data/finding_classification_choice/complication_generic_types.yaml +15 -0
  116. endoreg_db/data/finding_classification_choice/examination_setting_generic_types.yaml +15 -0
  117. endoreg_db/data/finding_classification_choice/histology.yaml +24 -0
  118. endoreg_db/data/finding_classification_choice/histology_polyp.yaml +20 -0
  119. endoreg_db/data/finding_classification_choice/outcome.yaml +19 -0
  120. endoreg_db/data/finding_classification_choice/yes_no_na.yaml +11 -0
  121. endoreg_db/data/finding_classification_type/colonoscopy_basic.yaml +48 -0
  122. endoreg_db/data/finding_intervention/endoscopy.yaml +43 -0
  123. endoreg_db/data/finding_intervention/endoscopy_colonoscopy.yaml +168 -0
  124. endoreg_db/data/finding_intervention/endoscopy_egd.yaml +128 -0
  125. endoreg_db/data/finding_intervention/endoscopy_ercp.yaml +32 -0
  126. endoreg_db/data/finding_intervention/endoscopy_eus_lower.yaml +9 -0
  127. endoreg_db/data/finding_intervention/endoscopy_eus_upper.yaml +36 -0
  128. endoreg_db/data/finding_intervention_type/endoscopy.yaml +15 -0
  129. endoreg_db/data/finding_morphology_classification_type/colonoscopy.yaml +79 -0
  130. endoreg_db/data/finding_type/data.yaml +43 -0
  131. endoreg_db/data/gender/data.yaml +42 -0
  132. endoreg_db/data/information_source/annotation.yaml +6 -0
  133. endoreg_db/data/information_source/data.yaml +30 -0
  134. endoreg_db/data/information_source/endoscopy_guidelines.yaml +7 -0
  135. endoreg_db/data/information_source/medication.yaml +6 -0
  136. endoreg_db/data/information_source/prediction.yaml +7 -0
  137. endoreg_db/data/information_source_type/data.yaml +8 -0
  138. endoreg_db/data/lab_value/cardiac_enzymes.yaml +37 -0
  139. endoreg_db/data/lab_value/coagulation.yaml +54 -0
  140. endoreg_db/data/lab_value/electrolytes.yaml +228 -0
  141. endoreg_db/data/lab_value/gastrointestinal_function.yaml +133 -0
  142. endoreg_db/data/lab_value/hematology.yaml +184 -0
  143. endoreg_db/data/lab_value/hormones.yaml +59 -0
  144. endoreg_db/data/lab_value/lipids.yaml +53 -0
  145. endoreg_db/data/lab_value/misc.yaml +76 -0
  146. endoreg_db/data/lab_value/renal_function.yaml +12 -0
  147. endoreg_db/data/log_type/data.yaml +57 -0
  148. endoreg_db/data/lx_client_tag/base.yaml +54 -0
  149. endoreg_db/data/lx_client_type/base.yaml +30 -0
  150. endoreg_db/data/lx_permission/base.yaml +24 -0
  151. endoreg_db/data/lx_permission/endoreg.yaml +52 -0
  152. endoreg_db/data/material/material.yaml +91 -0
  153. endoreg_db/data/medication/anticoagulation.yaml +65 -0
  154. endoreg_db/data/medication/tah.yaml +70 -0
  155. endoreg_db/data/medication_indication/anticoagulation.yaml +115 -0
  156. endoreg_db/data/medication_indication_type/data.yaml +11 -0
  157. endoreg_db/data/medication_indication_type/thrombembolism.yaml +41 -0
  158. endoreg_db/data/medication_intake_time/base.yaml +31 -0
  159. endoreg_db/data/medication_schedule/apixaban.yaml +95 -0
  160. endoreg_db/data/medication_schedule/ass.yaml +12 -0
  161. endoreg_db/data/medication_schedule/enoxaparin.yaml +26 -0
  162. endoreg_db/data/names_first/first_names.yaml +54 -0
  163. endoreg_db/data/names_last/last_names.yaml +51 -0
  164. endoreg_db/data/network_device/data.yaml +59 -0
  165. endoreg_db/data/network_device_type/data.yaml +12 -0
  166. endoreg_db/data/organ/data.yaml +29 -0
  167. endoreg_db/data/patient_lab_sample_type/generic.yaml +6 -0
  168. endoreg_db/data/pdf_type/data.yaml +46 -0
  169. endoreg_db/data/product/green_endoscopy_dashboard_Product.yaml +66 -0
  170. endoreg_db/data/product_group/green_endoscopy_dashboard_ProductGroup.yaml +33 -0
  171. endoreg_db/data/product_material/green_endoscopy_dashboard_ProductMaterial.yaml +308 -0
  172. endoreg_db/data/product_weight/green_endoscopy_dashboard_ProductWeight.yaml +88 -0
  173. endoreg_db/data/profession/data.yaml +70 -0
  174. endoreg_db/data/qualification/endoscopy.yaml +36 -0
  175. endoreg_db/data/qualification/m2.yaml +39 -0
  176. endoreg_db/data/qualification/outpatient_clinic.yaml +35 -0
  177. endoreg_db/data/qualification/sonography.yaml +36 -0
  178. endoreg_db/data/qualification_type/base.yaml +29 -0
  179. endoreg_db/data/reference_product/green_endoscopy_dashboard_ReferenceProduct.yaml +55 -0
  180. endoreg_db/data/report_reader_flag/rkh-histology-generic.yaml +10 -0
  181. endoreg_db/data/report_reader_flag/ukw-examination-generic.yaml +30 -0
  182. endoreg_db/data/report_reader_flag/ukw-histology-generic.yaml +24 -0
  183. endoreg_db/data/requirement/age.yaml +26 -0
  184. endoreg_db/data/requirement/colonoscopy_baseline_austria.yaml +45 -0
  185. endoreg_db/data/requirement/disease_cardiovascular.yaml +79 -0
  186. endoreg_db/data/requirement/disease_classification_choice_cardiovascular.yaml +41 -0
  187. endoreg_db/data/requirement/disease_hepatology.yaml +12 -0
  188. endoreg_db/data/requirement/disease_misc.yaml +12 -0
  189. endoreg_db/data/requirement/disease_renal.yaml +96 -0
  190. endoreg_db/data/requirement/endoscopy_bleeding_risk.yaml +59 -0
  191. endoreg_db/data/requirement/event_cardiology.yaml +251 -0
  192. endoreg_db/data/requirement/event_requirements.yaml +145 -0
  193. endoreg_db/data/requirement/finding_colon_polyp.yaml +50 -0
  194. endoreg_db/data/requirement/gender.yaml +25 -0
  195. endoreg_db/data/requirement/lab_value.yaml +441 -0
  196. endoreg_db/data/requirement/medication.yaml +93 -0
  197. endoreg_db/data/requirement_operator/age.yaml +13 -0
  198. endoreg_db/data/requirement_operator/lab_operators.yaml +129 -0
  199. endoreg_db/data/requirement_operator/model_operators.yaml +96 -0
  200. endoreg_db/data/requirement_set/01_endoscopy_generic.yaml +48 -0
  201. endoreg_db/data/requirement_set/colonoscopy_austria_screening.yaml +57 -0
  202. endoreg_db/data/requirement_set/endoscopy_bleeding_risk.yaml +52 -0
  203. endoreg_db/data/requirement_set_type/data.yaml +20 -0
  204. endoreg_db/data/requirement_type/requirement_types.yaml +165 -0
  205. endoreg_db/data/resource/green_endoscopy_dashboard_Resource.yaml +15 -0
  206. endoreg_db/data/risk/bleeding.yaml +26 -0
  207. endoreg_db/data/risk/thrombosis.yaml +37 -0
  208. endoreg_db/data/risk_type/data.yaml +27 -0
  209. endoreg_db/data/setup_config.yaml +38 -0
  210. endoreg_db/data/shift/endoscopy.yaml +21 -0
  211. endoreg_db/data/shift/m2.yaml +0 -0
  212. endoreg_db/data/shift_type/base.yaml +35 -0
  213. endoreg_db/data/tag/requirement_set_tags.yaml +11 -0
  214. endoreg_db/data/tmp/chronic_kidney_disease.yaml +0 -0
  215. endoreg_db/data/tmp/congestive_heart_failure.yaml +0 -0
  216. endoreg_db/data/transport_route/green_endoscopy_dashboard_TransportRoute.yaml +12 -0
  217. endoreg_db/data/unit/concentration.yaml +115 -0
  218. endoreg_db/data/unit/data.yaml +17 -0
  219. endoreg_db/data/unit/length.yaml +31 -0
  220. endoreg_db/data/unit/misc.yaml +20 -0
  221. endoreg_db/data/unit/rate.yaml +6 -0
  222. endoreg_db/data/unit/time.yaml +48 -0
  223. endoreg_db/data/unit/volume.yaml +35 -0
  224. endoreg_db/data/unit/weight.yaml +38 -0
  225. endoreg_db/data/waste/data.yaml +12 -0
  226. endoreg_db/exceptions.py +19 -0
  227. endoreg_db/factories/__init__.py +0 -0
  228. endoreg_db/forms/__init__.py +5 -0
  229. endoreg_db/forms/examination_form.py +11 -0
  230. endoreg_db/forms/patient_finding_intervention_form.py +18 -0
  231. endoreg_db/forms/patient_form.py +27 -0
  232. endoreg_db/forms/questionnaires/__init__.py +1 -0
  233. endoreg_db/forms/questionnaires/tto_questionnaire.py +23 -0
  234. endoreg_db/forms/settings/__init__.py +8 -0
  235. endoreg_db/forms/unit.py +6 -0
  236. endoreg_db/helpers/__init__.py +0 -0
  237. endoreg_db/helpers/count_db.py +45 -0
  238. endoreg_db/helpers/data_loader.py +208 -0
  239. endoreg_db/helpers/default_objects.py +378 -0
  240. endoreg_db/helpers/download_segmentation_model.py +31 -0
  241. endoreg_db/helpers/interact.py +6 -0
  242. endoreg_db/helpers/test_video_helper.py +119 -0
  243. endoreg_db/logger_conf.py +140 -0
  244. endoreg_db/management/__init__.py +1 -0
  245. endoreg_db/management/commands/__init__.py +1 -0
  246. endoreg_db/management/commands/anonymize_video.py +0 -0
  247. endoreg_db/management/commands/check_auth.py +125 -0
  248. endoreg_db/management/commands/create_model_meta_from_huggingface.py +115 -0
  249. endoreg_db/management/commands/create_multilabel_model_meta.py +214 -0
  250. endoreg_db/management/commands/fix_missing_patient_data.py +172 -0
  251. endoreg_db/management/commands/fix_video_paths.py +165 -0
  252. endoreg_db/management/commands/import_fallback_video.py +203 -0
  253. endoreg_db/management/commands/import_report.py +298 -0
  254. endoreg_db/management/commands/import_video.py +423 -0
  255. endoreg_db/management/commands/import_video_with_classification.py +367 -0
  256. endoreg_db/management/commands/init_default_ai_model.py +112 -0
  257. endoreg_db/management/commands/load_ai_model_data.py +77 -0
  258. endoreg_db/management/commands/load_ai_model_label_data.py +59 -0
  259. endoreg_db/management/commands/load_base_db_data.py +192 -0
  260. endoreg_db/management/commands/load_center_data.py +68 -0
  261. endoreg_db/management/commands/load_contraindication_data.py +41 -0
  262. endoreg_db/management/commands/load_disease_classification_choices_data.py +41 -0
  263. endoreg_db/management/commands/load_disease_classification_data.py +41 -0
  264. endoreg_db/management/commands/load_disease_data.py +62 -0
  265. endoreg_db/management/commands/load_distribution_data.py +66 -0
  266. endoreg_db/management/commands/load_endoscope_data.py +68 -0
  267. endoreg_db/management/commands/load_event_data.py +41 -0
  268. endoreg_db/management/commands/load_examination_data.py +75 -0
  269. endoreg_db/management/commands/load_examination_indication_data.py +86 -0
  270. endoreg_db/management/commands/load_finding_data.py +128 -0
  271. endoreg_db/management/commands/load_gender_data.py +44 -0
  272. endoreg_db/management/commands/load_green_endoscopy_wuerzburg_data.py +132 -0
  273. endoreg_db/management/commands/load_information_source.py +51 -0
  274. endoreg_db/management/commands/load_lab_value_data.py +50 -0
  275. endoreg_db/management/commands/load_medication_data.py +103 -0
  276. endoreg_db/management/commands/load_name_data.py +37 -0
  277. endoreg_db/management/commands/load_organ_data.py +43 -0
  278. endoreg_db/management/commands/load_pdf_type_data.py +61 -0
  279. endoreg_db/management/commands/load_profession_data.py +44 -0
  280. endoreg_db/management/commands/load_qualification_data.py +59 -0
  281. endoreg_db/management/commands/load_report_reader_flag_data.py +46 -0
  282. endoreg_db/management/commands/load_requirement_data.py +180 -0
  283. endoreg_db/management/commands/load_risk_data.py +56 -0
  284. endoreg_db/management/commands/load_shift_data.py +60 -0
  285. endoreg_db/management/commands/load_tag_data.py +57 -0
  286. endoreg_db/management/commands/load_unit_data.py +46 -0
  287. endoreg_db/management/commands/load_user_groups.py +28 -0
  288. endoreg_db/management/commands/register_ai_model.py +64 -0
  289. endoreg_db/management/commands/reset_celery_schedule.py +9 -0
  290. endoreg_db/management/commands/setup_endoreg_db.py +381 -0
  291. endoreg_db/management/commands/start_filewatcher.py +106 -0
  292. endoreg_db/management/commands/storage_management.py +548 -0
  293. endoreg_db/management/commands/summarize_db_content.py +189 -0
  294. endoreg_db/management/commands/validate_video.py +204 -0
  295. endoreg_db/management/commands/validate_video_files.py +161 -0
  296. endoreg_db/management/commands/video_validation.py +22 -0
  297. endoreg_db/mermaid/Overall_flow_patient_finding_intervention.md +10 -0
  298. endoreg_db/mermaid/anonymized_image_annotation.md +20 -0
  299. endoreg_db/mermaid/binary_classification_annotation.md +50 -0
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  607. endoreg_db/tasks/video_processing_tasks.py +327 -0
  608. endoreg_db/templates/admin/patient_finding_intervention.html +253 -0
  609. endoreg_db/templates/admin/start_examination.html +12 -0
  610. endoreg_db/templates/timeline.html +176 -0
  611. endoreg_db/urls/__init__.py +70 -0
  612. endoreg_db/urls/anonymization.py +32 -0
  613. endoreg_db/urls/auth.py +16 -0
  614. endoreg_db/urls/classification.py +39 -0
  615. endoreg_db/urls/examination.py +54 -0
  616. endoreg_db/urls/files.py +6 -0
  617. endoreg_db/urls/label_video_segment_validate.py +33 -0
  618. endoreg_db/urls/label_video_segments.py +44 -0
  619. endoreg_db/urls/media.py +226 -0
  620. endoreg_db/urls/patient.py +19 -0
  621. endoreg_db/urls/report.py +48 -0
  622. endoreg_db/urls/requirements.py +13 -0
  623. endoreg_db/urls/sensitive_meta.py +0 -0
  624. endoreg_db/urls/stats.py +46 -0
  625. endoreg_db/urls/upload.py +20 -0
  626. endoreg_db/urls/video.py +61 -0
  627. endoreg_db/urls.py +9 -0
  628. endoreg_db/utils/__init__.py +88 -0
  629. endoreg_db/utils/ai/__init__.py +9 -0
  630. endoreg_db/utils/ai/get.py +5 -0
  631. endoreg_db/utils/ai/inference_dataset.py +52 -0
  632. endoreg_db/utils/ai/multilabel_classification_net.py +159 -0
  633. endoreg_db/utils/ai/postprocess.py +63 -0
  634. endoreg_db/utils/ai/predict.py +291 -0
  635. endoreg_db/utils/ai/preprocess.py +68 -0
  636. endoreg_db/utils/calc_duration_seconds.py +24 -0
  637. endoreg_db/utils/case_generator/__init__.py +0 -0
  638. endoreg_db/utils/case_generator/case_generator.py +159 -0
  639. endoreg_db/utils/case_generator/lab_sample_factory.py +33 -0
  640. endoreg_db/utils/case_generator/utils.py +30 -0
  641. endoreg_db/utils/check_video_files.py +148 -0
  642. endoreg_db/utils/cropping.py +29 -0
  643. endoreg_db/utils/dataloader.py +175 -0
  644. endoreg_db/utils/dates.py +60 -0
  645. endoreg_db/utils/env.py +33 -0
  646. endoreg_db/utils/extract_specific_frames.py +72 -0
  647. endoreg_db/utils/file_operations.py +58 -0
  648. endoreg_db/utils/fix_video_path_direct.py +141 -0
  649. endoreg_db/utils/frame_anonymization_utils.py +463 -0
  650. endoreg_db/utils/hashs.py +153 -0
  651. endoreg_db/utils/links/__init__.py +0 -0
  652. endoreg_db/utils/links/requirement_link.py +193 -0
  653. endoreg_db/utils/mime_types.py +0 -0
  654. endoreg_db/utils/names.py +76 -0
  655. endoreg_db/utils/ocr.py +190 -0
  656. endoreg_db/utils/parse_and_generate_yaml.py +46 -0
  657. endoreg_db/utils/paths.py +95 -0
  658. endoreg_db/utils/permissions.py +143 -0
  659. endoreg_db/utils/pipelines/Readme.md +235 -0
  660. endoreg_db/utils/pipelines/__init__.py +0 -0
  661. endoreg_db/utils/pipelines/process_video_dir.py +120 -0
  662. endoreg_db/utils/product/__init__.py +0 -0
  663. endoreg_db/utils/product/sum_emissions.py +20 -0
  664. endoreg_db/utils/product/sum_weights.py +18 -0
  665. endoreg_db/utils/pydantic_models/__init__.py +6 -0
  666. endoreg_db/utils/pydantic_models/db_config.py +57 -0
  667. endoreg_db/utils/requirement_helpers.py +0 -0
  668. endoreg_db/utils/requirement_operator_logic/__init__.py +0 -0
  669. endoreg_db/utils/requirement_operator_logic/lab_value_operators.py +578 -0
  670. endoreg_db/utils/requirement_operator_logic/model_evaluators.py +368 -0
  671. endoreg_db/utils/setup_config.py +177 -0
  672. endoreg_db/utils/translation.py +27 -0
  673. endoreg_db/utils/uuid.py +4 -0
  674. endoreg_db/utils/validate_endo_roi.py +19 -0
  675. endoreg_db/utils/validate_subcategory_dict.py +91 -0
  676. endoreg_db/utils/validate_video_detailed.py +357 -0
  677. endoreg_db/utils/video/__init__.py +26 -0
  678. endoreg_db/utils/video/extract_frames.py +88 -0
  679. endoreg_db/utils/video/ffmpeg_wrapper.py +835 -0
  680. endoreg_db/utils/video/names.py +42 -0
  681. endoreg_db/utils/video/streaming_processor.py +312 -0
  682. endoreg_db/utils/video/video_splitter.py +94 -0
  683. endoreg_db/views/Frames_NICE_and_PARIS_classifications_views.py +238 -0
  684. endoreg_db/views/__init__.py +272 -0
  685. endoreg_db/views/anonymization/__init__.py +27 -0
  686. endoreg_db/views/anonymization/media_management.py +454 -0
  687. endoreg_db/views/anonymization/overview.py +216 -0
  688. endoreg_db/views/anonymization/validate.py +107 -0
  689. endoreg_db/views/auth/__init__.py +13 -0
  690. endoreg_db/views/auth/keycloak.py +113 -0
  691. endoreg_db/views/examination/__init__.py +33 -0
  692. endoreg_db/views/examination/examination.py +37 -0
  693. endoreg_db/views/examination/examination_manifest_cache.py +26 -0
  694. endoreg_db/views/examination/get_finding_classification_choices.py +59 -0
  695. endoreg_db/views/examination/get_finding_classifications.py +36 -0
  696. endoreg_db/views/examination/get_findings.py +41 -0
  697. endoreg_db/views/examination/get_instruments.py +18 -0
  698. endoreg_db/views/examination/get_interventions.py +14 -0
  699. endoreg_db/views/finding/__init__.py +9 -0
  700. endoreg_db/views/finding/finding.py +112 -0
  701. endoreg_db/views/finding/get_classifications.py +14 -0
  702. endoreg_db/views/finding/get_interventions.py +17 -0
  703. endoreg_db/views/finding_classification/__init__.py +13 -0
  704. endoreg_db/views/finding_classification/base.py +0 -0
  705. endoreg_db/views/finding_classification/finding_classification.py +42 -0
  706. endoreg_db/views/finding_classification/get_classification_choices.py +55 -0
  707. endoreg_db/views/label/__init__.py +5 -0
  708. endoreg_db/views/label/label.py +15 -0
  709. endoreg_db/views/label_video_segment/__init__.py +16 -0
  710. endoreg_db/views/label_video_segment/create_lvs_from_annotation.py +44 -0
  711. endoreg_db/views/label_video_segment/get_lvs_by_name_and_video.py +50 -0
  712. endoreg_db/views/label_video_segment/label_video_segment.py +77 -0
  713. endoreg_db/views/label_video_segment/label_video_segment_by_label.py +174 -0
  714. endoreg_db/views/label_video_segment/label_video_segment_detail.py +73 -0
  715. endoreg_db/views/label_video_segment/update_lvs_from_annotation.py +46 -0
  716. endoreg_db/views/label_video_segment/validate.py +226 -0
  717. endoreg_db/views/media/__init__.py +45 -0
  718. endoreg_db/views/media/pdf_media.py +386 -0
  719. endoreg_db/views/media/segments.py +71 -0
  720. endoreg_db/views/media/sensitive_metadata.py +314 -0
  721. endoreg_db/views/media/video_media.py +272 -0
  722. endoreg_db/views/media/video_segments.py +524 -0
  723. endoreg_db/views/meta/__init__.py +15 -0
  724. endoreg_db/views/meta/available_files_list.py +146 -0
  725. endoreg_db/views/meta/report_meta.py +53 -0
  726. endoreg_db/views/meta/sensitive_meta_detail.py +148 -0
  727. endoreg_db/views/meta/sensitive_meta_list.py +104 -0
  728. endoreg_db/views/meta/sensitive_meta_verification.py +71 -0
  729. endoreg_db/views/misc/__init__.py +63 -0
  730. endoreg_db/views/misc/center.py +13 -0
  731. endoreg_db/views/misc/csrf.py +7 -0
  732. endoreg_db/views/misc/gender.py +14 -0
  733. endoreg_db/views/misc/secure_file_serving_view.py +80 -0
  734. endoreg_db/views/misc/secure_file_url_view.py +84 -0
  735. endoreg_db/views/misc/secure_url_validate.py +79 -0
  736. endoreg_db/views/misc/stats.py +220 -0
  737. endoreg_db/views/misc/translation.py +182 -0
  738. endoreg_db/views/misc/upload_views.py +240 -0
  739. endoreg_db/views/patient/__init__.py +5 -0
  740. endoreg_db/views/patient/patient.py +210 -0
  741. endoreg_db/views/patient_examination/DEPRECATED_video_backup.py +164 -0
  742. endoreg_db/views/patient_examination/__init__.py +11 -0
  743. endoreg_db/views/patient_examination/patient_examination.py +140 -0
  744. endoreg_db/views/patient_examination/patient_examination_create.py +63 -0
  745. endoreg_db/views/patient_examination/patient_examination_detail.py +66 -0
  746. endoreg_db/views/patient_examination/patient_examination_list.py +68 -0
  747. endoreg_db/views/patient_examination/video.py +194 -0
  748. endoreg_db/views/patient_finding/__init__.py +7 -0
  749. endoreg_db/views/patient_finding/base.py +0 -0
  750. endoreg_db/views/patient_finding/patient_finding.py +64 -0
  751. endoreg_db/views/patient_finding/patient_finding_optimized.py +259 -0
  752. endoreg_db/views/patient_finding_classification/__init__.py +5 -0
  753. endoreg_db/views/patient_finding_classification/pfc_create.py +67 -0
  754. endoreg_db/views/patient_finding_location/__init__.py +5 -0
  755. endoreg_db/views/patient_finding_location/pfl_create.py +70 -0
  756. endoreg_db/views/patient_finding_morphology/__init__.py +5 -0
  757. endoreg_db/views/patient_finding_morphology/pfm_create.py +70 -0
  758. endoreg_db/views/pdf/__init__.py +11 -0
  759. endoreg_db/views/pdf/pdf_media.py +239 -0
  760. endoreg_db/views/pdf/pdf_stream_views.py +127 -0
  761. endoreg_db/views/pdf/reimport.py +161 -0
  762. endoreg_db/views/report/__init__.py +9 -0
  763. endoreg_db/views/report/report_list.py +112 -0
  764. endoreg_db/views/report/report_with_secure_url.py +28 -0
  765. endoreg_db/views/report/start_examination.py +7 -0
  766. endoreg_db/views/requirement/__init__.py +10 -0
  767. endoreg_db/views/requirement/evaluate.py +279 -0
  768. endoreg_db/views/requirement/lookup.py +483 -0
  769. endoreg_db/views/requirement/lookup_store.py +252 -0
  770. endoreg_db/views/requirement_lookup/lookup.py +0 -0
  771. endoreg_db/views/requirement_lookup/lookup_store.py +0 -0
  772. endoreg_db/views/stats/__init__.py +13 -0
  773. endoreg_db/views/stats/stats_views.py +229 -0
  774. endoreg_db/views/video/__init__.py +61 -0
  775. endoreg_db/views/video/correction.py +530 -0
  776. endoreg_db/views/video/reimport.py +195 -0
  777. endoreg_db/views/video/segmentation.py +274 -0
  778. endoreg_db/views/video/task_status.py +49 -0
  779. endoreg_db/views/video/timeline.py +46 -0
  780. endoreg_db/views/video/video_analyze.py +52 -0
  781. endoreg_db/views/video/video_apply_mask.py +48 -0
  782. endoreg_db/views/video/video_correction.py +21 -0
  783. endoreg_db/views/video/video_download_processed.py +58 -0
  784. endoreg_db/views/video/video_examination_viewset.py +329 -0
  785. endoreg_db/views/video/video_media.py +158 -0
  786. endoreg_db/views/video/video_meta.py +29 -0
  787. endoreg_db/views/video/video_processing_history.py +24 -0
  788. endoreg_db/views/video/video_remove_frames.py +48 -0
  789. endoreg_db/views/video/video_stream.py +306 -0
  790. endoreg_db/views.py +0 -0
  791. endoreg_db-0.8.5.1.dist-info/METADATA +383 -0
  792. endoreg_db-0.8.5.1.dist-info/RECORD +794 -0
  793. endoreg_db-0.8.5.1.dist-info/WHEEL +4 -0
  794. endoreg_db-0.8.5.1.dist-info/licenses/LICENSE +674 -0
@@ -0,0 +1,730 @@
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(s, settings={"DATE_ORDER": "DMY", "PREFER_DAY_OF_MONTH": "first"})
84
+ return dt.date() if dt else None
85
+ except Exception as e:
86
+ logger.debug(f"Dateparser fallback failed for '{s}': {e}")
87
+ return None
88
+
89
+
90
+ def format_date_german(d: Optional[date]) -> str:
91
+ """
92
+ Formatiert date-Objekt als deutsches Datumsformat (DD.MM.YYYY).
93
+
94
+ Args:
95
+ d: date-Objekt oder None
96
+
97
+ Returns:
98
+ Formatiertes Datum als String oder leerer String bei None
99
+ """
100
+ if not d:
101
+ return ""
102
+ return d.strftime("%d.%m.%Y")
103
+
104
+
105
+ def format_date_iso(d: Optional[date]) -> str:
106
+ """
107
+ Formatiert date-Objekt als ISO-Format (YYYY-MM-DD).
108
+
109
+ Args:
110
+ d: date-Objekt oder None
111
+
112
+ Returns:
113
+ Formatiertes Datum als String oder leerer String bei None
114
+ """
115
+ if not d:
116
+ return ""
117
+ return d.isoformat()
118
+
119
+
120
+ def generate_random_dob() -> datetime:
121
+ """Generates a random timezone-aware datetime between 1920-01-01 and 2000-12-31."""
122
+ start_date = date(1920, 1, 1)
123
+ end_date = date(2000, 12, 31)
124
+ time_between_dates = end_date - start_date
125
+ days_between_dates = time_between_dates.days
126
+ random_number_of_days = random.randrange(days_between_dates)
127
+ random_date = start_date + timedelta(days=random_number_of_days)
128
+ random_datetime = datetime.combine(random_date, datetime.min.time())
129
+ return timezone.make_aware(random_datetime)
130
+
131
+
132
+ def generate_random_examination_date() -> date:
133
+ """Generates a random date within the last 20 years."""
134
+ today = date.today()
135
+ start_date = today - timedelta(days=20 * 365) # Approximate 20 years back
136
+ time_between_dates = today - start_date
137
+ days_between_dates = time_between_dates.days
138
+ random_number_of_days = random.randrange(days_between_dates)
139
+ random_date = start_date + timedelta(days=random_number_of_days)
140
+ return random_date
141
+
142
+
143
+ def update_name_db(first_name: Optional[str], last_name: Optional[str]):
144
+ """Adds first and last names to the respective lookup tables if they don't exist."""
145
+ if first_name:
146
+ FirstName.objects.get_or_create(name=first_name)
147
+ if last_name:
148
+ LastName.objects.get_or_create(name=last_name)
149
+
150
+
151
+ def calculate_patient_hash(instance: "SensitiveMeta", salt: str = SECRET_SALT) -> str:
152
+ """Calculates the patient hash for the instance."""
153
+ dob = instance.patient_dob
154
+ first_name = instance.patient_first_name
155
+ last_name = instance.patient_last_name
156
+ center = instance.center
157
+
158
+ if not dob:
159
+ raise ValueError("Patient DOB is required to calculate patient hash.")
160
+ if not center:
161
+ raise ValueError("Center is required to calculate patient hash.")
162
+
163
+ assert first_name is not None, "First name is required to calculate patient hash."
164
+ assert last_name is not None, "Last name is required to calculate patient hash."
165
+
166
+ hash_str = get_patient_hash(
167
+ first_name=first_name,
168
+ last_name=last_name,
169
+ dob=dob,
170
+ center=center.name, # Use center name
171
+ salt=salt,
172
+ )
173
+ return sha256(hash_str.encode()).hexdigest()
174
+
175
+
176
+ def calculate_examination_hash(instance: "SensitiveMeta", salt: str = SECRET_SALT) -> str:
177
+ """Calculates the examination hash for the instance."""
178
+ dob = instance.patient_dob
179
+ first_name = instance.patient_first_name
180
+ last_name = instance.patient_last_name
181
+ examination_date = instance.examination_date
182
+ center = instance.center
183
+
184
+ if not dob:
185
+ raise ValueError("Patient DOB is required to calculate examination hash.")
186
+ if not examination_date:
187
+ raise ValueError("Examination date is required to calculate examination hash.")
188
+ if not center:
189
+ raise ValueError("Center is required to calculate examination hash.")
190
+
191
+ hash_str = get_patient_examination_hash(
192
+ first_name=first_name,
193
+ last_name=last_name,
194
+ dob=dob,
195
+ examination_date=examination_date,
196
+ center=center.name, # Use center name
197
+ salt=salt,
198
+ )
199
+ return sha256(hash_str.encode()).hexdigest()
200
+
201
+
202
+ def create_pseudo_examiner_logic(instance: "SensitiveMeta") -> "Examiner":
203
+ """Creates or retrieves the pseudo examiner based on instance data."""
204
+ first_name = instance.examiner_first_name
205
+ last_name = instance.examiner_last_name
206
+ center = instance.center # Should be set before calling save
207
+
208
+ if not first_name or not last_name or not center:
209
+ logger.warning(f"Incomplete examiner info for SensitiveMeta (pk={instance.pk or 'new'}). Using default examiner.")
210
+ # Ensure default center exists or handle appropriately
211
+ try:
212
+ default_center = Center.objects.get_by_natural_key("endoreg_db_demo")
213
+ except Center.DoesNotExist:
214
+ logger.error("Default center 'endoreg_db_demo' not found. Cannot create default examiner.")
215
+ raise ValueError("Default center 'endoreg_db_demo' not found.")
216
+
217
+ examiner, _created = Examiner.custom_get_or_create(first_name="Unknown", last_name="Unknown", center=default_center)
218
+ else:
219
+ examiner, _created = Examiner.custom_get_or_create(first_name=first_name, last_name=last_name, center=center)
220
+
221
+ return examiner
222
+
223
+
224
+ def get_or_create_pseudo_patient_logic(instance: "SensitiveMeta") -> "Patient":
225
+ """Gets or creates the pseudo patient based on instance data."""
226
+ # Ensure necessary fields are set
227
+ if not instance.patient_hash:
228
+ instance.patient_hash = calculate_patient_hash(instance)
229
+ if not instance.center:
230
+ raise ValueError("Center must be set before creating pseudo patient.")
231
+ if not instance.patient_gender:
232
+ raise ValueError("Patient gender must be set before creating pseudo patient.")
233
+ if not instance.patient_dob:
234
+ raise ValueError("Patient DOB must be set before creating pseudo patient.")
235
+
236
+ dob = instance.patient_dob
237
+ year = dob.year
238
+ month = dob.month
239
+
240
+ patient, _created = Patient.get_or_create_pseudo_patient_by_hash(
241
+ patient_hash=instance.patient_hash,
242
+ center=instance.center,
243
+ gender=instance.patient_gender,
244
+ birth_year=year,
245
+ birth_month=month,
246
+ )
247
+ return patient
248
+
249
+
250
+ def get_or_create_pseudo_patient_examination_logic(
251
+ instance: "SensitiveMeta",
252
+ ) -> "PatientExamination":
253
+ """Gets or creates the pseudo patient examination based on instance data."""
254
+ # Ensure necessary fields are set
255
+ if not instance.patient_hash:
256
+ instance.patient_hash = calculate_patient_hash(instance)
257
+ if not instance.examination_hash:
258
+ instance.examination_hash = calculate_examination_hash(instance)
259
+
260
+ # Ensure the pseudo patient exists first, as PatientExamination might depend on it
261
+ if not instance.pseudo_patient_id:
262
+ pseudo_patient = get_or_create_pseudo_patient_logic(instance)
263
+ instance.pseudo_patient_id = pseudo_patient.pk # Assign FK directly
264
+
265
+ patient_examination, _created = PatientExamination.get_or_create_pseudo_patient_examination_by_hash(
266
+ patient_hash=instance.patient_hash,
267
+ examination_hash=instance.examination_hash,
268
+ # Optionally pass pseudo_patient if the method requires it
269
+ # pseudo_patient=instance.pseudo_patient
270
+ )
271
+ return patient_examination
272
+
273
+
274
+ @transaction.atomic # Ensure all operations within save succeed or fail together
275
+ def perform_save_logic(instance: "SensitiveMeta") -> "Examiner":
276
+ """
277
+ Contains the core logic for preparing a SensitiveMeta instance for saving.
278
+ Handles data generation (dates), hash calculation, and linking pseudo-entities.
279
+ Returns the Examiner instance to be linked via M2M after the main save.
280
+ """
281
+
282
+ # --- Pre-Save Checks and Data Generation ---
283
+
284
+ # 1. Ensure DOB and Examination Date exist
285
+ if not instance.patient_dob:
286
+ logger.debug(f"SensitiveMeta (pk={instance.pk or 'new'}): Patient DOB missing, generating random.")
287
+ instance.patient_dob = generate_random_dob()
288
+ if not instance.examination_date:
289
+ logger.debug(f"SensitiveMeta (pk={instance.pk or 'new'}): Examination date missing, generating random.")
290
+ instance.examination_date = generate_random_examination_date()
291
+
292
+ # 2. Ensure Center exists (should be set before calling save)
293
+ if not instance.center:
294
+ raise ValueError("Center must be set before saving SensitiveMeta.")
295
+
296
+ # 3. Ensure Gender exists (should be set before calling save, e.g., during creation/update)
297
+ if not instance.patient_gender:
298
+ # Attempt to guess if names are available
299
+ first_name = instance.patient_first_name or DEFAULT_UNKNOWN_NAME
300
+ gender = guess_name_gender(first_name)
301
+ if not gender:
302
+ raise ValueError("Patient gender could not be determined and must be set before saving.")
303
+ instance.patient_gender = gender
304
+
305
+ # 4. Calculate Hashes (depends on DOB, Exam Date, Center, Names)
306
+ instance.patient_hash = calculate_patient_hash(instance)
307
+ instance.examination_hash = calculate_examination_hash(instance)
308
+
309
+ # 5. Get or Create Pseudo Patient (depends on hash, center, gender, dob)
310
+ # Assign directly to the FK field to avoid premature saving issues
311
+ pseudo_patient = get_or_create_pseudo_patient_logic(instance)
312
+ instance.pseudo_patient_id = pseudo_patient.pk
313
+
314
+ # 6. Get or Create Pseudo Examination (depends on hashes)
315
+ # Assign directly to the FK field
316
+ pseudo_examination = get_or_create_pseudo_patient_examination_logic(instance)
317
+ instance.pseudo_examination_id = pseudo_examination.pk
318
+
319
+ # 7. Get or Create Pseudo Examiner (depends on names, center)
320
+ # This needs to happen *after* the main instance has a PK for M2M linking.
321
+ # We create/get it here and return it to the main save method.
322
+ examiner_instance = create_pseudo_examiner_logic(instance)
323
+
324
+ # 8. Ensure SensitiveMetaState exists (will be checked/created *after* main save)
325
+
326
+ # Return the examiner instance so the model's save method can handle M2M linking
327
+ return examiner_instance
328
+
329
+
330
+ def create_sensitive_meta_from_dict(cls: Type["SensitiveMeta"], data: Dict[str, Any]) -> "SensitiveMeta":
331
+ """Logic to create a SensitiveMeta instance from a dictionary."""
332
+
333
+ field_names = {f.name for f in cls._meta.get_fields() if not f.is_relation or f.one_to_one or (f.many_to_one and f.related_model)}
334
+ selected_data = {k: v for k, v in data.items() if k in field_names}
335
+
336
+ # --- Convert patient_dob if it's a date object ---
337
+ dob = selected_data.get("patient_dob")
338
+ if isinstance(dob, date) and not isinstance(dob, datetime):
339
+ # Convert date to datetime at the start of the day and make it timezone-aware
340
+ aware_dob = timezone.make_aware(datetime.combine(dob, datetime.min.time()))
341
+ selected_data["patient_dob"] = aware_dob
342
+ logger.debug("Converted patient_dob from date to aware datetime: %s", aware_dob)
343
+ elif isinstance(dob, str):
344
+ # Handle string DOB - check if it's a field name or actual date
345
+ if dob == "patient_dob" or dob in [
346
+ "patient_first_name",
347
+ "patient_last_name",
348
+ "examination_date",
349
+ ]:
350
+ logger.warning(
351
+ "Skipping invalid patient_dob value '%s' - appears to be field name",
352
+ dob,
353
+ )
354
+ selected_data.pop("patient_dob", None) # Remove invalid value
355
+ else:
356
+ # Try to parse as date string
357
+ try:
358
+ import dateparser
359
+
360
+ parsed_dob = dateparser.parse(dob, languages=["de"], settings={"DATE_ORDER": "DMY"})
361
+ if parsed_dob:
362
+ aware_dob = timezone.make_aware(parsed_dob.replace(hour=0, minute=0, second=0, microsecond=0))
363
+ selected_data["patient_dob"] = aware_dob
364
+ logger.debug(
365
+ "Parsed string patient_dob '%s' to aware datetime: %s",
366
+ dob,
367
+ aware_dob,
368
+ )
369
+ else:
370
+ logger.warning(
371
+ "Could not parse patient_dob string '%s', removing from data",
372
+ dob,
373
+ )
374
+ selected_data.pop("patient_dob", None)
375
+ except Exception as e:
376
+ logger.warning(
377
+ "Error parsing patient_dob string '%s': %s, removing from data",
378
+ dob,
379
+ e,
380
+ )
381
+ selected_data.pop("patient_dob", None)
382
+ # --- End Conversion ---
383
+
384
+ # Similar validation for examination_date
385
+ exam_date = selected_data.get("examination_date")
386
+ if isinstance(exam_date, str):
387
+ if exam_date == "examination_date" or exam_date in [
388
+ "patient_first_name",
389
+ "patient_last_name",
390
+ "patient_dob",
391
+ ]:
392
+ logger.warning(
393
+ "Skipping invalid examination_date value '%s' - appears to be field name",
394
+ exam_date,
395
+ )
396
+ selected_data.pop("examination_date", None)
397
+ else:
398
+ # Try to parse as date string
399
+ try:
400
+ # First try simple ISO format for YYYY-MM-DD
401
+ if len(exam_date) == 10 and exam_date.count("-") == 2:
402
+ try:
403
+ from datetime import datetime as dt
404
+
405
+ parsed_date = dt.strptime(exam_date, "%Y-%m-%d").date()
406
+ selected_data["examination_date"] = parsed_date
407
+ logger.debug(
408
+ "Parsed ISO examination_date '%s' to date: %s",
409
+ exam_date,
410
+ parsed_date,
411
+ )
412
+ except ValueError:
413
+ # Fall back to dateparser for complex formats
414
+ import dateparser
415
+
416
+ parsed_date = dateparser.parse(exam_date, languages=["de"], settings={"DATE_ORDER": "DMY"})
417
+ if parsed_date:
418
+ selected_data["examination_date"] = parsed_date.date()
419
+ logger.debug(
420
+ "Parsed string examination_date '%s' to date: %s",
421
+ exam_date,
422
+ parsed_date.date(),
423
+ )
424
+ else:
425
+ logger.warning(
426
+ "Could not parse examination_date string '%s', removing from data",
427
+ exam_date,
428
+ )
429
+ selected_data.pop("examination_date", None)
430
+ else:
431
+ # Use dateparser for non-ISO formats
432
+ import dateparser
433
+
434
+ parsed_date = dateparser.parse(exam_date, languages=["de"], settings={"DATE_ORDER": "DMY"})
435
+ if parsed_date:
436
+ selected_data["examination_date"] = parsed_date.date()
437
+ logger.debug(
438
+ "Parsed string examination_date '%s' to date: %s",
439
+ exam_date,
440
+ parsed_date.date(),
441
+ )
442
+ else:
443
+ logger.warning(
444
+ "Could not parse examination_date string '%s', removing from data",
445
+ exam_date,
446
+ )
447
+ selected_data.pop("examination_date", None)
448
+ except Exception as e:
449
+ logger.warning(
450
+ "Error parsing examination_date string '%s': %s, removing from data",
451
+ exam_date,
452
+ e,
453
+ )
454
+ selected_data.pop("examination_date", None)
455
+
456
+ # Handle Center
457
+ center_name = data.get("center_name")
458
+ if not center_name:
459
+ raise ValueError("center_name is required in data dictionary.")
460
+ try:
461
+ center = Center.objects.get_by_natural_key(center_name)
462
+ selected_data["center"] = center
463
+ except Center.DoesNotExist as exc:
464
+ raise ValueError(f"Center with name '{center_name}' does not exist.") from exc
465
+
466
+ # Handle Names and Gender
467
+ first_name = selected_data.get("patient_first_name") or DEFAULT_UNKNOWN_NAME
468
+ last_name = selected_data.get("patient_last_name") or DEFAULT_UNKNOWN_NAME
469
+ selected_data["patient_first_name"] = first_name # Ensure defaults are set
470
+ selected_data["patient_last_name"] = last_name
471
+
472
+ patient_gender_input = selected_data.get("patient_gender")
473
+
474
+ if isinstance(patient_gender_input, Gender):
475
+ # Already a Gender object, nothing to do
476
+ pass
477
+ elif isinstance(patient_gender_input, str):
478
+ # Input is a string (gender name)
479
+ try:
480
+ selected_data["patient_gender"] = Gender.objects.get(name=patient_gender_input)
481
+ except Gender.DoesNotExist:
482
+ logger.warning(f"Gender with name '{patient_gender_input}' provided but not found. Attempting to guess or use default.")
483
+ # Fall through to guessing logic if provided string name is invalid
484
+ patient_gender_input = None # Reset to trigger guessing
485
+
486
+ if not isinstance(selected_data.get("patient_gender"), Gender): # If not already a Gender object (e.g. was None, or string lookup failed)
487
+ gender_name_to_use = guess_name_gender(first_name)
488
+ if not gender_name_to_use:
489
+ logger.warning(f"Could not guess gender for name '{first_name}'. Setting Gender to unknown.")
490
+ gender_name_to_use = "unknown"
491
+ try:
492
+ selected_data["patient_gender"] = Gender.objects.get(name=gender_name_to_use)
493
+ except Gender.DoesNotExist:
494
+ # This should ideally not happen if "unknown" gender is guaranteed to exist
495
+ raise ValueError(f"Default or guessed gender '{gender_name_to_use}' does not exist in Gender table.")
496
+
497
+ # Update name DB
498
+ update_name_db(first_name, last_name)
499
+
500
+ # Instantiate without saving yet
501
+ sensitive_meta = cls(**selected_data)
502
+
503
+ # Call save once at the end. This triggers the custom save logic.
504
+ sensitive_meta.save() # This will call perform_save_logic internally
505
+
506
+ return sensitive_meta
507
+
508
+
509
+ def update_sensitive_meta_from_dict(instance: "SensitiveMeta", data: Dict[str, Any]) -> "SensitiveMeta":
510
+ """Logic to update a SensitiveMeta instance from a dictionary."""
511
+ field_names = {f.name for f in instance._meta.get_fields() if not f.is_relation or f.one_to_one or (f.many_to_one and f.related_model)}
512
+ # Exclude FKs that should not be updated directly from dict keys (handled separately or via save logic)
513
+ excluded_fields = {"pseudo_patient", "pseudo_examination"}
514
+ selected_data = {k: v for k, v in data.items() if k in field_names and k not in excluded_fields}
515
+
516
+ # Handle potential Center update
517
+ center_name = data.get("center_name")
518
+ if center_name:
519
+ try:
520
+ center = Center.objects.get_by_natural_key(center_name)
521
+ instance.center = center # Update center directly
522
+ except Center.DoesNotExist as exc:
523
+ logger.warning(f"Center '{center_name}' not found during update. Keeping existing center.")
524
+ selected_data.pop("center", None) # Remove from dict if not found
525
+
526
+ # Set examiner names if provided, before calling save
527
+ examiner_first_name = data.get("examiner_first_name")
528
+ examiner_last_name = data.get("examiner_last_name")
529
+ if examiner_first_name is not None: # Allow setting empty strings
530
+ instance.examiner_first_name = examiner_first_name
531
+ if examiner_last_name is not None:
532
+ instance.examiner_last_name = examiner_last_name
533
+
534
+ # Handle patient_gender specially with graceful error handling
535
+ patient_gender_input = data.get("patient_gender")
536
+ if patient_gender_input is not None:
537
+ try:
538
+ if isinstance(patient_gender_input, Gender):
539
+ selected_data["patient_gender"] = patient_gender_input
540
+ elif isinstance(patient_gender_input, str):
541
+ gender_input_clean = patient_gender_input.strip()
542
+ # Try direct case-insensitive DB lookup first
543
+ gender_obj = Gender.objects.filter(name__iexact=gender_input_clean).first()
544
+ if gender_obj:
545
+ selected_data["patient_gender"] = gender_obj
546
+ logger.debug(f"Successfully matched gender string '{patient_gender_input}' to Gender object via iexact lookup")
547
+ else:
548
+ # Use mapping helper for fallback
549
+ mapped = _map_gender_string_to_standard(gender_input_clean)
550
+ if mapped:
551
+ gender_obj = Gender.objects.filter(name__iexact=mapped).first()
552
+ if gender_obj:
553
+ selected_data["patient_gender"] = gender_obj
554
+ logger.info(f"Mapped gender '{patient_gender_input}' to '{mapped}' via fallback mapping")
555
+ else:
556
+ logger.warning(f"Mapped gender '{patient_gender_input}' to '{mapped}', but no such Gender in DB. Trying 'unknown'.")
557
+ unknown_gender = Gender.objects.filter(name__iexact="unknown").first()
558
+ if unknown_gender:
559
+ selected_data["patient_gender"] = unknown_gender
560
+ logger.warning(f"Using 'unknown' gender as fallback for '{patient_gender_input}'")
561
+ else:
562
+ logger.error(f"No 'unknown' gender found in database. Cannot handle gender '{patient_gender_input}'. Skipping gender update.")
563
+ selected_data.pop("patient_gender", None)
564
+ else:
565
+ # Last resort: try to get 'unknown' gender
566
+ unknown_gender = Gender.objects.filter(name__iexact="unknown").first()
567
+ if unknown_gender:
568
+ selected_data["patient_gender"] = unknown_gender
569
+ logger.warning(f"Using 'unknown' gender as fallback for '{patient_gender_input}' (no mapping)")
570
+ else:
571
+ logger.error(f"No 'unknown' gender found in database. Cannot handle gender '{patient_gender_input}'. Skipping gender update.")
572
+ selected_data.pop("patient_gender", None)
573
+ else:
574
+ logger.warning(f"Unexpected patient_gender type {type(patient_gender_input)}: {patient_gender_input}. Skipping gender update.")
575
+ selected_data.pop("patient_gender", None)
576
+ except Exception as e:
577
+ logger.exception(f"Error handling patient_gender '{patient_gender_input}': {e}. Skipping gender update.")
578
+ selected_data.pop("patient_gender", None)
579
+
580
+ # Update other attributes from selected_data
581
+ patient_name_changed = False
582
+ for k, v in selected_data.items():
583
+ # Avoid overwriting examiner names if they were just explicitly set
584
+ if (
585
+ k not in ["examiner_first_name", "examiner_last_name"]
586
+ or (k == "examiner_first_name" and examiner_first_name is None)
587
+ or (k == "examiner_last_name" and examiner_last_name is None)
588
+ ):
589
+ try:
590
+ # --- Convert patient_dob if it's a date object ---
591
+ value_to_set = v
592
+ if k == "patient_dob":
593
+ if isinstance(v, date) and not isinstance(v, datetime):
594
+ aware_dob = timezone.make_aware(datetime.combine(v, datetime.min.time()))
595
+ value_to_set = aware_dob
596
+ logger.debug(
597
+ "Converted patient_dob from date to aware datetime during update: %s",
598
+ aware_dob,
599
+ )
600
+ elif isinstance(v, str):
601
+ # Handle string DOB - check if it's a field name or actual date
602
+ if v == "patient_dob" or v in [
603
+ "patient_first_name",
604
+ "patient_last_name",
605
+ "examination_date",
606
+ ]:
607
+ logger.warning(
608
+ "Skipping invalid patient_dob value '%s' during update - appears to be field name",
609
+ v,
610
+ )
611
+ continue # Skip this field
612
+ else:
613
+ # Try to parse as date string
614
+ try:
615
+ import dateparser
616
+
617
+ parsed_dob = dateparser.parse(v, languages=["de"], settings={"DATE_ORDER": "DMY"})
618
+ if parsed_dob:
619
+ value_to_set = timezone.make_aware(parsed_dob.replace(hour=0, minute=0, second=0, microsecond=0))
620
+ logger.debug(
621
+ "Parsed string patient_dob '%s' during update to aware datetime: %s",
622
+ v,
623
+ value_to_set,
624
+ )
625
+ else:
626
+ logger.warning(
627
+ "Could not parse patient_dob string '%s' during update, skipping",
628
+ v,
629
+ )
630
+ continue
631
+ except Exception as e:
632
+ logger.warning(
633
+ "Error parsing patient_dob string '%s' during update: %s, skipping",
634
+ v,
635
+ e,
636
+ )
637
+ continue
638
+ elif k == "examination_date" and isinstance(v, str):
639
+ if v == "examination_date" or v in [
640
+ "patient_first_name",
641
+ "patient_last_name",
642
+ "patient_dob",
643
+ ]:
644
+ logger.warning(
645
+ "Skipping invalid examination_date value '%s' during update - appears to be field name",
646
+ v,
647
+ )
648
+ continue
649
+ else:
650
+ # Try to parse as date string
651
+ try:
652
+ import dateparser
653
+
654
+ parsed_date = dateparser.parse(v, languages=["de"], settings={"DATE_ORDER": "DMY"})
655
+ if parsed_date:
656
+ value_to_set = parsed_date.date()
657
+ logger.debug(
658
+ "Parsed string examination_date '%s' during update to date: %s",
659
+ v,
660
+ value_to_set,
661
+ )
662
+ else:
663
+ logger.warning(
664
+ "Could not parse examination_date string '%s' during update, skipping",
665
+ v,
666
+ )
667
+ continue
668
+ except Exception as e:
669
+ logger.warning(
670
+ "Error parsing examination_date string '%s' during update: %s, skipping",
671
+ v,
672
+ e,
673
+ )
674
+ continue
675
+ # --- End Conversion ---
676
+
677
+ # Check if patient name is changing
678
+ if k in ["patient_first_name", "patient_last_name"] and getattr(instance, k) != value_to_set:
679
+ patient_name_changed = True
680
+
681
+ setattr(instance, k, value_to_set) # Use value_to_set
682
+
683
+ except Exception as e:
684
+ logger.error(f"Error setting attribute '{k}' to '{v}': {e}. Skipping this field.")
685
+ continue
686
+
687
+ # Update name DB if patient names changed
688
+ if patient_name_changed:
689
+ try:
690
+ update_name_db(instance.patient_first_name, instance.patient_last_name)
691
+ except Exception as e:
692
+ logger.warning(f"Error updating name database: {e}")
693
+
694
+ # Call save - this will trigger the full save logic including hash recalculation etc.
695
+ try:
696
+ instance.save()
697
+ except Exception as e:
698
+ logger.error(f"Error saving SensitiveMeta instance: {e}")
699
+ raise
700
+
701
+ return instance
702
+
703
+
704
+ def update_or_create_sensitive_meta_from_dict(
705
+ cls: Type["SensitiveMeta"],
706
+ data: Dict[str, Any],
707
+ instance: Optional["SensitiveMeta"] = None,
708
+ ) -> "SensitiveMeta":
709
+ """Logic to update or create a SensitiveMeta instance from a dictionary."""
710
+ # Check if the instance already exists based on unique fields
711
+ if instance:
712
+ # Update the existing instance
713
+ return update_sensitive_meta_from_dict(instance, data), False
714
+ else:
715
+ # Create a new instance
716
+ return create_sensitive_meta_from_dict(cls, data), True
717
+
718
+
719
+ def _map_gender_string_to_standard(gender_str: str) -> Optional[str]:
720
+ """Maps various gender string inputs to standard gender names used in the DB."""
721
+ mapping = {
722
+ "male": ["male", "m", "männlich", "man"],
723
+ "female": ["female", "f", "weiblich", "woman"],
724
+ "unknown": ["unknown", "unbekannt", "other", "diverse", ""],
725
+ }
726
+ gender_lower = gender_str.strip().lower()
727
+ for standard, variants in mapping.items():
728
+ if gender_lower in variants:
729
+ return standard
730
+ return None