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
@@ -0,0 +1,35 @@
1
+ from django.db import models
2
+ from typing import TYPE_CHECKING
3
+
4
+ class FindingTypeManager(models.Manager):
5
+ def get_by_natural_key(self, name):
6
+ """
7
+ Retrieve a FindingType instance by its unique name for natural key deserialization.
8
+
9
+ Parameters:
10
+ name (str): The unique name of the FindingType to retrieve.
11
+
12
+ Returns:
13
+ FindingType: The instance matching the given name.
14
+ """
15
+ return self.get(name=name)
16
+
17
+ class FindingType(models.Model):
18
+ name = models.CharField(max_length=100, unique=True)
19
+ description = models.TextField(blank=True, null=True)
20
+
21
+ objects = FindingTypeManager()
22
+
23
+ if TYPE_CHECKING:
24
+ from endoreg_db.models import (
25
+ Finding, Examination, FindingClassification, FindingMorphologyClassification
26
+ )
27
+ finding_classifications: models.QuerySet['FindingClassification']
28
+ morphology_classifications: models.QuerySet['FindingMorphologyClassification']
29
+
30
+
31
+ def natural_key(self):
32
+ return (self.name,)
33
+
34
+ def __str__(self):
35
+ return self.name
@@ -0,0 +1,8 @@
1
+ from .endoscopy_processor import EndoscopyProcessor
2
+ from .endoscope import Endoscope, EndoscopeType
3
+
4
+ __all__ = [
5
+ "Endoscope",
6
+ "EndoscopeType",
7
+ "EndoscopyProcessor",
8
+ ]
@@ -1,37 +1,41 @@
1
- from django.db import models
1
+ from django.db import models#
2
+ from typing import TYPE_CHECKING
2
3
 
3
4
  class EndoscopeManager(models.Manager):
4
5
  def get_by_natural_key(self, name, sn):
5
6
  return self.get(name=name, sn=sn)
6
-
7
+
7
8
  class Endoscope(models.Model):
8
9
  objects = EndoscopeManager()
9
-
10
- name = models.CharField(max_length=255)
11
- name_de = models.CharField(max_length=255, blank=True, null=True)
12
- name_en = models.CharField(max_length=255, blank=True, null=True)
10
+
11
+ name = models.CharField(max_length=255)
13
12
  sn = models.CharField(max_length=255)
14
13
  center = models.ForeignKey(
15
14
  'Center',
16
- blank=True,
17
- null=True,
15
+ blank=True,
16
+ null=True,
18
17
  on_delete=models.CASCADE,
19
18
  related_name='endoscopes'
20
19
  )
21
20
  endoscope_type = models.ForeignKey(
22
21
  'EndoscopeType',
23
- blank=True,
24
- null=True,
22
+ blank=True,
23
+ null=True,
25
24
  on_delete=models.CASCADE,
26
25
  related_name='endoscopes'
27
26
  )
28
-
27
+
28
+ if TYPE_CHECKING:
29
+ from endoreg_db.models.center.center import Center
30
+ center: "Center"
31
+ endoscope_type: "EndoscopeType"
32
+
29
33
  def natural_key(self):
30
34
  return (self.name, self.sn)
31
-
35
+
32
36
  def __str__(self):
33
- return self.name
34
-
37
+ return str(self.name)
38
+
35
39
  class Meta:
36
40
  ordering = ['name']
37
41
  verbose_name = 'Endoscope'
@@ -40,20 +44,21 @@ class Endoscope(models.Model):
40
44
  class EndoscopeTypeManager(models.Manager):
41
45
  def get_by_natural_key(self, name):
42
46
  return self.get(name=name)
43
-
47
+
44
48
  class EndoscopeType(models.Model):
45
49
  objects = EndoscopeTypeManager()
46
-
47
- name = models.CharField(max_length=255)
48
- name_de = models.CharField(max_length=255, blank=True, null=True)
49
- name_en = models.CharField(max_length=255, blank=True, null=True)
50
-
51
- def natural_key(self):
50
+
51
+ name = models.CharField(max_length=255, unique=True)
52
+
53
+ if TYPE_CHECKING:
54
+ endoscopes: models.QuerySet["Endoscope"]
55
+
56
+ def natural_key(self) -> tuple[str]:
52
57
  return (self.name,)
53
58
 
54
59
  def __str__(self):
55
- return self.name
56
-
60
+ return str(self.name)
61
+
57
62
  class Meta:
58
63
  ordering = ['name']
59
64
  verbose_name = 'Endoscope Type'
@@ -0,0 +1,5 @@
1
+ from .lab_value import LabValue
2
+
3
+ __all__ = [
4
+ "LabValue",
5
+ ]
@@ -0,0 +1,419 @@
1
+ from django.db import models
2
+ import warnings
3
+ from typing import TYPE_CHECKING
4
+
5
+ if TYPE_CHECKING:
6
+ from endoreg_db.models.other.unit import Unit
7
+ from ...other.distribution import (
8
+ SingleCategoricalValueDistribution,
9
+ NumericValueDistribution,
10
+ MultipleCategoricalValueDistribution,
11
+ DateValueDistribution,
12
+ )
13
+ from ...administration.person.patient import Patient # Added Patient for type hinting
14
+
15
+ LANG = "de"
16
+
17
+ from pydantic import BaseModel, ConfigDict
18
+
19
+ class CommonLabValues(BaseModel):
20
+ """
21
+ A Pydantic model representing a lookup for common lab values.
22
+ It is used to provide a structured way to access common lab values like
23
+ hemoglobin, creatinine, and others
24
+ """
25
+ hb: "LabValue"
26
+ wbc: "LabValue"
27
+ plt: "LabValue"
28
+ cr: "LabValue"
29
+ na: "LabValue"
30
+ k: "LabValue"
31
+ glc: "LabValue"
32
+ inr: "LabValue"
33
+ crp: "LabValue"
34
+
35
+ model_config = ConfigDict(
36
+ from_attributes = True,
37
+ arbitrary_types_allowed = True
38
+ )
39
+
40
+ class LabValueManager(models.Manager):
41
+ def get_by_natural_key(self, name):
42
+ """
43
+ Retrieves a LabValue instance by its unique name.
44
+
45
+ Args:
46
+ name: The unique name of the LabValue.
47
+
48
+ Returns:
49
+ The LabValue instance with the specified name.
50
+ """
51
+ return self.get(name=name)
52
+
53
+
54
+ class LabValue(models.Model):
55
+ name = models.CharField(max_length=255, unique=True)
56
+ abbreviation = models.CharField(max_length=10, blank=True, null=True)
57
+ default_unit = models.ForeignKey(
58
+ "Unit", on_delete=models.CASCADE, blank=True, null=True
59
+ )
60
+ numeric_precision = models.IntegerField(default=3)
61
+ default_single_categorical_value_distribution = models.ForeignKey(
62
+ "SingleCategoricalValueDistribution",
63
+ on_delete=models.CASCADE,
64
+ blank=True,
65
+ null=True,
66
+ related_name="default_single_categorical_value_distribution",
67
+ )
68
+ default_numerical_value_distribution = models.ForeignKey(
69
+ "NumericValueDistribution",
70
+ on_delete=models.CASCADE,
71
+ blank=True,
72
+ null=True,
73
+ related_name="default_numerical_value_distribution",
74
+ )
75
+ default_multiple_categorical_value_distribution = models.ForeignKey(
76
+ "MultipleCategoricalValueDistribution",
77
+ on_delete=models.CASCADE,
78
+ blank=True,
79
+ null=True,
80
+ related_name="default_multiple_categorical_value_distribution",
81
+ )
82
+ default_date_value_distribution = models.ForeignKey(
83
+ "DateValueDistribution",
84
+ on_delete=models.CASCADE,
85
+ blank=True,
86
+ null=True,
87
+ related_name="default_date_value_distribution",
88
+ )
89
+ default_normal_range = models.JSONField(blank=True, null=True)
90
+ normal_range_age_dependent = models.BooleanField(default=False)
91
+ normal_range_gender_dependent = models.BooleanField(default=False)
92
+ normal_range_special_case = models.BooleanField(default=False)
93
+ bound_adjustment_factor = models.FloatField(
94
+ default=0.1,
95
+ help_text="Factor for adjusting bounds when generating increased/decreased values, e.g., 0.1 for 10%."
96
+ )
97
+ objects = LabValueManager()
98
+
99
+ if TYPE_CHECKING:
100
+ default_unit: "Unit"
101
+ default_single_categorical_value_distribution: "SingleCategoricalValueDistribution"
102
+ default_numerical_value_distribution: "NumericValueDistribution"
103
+ default_multiple_categorical_value_distribution: "MultipleCategoricalValueDistribution"
104
+ default_date_value_distribution: "DateValueDistribution"
105
+
106
+ @classmethod
107
+ def get_common_lab_values(cls):
108
+ """
109
+ Retrieves a structured set of common laboratory values as a CommonLabValues instance.
110
+
111
+ Returns:
112
+ A CommonLabValues Pydantic model populated with LabValue objects for hemoglobin, white blood cells, platelets, creatinine, sodium, potassium, glucose, international normalized ratio, and C-reactive protein.
113
+ """
114
+ from endoreg_db.models.medical.laboratory.lab_value import CommonLabValues
115
+
116
+ return CommonLabValues(
117
+ hb=cls.objects.get(name="hemoglobin"),
118
+ wbc=cls.objects.get(name="white_blood_cells"),
119
+ plt=cls.objects.get(name="platelets"),
120
+ cr=cls.objects.get(name="creatinine"),
121
+ na=cls.objects.get(name="sodium"),
122
+ k=cls.objects.get(name="potassium"),
123
+ glc=cls.objects.get(name="glucose"),
124
+ inr=cls.objects.get(name="international_normalized_ratio"),
125
+ crp=cls.objects.get(name="c_reactive_protein")
126
+ )
127
+
128
+
129
+ def natural_key(self):
130
+ """Returns a tuple containing the unique name of this lab value instance."""
131
+ return (self.name,)
132
+
133
+ def __str__(self):
134
+ """
135
+ Return the lab value name as a string.
136
+
137
+ Converts the lab value's `name` attribute into its string representation for
138
+ display purposes.
139
+ """
140
+ return str(self.name)
141
+
142
+ def get_default_default_distribution(self):
143
+ """
144
+ Returns the first available default distribution for the lab value.
145
+
146
+ Checks the default distribution fields in the following order:
147
+ default_single_categorical_value_distribution, default_numerical_value_distribution,
148
+ default_multiple_categorical_value_distribution, and default_date_value_distribution.
149
+ If none are set, a warning is issued and None is returned.
150
+ """
151
+ if self.default_single_categorical_value_distribution:
152
+ return self.default_single_categorical_value_distribution
153
+ elif self.default_numerical_value_distribution:
154
+ return self.default_numerical_value_distribution
155
+ elif self.default_multiple_categorical_value_distribution:
156
+ return self.default_multiple_categorical_value_distribution
157
+ elif self.default_date_value_distribution:
158
+ return self.default_date_value_distribution
159
+ else:
160
+ warnings.warn("No default distribution set for lab value")
161
+ return None
162
+
163
+ def get_normal_range(self, age: int = None, gender=None):
164
+ """
165
+ Returns the normal range for this lab value, considering age and gender dependencies.
166
+
167
+ If the normal range is gender-dependent, attempts to use the provided gender; defaults to "male" if gender is missing or unknown. Falls back to general min/max values if gender-specific data is unavailable. Issues warnings for unimplemented age-dependent or special case ranges, and when min or max values cannot be determined. Returns a dictionary with keys "min" and "max", which may be None if the range is not defined.
168
+ """
169
+ from ...other.gender import Gender
170
+
171
+ assert isinstance(age, int) or age is None
172
+ assert isinstance(gender, Gender) or gender is None
173
+
174
+ age_dependent = self.normal_range_age_dependent
175
+ gender_dependent = self.normal_range_gender_dependent
176
+ special_case = self.normal_range_special_case
177
+
178
+ min_value = None
179
+ max_value = None
180
+ current_range_source = self.default_normal_range or {}
181
+
182
+ gender_name_to_use = None
183
+ if gender_dependent:
184
+ if gender and hasattr(gender, 'name') and gender.name:
185
+ gender_name_to_use = gender.name
186
+ if gender_name_to_use not in current_range_source:
187
+ warnings.warn(
188
+ f"Normal range for gender '{gender_name_to_use}' not found for LabValue '{self.name}'. "
189
+ f"Defaulting to 'male' range.",
190
+ UserWarning
191
+ )
192
+ gender_name_to_use = "male"
193
+ else:
194
+ warnings.warn(
195
+ f"Gender not provided for gender-dependent LabValue '{self.name}'. Defaulting to 'male' range.",
196
+ UserWarning
197
+ )
198
+ gender_name_to_use = "male"
199
+
200
+ # Attempt gender-specific lookup
201
+ gender_specific_data = current_range_source.get(gender_name_to_use)
202
+ if isinstance(gender_specific_data, dict):
203
+ min_value = gender_specific_data.get("min")
204
+ max_value = gender_specific_data.get("max")
205
+ else:
206
+ warnings.warn(
207
+ f"No gender-specific data found for '{gender_name_to_use}' in LabValue '{self.name}'. "
208
+ f"Falling back to general range if available.",
209
+ UserWarning
210
+ )
211
+
212
+ # Fallback to general min/max if needed
213
+ if (min_value is None or max_value is None) and isinstance(current_range_source, dict):
214
+ if min_value is None:
215
+ min_value = current_range_source.get("min")
216
+ if max_value is None:
217
+ max_value = current_range_source.get("max")
218
+
219
+ if age_dependent:
220
+ warnings.warn(f"Age dependent normal range not implemented yet for LabValue '{self.name}'. Age: {age}.")
221
+
222
+ if special_case:
223
+ warnings.warn(f"Special case normal range not implemented yet for LabValue '{self.name}'.")
224
+
225
+ # Final contextual warning
226
+ if min_value is None and max_value is None:
227
+ # Do not warn here; let get_normal_value handle the warning for missing range
228
+ return {"min": min_value, "max": max_value}
229
+ if min_value is None:
230
+ context_parts = []
231
+ if gender_dependent:
232
+ gender_repr = (gender.name if gender and hasattr(gender, 'name') else 'None')
233
+ if gender_name_to_use and gender_name_to_use != gender_repr:
234
+ gender_repr = f"{gender_repr} (lookup attempted for: {gender_name_to_use})"
235
+ context_parts.append(f"gender: {gender_repr}")
236
+ if age_dependent:
237
+ context_parts.append(f"age: {age}")
238
+
239
+ warning_message = (
240
+ f"Could not determine a 'min' normal range for LabValue '{self.name}'"
241
+ )
242
+ if context_parts:
243
+ warning_message += f" with context ({', '.join(context_parts)})."
244
+ else:
245
+ warning_message += " (general context)."
246
+ warning_message += " Check LabValue's default_normal_range definition."
247
+ warnings.warn(warning_message, UserWarning)
248
+
249
+ return {"min": min_value, "max": max_value}
250
+
251
+ def get_increased_value(self, patient: "Patient" = None):
252
+ """
253
+ Returns a value that is considered increased for this lab value.
254
+ It prioritizes sampling from a numerical distribution if available,
255
+ otherwise uses the upper bound of the normal range.
256
+ """
257
+ _age = patient.age() if patient else None
258
+ _gender = patient.gender if patient else None
259
+ normal_range = self.get_normal_range(age=_age, gender=_gender)
260
+ upper_bound = normal_range.get("max")
261
+
262
+ if self.default_numerical_value_distribution:
263
+ if patient:
264
+ # Attempt to sample above the upper bound, or a high value if no bound
265
+ for _ in range(10): # Try a few times to get a value if bounds are restrictive
266
+ generated_value = self.default_numerical_value_distribution.generate_value(
267
+ lab_value=self, patient=patient
268
+ )
269
+ if upper_bound is not None:
270
+ if generated_value > upper_bound:
271
+ return generated_value
272
+ # Heuristic for "high" if no upper_bound, compare against mean + stddev
273
+ elif hasattr(self.default_numerical_value_distribution, "mean") and \
274
+ hasattr(self.default_numerical_value_distribution, "stddev") and \
275
+ self.default_numerical_value_distribution.mean is not None and \
276
+ self.default_numerical_value_distribution.stddev is not None and \
277
+ generated_value > (
278
+ self.default_numerical_value_distribution.mean + self.default_numerical_value_distribution.stddev
279
+ ):
280
+ return generated_value
281
+ # Fallback if sampling fails to produce a clearly increased value
282
+ if upper_bound is not None:
283
+ return upper_bound + (abs(upper_bound * self.bound_adjustment_factor) if upper_bound != 0 else 1) # Increase by factor or 1
284
+ # If no upper bound and sampling didn't provide a clear high value, return a generated value as last resort
285
+ return self.default_numerical_value_distribution.generate_value(lab_value=self, patient=patient)
286
+ else: # No patient, cannot use distribution
287
+ warnings.warn(
288
+ f"Cannot use numerical distribution for {self.name} without patient context. Falling back to normal range logic for increased value."
289
+ )
290
+ if upper_bound is not None:
291
+ return upper_bound + (abs(upper_bound * self.bound_adjustment_factor) if upper_bound != 0 else 1)
292
+ else:
293
+ warnings.warn(
294
+ f"Cannot determine an increased value for {self.name} without an upper normal range or patient context for distribution."
295
+ )
296
+ return None
297
+
298
+ elif upper_bound is not None:
299
+ return upper_bound + (abs(upper_bound * self.bound_adjustment_factor) if upper_bound != 0 else 1)
300
+ else:
301
+ warnings.warn(
302
+ f"Cannot determine an increased value for {self.name} without a numerical distribution or an upper normal range."
303
+ )
304
+ return None
305
+
306
+ def get_normal_value(self, patient: "Patient" = None):
307
+ """
308
+ Returns a value considered normal for this lab value.
309
+
310
+ If a numerical distribution and patient context are available, attempts to generate a value within the normal range. Falls back to the midpoint of the normal range or to available bounds if sampling fails or context is insufficient. Returns None if neither a normal range nor a distribution is available.
311
+ """
312
+ _age = patient.age() if patient else None
313
+ _gender = patient.gender if patient else None
314
+ normal_range = self.get_normal_range(age=_age, gender=_gender)
315
+ lower_bound = normal_range.get("min")
316
+ upper_bound = normal_range.get("max")
317
+
318
+ if self.default_numerical_value_distribution:
319
+ if patient:
320
+ for _ in range(10): # Try a few times
321
+ generated_value = self.default_numerical_value_distribution.generate_value(
322
+ lab_value=self, patient=patient
323
+ )
324
+ if lower_bound is not None and upper_bound is not None:
325
+ if lower_bound <= generated_value <= upper_bound:
326
+ return generated_value
327
+ elif lower_bound is not None and generated_value >= lower_bound: # No upper bound
328
+ return generated_value
329
+ elif upper_bound is not None and generated_value <= upper_bound: # No lower bound
330
+ return generated_value
331
+ elif lower_bound is None and upper_bound is None: # No range defined
332
+ return generated_value
333
+ # Fallback if sampling fails to produce a value in range
334
+ if lower_bound is not None and upper_bound is not None:
335
+ return (lower_bound + upper_bound) / 2.0
336
+ # Return any generated value as last resort
337
+ return self.default_numerical_value_distribution.generate_value(lab_value=self, patient=patient)
338
+ else: # No patient, cannot use distribution
339
+ warnings.warn(
340
+ f"Cannot use numerical distribution for {self.name} without patient context. Falling back to normal range logic for normal value."
341
+ )
342
+ if lower_bound is not None and upper_bound is not None:
343
+ return (lower_bound + upper_bound) / 2.0
344
+ elif lower_bound is not None:
345
+ return lower_bound
346
+ elif upper_bound is not None:
347
+ return upper_bound
348
+ else:
349
+ warnings.warn(
350
+ f"Cannot determine a normal value for {self.name} without a normal range or patient context for distribution.",
351
+ UserWarning
352
+ )
353
+ return None
354
+
355
+ elif lower_bound is not None and upper_bound is not None:
356
+ return (lower_bound + upper_bound) / 2.0
357
+ elif lower_bound is not None: # Only min is defined
358
+ return lower_bound
359
+ elif upper_bound is not None: # Only max is defined
360
+ return upper_bound
361
+ else:
362
+ warnings.warn(
363
+ f"Cannot determine a normal value for {self.name} without a numerical distribution or a normal range."
364
+ )
365
+ return None
366
+
367
+ def get_decreased_value(self, patient: "Patient" = None):
368
+ """
369
+ Returns a value that is considered decreased for this lab value.
370
+ It prioritizes sampling from a numerical distribution if available,
371
+ otherwise uses the lower bound of the normal range.
372
+ """
373
+ _age = patient.age() if patient else None
374
+ _gender = patient.gender if patient else None
375
+ normal_range = self.get_normal_range(age=_age, gender=_gender)
376
+ lower_bound = normal_range.get("min")
377
+
378
+ if self.default_numerical_value_distribution:
379
+ if patient:
380
+ for _ in range(10): # Try a few times
381
+ generated_value = self.default_numerical_value_distribution.generate_value(
382
+ lab_value=self, patient=patient
383
+ )
384
+ if lower_bound is not None:
385
+ if generated_value < lower_bound:
386
+ return generated_value
387
+ # Heuristic for "low" if no lower_bound, compare against mean - stddev
388
+ elif hasattr(self.default_numerical_value_distribution, "mean") and \
389
+ hasattr(self.default_numerical_value_distribution, "stddev") and \
390
+ self.default_numerical_value_distribution.mean is not None and \
391
+ self.default_numerical_value_distribution.stddev is not None and \
392
+ generated_value < (
393
+ self.default_numerical_value_distribution.mean - self.default_numerical_value_distribution.stddev
394
+ ):
395
+ return generated_value
396
+ # Fallback
397
+ if lower_bound is not None:
398
+ return lower_bound - (abs(lower_bound * self.bound_adjustment_factor) if lower_bound != 0 else 1) # Decrease by factor or 1
399
+ # Return any generated value as last resort
400
+ return self.default_numerical_value_distribution.generate_value(lab_value=self, patient=patient)
401
+ else: # No patient, cannot use distribution
402
+ warnings.warn(
403
+ f"Cannot use numerical distribution for {self.name} without patient context. Falling back to normal range logic for decreased value."
404
+ )
405
+ if lower_bound is not None:
406
+ return lower_bound - (abs(lower_bound * self.bound_adjustment_factor) if lower_bound != 0 else 1)
407
+ else:
408
+ warnings.warn(
409
+ f"Cannot determine a decreased value for {self.name} without a lower normal range or patient context for distribution."
410
+ )
411
+ return None
412
+
413
+ elif lower_bound is not None:
414
+ return lower_bound - (abs(lower_bound * self.bound_adjustment_factor) if lower_bound != 0 else 1)
415
+ else:
416
+ warnings.warn(
417
+ f"Cannot determine a decreased value for {self.name} without a numerical distribution or a lower normal range."
418
+ )
419
+ return None
@@ -10,9 +10,7 @@ class MedicationManager(models.Manager):
10
10
 
11
11
  class Medication(models.Model):
12
12
  '''Model representing a medication.'''
13
- name = models.CharField(max_length=255, unique=True)
14
- name_de = models.CharField(max_length=255, blank=True, null=True)
15
- name_en = models.CharField(max_length=255, blank=True, null=True)
13
+ name = models.CharField(max_length=255, unique=True)
16
14
  adapt_to_renal_function = models.BooleanField(default = False)
17
15
  adapt_to_hepatic_function = models.BooleanField(default=False)
18
16
  adapt_to_indication = models.BooleanField(default=False)
@@ -1,5 +1,9 @@
1
1
  '''Model for medication indication type.'''
2
2
  from django.db import models
3
+ from typing import TYPE_CHECKING
4
+
5
+ if TYPE_CHECKING:
6
+ from endoreg_db.models import MedicationIndication
3
7
 
4
8
  class MedicationIndicationTypeManager(models.Manager):
5
9
  '''Manager for the medication indication type model.'''
@@ -9,12 +13,13 @@ class MedicationIndicationTypeManager(models.Manager):
9
13
 
10
14
  class MedicationIndicationType(models.Model):
11
15
  '''Model representing a medication indication type.'''
12
- name = models.CharField(max_length=255, unique=True)
13
- name_de = models.CharField(max_length=255, blank=True, null=True)
14
- name_en = models.CharField(max_length=255, blank=True, null=True)
16
+ name = models.CharField(max_length=255, unique=True)
15
17
 
16
18
  objects = MedicationIndicationTypeManager()
17
19
 
20
+ if TYPE_CHECKING:
21
+ medication_indications: models.QuerySet["MedicationIndication"]
22
+
18
23
  def natural_key(self):
19
24
  '''Return the natural key for the medication indication type.'''
20
25
  return (self.name,)
@@ -10,14 +10,32 @@ class MedicationIntakeTimeManager(models.Manager):
10
10
 
11
11
  class MedicationIntakeTime(models.Model):
12
12
  '''Model representing a medication intake time.'''
13
- name = models.CharField(max_length=255)
14
- name_de = models.CharField(max_length=255, blank=True, null=True)
15
- name_en = models.CharField(max_length=255, blank=True, null=True)
13
+ name = models.CharField(max_length=255, unique=True) # Made unique=True
16
14
  repeats = models.CharField(max_length=20, default = "daily")
17
15
  time = models.TimeField()
18
16
 
19
17
  objects = MedicationIntakeTimeManager()
20
18
 
19
+ @classmethod
20
+ def dm(cls):
21
+ '''Return the daily morning intake time object.'''
22
+ return cls.objects.get(name='daily-morning')
23
+
24
+ @classmethod
25
+ def dno(cls):
26
+ '''Return the daily noon intake time object.'''
27
+ return cls.objects.get(name='daily-noon')
28
+
29
+ @classmethod
30
+ def de(cls):
31
+ '''Return the daily evening intake time object.'''
32
+ return cls.objects.get(name='daily-evening')
33
+
34
+ @classmethod
35
+ def dn(cls):
36
+ '''Return the daily night intake time object.'''
37
+ return cls.objects.get(name='daily-night')
38
+
21
39
  def natural_key(self):
22
40
  '''Return the natural key for the medication intake time.'''
23
41
  return (self.name,)
@@ -1,18 +1,26 @@
1
1
  '''Model for the medication schedule.'''
2
- from typing import List
2
+ from typing import List, TYPE_CHECKING
3
3
  from django.db import models
4
4
 
5
+ if TYPE_CHECKING:
6
+ from endoreg_db.models import MedicationIntakeTime
5
7
  class MedicationScheduleManager(models.Manager):
6
8
  '''Manager for the medication schedule model.'''
7
9
  def get_by_natural_key(self, name):
8
- '''Retrieve a medication schedule by its natural key.'''
10
+ """
11
+ Retrieve a MedicationSchedule instance by its name.
12
+
13
+ Parameters:
14
+ name (str): The name of the medication schedule to retrieve.
15
+
16
+ Returns:
17
+ MedicationSchedule: The matching medication schedule instance.
18
+ """
9
19
  return self.get(name=name)
10
20
 
11
21
  class MedicationSchedule(models.Model):
12
22
  '''Model representing a medication schedule.'''
13
- name = models.CharField(max_length=255)
14
- name_de = models.CharField(max_length=255, blank=True, null=True)
15
- name_en = models.CharField(max_length=255, blank=True, null=True)
23
+ name = models.CharField(max_length=255, unique=True)
16
24
  description = models.TextField(blank=True, null=True)
17
25
  medication = models.ForeignKey("Medication", on_delete=models.CASCADE)
18
26
  unit = models.ForeignKey("Unit", on_delete=models.CASCADE)