endoreg-db 0.6.3__py3-none-any.whl → 0.8.1__py3-none-any.whl

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  1. endoreg_db/admin.py +26 -26
  2. endoreg_db/api_urls.py +4 -0
  3. endoreg_db/apps.py +12 -0
  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 +26 -0
  9. endoreg_db/data/ai_model/data.yaml +1 -1
  10. endoreg_db/data/ai_model_label/label/polyp_classification.yaml +52 -0
  11. endoreg_db/data/ai_model_label/label-set/data.yaml +20 -1
  12. endoreg_db/data/ai_model_label/label-set/polyp_classifications.yaml +25 -0
  13. endoreg_db/data/center/data.yaml +13 -12
  14. endoreg_db/data/center_shift/ukw.yaml +9 -0
  15. endoreg_db/data/db_summary.csv +58 -0
  16. endoreg_db/data/db_summary.xlsx +0 -0
  17. endoreg_db/data/disease/misc.yaml +1 -2
  18. endoreg_db/data/disease_classification/chronic_kidney_disease.yaml +2 -2
  19. endoreg_db/data/disease_classification_choice/chronic_kidney_disease.yaml +6 -6
  20. endoreg_db/data/endoscopy_processor/data.yaml +3 -0
  21. endoreg_db/data/event/cardiology.yaml +0 -13
  22. endoreg_db/data/examination/examinations/data.yaml +34 -28
  23. endoreg_db/data/examination/type/data.yaml +12 -0
  24. endoreg_db/data/examination_indication/endoscopy.yaml +418 -2
  25. endoreg_db/data/examination_indication_classification/endoscopy.yaml +157 -5
  26. endoreg_db/data/examination_requirement_set/colonoscopy.yaml +15 -0
  27. endoreg_db/data/finding/anatomy_colon.yaml +128 -0
  28. endoreg_db/data/finding/colonoscopy.yaml +40 -0
  29. endoreg_db/data/finding/colonoscopy_bowel_prep.yaml +56 -0
  30. endoreg_db/data/finding/complication.yaml +16 -0
  31. endoreg_db/data/finding/data.yaml +8 -44
  32. endoreg_db/data/finding/examination_setting.yaml +16 -0
  33. endoreg_db/data/finding/medication_related.yaml +18 -0
  34. endoreg_db/data/finding/outcome.yaml +12 -0
  35. endoreg_db/data/finding_classification/colonoscopy_bowel_preparation.yaml +95 -0
  36. endoreg_db/data/finding_classification/colonoscopy_jnet.yaml +22 -0
  37. endoreg_db/data/finding_classification/colonoscopy_kudo.yaml +25 -0
  38. endoreg_db/data/finding_classification/colonoscopy_lesion_circularity.yaml +20 -0
  39. endoreg_db/data/finding_classification/colonoscopy_lesion_planarity.yaml +24 -0
  40. endoreg_db/data/finding_classification/colonoscopy_lesion_size.yaml +68 -0
  41. endoreg_db/data/finding_classification/colonoscopy_lesion_surface.yaml +20 -0
  42. endoreg_db/data/finding_classification/colonoscopy_location.yaml +80 -0
  43. endoreg_db/data/finding_classification/colonoscopy_lst.yaml +21 -0
  44. endoreg_db/data/finding_classification/colonoscopy_nice.yaml +20 -0
  45. endoreg_db/data/finding_classification/colonoscopy_paris.yaml +26 -0
  46. endoreg_db/data/finding_classification/colonoscopy_sano.yaml +22 -0
  47. endoreg_db/data/finding_classification/colonoscopy_summary.yaml +53 -0
  48. endoreg_db/data/finding_classification/complication_generic.yaml +25 -0
  49. endoreg_db/data/finding_classification/examination_setting_generic.yaml +40 -0
  50. endoreg_db/data/finding_classification/histology_colo.yaml +51 -0
  51. endoreg_db/data/finding_classification/intervention_required.yaml +26 -0
  52. endoreg_db/data/finding_classification/medication_related.yaml +23 -0
  53. endoreg_db/data/finding_classification/visualized.yaml +33 -0
  54. endoreg_db/data/finding_classification_choice/bowel_preparation.yaml +78 -0
  55. endoreg_db/data/{finding_morphology_classification_choice → finding_classification_choice}/colon_lesion_circularity_default.yaml +0 -2
  56. endoreg_db/data/finding_classification_choice/colon_lesion_jnet.yaml +15 -0
  57. endoreg_db/data/finding_classification_choice/colon_lesion_kudo.yaml +23 -0
  58. endoreg_db/data/finding_classification_choice/colon_lesion_lst.yaml +15 -0
  59. endoreg_db/data/{finding_morphology_classification_choice → finding_classification_choice}/colon_lesion_nice.yaml +4 -7
  60. endoreg_db/data/{finding_morphology_classification_choice → finding_classification_choice}/colon_lesion_paris.yaml +0 -8
  61. endoreg_db/data/{finding_morphology_classification_choice → finding_classification_choice}/colon_lesion_planarity_default.yaml +6 -13
  62. endoreg_db/data/finding_classification_choice/colon_lesion_sano.yaml +14 -0
  63. endoreg_db/data/{finding_morphology_classification_choice → finding_classification_choice}/colon_lesion_surface_intact_default.yaml +3 -6
  64. endoreg_db/data/{finding_location_classification_choice/colonoscopy.yaml → finding_classification_choice/colonoscopy_location.yaml} +11 -22
  65. endoreg_db/data/finding_classification_choice/colonoscopy_not_complete_reason.yaml +19 -0
  66. endoreg_db/data/finding_classification_choice/colonoscopy_size.yaml +82 -0
  67. endoreg_db/data/finding_classification_choice/colonoscopy_summary_worst_finding.yaml +15 -0
  68. endoreg_db/data/finding_classification_choice/complication_generic_types.yaml +15 -0
  69. endoreg_db/data/finding_classification_choice/examination_setting_generic_types.yaml +15 -0
  70. endoreg_db/data/finding_classification_choice/histology.yaml +24 -0
  71. endoreg_db/data/finding_classification_choice/histology_polyp.yaml +20 -0
  72. endoreg_db/data/finding_classification_choice/outcome.yaml +19 -0
  73. endoreg_db/data/finding_classification_choice/yes_no_na.yaml +11 -0
  74. endoreg_db/data/finding_classification_type/colonoscopy_basic.yaml +48 -0
  75. endoreg_db/data/finding_intervention/endoscopy.yaml +26 -121
  76. endoreg_db/data/finding_intervention/endoscopy_colonoscopy.yaml +168 -0
  77. endoreg_db/data/finding_intervention/endoscopy_egd.yaml +128 -0
  78. endoreg_db/data/finding_intervention/endoscopy_ercp.yaml +32 -0
  79. endoreg_db/data/finding_intervention/endoscopy_eus_lower.yaml +9 -0
  80. endoreg_db/data/finding_intervention/endoscopy_eus_upper.yaml +36 -0
  81. endoreg_db/data/finding_morphology_classification_type/colonoscopy.yaml +6 -6
  82. endoreg_db/data/finding_type/data.yaml +23 -10
  83. endoreg_db/data/gender/data.yaml +8 -1
  84. endoreg_db/data/information_source/annotation.yaml +6 -0
  85. endoreg_db/data/information_source/endoscopy_guidelines.yaml +7 -0
  86. endoreg_db/data/information_source/prediction.yaml +7 -0
  87. endoreg_db/data/information_source_type/data.yaml +8 -0
  88. endoreg_db/data/lab_value/misc.yaml +43 -0
  89. endoreg_db/data/medication/anticoagulation.yaml +5 -5
  90. endoreg_db/data/medication/tah.yaml +5 -5
  91. endoreg_db/data/medication_indication/anticoagulation.yaml +4 -4
  92. endoreg_db/data/medication_intake_time/base.yaml +4 -4
  93. endoreg_db/data/names_first/first_names.yaml +3 -0
  94. endoreg_db/data/pdf_type/data.yaml +27 -10
  95. endoreg_db/data/qualification/endoscopy.yaml +36 -0
  96. endoreg_db/data/qualification/m2.yaml +39 -0
  97. endoreg_db/data/qualification/outpatient_clinic.yaml +35 -0
  98. endoreg_db/data/qualification/sonography.yaml +36 -0
  99. endoreg_db/data/qualification_type/base.yaml +29 -0
  100. endoreg_db/data/report_reader_flag/rkh-histology-generic.yaml +10 -0
  101. endoreg_db/data/report_reader_flag/ukw-histology-generic.yaml +5 -0
  102. endoreg_db/data/requirement/age.yaml +26 -0
  103. endoreg_db/data/requirement/colonoscopy_baseline_austria.yaml +45 -0
  104. endoreg_db/data/requirement/disease_cardiovascular.yaml +79 -0
  105. endoreg_db/data/requirement/disease_classification_choice_cardiovascular.yaml +41 -0
  106. endoreg_db/data/requirement/disease_hepatology.yaml +12 -0
  107. endoreg_db/data/requirement/disease_misc.yaml +12 -0
  108. endoreg_db/data/requirement/disease_renal.yaml +96 -0
  109. endoreg_db/data/requirement/endoscopy_bleeding_risk.yaml +59 -0
  110. endoreg_db/data/requirement/event_cardiology.yaml +251 -0
  111. endoreg_db/data/requirement/event_requirements.yaml +145 -0
  112. endoreg_db/data/requirement/finding_colon_polyp.yaml +50 -0
  113. endoreg_db/data/requirement/gender.yaml +25 -0
  114. endoreg_db/data/requirement/lab_value.yaml +441 -0
  115. endoreg_db/data/requirement/medication.yaml +93 -0
  116. endoreg_db/data/requirement_operator/age.yaml +13 -0
  117. endoreg_db/data/requirement_operator/lab_operators.yaml +129 -0
  118. endoreg_db/data/requirement_operator/model_operators.yaml +96 -0
  119. endoreg_db/data/requirement_set/01_endoscopy_generic.yaml +48 -0
  120. endoreg_db/data/requirement_set/colonoscopy_austria_screening.yaml +57 -0
  121. endoreg_db/data/requirement_set/endoscopy_bleeding_risk.yaml +52 -0
  122. endoreg_db/data/requirement_set_type/data.yaml +20 -0
  123. endoreg_db/data/requirement_type/requirement_types.yaml +165 -0
  124. endoreg_db/data/risk/bleeding.yaml +26 -0
  125. endoreg_db/data/risk/thrombosis.yaml +37 -0
  126. endoreg_db/data/risk_type/data.yaml +27 -0
  127. endoreg_db/data/shift/endoscopy.yaml +21 -0
  128. endoreg_db/data/shift_type/base.yaml +35 -0
  129. endoreg_db/data/tag/requirement_set_tags.yaml +11 -0
  130. endoreg_db/data/unit/concentration.yaml +23 -0
  131. endoreg_db/data/unit/time.yaml +36 -1
  132. endoreg_db/exceptions.py +19 -0
  133. endoreg_db/forms/patient_finding_intervention_form.py +4 -5
  134. endoreg_db/forms/patient_form.py +7 -6
  135. endoreg_db/forms/questionnaires/__init__.py +1 -1
  136. endoreg_db/forms/questionnaires/tto_questionnaire.py +19 -19
  137. endoreg_db/helpers/count_db.py +45 -0
  138. endoreg_db/helpers/data_loader.py +208 -0
  139. endoreg_db/helpers/default_objects.py +359 -0
  140. endoreg_db/helpers/interact.py +6 -0
  141. endoreg_db/helpers/test_video_helper.py +119 -0
  142. endoreg_db/logger_conf.py +140 -0
  143. endoreg_db/management/__init__.py +1 -0
  144. endoreg_db/management/commands/__init__.py +1 -0
  145. endoreg_db/management/commands/anonymize_video.py +0 -0
  146. endoreg_db/management/commands/check_auth.py +125 -0
  147. endoreg_db/management/commands/create_multilabel_model_meta.py +214 -0
  148. endoreg_db/management/commands/fix_missing_patient_data.py +172 -0
  149. endoreg_db/management/commands/fix_video_paths.py +165 -0
  150. endoreg_db/management/commands/import_fallback_video.py +203 -0
  151. endoreg_db/management/commands/import_report.py +298 -0
  152. endoreg_db/management/commands/import_video.py +422 -0
  153. endoreg_db/management/commands/import_video_with_classification.py +367 -0
  154. endoreg_db/management/commands/init_default_ai_model.py +112 -0
  155. endoreg_db/management/commands/load_ai_model_data.py +2 -7
  156. endoreg_db/management/commands/load_base_db_data.py +15 -1
  157. endoreg_db/management/commands/load_center_data.py +46 -21
  158. endoreg_db/management/commands/load_endoscope_data.py +2 -2
  159. endoreg_db/management/commands/load_examination_indication_data.py +49 -28
  160. endoreg_db/management/commands/load_finding_data.py +49 -92
  161. endoreg_db/management/commands/load_green_endoscopy_wuerzburg_data.py +0 -1
  162. endoreg_db/management/commands/load_information_source.py +13 -7
  163. endoreg_db/management/commands/load_qualification_data.py +59 -0
  164. endoreg_db/management/commands/load_requirement_data.py +180 -0
  165. endoreg_db/management/commands/load_risk_data.py +56 -0
  166. endoreg_db/management/commands/load_shift_data.py +60 -0
  167. endoreg_db/management/commands/load_tag_data.py +57 -0
  168. endoreg_db/management/commands/register_ai_model.py +1 -1
  169. endoreg_db/management/commands/start_filewatcher.py +106 -0
  170. endoreg_db/management/commands/storage_management.py +548 -0
  171. endoreg_db/management/commands/summarize_db_content.py +189 -0
  172. endoreg_db/management/commands/validate_video.py +204 -0
  173. endoreg_db/management/commands/validate_video_files.py +161 -0
  174. endoreg_db/management/commands/video_validation.py +22 -0
  175. endoreg_db/migrations/0001_initial.py +625 -813
  176. endoreg_db/migrations/0002_add_video_correction_models.py +52 -0
  177. endoreg_db/models/__init__.py +274 -291
  178. endoreg_db/models/administration/__init__.py +116 -0
  179. endoreg_db/models/{ai_model → administration/ai}/__init__.py +6 -1
  180. endoreg_db/models/administration/ai/active_model.py +35 -0
  181. endoreg_db/models/administration/ai/ai_model.py +156 -0
  182. endoreg_db/models/{ai_model → administration/ai}/model_type.py +6 -1
  183. endoreg_db/models/administration/case/__init__.py +19 -0
  184. endoreg_db/models/administration/case/case.py +114 -0
  185. endoreg_db/models/{case_template → administration/case/case_template}/case_template.py +3 -3
  186. endoreg_db/models/{case_template → administration/case/case_template}/case_template_rule.py +3 -10
  187. endoreg_db/models/{case_template → administration/case/case_template}/case_template_rule_value.py +2 -4
  188. endoreg_db/models/{case_template → administration/case/case_template}/case_template_type.py +1 -3
  189. endoreg_db/models/{center → administration/center}/__init__.py +3 -1
  190. endoreg_db/models/administration/center/center.py +61 -0
  191. endoreg_db/models/administration/center/center_product.py +64 -0
  192. endoreg_db/models/{center → administration/center}/center_resource.py +19 -3
  193. endoreg_db/models/administration/center/center_shift.py +88 -0
  194. endoreg_db/models/administration/center/center_waste.py +30 -0
  195. endoreg_db/models/administration/permissions/__init__.py +44 -0
  196. endoreg_db/models/administration/person/__init__.py +24 -0
  197. endoreg_db/models/administration/person/employee/__init__.py +3 -0
  198. endoreg_db/models/administration/person/employee/employee.py +35 -0
  199. endoreg_db/models/administration/person/employee/employee_qualification.py +39 -0
  200. endoreg_db/models/administration/person/employee/employee_type.py +42 -0
  201. endoreg_db/models/administration/person/examiner/__init__.py +4 -0
  202. endoreg_db/models/administration/person/examiner/examiner.py +54 -0
  203. endoreg_db/models/administration/person/names/__init__.py +0 -0
  204. endoreg_db/models/{persons → administration/person/names}/first_name.py +1 -1
  205. endoreg_db/models/{persons → administration/person/names}/last_name.py +2 -3
  206. endoreg_db/models/administration/person/patient/__init__.py +5 -0
  207. endoreg_db/models/administration/person/patient/patient.py +460 -0
  208. endoreg_db/models/administration/person/profession/__init__.py +24 -0
  209. endoreg_db/models/administration/person/user/__init__.py +5 -0
  210. endoreg_db/models/administration/person/user/portal_user_information.py +37 -0
  211. endoreg_db/models/administration/product/product.py +97 -0
  212. endoreg_db/models/administration/product/product_group.py +39 -0
  213. endoreg_db/models/administration/product/product_material.py +54 -0
  214. endoreg_db/models/{product → administration/product}/product_weight.py +9 -0
  215. endoreg_db/models/{product → administration/product}/reference_product.py +26 -11
  216. endoreg_db/models/administration/qualification/__init__.py +7 -0
  217. endoreg_db/models/administration/qualification/qualification.py +37 -0
  218. endoreg_db/models/administration/qualification/qualification_type.py +35 -0
  219. endoreg_db/models/administration/shift/__init__.py +9 -0
  220. endoreg_db/models/administration/shift/scheduled_days.py +69 -0
  221. endoreg_db/models/administration/shift/shift.py +51 -0
  222. endoreg_db/models/administration/shift/shift_type.py +108 -0
  223. endoreg_db/models/label/__init__.py +24 -1
  224. endoreg_db/models/label/annotation/__init__.py +12 -0
  225. endoreg_db/models/label/annotation/image_classification.py +84 -0
  226. endoreg_db/models/label/annotation/video_segmentation_annotation.py +66 -0
  227. endoreg_db/models/label/label.py +45 -74
  228. endoreg_db/models/label/label_set.py +53 -0
  229. endoreg_db/models/label/label_type.py +29 -0
  230. endoreg_db/models/label/label_video_segment/__init__.py +3 -0
  231. endoreg_db/models/label/label_video_segment/_create_from_video.py +41 -0
  232. endoreg_db/models/label/label_video_segment/label_video_segment.py +511 -0
  233. endoreg_db/models/label/video_segmentation_label.py +31 -0
  234. endoreg_db/models/{annotation → label}/video_segmentation_labelset.py +7 -0
  235. endoreg_db/models/media/__init__.py +14 -0
  236. endoreg_db/models/media/frame/__init__.py +3 -0
  237. endoreg_db/models/media/frame/frame.py +111 -0
  238. endoreg_db/models/media/pdf/__init__.py +11 -0
  239. endoreg_db/models/media/pdf/raw_pdf.py +608 -0
  240. endoreg_db/models/media/pdf/report_file.py +162 -0
  241. endoreg_db/models/media/pdf/report_reader/report_reader_config.py +77 -0
  242. endoreg_db/models/media/video/__init__.py +4 -0
  243. endoreg_db/models/media/video/create_from_file.py +336 -0
  244. endoreg_db/models/media/video/pipe_1.py +195 -0
  245. endoreg_db/models/media/video/pipe_2.py +105 -0
  246. endoreg_db/models/media/video/refactor_plan.md +0 -0
  247. endoreg_db/models/media/video/video_file.py +680 -0
  248. endoreg_db/models/media/video/video_file_ai.py +443 -0
  249. endoreg_db/models/media/video/video_file_anonymize.py +348 -0
  250. endoreg_db/models/media/video/video_file_frames/__init__.py +47 -0
  251. endoreg_db/models/media/video/video_file_frames/_bulk_create_frames.py +22 -0
  252. endoreg_db/models/media/video/video_file_frames/_create_frame_object.py +23 -0
  253. endoreg_db/models/media/video/video_file_frames/_delete_frames.py +104 -0
  254. endoreg_db/models/media/video/video_file_frames/_extract_frames.py +174 -0
  255. endoreg_db/models/media/video/video_file_frames/_get_frame.py +28 -0
  256. endoreg_db/models/media/video/video_file_frames/_get_frame_number.py +27 -0
  257. endoreg_db/models/media/video/video_file_frames/_get_frame_path.py +20 -0
  258. endoreg_db/models/media/video/video_file_frames/_get_frame_paths.py +27 -0
  259. endoreg_db/models/media/video/video_file_frames/_get_frame_range.py +34 -0
  260. endoreg_db/models/media/video/video_file_frames/_get_frames.py +27 -0
  261. endoreg_db/models/media/video/video_file_frames/_initialize_frames.py +129 -0
  262. endoreg_db/models/media/video/video_file_frames/_manage_frame_range.py +129 -0
  263. endoreg_db/models/media/video/video_file_frames/_mark_frames_extracted_status.py +65 -0
  264. endoreg_db/models/media/video/video_file_frames.py +0 -0
  265. endoreg_db/models/media/video/video_file_io.py +166 -0
  266. endoreg_db/models/media/video/video_file_meta/__init__.py +22 -0
  267. endoreg_db/models/media/video/video_file_meta/get_crop_template.py +45 -0
  268. endoreg_db/models/media/video/video_file_meta/get_endo_roi.py +39 -0
  269. endoreg_db/models/media/video/video_file_meta/get_fps.py +147 -0
  270. endoreg_db/models/media/video/video_file_meta/initialize_video_specs.py +143 -0
  271. endoreg_db/models/media/video/video_file_meta/text_meta.py +134 -0
  272. endoreg_db/models/media/video/video_file_meta/video_meta.py +70 -0
  273. endoreg_db/models/media/video/video_file_meta.py +11 -0
  274. endoreg_db/models/media/video/video_file_segments.py +209 -0
  275. endoreg_db/models/medical/__init__.py +146 -0
  276. endoreg_db/models/{contraindication → medical/contraindication}/__init__.py +1 -5
  277. endoreg_db/models/medical/disease.py +156 -0
  278. endoreg_db/models/medical/event.py +137 -0
  279. endoreg_db/models/{examination → medical/examination}/__init__.py +1 -1
  280. endoreg_db/models/medical/examination/examination.py +148 -0
  281. endoreg_db/models/medical/examination/examination_indication.py +278 -0
  282. endoreg_db/models/{examination → medical/examination}/examination_time.py +0 -4
  283. endoreg_db/models/{examination → medical/examination}/examination_time_type.py +1 -8
  284. endoreg_db/models/{examination → medical/examination}/examination_type.py +18 -10
  285. endoreg_db/models/medical/finding/__init__.py +18 -0
  286. endoreg_db/models/medical/finding/finding.py +96 -0
  287. endoreg_db/models/medical/finding/finding_classification.py +142 -0
  288. endoreg_db/models/{finding → medical/finding}/finding_intervention.py +2 -10
  289. endoreg_db/models/medical/finding/finding_type.py +35 -0
  290. endoreg_db/models/medical/hardware/__init__.py +8 -0
  291. endoreg_db/models/{hardware → medical/hardware}/endoscope.py +28 -23
  292. endoreg_db/models/medical/laboratory/__init__.py +5 -0
  293. endoreg_db/models/medical/laboratory/lab_value.py +419 -0
  294. endoreg_db/models/{medication → medical/medication}/medication.py +1 -3
  295. endoreg_db/models/{medication → medical/medication}/medication_indication_type.py +8 -3
  296. endoreg_db/models/{medication → medical/medication}/medication_intake_time.py +21 -3
  297. endoreg_db/models/{medication → medical/medication}/medication_schedule.py +13 -5
  298. endoreg_db/models/{organ → medical/organ}/__init__.py +3 -6
  299. endoreg_db/models/medical/patient/__init__.py +56 -0
  300. endoreg_db/models/medical/patient/medication_examples.py +38 -0
  301. endoreg_db/models/medical/patient/patient_disease.py +63 -0
  302. endoreg_db/models/medical/patient/patient_event.py +75 -0
  303. endoreg_db/models/medical/patient/patient_examination.py +249 -0
  304. endoreg_db/models/{persons → medical}/patient/patient_examination_indication.py +21 -9
  305. endoreg_db/models/medical/patient/patient_finding.py +357 -0
  306. endoreg_db/models/medical/patient/patient_finding_classification.py +207 -0
  307. endoreg_db/models/{patient → medical/patient}/patient_finding_intervention.py +15 -1
  308. endoreg_db/models/medical/patient/patient_lab_sample.py +148 -0
  309. endoreg_db/models/{persons → medical}/patient/patient_lab_value.py +40 -15
  310. endoreg_db/models/medical/patient/patient_medication.py +104 -0
  311. endoreg_db/models/medical/patient/patient_medication_schedule.py +136 -0
  312. endoreg_db/models/medical/risk/__init__.py +7 -0
  313. endoreg_db/models/medical/risk/risk.py +72 -0
  314. endoreg_db/models/medical/risk/risk_type.py +51 -0
  315. endoreg_db/models/{data_file/metadata → metadata}/__init__.py +6 -0
  316. endoreg_db/models/metadata/frame_ocr_result.py +0 -0
  317. endoreg_db/models/metadata/model_meta.py +193 -0
  318. endoreg_db/models/metadata/model_meta_logic.py +236 -0
  319. endoreg_db/models/{data_file/metadata → metadata}/pdf_meta.py +28 -13
  320. endoreg_db/models/metadata/sensitive_meta.py +288 -0
  321. endoreg_db/models/metadata/sensitive_meta_logic.py +643 -0
  322. endoreg_db/models/metadata/video_meta.py +332 -0
  323. endoreg_db/models/metadata/video_prediction_logic.py +190 -0
  324. endoreg_db/models/metadata/video_prediction_meta.py +270 -0
  325. endoreg_db/models/other/__init__.py +17 -0
  326. endoreg_db/models/other/distribution/date_value_distribution.py +0 -2
  327. endoreg_db/models/other/distribution/numeric_value_distribution.py +30 -2
  328. endoreg_db/models/{emission → other/emission}/emission_factor.py +15 -6
  329. endoreg_db/models/{persons → other}/gender.py +8 -3
  330. endoreg_db/models/other/information_source.py +159 -0
  331. endoreg_db/models/other/material.py +10 -2
  332. endoreg_db/models/other/resource.py +6 -2
  333. endoreg_db/models/other/tag.py +27 -0
  334. endoreg_db/models/other/transport_route.py +13 -2
  335. endoreg_db/models/{unit.py → other/unit.py} +16 -6
  336. endoreg_db/models/other/waste.py +10 -3
  337. endoreg_db/models/requirement/__init__.py +11 -0
  338. endoreg_db/models/requirement/requirement.py +767 -0
  339. endoreg_db/models/requirement/requirement_evaluation/__init__.py +6 -0
  340. endoreg_db/models/requirement/requirement_evaluation/get_values.py +40 -0
  341. endoreg_db/models/requirement/requirement_evaluation/operator_evaluation_models.py +9 -0
  342. endoreg_db/models/requirement/requirement_evaluation/requirement_type_parser.py +95 -0
  343. endoreg_db/models/requirement/requirement_operator.py +176 -0
  344. endoreg_db/models/requirement/requirement_set.py +287 -0
  345. endoreg_db/models/rule/__init__.py +13 -0
  346. endoreg_db/models/{rules → rule}/rule.py +6 -3
  347. endoreg_db/models/{rules → rule}/rule_attribute_dtype.py +0 -2
  348. endoreg_db/models/{rules → rule}/rule_type.py +0 -2
  349. endoreg_db/models/{rules → rule}/ruleset.py +0 -2
  350. endoreg_db/models/state/__init__.py +12 -0
  351. endoreg_db/models/state/abstract.py +11 -0
  352. endoreg_db/models/state/audit_ledger.py +150 -0
  353. endoreg_db/models/state/label_video_segment.py +22 -0
  354. endoreg_db/models/state/raw_pdf.py +187 -0
  355. endoreg_db/models/state/sensitive_meta.py +46 -0
  356. endoreg_db/models/state/video.py +232 -0
  357. endoreg_db/models/upload_job.py +99 -0
  358. endoreg_db/models/utils.py +135 -0
  359. endoreg_db/models/video_metadata.py +66 -0
  360. endoreg_db/models/video_processing.py +153 -0
  361. endoreg_db/renames.yml +8 -0
  362. endoreg_db/root_urls.py +9 -0
  363. endoreg_db/schemas/__init__.py +0 -0
  364. endoreg_db/schemas/examination_evaluation.py +27 -0
  365. endoreg_db/serializers/Frames_NICE_and_PARIS_classifications.py +775 -0
  366. endoreg_db/serializers/__init__.py +147 -10
  367. endoreg_db/serializers/{raw_pdf_meta_validation.py → _old/raw_pdf_meta_validation.py} +3 -3
  368. endoreg_db/serializers/{raw_video_meta_validation.py → _old/raw_video_meta_validation.py} +18 -14
  369. endoreg_db/serializers/_old/video.py +71 -0
  370. endoreg_db/serializers/administration/__init__.py +14 -0
  371. endoreg_db/serializers/administration/ai/__init__.py +10 -0
  372. endoreg_db/serializers/administration/ai/active_model.py +10 -0
  373. endoreg_db/serializers/administration/ai/ai_model.py +18 -0
  374. endoreg_db/serializers/administration/ai/model_type.py +10 -0
  375. endoreg_db/serializers/administration/center.py +9 -0
  376. endoreg_db/serializers/administration/gender.py +9 -0
  377. endoreg_db/serializers/anonymization.py +66 -0
  378. endoreg_db/serializers/evaluation/examination_evaluation.py +1 -0
  379. endoreg_db/serializers/examination/__init__.py +10 -0
  380. endoreg_db/serializers/examination/base.py +46 -0
  381. endoreg_db/serializers/examination/dropdown.py +21 -0
  382. endoreg_db/serializers/examination_serializer.py +12 -0
  383. endoreg_db/serializers/finding/__init__.py +5 -0
  384. endoreg_db/serializers/finding/finding.py +54 -0
  385. endoreg_db/serializers/finding_classification/__init__.py +7 -0
  386. endoreg_db/serializers/finding_classification/choice.py +19 -0
  387. endoreg_db/serializers/finding_classification/classification.py +13 -0
  388. endoreg_db/serializers/label/__init__.py +7 -0
  389. endoreg_db/serializers/label/image_classification_annotation.py +62 -0
  390. endoreg_db/serializers/label/label.py +15 -0
  391. endoreg_db/serializers/label_video_segment/__init__.py +7 -0
  392. endoreg_db/serializers/label_video_segment/_lvs_create.py +149 -0
  393. endoreg_db/serializers/label_video_segment/_lvs_update.py +138 -0
  394. endoreg_db/serializers/label_video_segment/_lvs_validate.py +149 -0
  395. endoreg_db/serializers/label_video_segment/label_video_segment.py +344 -0
  396. endoreg_db/serializers/label_video_segment/label_video_segment_annotation.py +99 -0
  397. endoreg_db/serializers/label_video_segment/label_video_segment_update.py +163 -0
  398. endoreg_db/serializers/meta/__init__.py +19 -0
  399. endoreg_db/serializers/meta/pdf_file_meta_extraction.py +115 -0
  400. endoreg_db/serializers/meta/report_meta.py +53 -0
  401. endoreg_db/serializers/meta/sensitive_meta_detail.py +162 -0
  402. endoreg_db/serializers/meta/sensitive_meta_update.py +148 -0
  403. endoreg_db/serializers/meta/sensitive_meta_verification.py +59 -0
  404. endoreg_db/serializers/meta/video_meta.py +39 -0
  405. endoreg_db/serializers/misc/__init__.py +14 -0
  406. endoreg_db/serializers/misc/file_overview.py +152 -0
  407. endoreg_db/serializers/misc/stats.py +33 -0
  408. endoreg_db/serializers/misc/translatable_field_mix_in.py +44 -0
  409. endoreg_db/serializers/misc/upload_job.py +71 -0
  410. endoreg_db/serializers/misc/vop_patient_data.py +120 -0
  411. endoreg_db/serializers/patient/__init__.py +11 -0
  412. endoreg_db/serializers/patient/patient.py +86 -0
  413. endoreg_db/serializers/patient/patient_dropdown.py +27 -0
  414. endoreg_db/serializers/patient_examination/__init__.py +7 -0
  415. endoreg_db/serializers/patient_examination/patient_examination.py +141 -0
  416. endoreg_db/serializers/patient_finding/__init__.py +15 -0
  417. endoreg_db/serializers/patient_finding/patient_finding.py +31 -0
  418. endoreg_db/serializers/patient_finding/patient_finding_classification.py +39 -0
  419. endoreg_db/serializers/patient_finding/patient_finding_detail.py +53 -0
  420. endoreg_db/serializers/patient_finding/patient_finding_intervention.py +26 -0
  421. endoreg_db/serializers/patient_finding/patient_finding_list.py +41 -0
  422. endoreg_db/serializers/patient_finding/patient_finding_write.py +126 -0
  423. endoreg_db/serializers/pdf/__init__.py +5 -0
  424. endoreg_db/serializers/pdf/anony_text_validation.py +85 -0
  425. endoreg_db/serializers/report/__init__.py +9 -0
  426. endoreg_db/serializers/report/mixins.py +45 -0
  427. endoreg_db/serializers/report/report.py +105 -0
  428. endoreg_db/serializers/report/report_list.py +22 -0
  429. endoreg_db/serializers/report/secure_file_url.py +26 -0
  430. endoreg_db/serializers/requirements/requirement_schema.py +25 -0
  431. endoreg_db/serializers/requirements/requirement_sets.py +29 -0
  432. endoreg_db/serializers/sensitive_meta_serializer.py +282 -0
  433. endoreg_db/serializers/video/__init__.py +7 -0
  434. endoreg_db/serializers/video/segmentation.py +263 -0
  435. endoreg_db/serializers/video/video_file_brief.py +10 -0
  436. endoreg_db/serializers/video/video_file_detail.py +83 -0
  437. endoreg_db/serializers/video/video_file_list.py +67 -0
  438. endoreg_db/serializers/video/video_metadata.py +105 -0
  439. endoreg_db/serializers/video/video_processing_history.py +153 -0
  440. endoreg_db/services/__init__.py +5 -0
  441. endoreg_db/services/anonymization.py +223 -0
  442. endoreg_db/services/examination_evaluation.py +149 -0
  443. endoreg_db/services/finding_description_service.py +0 -0
  444. endoreg_db/services/lookup_service.py +241 -0
  445. endoreg_db/services/lookup_store.py +122 -0
  446. endoreg_db/services/ollama_api_docs.py +1528 -0
  447. endoreg_db/services/pdf_import.py +993 -0
  448. endoreg_db/services/polling_coordinator.py +288 -0
  449. endoreg_db/services/pseudonym_service.py +89 -0
  450. endoreg_db/services/requirements_object.py +147 -0
  451. endoreg_db/services/segment_sync.py +155 -0
  452. endoreg_db/services/storage_aware_video_processor.py +344 -0
  453. endoreg_db/services/video_import.py +915 -0
  454. endoreg_db/tasks/upload_tasks.py +207 -0
  455. endoreg_db/tasks/video_ingest.py +157 -0
  456. endoreg_db/tasks/video_processing_tasks.py +327 -0
  457. endoreg_db/urls/__init__.py +72 -0
  458. endoreg_db/urls/anonymization.py +32 -0
  459. endoreg_db/urls/auth.py +16 -0
  460. endoreg_db/urls/classification.py +39 -0
  461. endoreg_db/urls/examination.py +54 -0
  462. endoreg_db/urls/files.py +6 -0
  463. endoreg_db/urls/label_video_segment_validate.py +33 -0
  464. endoreg_db/urls/label_video_segments.py +44 -0
  465. endoreg_db/urls/media.py +32 -0
  466. endoreg_db/urls/patient.py +19 -0
  467. endoreg_db/urls/pdf.py +0 -0
  468. endoreg_db/urls/report.py +78 -0
  469. endoreg_db/urls/requirements.py +13 -0
  470. endoreg_db/urls/sensitive_meta.py +36 -0
  471. endoreg_db/urls/stats.py +46 -0
  472. endoreg_db/urls/upload.py +20 -0
  473. endoreg_db/urls/video.py +119 -0
  474. endoreg_db/urls.py +6 -269
  475. endoreg_db/utils/__init__.py +68 -16
  476. endoreg_db/utils/ai/__init__.py +9 -0
  477. endoreg_db/{models/ai_model/utils.py → utils/ai/get.py} +1 -4
  478. endoreg_db/{models/ai_model/lightning → utils/ai}/inference_dataset.py +0 -1
  479. endoreg_db/{models/ai_model/lightning → utils/ai}/multilabel_classification_net.py +14 -10
  480. endoreg_db/{models/ai_model/lightning → utils/ai}/postprocess.py +15 -5
  481. endoreg_db/utils/ai/predict.py +291 -0
  482. endoreg_db/{models/ai_model/lightning → utils/ai}/preprocess.py +1 -1
  483. endoreg_db/utils/calc_duration_seconds.py +24 -0
  484. endoreg_db/utils/case_generator/__init__.py +0 -0
  485. endoreg_db/utils/check_video_files.py +148 -0
  486. endoreg_db/utils/dataloader.py +88 -31
  487. endoreg_db/utils/dates.py +21 -0
  488. endoreg_db/utils/env.py +33 -0
  489. endoreg_db/utils/extract_specific_frames.py +72 -0
  490. endoreg_db/utils/file_operations.py +29 -1
  491. endoreg_db/utils/fix_video_path_direct.py +141 -0
  492. endoreg_db/utils/frame_anonymization_utils.py +463 -0
  493. endoreg_db/utils/hashs.py +1 -0
  494. endoreg_db/utils/links/__init__.py +0 -0
  495. endoreg_db/utils/links/requirement_link.py +193 -0
  496. endoreg_db/utils/mime_types.py +0 -0
  497. endoreg_db/utils/names.py +2 -0
  498. endoreg_db/utils/paths.py +104 -0
  499. endoreg_db/utils/permissions.py +143 -0
  500. endoreg_db/utils/pipelines/Readme.md +235 -0
  501. endoreg_db/utils/pipelines/__init__.py +0 -0
  502. endoreg_db/utils/pipelines/process_video_dir.py +120 -0
  503. endoreg_db/utils/product/__init__.py +0 -0
  504. endoreg_db/utils/product/sum_emissions.py +20 -0
  505. endoreg_db/utils/product/sum_weights.py +18 -0
  506. endoreg_db/utils/pydantic_models/db_config.py +1 -1
  507. endoreg_db/utils/requirement_helpers.py +0 -0
  508. endoreg_db/utils/requirement_operator_logic/__init__.py +0 -0
  509. endoreg_db/utils/requirement_operator_logic/lab_value_operators.py +578 -0
  510. endoreg_db/utils/requirement_operator_logic/model_evaluators.py +368 -0
  511. endoreg_db/utils/translation.py +27 -0
  512. endoreg_db/utils/validate_video_detailed.py +357 -0
  513. endoreg_db/utils/video/__init__.py +19 -6
  514. endoreg_db/utils/video/extract_frames.py +37 -70
  515. endoreg_db/utils/video/ffmpeg_wrapper.py +772 -0
  516. endoreg_db/utils/video/names.py +42 -0
  517. endoreg_db/utils/video/streaming_processor.py +312 -0
  518. endoreg_db/utils/video/video_splitter.py +94 -0
  519. endoreg_db/views/Frames_NICE_and_PARIS_classifications_views.py +238 -0
  520. endoreg_db/views/__init__.py +282 -2
  521. endoreg_db/views/anonymization/__init__.py +27 -0
  522. endoreg_db/views/anonymization/media_management.py +454 -0
  523. endoreg_db/views/anonymization/overview.py +216 -0
  524. endoreg_db/views/anonymization/validate.py +63 -0
  525. endoreg_db/views/auth/__init__.py +13 -0
  526. endoreg_db/views/auth/keycloak.py +113 -0
  527. endoreg_db/views/examination/__init__.py +33 -0
  528. endoreg_db/views/examination/examination.py +37 -0
  529. endoreg_db/views/examination/examination_manifest_cache.py +26 -0
  530. endoreg_db/views/examination/get_finding_classification_choices.py +59 -0
  531. endoreg_db/views/examination/get_finding_classifications.py +36 -0
  532. endoreg_db/views/examination/get_findings.py +41 -0
  533. endoreg_db/views/examination/get_instruments.py +18 -0
  534. endoreg_db/views/examination/get_interventions.py +14 -0
  535. endoreg_db/views/finding/__init__.py +9 -0
  536. endoreg_db/views/finding/finding.py +112 -0
  537. endoreg_db/views/finding/get_classifications.py +14 -0
  538. endoreg_db/views/finding/get_interventions.py +17 -0
  539. endoreg_db/views/finding_classification/__init__.py +13 -0
  540. endoreg_db/views/finding_classification/base.py +0 -0
  541. endoreg_db/views/finding_classification/finding_classification.py +42 -0
  542. endoreg_db/views/finding_classification/get_classification_choices.py +55 -0
  543. endoreg_db/views/label/__init__.py +5 -0
  544. endoreg_db/views/label/label.py +15 -0
  545. endoreg_db/views/label_video_segment/__init__.py +16 -0
  546. endoreg_db/views/label_video_segment/create_lvs_from_annotation.py +44 -0
  547. endoreg_db/views/label_video_segment/get_lvs_by_name_and_video.py +50 -0
  548. endoreg_db/views/label_video_segment/label_video_segment.py +77 -0
  549. endoreg_db/views/label_video_segment/label_video_segment_by_label.py +174 -0
  550. endoreg_db/views/label_video_segment/label_video_segment_detail.py +73 -0
  551. endoreg_db/views/label_video_segment/update_lvs_from_annotation.py +46 -0
  552. endoreg_db/views/label_video_segment/validate.py +226 -0
  553. endoreg_db/views/media/__init__.py +9 -0
  554. endoreg_db/views/media/pdf_media.py +386 -0
  555. endoreg_db/views/media/video_media.py +272 -0
  556. endoreg_db/views/meta/__init__.py +15 -0
  557. endoreg_db/views/meta/available_files_list.py +146 -0
  558. endoreg_db/views/meta/report_meta.py +53 -0
  559. endoreg_db/views/meta/sensitive_meta_detail.py +148 -0
  560. endoreg_db/views/meta/sensitive_meta_list.py +104 -0
  561. endoreg_db/views/meta/sensitive_meta_verification.py +71 -0
  562. endoreg_db/views/misc/__init__.py +63 -0
  563. endoreg_db/views/misc/center.py +13 -0
  564. endoreg_db/views/misc/gender.py +14 -0
  565. endoreg_db/views/misc/secure_file_serving_view.py +80 -0
  566. endoreg_db/views/misc/secure_file_url_view.py +84 -0
  567. endoreg_db/views/misc/secure_url_validate.py +79 -0
  568. endoreg_db/views/misc/stats.py +220 -0
  569. endoreg_db/views/misc/translation.py +182 -0
  570. endoreg_db/views/misc/upload_views.py +240 -0
  571. endoreg_db/views/patient/__init__.py +5 -0
  572. endoreg_db/views/patient/patient.py +210 -0
  573. endoreg_db/views/patient_examination/DEPRECATED_video_backup.py +164 -0
  574. endoreg_db/views/patient_examination/__init__.py +11 -0
  575. endoreg_db/views/patient_examination/patient_examination.py +140 -0
  576. endoreg_db/views/patient_examination/patient_examination_create.py +63 -0
  577. endoreg_db/views/patient_examination/patient_examination_detail.py +66 -0
  578. endoreg_db/views/patient_examination/patient_examination_list.py +68 -0
  579. endoreg_db/views/patient_examination/video.py +194 -0
  580. endoreg_db/views/patient_finding/__init__.py +7 -0
  581. endoreg_db/views/patient_finding/base.py +0 -0
  582. endoreg_db/views/patient_finding/patient_finding.py +64 -0
  583. endoreg_db/views/patient_finding/patient_finding_optimized.py +259 -0
  584. endoreg_db/views/patient_finding_classification/__init__.py +5 -0
  585. endoreg_db/views/patient_finding_classification/pfc_create.py +67 -0
  586. endoreg_db/views/patient_finding_location/__init__.py +5 -0
  587. endoreg_db/views/patient_finding_location/pfl_create.py +70 -0
  588. endoreg_db/views/patient_finding_morphology/__init__.py +5 -0
  589. endoreg_db/views/patient_finding_morphology/pfm_create.py +70 -0
  590. endoreg_db/views/pdf/__init__.py +11 -0
  591. endoreg_db/views/pdf/pdf_media.py +239 -0
  592. endoreg_db/views/pdf/pdf_stream_views.py +127 -0
  593. endoreg_db/views/pdf/reimport.py +151 -0
  594. endoreg_db/views/report/__init__.py +9 -0
  595. endoreg_db/views/report/report_list.py +112 -0
  596. endoreg_db/views/report/report_with_secure_url.py +28 -0
  597. endoreg_db/views/report/start_examination.py +7 -0
  598. endoreg_db/views/requirement/__init__.py +10 -0
  599. endoreg_db/views/requirement/evaluate.py +279 -0
  600. endoreg_db/views/requirement/lookup.py +483 -0
  601. endoreg_db/views/requirement/lookup_store.py +252 -0
  602. endoreg_db/views/requirement_lookup/lookup.py +0 -0
  603. endoreg_db/views/requirement_lookup/lookup_store.py +0 -0
  604. endoreg_db/views/stats/__init__.py +13 -0
  605. endoreg_db/views/stats/stats_views.py +229 -0
  606. endoreg_db/views/video/__init__.py +72 -0
  607. endoreg_db/views/video/correction.py +672 -0
  608. endoreg_db/views/video/media/__init__.py +23 -0
  609. endoreg_db/views/video/media/task_status.py +49 -0
  610. endoreg_db/views/video/media/video_analyze.py +52 -0
  611. endoreg_db/views/video/media/video_apply_mask.py +48 -0
  612. endoreg_db/views/video/media/video_correction.py +21 -0
  613. endoreg_db/views/video/media/video_download_processed.py +58 -0
  614. endoreg_db/views/video/media/video_media.py +158 -0
  615. endoreg_db/views/video/media/video_meta.py +29 -0
  616. endoreg_db/views/video/media/video_processing_history.py +24 -0
  617. endoreg_db/views/video/media/video_remove_frames.py +48 -0
  618. endoreg_db/views/video/media/video_reprocess.py +40 -0
  619. endoreg_db/views/video/reimport.py +192 -0
  620. endoreg_db/views/video/segmentation.py +274 -0
  621. endoreg_db/views/{views_for_timeline.py → video/timeline.py} +3 -3
  622. endoreg_db/views/video/video_examination_viewset.py +329 -0
  623. endoreg_db/views/video/video_stream.py +188 -0
  624. endoreg_db-0.8.1.dist-info/METADATA +384 -0
  625. endoreg_db-0.8.1.dist-info/RECORD +789 -0
  626. endoreg_db/data/agl_service/data.yaml +0 -19
  627. endoreg_db/data/finding_location_classification/colonoscopy.yaml +0 -46
  628. endoreg_db/data/finding_morphology_classification/colonoscopy.yaml +0 -48
  629. endoreg_db/data/finding_morphology_classification_choice/colonoscopy_size.yaml +0 -57
  630. endoreg_db/management/commands/_load_model_template.py +0 -41
  631. endoreg_db/management/commands/delete_all.py +0 -18
  632. endoreg_db/management/commands/fetch_legacy_image_dataset.py +0 -32
  633. endoreg_db/management/commands/fix_auth_permission.py +0 -20
  634. endoreg_db/management/commands/load_active_model_data.py +0 -45
  635. endoreg_db/management/commands/load_g_play_data.py +0 -113
  636. endoreg_db/management/commands/load_logging_data.py +0 -39
  637. endoreg_db/management/commands/load_lx_data.py +0 -64
  638. endoreg_db/management/commands/load_medication_indication_data.py +0 -63
  639. endoreg_db/management/commands/load_medication_indication_type_data.py +0 -41
  640. endoreg_db/management/commands/load_medication_intake_time_data.py +0 -41
  641. endoreg_db/management/commands/load_medication_schedule_data.py +0 -55
  642. endoreg_db/management/commands/load_network_data.py +0 -57
  643. endoreg_db/migrations/0002_alter_frame_image_alter_rawframe_image.py +0 -23
  644. endoreg_db/migrations/0003_alter_frame_image_alter_rawframe_image.py +0 -23
  645. endoreg_db/migrations/0004_alter_rawvideofile_file_alter_video_file.py +0 -25
  646. endoreg_db/migrations/0005_rawvideofile_frame_count_and_more.py +0 -33
  647. endoreg_db/migrations/0006_frame_extracted_rawframe_extracted.py +0 -23
  648. endoreg_db/migrations/0007_rename_pseudo_patient_video_patient_and_more.py +0 -24
  649. endoreg_db/migrations/0008_remove_reportfile_patient_examination_and_more.py +0 -48
  650. endoreg_db/models/ai_model/active_model.py +0 -9
  651. endoreg_db/models/ai_model/ai_model.py +0 -103
  652. endoreg_db/models/ai_model/lightning/__init__.py +0 -3
  653. endoreg_db/models/ai_model/lightning/predict.py +0 -172
  654. endoreg_db/models/ai_model/lightning/prediction_visualizer.py +0 -55
  655. endoreg_db/models/ai_model/lightning/run_visualizer.py +0 -21
  656. endoreg_db/models/ai_model/model_meta.py +0 -250
  657. endoreg_db/models/annotation/__init__.py +0 -32
  658. endoreg_db/models/annotation/anonymized_image_annotation.py +0 -115
  659. endoreg_db/models/annotation/binary_classification_annotation_task.py +0 -117
  660. endoreg_db/models/annotation/image_classification.py +0 -86
  661. endoreg_db/models/annotation/video_segmentation_annotation.py +0 -52
  662. endoreg_db/models/case/__init__.py +0 -1
  663. endoreg_db/models/case/case.py +0 -34
  664. endoreg_db/models/center/center.py +0 -51
  665. endoreg_db/models/center/center_product.py +0 -33
  666. endoreg_db/models/center/center_waste.py +0 -16
  667. endoreg_db/models/data_file/__init__.py +0 -39
  668. endoreg_db/models/data_file/base_classes/__init__.py +0 -7
  669. endoreg_db/models/data_file/base_classes/abstract_frame.py +0 -100
  670. endoreg_db/models/data_file/base_classes/abstract_pdf.py +0 -136
  671. endoreg_db/models/data_file/base_classes/abstract_video.py +0 -807
  672. endoreg_db/models/data_file/base_classes/frame_helpers.py +0 -17
  673. endoreg_db/models/data_file/base_classes/prepare_bulk_frames.py +0 -19
  674. endoreg_db/models/data_file/base_classes/utils.py +0 -80
  675. endoreg_db/models/data_file/frame.py +0 -29
  676. endoreg_db/models/data_file/import_classes/__init__.py +0 -18
  677. endoreg_db/models/data_file/import_classes/processing_functions/__init__.py +0 -35
  678. endoreg_db/models/data_file/import_classes/processing_functions/pdf.py +0 -28
  679. endoreg_db/models/data_file/import_classes/processing_functions/video.py +0 -260
  680. endoreg_db/models/data_file/import_classes/raw_pdf.py +0 -260
  681. endoreg_db/models/data_file/import_classes/raw_video.py +0 -288
  682. endoreg_db/models/data_file/metadata/sensitive_meta.py +0 -290
  683. endoreg_db/models/data_file/metadata/video_meta.py +0 -199
  684. endoreg_db/models/data_file/report_file.py +0 -56
  685. endoreg_db/models/data_file/video/__init__.py +0 -11
  686. endoreg_db/models/data_file/video/import_meta.py +0 -25
  687. endoreg_db/models/data_file/video/video.py +0 -196
  688. endoreg_db/models/data_file/video_segment.py +0 -214
  689. endoreg_db/models/disease.py +0 -79
  690. endoreg_db/models/event.py +0 -73
  691. endoreg_db/models/examination/examination.py +0 -67
  692. endoreg_db/models/examination/examination_indication.py +0 -170
  693. endoreg_db/models/finding/__init__.py +0 -11
  694. endoreg_db/models/finding/finding.py +0 -75
  695. endoreg_db/models/finding/finding_location_classification.py +0 -94
  696. endoreg_db/models/finding/finding_morphology_classification.py +0 -89
  697. endoreg_db/models/finding/finding_type.py +0 -22
  698. endoreg_db/models/hardware/__init__.py +0 -2
  699. endoreg_db/models/information_source.py +0 -29
  700. endoreg_db/models/laboratory/__init__.py +0 -1
  701. endoreg_db/models/laboratory/lab_value.py +0 -111
  702. endoreg_db/models/logging/__init__.py +0 -11
  703. endoreg_db/models/logging/agl_service.py +0 -19
  704. endoreg_db/models/logging/base.py +0 -22
  705. endoreg_db/models/logging/log_type.py +0 -23
  706. endoreg_db/models/logging/network_device.py +0 -27
  707. endoreg_db/models/lx/__init__.py +0 -4
  708. endoreg_db/models/lx/client.py +0 -57
  709. endoreg_db/models/lx/identity.py +0 -34
  710. endoreg_db/models/lx/permission.py +0 -18
  711. endoreg_db/models/lx/user.py +0 -16
  712. endoreg_db/models/network/__init__.py +0 -9
  713. endoreg_db/models/network/agl_service.py +0 -38
  714. endoreg_db/models/network/network_device.py +0 -58
  715. endoreg_db/models/network/network_device_type.py +0 -23
  716. endoreg_db/models/other/distribution.py +0 -5
  717. endoreg_db/models/patient/__init__.py +0 -24
  718. endoreg_db/models/patient/patient_examination.py +0 -182
  719. endoreg_db/models/patient/patient_finding.py +0 -143
  720. endoreg_db/models/patient/patient_finding_location.py +0 -120
  721. endoreg_db/models/patient/patient_finding_morphology.py +0 -166
  722. endoreg_db/models/permissions/__init__.py +0 -44
  723. endoreg_db/models/persons/__init__.py +0 -34
  724. endoreg_db/models/persons/examiner/__init__.py +0 -2
  725. endoreg_db/models/persons/examiner/examiner.py +0 -60
  726. endoreg_db/models/persons/examiner/examiner_type.py +0 -2
  727. endoreg_db/models/persons/patient/__init__.py +0 -8
  728. endoreg_db/models/persons/patient/patient.py +0 -389
  729. endoreg_db/models/persons/patient/patient_disease.py +0 -22
  730. endoreg_db/models/persons/patient/patient_event.py +0 -52
  731. endoreg_db/models/persons/patient/patient_lab_sample.py +0 -108
  732. endoreg_db/models/persons/patient/patient_medication.py +0 -59
  733. endoreg_db/models/persons/patient/patient_medication_schedule.py +0 -88
  734. endoreg_db/models/persons/portal_user_information.py +0 -27
  735. endoreg_db/models/prediction/__init__.py +0 -8
  736. endoreg_db/models/prediction/image_classification.py +0 -51
  737. endoreg_db/models/prediction/video_prediction_meta.py +0 -306
  738. endoreg_db/models/product/product.py +0 -110
  739. endoreg_db/models/product/product_group.py +0 -27
  740. endoreg_db/models/product/product_material.py +0 -28
  741. endoreg_db/models/questionnaires/__init__.py +0 -114
  742. endoreg_db/models/quiz/__init__.py +0 -9
  743. endoreg_db/models/quiz/quiz_answer.py +0 -41
  744. endoreg_db/models/quiz/quiz_question.py +0 -54
  745. endoreg_db/models/report_reader/report_reader_config.py +0 -53
  746. endoreg_db/models/rules/__init__.py +0 -5
  747. endoreg_db/queries/get/__init__.py +0 -6
  748. endoreg_db/queries/get/center.py +0 -42
  749. endoreg_db/queries/get/model.py +0 -13
  750. endoreg_db/queries/get/patient.py +0 -14
  751. endoreg_db/queries/get/patient_examination.py +0 -20
  752. endoreg_db/queries/get/report_file.py +0 -33
  753. endoreg_db/queries/get/video.py +0 -31
  754. endoreg_db/serializers/ai_model.py +0 -19
  755. endoreg_db/serializers/annotation.py +0 -14
  756. endoreg_db/serializers/center.py +0 -11
  757. endoreg_db/serializers/examination.py +0 -33
  758. endoreg_db/serializers/frame.py +0 -9
  759. endoreg_db/serializers/hardware.py +0 -21
  760. endoreg_db/serializers/label.py +0 -22
  761. endoreg_db/serializers/patient.py +0 -33
  762. endoreg_db/serializers/prediction.py +0 -10
  763. endoreg_db/serializers/raw_pdf_anony_text_validation.py +0 -137
  764. endoreg_db/serializers/report_file.py +0 -7
  765. endoreg_db/serializers/video.py +0 -20
  766. endoreg_db/serializers/video_segmentation.py +0 -587
  767. endoreg_db/tests.py +0 -3
  768. endoreg_db/utils/legacy_ocr.py +0 -201
  769. endoreg_db/utils/video/transcode_videofile.py +0 -111
  770. endoreg_db/views/patient_views.py +0 -90
  771. endoreg_db/views/raw_pdf_anony_text_validation_views.py +0 -95
  772. endoreg_db/views/raw_pdf_meta_validation_views.py +0 -111
  773. endoreg_db/views/raw_video_meta_validation_views.py +0 -148
  774. endoreg_db/views/report_views.py +0 -96
  775. endoreg_db/views/video_segmentation_views.py +0 -166
  776. endoreg_db-0.6.3.dist-info/METADATA +0 -161
  777. endoreg_db-0.6.3.dist-info/RECORD +0 -435
  778. /endoreg_db/{case_generator/__init__.py → api/serializers/finding_descriptions.py} +0 -0
  779. /endoreg_db/{queries/get/annotation.py → api/views/finding_descriptions.py} +0 -0
  780. /endoreg_db/{queries/get/prediction.py → data/shift/m2.yaml} +0 -0
  781. /endoreg_db/{queries/get/video_import_meta.py → factories/__init__.py} +0 -0
  782. /endoreg_db/{queries/get/video_prediction_meta.py → helpers/__init__.py} +0 -0
  783. /endoreg_db/models/{case_template → administration/case/case_template}/__init__.py +0 -0
  784. /endoreg_db/models/{persons → administration/person}/person.py +0 -0
  785. /endoreg_db/models/{product → administration/product}/__init__.py +0 -0
  786. /endoreg_db/models/{report_reader → media/pdf/report_reader}/__init__.py +0 -0
  787. /endoreg_db/models/{report_reader → media/pdf/report_reader}/report_reader_flag.py +0 -0
  788. /endoreg_db/models/{hardware → medical/hardware}/endoscopy_processor.py +0 -0
  789. /endoreg_db/models/{medication → medical/medication}/__init__.py +0 -0
  790. /endoreg_db/models/{medication → medical/medication}/medication_indication.py +0 -0
  791. /endoreg_db/models/{emission → other/emission}/__init__.py +0 -0
  792. /endoreg_db/models/{rules → rule}/rule_applicator.py +0 -0
  793. /endoreg_db/{case_generator → utils/case_generator}/case_generator.py +0 -0
  794. /endoreg_db/{case_generator → utils/case_generator}/lab_sample_factory.py +0 -0
  795. /endoreg_db/{case_generator → utils/case_generator}/utils.py +0 -0
  796. /endoreg_db/views/{csrf.py → misc/csrf.py} +0 -0
  797. {endoreg_db-0.6.3.dist-info → endoreg_db-0.8.1.dist-info}/WHEEL +0 -0
  798. {endoreg_db-0.6.3.dist-info → endoreg_db-0.8.1.dist-info}/licenses/LICENSE +0 -0
endoreg_db/admin.py CHANGED
@@ -4,18 +4,16 @@ from django.http import JsonResponse
4
4
  from endoreg_db.models import (
5
5
  Patient,
6
6
  Examination,
7
- PatientExamination,
7
+ # PatientExamination,
8
8
  Finding,
9
- FindingLocationClassification,
10
- FindingMorphologyClassification,
9
+ FindingClassification,
10
+ FindingClassificationChoice,
11
11
  FindingIntervention, # Import Finding Interventions
12
12
  PatientFindingIntervention,
13
- FindingLocationClassificationChoice,
14
- FindingMorphologyClassificationChoice,
15
- )
16
- from endoreg_db.forms.patient_finding_intervention_form import (
17
- PatientFindingInterventionForm,
18
13
  )
14
+ # from endoreg_db.forms.patient_finding_intervention_form import (
15
+ # PatientFindingInterventionForm,
16
+ # )
19
17
  from endoreg_db.forms.patient_form import PatientForm
20
18
 
21
19
 
@@ -31,7 +29,7 @@ class PatientAdmin(admin.ModelAdmin):
31
29
  @admin.register(Examination)
32
30
  class ExaminationAdmin(admin.ModelAdmin):
33
31
  list_display = ("id", "name")
34
- search_fields = ("name", "name_de", "name_en")
32
+ search_fields = ("name", )
35
33
  list_filter = ("name",)
36
34
  ordering = ("name",)
37
35
 
@@ -40,39 +38,41 @@ class PatientFindingInterventionAdmin(admin.ModelAdmin):
40
38
  change_list_template = "admin/patient_finding_intervention.html"
41
39
 
42
40
  def changelist_view(self, request, extra_context=None):
43
- """Pass Patients, Examinations, Findings, Locations, Location Choices, Morphologies, Morphology Choices, and Finding Interventions to the template"""
41
+ """
42
+ Overrides the admin changelist view to provide additional context data for the template, including all patients, examinations, findings, classifications, and interventions relevant to patient finding interventions.
43
+ """
44
44
  extra_context = {
45
45
  "patients": Patient.objects.all(),
46
46
  "examinations": Examination.objects.all(),
47
47
  "findings": Finding.objects.all(),
48
- "locations": FindingLocationClassification.objects.all(),
49
- "location_choices": FindingLocationClassificationChoice.objects.none(),
50
- "morphologies": FindingMorphologyClassification.objects.all(),
51
- "morphology_choices": FindingMorphologyClassificationChoice.objects.all(),
52
- "finding_interventions": FindingIntervention.objects.all(), # Pass Finding Interventions
48
+ "locations": FindingClassification.objects.filter(classification_types__name__iexact="location"),
49
+ "location_choices": FindingClassificationChoice.objects.none(),
50
+ "morphologies": FindingClassification.objects.filter(classification_types__name__iexact="morphology"),
51
+ "morphology_choices": FindingClassificationChoice.objects.none(),
52
+ "finding_interventions": FindingIntervention.objects.all(),
53
53
  }
54
54
  return super().changelist_view(request, extra_context=extra_context)
55
55
 
56
56
  def get_location_choices_json(self, request):
57
- """Ensure Django Admin returns JSON response for Location Choices"""
57
+ """
58
+ Handles AJAX requests to retrieve location classification choices as JSON.
59
+
60
+ Expects a "location" parameter in the GET request and returns a list of matching FindingClassificationChoice objects with their IDs and names. Returns an error message with appropriate HTTP status if the parameter is missing or an exception occurs.
61
+ """
58
62
  location_id = request.GET.get("location")
59
63
  if not location_id:
60
64
  return JsonResponse({"error": "Location ID is required"}, status=400)
61
65
 
62
66
  try:
63
67
  choices = list(
64
- FindingLocationClassificationChoice.objects.filter(
65
- location_classifications__id=location_id
68
+ FindingClassificationChoice.objects.filter(
69
+ classifications__id=location_id,
70
+ classifications__classification_types__name__iexact="location"
66
71
  ).values("id", "name")
67
- ) # Convert QuerySet to List
68
-
72
+ )
69
73
  if not choices:
70
- return JsonResponse(
71
- [], safe=False
72
- ) # Return an empty list if no data found
73
-
74
- return JsonResponse(choices, safe=False) # Return valid JSON
75
-
74
+ return JsonResponse([], safe=False)
75
+ return JsonResponse(choices, safe=False)
76
76
  except Exception as e:
77
77
  return JsonResponse({"error": str(e)}, status=500)
78
78
 
endoreg_db/api_urls.py ADDED
@@ -0,0 +1,4 @@
1
+ # Export raw API URL patterns so the project-level router can add the single `/api/` prefix.
2
+ from endoreg_db.urls import urlpatterns as api_urlpatterns
3
+
4
+ urlpatterns = api_urlpatterns
endoreg_db/apps.py CHANGED
@@ -4,3 +4,15 @@ from django.apps import AppConfig
4
4
  class EndoregDbConfig(AppConfig):
5
5
  default_auto_field = 'django.db.models.BigAutoField'
6
6
  name = 'endoreg_db'
7
+
8
+ def ready(self):
9
+ """
10
+ Performs application startup tasks when the Django app is fully loaded.
11
+
12
+ This method imports media-related model modules to ensure they are registered
13
+ and ready for use when the application starts.
14
+ """
15
+ import endoreg_db.models.media.video
16
+ import endoreg_db.models.media.frame
17
+ import endoreg_db.models.media.pdf
18
+ pass
@@ -0,0 +1 @@
1
+ dummy weights content
@@ -0,0 +1,88 @@
1
+ ### install
2
+ ```
3
+ uv add bowler fissix
4
+ ```
5
+
6
+ ### Dry-run (preview only)
7
+ ```
8
+ python endoreg_db/codemods/rename_datetime_fields.py
9
+ ```
10
+
11
+ ### Run it (models only):
12
+ ```
13
+ python endoreg_db/codemods/rename_datetime_fields.py --yes
14
+ ```
15
+
16
+ ### Verify what changed
17
+ ```
18
+ git status
19
+ git diff --name-only
20
+ git diff
21
+ ```
22
+
23
+ ### Then check for any leftover legacy names in models (excluding migration history):
24
+ ```
25
+ grep -RIn --exclude-dir='migrations' \
26
+ -E '\b(date_created|date_modified|last_update|date_updated|createdOn|updatedOn|modified_at|lastModified)\b' \
27
+ endoreg_db/models || true
28
+
29
+ grep -RIn --exclude-dir='migrations' -E '\b(date_created|date_modified|last_update|date_updated|createdOn|updatedOn|modified_at|lastModified)\b' endoreg_db/models || true
30
+ ```
31
+
32
+ ### Fix F(..) expressions (if any)
33
+ ```
34
+ # date_created -> created_at
35
+ grep -Rl --exclude-dir='migrations' "F('date_created')" endoreg_db/models | xargs -r sed -i "s/F('date_created')/F('created_at')/g"
36
+ grep -Rl --exclude-dir='migrations' 'F("date_created")' endoreg_db/models | xargs -r sed -i 's/F("date_created")/F("created_at")/g'
37
+
38
+ # date_modified -> updated_at
39
+ grep -Rl --exclude-dir='migrations' "F('date_modified')" endoreg_db/models | xargs -r sed -i "s/F('date_modified')/F('updated_at')/g"
40
+ grep -Rl --exclude-dir='migrations' 'F("date_modified")' endoreg_db/models | xargs -r sed -i 's/F("date_modified")/F("updated_at")/g'
41
+ ```
42
+
43
+
44
+ ### Example: Fix f-strings / attribute refs (seen in raw_pdf.py, video.py)
45
+ ```
46
+ # self.date_created -> self.created_at
47
+ grep -Rl --exclude-dir='migrations' 'self\.date_created' endoreg_db/models | xargs -r sed -i 's/self\.date_created/self.created_at/g'
48
+ # self.date_modified -> self.updated_at
49
+ grep -Rl --exclude-dir='migrations' 'self\.date_modified' endoreg_db/models | xargs -r sed -i 's/self\.date_modified/self.updated_at/g'
50
+ ```
51
+
52
+ ### Fix string literals in .values(), .order_by(), dict keys
53
+ ```
54
+ # double-quoted keys
55
+ grep -Rl --exclude-dir='migrations' --include="*.py" '"date_created"' endoreg_db/models | xargs -r sed -i 's/"date_created"/"created_at"/g'
56
+ grep -Rl --exclude-dir='migrations' --include="*.py" '"date_modified"' endoreg_db/models | xargs -r sed -i 's/"date_modified"/"updated_at"/g'
57
+ grep -Rl --exclude-dir='migrations' --include="*.py" '"last_update"' endoreg_db/models | xargs -r sed -i 's/"last_update"/"updated_at"/g'
58
+ grep -Rl --exclude-dir='migrations' --include="*.py" '"date_updated"' endoreg_db/models | xargs -r sed -i 's/"date_updated"/"updated_at"/g'
59
+
60
+ # single-quoted keys
61
+ grep -Rl --exclude-dir='migrations' --include="*.py" "'date_created'" endoreg_db/models | xargs -r sed -i "s/'date_created'/'created_at'/g"
62
+ grep -Rl --exclude-dir='migrations' --include="*.py" "'date_modified'" endoreg_db/models | xargs -r sed -i "s/'date_modified'/'updated_at'/g"
63
+ grep -Rl --exclude-dir='migrations' --include="*.py" "'last_update'" endoreg_db/models | xargs -r sed -i "s/'last_update'/'updated_at'/g"
64
+ grep -Rl --exclude-dir='migrations' --include="*.py" "'date_updated'" endoreg_db/models | xargs -r sed -i "s/'date_updated'/'updated_at'/g"
65
+
66
+ # order_by("-...") style
67
+ grep -Rl --exclude-dir='migrations' --include="*.py" '"-date_created"' endoreg_db/models | xargs -r sed -i 's/"-date_created"/"-created_at"/g'
68
+ grep -Rl --exclude-dir='migrations' --include="*.py" "'-date_created'" endoreg_db/models | xargs -r sed -i "s/'-date_created'/'-created_at'/g"
69
+ grep -Rl --exclude-dir='migrations' --include="*.py" '"-date_modified"' endoreg_db/models | xargs -r sed -i 's/"-date_modified"/"-updated_at"/g'
70
+ grep -Rl --exclude-dir='migrations' --include="*.py" "'-date_modified'" endoreg_db/models | xargs -r sed -i "s/'-date_modified'/'-updated_at'/g"
71
+ ```
72
+
73
+
74
+ ### Re-scan to confirm
75
+ ```
76
+ grep -RIn --exclude-dir='migrations' \
77
+ -E '\b(date_created|date_modified|last_update|date_updated|createdOn|updatedOn|modified_at|lastModified)\b' \
78
+ endoreg_db/models || true
79
+ ```
80
+
81
+
82
+ ### Migrations
83
+ ```
84
+ python manage.py makemigrations endoreg_db
85
+ python manage.py migrate
86
+ ```
87
+
88
+
@@ -0,0 +1,92 @@
1
+ # endoreg_db/codemods/rename_datetime_fields.py
2
+ from bowler import Query
3
+ from pathlib import Path
4
+ import argparse, yaml, sys
5
+
6
+ # Paths
7
+ BASE = Path(__file__).resolve().parents[1] # .../endoreg_db
8
+ RENAMES_YML = BASE / "renames.yml"
9
+ DEFAULT_TARGETS = ["endoreg_db/models"] # safer default
10
+ EXCLUDE_DIR_NAMES = {"migrations", "__pycache__"}
11
+
12
+ def load_renames():
13
+ if not RENAMES_YML.exists():
14
+ print(f"ERROR: renames.yml not found at {RENAMES_YML}", file=sys.stderr)
15
+ sys.exit(2)
16
+ data = yaml.safe_load(RENAMES_YML.read_text()) or {}
17
+ if not isinstance(data, dict) or not data:
18
+ print("ERROR: renames.yml is empty or not a mapping.", file=sys.stderr)
19
+ sys.exit(2)
20
+ return data
21
+
22
+ def iter_python_targets(paths):
23
+ """Yield *.py files under given paths, excluding migrations and caches."""
24
+ for p in map(Path, paths):
25
+ if p.is_file() and p.suffix == ".py":
26
+ if not any(part in EXCLUDE_DIR_NAMES for part in p.parts):
27
+ yield str(p)
28
+ elif p.is_dir():
29
+ for f in p.rglob("*.py"):
30
+ if any(part in EXCLUDE_DIR_NAMES for part in f.parts):
31
+ continue
32
+ yield str(f)
33
+
34
+ def build_query(files):
35
+ # Bowler can take a list of files; we’ve already filtered them
36
+ return Query(list(files))
37
+
38
+ def main(argv=None):
39
+ parser = argparse.ArgumentParser(
40
+ description="Rename legacy datetime fields to standardized names."
41
+ )
42
+ parser.add_argument(
43
+ "targets",
44
+ nargs="*",
45
+ help="Files/dirs to process. Default: endoreg_db/models",
46
+ )
47
+ parser.add_argument(
48
+ "--yes",
49
+ action="store_true",
50
+ help="Apply changes (write). Omit for a dry run.",
51
+ )
52
+ parser.add_argument(
53
+ "--silent",
54
+ action="store_true",
55
+ help="Reduce output verbosity.",
56
+ )
57
+ args = parser.parse_args(argv)
58
+
59
+ targets = args.targets or DEFAULT_TARGETS
60
+ if args.targets == []:
61
+ print(
62
+ "NOTICE: Using default target 'endoreg_db/models'. "
63
+ "Pass explicit paths to broaden scope.",
64
+ file=sys.stderr,
65
+ )
66
+
67
+ files = list(iter_python_targets(targets))
68
+ if not files:
69
+ print("No Python files found to process.", file=sys.stderr)
70
+ return 0
71
+
72
+ renames = load_renames()
73
+ q = build_query(files)
74
+
75
+ # Build transforms
76
+ for old, new in renames.items():
77
+ # obj.date_created -> obj.created_at
78
+ q.select_attribute(old).rename(new)
79
+ # LHS or bare names: date_created = models.DateTimeField(...)
80
+ q.select_var(old).rename(new)
81
+
82
+ # Execute (dry-run by default)
83
+ q.execute(write=args.yes, silent=args.silent)
84
+ if not args.yes:
85
+ print(
86
+ "\nDry run complete. Re-run with --yes to apply changes.",
87
+ file=sys.stderr,
88
+ )
89
+ return 0
90
+
91
+ if __name__ == "__main__":
92
+ raise SystemExit(main())
@@ -0,0 +1,101 @@
1
+ """
2
+ Centralized environment configuration for EndoReg-DB.
3
+
4
+ This module is the single place to read environment variables and .env files.
5
+ It avoids loading .env during pytest, and provides typed helpers.
6
+ No Django imports here to prevent early settings configuration.
7
+ """
8
+ from __future__ import annotations
9
+
10
+ from pathlib import Path
11
+ import os
12
+ from typing import Optional, Dict, Any
13
+
14
+ # Detect pytest early to avoid loading .env in test runs
15
+ IS_PYTEST = bool(os.environ.get("PYTEST_CURRENT_TEST"))
16
+
17
+ # Compute repository BASE_DIR (repo root). This file is endoreg_db/config/env.py.
18
+ BASE_DIR = Path(__file__).resolve().parents[2]
19
+
20
+ # Optional: load .env only when not under pytest
21
+ _DOTENV_LOADED = False
22
+ try:
23
+ if not IS_PYTEST:
24
+ import dotenv # type: ignore
25
+ dotenv.load_dotenv()
26
+ _DOTENV_LOADED = True
27
+ except Exception:
28
+ # dotenv is optional, ignore errors
29
+ _DOTENV_LOADED = False
30
+
31
+
32
+ def _get(key: str, default: Optional[str] = None) -> Optional[str]:
33
+ return os.environ.get(key, default)
34
+
35
+
36
+ def env_str(key: str, default: str = "") -> str:
37
+ val = _get(key)
38
+ return val if val is not None else default
39
+
40
+
41
+ def env_bool(key: str, default: bool = False) -> bool:
42
+ val = _get(key)
43
+ if val is None:
44
+ return default
45
+ return str(val).strip().lower() in {"1", "true", "yes", "on"}
46
+
47
+
48
+ def env_int(key: str, default: int = 0) -> int:
49
+ val = _get(key)
50
+ if val is None:
51
+ return default
52
+ try:
53
+ return int(str(val).strip())
54
+ except Exception:
55
+ return default
56
+
57
+
58
+ def env_path(key: str, default_relative: str) -> Path:
59
+ """Return an absolute path. If env is relative, resolve under BASE_DIR."""
60
+ val = _get(key)
61
+ if not val:
62
+ p = BASE_DIR / default_relative
63
+ else:
64
+ p = Path(val)
65
+ if not p.is_absolute():
66
+ p = (BASE_DIR / p).resolve()
67
+ return p
68
+
69
+
70
+ def snapshot() -> Dict[str, Any]:
71
+ """Return a snapshot of relevant config for debugging/logging."""
72
+ keys = [
73
+ # Core
74
+ "DJANGO_SETTINGS_MODULE",
75
+ "TIME_ZONE",
76
+ # Paths
77
+ "STORAGE_DIR",
78
+ "ASSET_DIR",
79
+ "STATIC_URL",
80
+ "MEDIA_URL",
81
+ # Dev DB
82
+ "DEV_DB_ENGINE",
83
+ "DEV_DB_NAME",
84
+ # Test DB
85
+ "TEST_DB_ENGINE",
86
+ "TEST_DB_NAME",
87
+ "TEST_DB_FILE",
88
+ # Flags
89
+ "RUN_VIDEO_TESTS",
90
+ "SKIP_EXPENSIVE_TESTS",
91
+ ]
92
+ data: Dict[str, Any] = {k: os.environ.get(k) for k in keys}
93
+ data.update({
94
+ "IS_PYTEST": IS_PYTEST,
95
+ "DOTENV_LOADED": _DOTENV_LOADED,
96
+ "BASE_DIR": str(BASE_DIR),
97
+ })
98
+ return data
99
+
100
+ # Back-compat short aliases used by settings modules
101
+ ENV = os.environ.get
@@ -3,6 +3,7 @@ from pathlib import Path
3
3
  DATA_DIR = Path(__file__).parent
4
4
 
5
5
  INFORMATION_DATA_DIR = DATA_DIR / "information_source"
6
+ INFORMATION_SOURCE_TYPE_DATA_DIR = DATA_DIR / "information_source_type"
6
7
  UNIT_DATA_DIR = DATA_DIR / "unit"
7
8
  CENTER_DATA_DIR = DATA_DIR / "center"
8
9
  EXAMINATION_DATA_DIR = DATA_DIR / "examination"
@@ -17,6 +18,9 @@ REPORT_READER_FLAG_DATA_DIR = DATA_DIR / "report_reader_flag"
17
18
  EVENT_DATA_DIR = DATA_DIR / "event"
18
19
  GENDER_DATA_DIR = DATA_DIR / "gender"
19
20
  ORGAN_DATA_DIR = DATA_DIR / "organ"
21
+ NAMES_FIRST_DATA_DIR = DATA_DIR / "names_first"
22
+ NAMES_LAST_DATA_DIR = DATA_DIR / "names_last"
23
+
20
24
 
21
25
  # Contraindication
22
26
  CONTRAINDICATION_DATA_DIR = DATA_DIR / "contraindication"
@@ -49,6 +53,11 @@ FINDING_MORPGOLOGY_CLASSIFICATION_TYPE_DATA_DIR = (
49
53
  FINDING_INTERVETION_DATA_DIR = DATA_DIR / "finding_intervention"
50
54
  FINIDNG_INTERVENTION_TYPE_DATA_DIR = DATA_DIR / "finding_intervention_type"
51
55
 
56
+
57
+ FINDING_CLASSIFICATION_TYPE_DATA_DIR = DATA_DIR / "finding_classification_type"
58
+ FINDING_CLASSIFICATION_DATA_DIR = DATA_DIR / "finding_classification"
59
+ FINDING_CLASSIFICATION_CHOICE_DATA_DIR = DATA_DIR / "finding_classification_choice"
60
+
52
61
  # Green Endoscopy Dashboard Stuffs
53
62
  CENTER_RESOURCE_DATA_DIR = DATA_DIR / "center_resource"
54
63
  CENTER_WASTE_DATA_DIR = DATA_DIR / "center_waste"
@@ -102,6 +111,17 @@ LABEL_DATA_DIR = DATA_DIR / "ai_model_label"
102
111
  VIDEO_SEGMENTATION_LABEL_DATA_DIR = DATA_DIR / "ai_model_video_segmentation_label"
103
112
  VIDEO_SEGMENTATION_LABELSET_DATA_DIR = DATA_DIR / "ai_model_video_segmentation_labelset"
104
113
 
114
+ # RISK
115
+ RISK_DATA_DIR = DATA_DIR / "risk"
116
+ RISK_TYPE_DATA_DIR = DATA_DIR / "risk_type"
117
+
118
+ # REQUIREMENT
119
+ REQUIREMENT_DATA_DIR = DATA_DIR / "requirement"
120
+ REQUIREMENT_OPERATOR_DATA_DIR = DATA_DIR / "requirement_operator"
121
+ REQUIREMENT_SET_DATA_DIR = DATA_DIR / "requirement_set"
122
+ REQUIREMENT_SET_TYPE_DATA_DIR = DATA_DIR / "requirement_set_type"
123
+ REQUIREMENT_TYPE_DATA_DIR = DATA_DIR / "requirement_type"
124
+
105
125
  # To Do
106
126
  LAB_VALUE_DATA_DIR = DATA_DIR / "lab_value"
107
127
  PATIENT_LAB_SAMPLE_TYPE_DATA_DIR = DATA_DIR / "patient_lab_sample_type"
@@ -116,3 +136,9 @@ RULESET_DATA_DIR = DATA_DIR / "ruleset"
116
136
  LX_PERMISSION_DATA_DIR = DATA_DIR / "lx_permission"
117
137
  LX_CLIENT_TAG_DATA_DIR = DATA_DIR / "lx_client_tag"
118
138
  LX_CLIENT_TYPE_DATA_DIR = DATA_DIR / "lx_client_type"
139
+
140
+ QUALIFICATION_DATA_DIR = DATA_DIR / "qualification"
141
+
142
+ TAG_DATA_DIR = DATA_DIR / "tag"
143
+
144
+ EXAMINATION_REQUIREMENT_SET_DATA_DIR = DATA_DIR / "examination_requirement_set"
@@ -2,6 +2,6 @@
2
2
  fields:
3
3
  name: "image_multilabel_classification_colonoscopy_default"
4
4
  description: "Image multilabel classification model"
5
- model_type: "image"
5
+ model_type: "multilabel_classification"
6
6
  model_subtype: "multilabel"
7
7
  video_segmentation_labelset: "colonoscopy_video_segmentation_raw"
@@ -0,0 +1,52 @@
1
+ # Paris
2
+ - model: endoreg_db.Label
3
+ fields:
4
+ name: "paris_1s"
5
+ label_type: "classification"
6
+
7
+ - model: endoreg_db.Label
8
+ fields:
9
+ name: "paris_1p"
10
+ label_type: "classification"
11
+
12
+ - model: endoreg_db.Label
13
+ fields:
14
+ name: "paris_2a"
15
+ label_type: "classification"
16
+
17
+ - model: endoreg_db.Label
18
+ fields:
19
+ name: "paris_2b"
20
+ label_type: "classification"
21
+
22
+ - model: endoreg_db.Label
23
+ fields:
24
+ name: "paris_2c"
25
+ label_type: "classification"
26
+
27
+ - model: endoreg_db.Label
28
+ fields:
29
+ name: "paris_3"
30
+ label_type: "classification"
31
+
32
+ # NICE Classification
33
+ - model: endoreg_db.Label
34
+ fields:
35
+ name: "nice_1"
36
+ label_type: "classification"
37
+
38
+ - model: endoreg_db.Label
39
+ fields:
40
+ name: "nice_2a"
41
+ label_type: "classification"
42
+
43
+ - model: endoreg_db.Label
44
+ fields:
45
+ name: "nice_2b"
46
+ label_type: "classification"
47
+
48
+ - model: endoreg_db.Label
49
+ fields:
50
+ name: "nice_3"
51
+ label_type: "classification"
52
+
@@ -1,4 +1,4 @@
1
- - model: endoreg_db.LabelSet
1
+ - model: endoreg_db.label_set
2
2
  fields:
3
3
  name: "multilabel_classification_colonoscopy_default"
4
4
  version: 1
@@ -19,3 +19,22 @@
19
19
  "water_jet",
20
20
  "wound",
21
21
  ]
22
+
23
+ - model: endoreg_db.label_set
24
+ fields:
25
+ name: "multilabel_classification_colonoscopy_default"
26
+ version: 2
27
+ labels:
28
+ [
29
+ "appendix",
30
+ "blood",
31
+ "ileocaecalvalve",
32
+ "ileum",
33
+ "low_quality",
34
+ "instrument",
35
+ "digital_chromo_endoscopy",
36
+ "outside",
37
+ "polyp",
38
+ "water_jet",
39
+ "wound",
40
+ ]
@@ -0,0 +1,25 @@
1
+ - model: endoreg_db.LabelSet
2
+ fields:
3
+ name: "endoscopy_paris_classification"
4
+ version: 1
5
+ labels:
6
+ [
7
+ "paris_1s",
8
+ "paris_1p",
9
+ "paris_2a",
10
+ "paris_2b",
11
+ "paris_2c",
12
+ "paris_3",
13
+ ]
14
+
15
+ - model: endoreg_db.LabelSet
16
+ fields:
17
+ name: "endoscopy_nice_classification"
18
+ version: 1
19
+ labels:
20
+ [
21
+ "nice_1",
22
+ "nice_2a",
23
+ "nice_2b",
24
+ "nice_3",
25
+ ]
@@ -3,8 +3,8 @@
3
3
  - model: endoreg_db.center
4
4
  fields:
5
5
  name: "university_hospital_wuerzburg"
6
- name_de: "Universitätsklinikum Würzburg"
7
- name_en: "University Hospital Würzburg"
6
+ # name_de: "Universitätsklinikum Würzburg"
7
+ # name_en: "University Hospital Würzburg"
8
8
 
9
9
  first_names: [
10
10
  "Markus",
@@ -24,6 +24,7 @@
24
24
  "Philip",
25
25
  "Laura",
26
26
  "Tanja",
27
+ "Thomas"
27
28
  ]
28
29
 
29
30
  last_names: [
@@ -49,8 +50,8 @@
49
50
  - model: endoreg_db.center
50
51
  fields:
51
52
  name: "rbk_stuttgart"
52
- name_de: "Robert-Bosch-Krankenhaus Stuttgart"
53
- name_en: "Robert Bosch Hospital Stuttgart"
53
+ # name_de: "Robert-Bosch-Krankenhaus Stuttgart"
54
+ # name_en: "Robert Bosch Hospital Stuttgart"
54
55
  first_names: [] # many to many; if foreign key, we would just have a string; strings represent "name" attribute
55
56
  last_names: []
56
57
 
@@ -58,8 +59,8 @@
58
59
  - model: endoreg_db.center
59
60
  fields:
60
61
  name: "bbk_regensburg"
61
- name_de: "Barmherzige Brüder Krankenhaus Regensburg"
62
- name_en: "Barmherzige Brüder Hospital Regensburg"
62
+ # name_de: "Barmherzige Brüder Krankenhaus Regensburg"
63
+ # name_en: "Barmherzige Brüder Hospital Regensburg"
63
64
  first_names: []
64
65
  last_names: []
65
66
 
@@ -67,8 +68,8 @@
67
68
  - model: endoreg_db.center
68
69
  fields:
69
70
  name: "uke_hamburg"
70
- name_de: "Universitätsklinikum Hamburg-Eppendorf"
71
- name_en: "University Hospital Hamburg-Eppendorf"
71
+ # name_de: "Universitätsklinikum Hamburg-Eppendorf"
72
+ # name_en: "University Hospital Hamburg-Eppendorf"
72
73
  first_names: []
73
74
  last_names: []
74
75
 
@@ -76,15 +77,15 @@
76
77
  - model: endoreg_db.center
77
78
  fields:
78
79
  name: "rkh_ludwigsburg"
79
- name_de: "RKH Krankenhaus Ludwigsburg"
80
- name_en: "RKH Hospital Ludwigsburg"
80
+ # name_de: "RKH Krankenhaus Ludwigsburg"
81
+ # name_en: "RKH Hospital Ludwigsburg"
81
82
  first_names: []
82
83
  last_names: []
83
84
 
84
85
  - model: endoreg_db.center
85
86
  fields:
86
87
  name: "endoreg_db_demo"
87
- name_de: "Demo Center"
88
- name_en: "Demo Center"
88
+ # name_de: "Demo Center"
89
+ # name_en: "Demo Center"
89
90
  first_names: []
90
91
  last_names: []
@@ -0,0 +1,9 @@
1
+ - model: endoreg_db.center_shift
2
+ fields:
3
+ name: "ukw_endoscopy"
4
+ name_de: "Endoskopie (Koloskopie Raum)"
5
+ name_en: "Endoscopy (Colonoscopy Room)"
6
+ description: "This shift represents the UKW's colonoscopy room."
7
+ shift: "endoscopy_base"
8
+ center: "university_hospital_wuerzburg"
9
+