endoreg-db 0.8.9.32__py3-none-any.whl

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Potentially problematic release.

This version of endoreg-db might be problematic. Click here for more details.

Files changed (787) hide show
  1. endoreg_db/__init__.py +0 -0
  2. endoreg_db/_version.py +34 -0
  3. endoreg_db/admin.py +97 -0
  4. endoreg_db/api/serializers/finding_descriptions.py +0 -0
  5. endoreg_db/api/views/finding_descriptions.py +0 -0
  6. endoreg_db/api_urls.py +4 -0
  7. endoreg_db/apps.py +17 -0
  8. endoreg_db/assets/dummy_model.ckpt +1 -0
  9. endoreg_db/authz/auth.py +78 -0
  10. endoreg_db/authz/backends.py +168 -0
  11. endoreg_db/authz/management/commands/list_routes.py +20 -0
  12. endoreg_db/authz/middleware.py +84 -0
  13. endoreg_db/authz/permissions.py +138 -0
  14. endoreg_db/authz/policy.py +224 -0
  15. endoreg_db/authz/settings.py +64 -0
  16. endoreg_db/authz/views_auth.py +70 -0
  17. endoreg_db/codemods/readme.md +88 -0
  18. endoreg_db/codemods/rename_datetime_fields.py +99 -0
  19. endoreg_db/config/__init__.py +0 -0
  20. endoreg_db/config/env.py +106 -0
  21. endoreg_db/config/settings/__init__.py +6 -0
  22. endoreg_db/config/settings/base.py +148 -0
  23. endoreg_db/config/settings/case_gen.py +32 -0
  24. endoreg_db/config/settings/dev.py +108 -0
  25. endoreg_db/config/settings/keycloak.py +177 -0
  26. endoreg_db/config/settings/prod.py +66 -0
  27. endoreg_db/config/settings/test.py +72 -0
  28. endoreg_db/data/__init__.py +135 -0
  29. endoreg_db/data/ai_model/data.yaml +7 -0
  30. endoreg_db/data/ai_model_label/label/data.yaml +88 -0
  31. endoreg_db/data/ai_model_label/label/polyp_classification.yaml +52 -0
  32. endoreg_db/data/ai_model_label/label-set/data.yaml +40 -0
  33. endoreg_db/data/ai_model_label/label-set/polyp_classifications.yaml +25 -0
  34. endoreg_db/data/ai_model_label/label-type/data.yaml +7 -0
  35. endoreg_db/data/ai_model_meta/default_multilabel_classification.yaml +27 -0
  36. endoreg_db/data/ai_model_type/data.yaml +7 -0
  37. endoreg_db/data/ai_model_video_segmentation_label/base_segmentation.yaml +176 -0
  38. endoreg_db/data/ai_model_video_segmentation_labelset/data.yaml +20 -0
  39. endoreg_db/data/case_template/rule/00_patient_lab_sample_add_default_value.yaml +167 -0
  40. endoreg_db/data/case_template/rule/01_patient-set-age.yaml +8 -0
  41. endoreg_db/data/case_template/rule/01_patient-set-gender.yaml +9 -0
  42. endoreg_db/data/case_template/rule/11_create_patient_lab_sample.yaml +23 -0
  43. endoreg_db/data/case_template/rule/12_create-patient_medication-anticoagulation.yaml +19 -0
  44. endoreg_db/data/case_template/rule/13_create-patient_medication_schedule-anticoagulation.yaml +19 -0
  45. endoreg_db/data/case_template/rule/19_create_patient.yaml +17 -0
  46. endoreg_db/data/case_template/rule_type/base_types.yaml +35 -0
  47. endoreg_db/data/case_template/rule_value/.init +0 -0
  48. endoreg_db/data/case_template/rule_value_type/base_types.yaml +59 -0
  49. endoreg_db/data/case_template/template/base.yaml +8 -0
  50. endoreg_db/data/case_template/template_type/pre_endoscopy.yaml +3 -0
  51. endoreg_db/data/case_template/tmp/_rule_value +13 -0
  52. endoreg_db/data/case_template/tmp/rule/01_atrial_fibrillation.yaml +21 -0
  53. endoreg_db/data/case_template/tmp/rule/02_create_object.yaml +10 -0
  54. endoreg_db/data/case_template/tmp/template/atrial_fibrillation_low_risk.yaml +7 -0
  55. endoreg_db/data/center/data.yaml +99 -0
  56. endoreg_db/data/center_resource/green_endoscopy_dashboard_CenterResource.yaml +144 -0
  57. endoreg_db/data/center_shift/ukw.yaml +9 -0
  58. endoreg_db/data/center_waste/green_endoscopy_dashboard_CenterWaste.yaml +48 -0
  59. endoreg_db/data/contraindication/bleeding.yaml +11 -0
  60. endoreg_db/data/db_summary.csv +58 -0
  61. endoreg_db/data/db_summary.xlsx +0 -0
  62. endoreg_db/data/disease/cardiovascular.yaml +37 -0
  63. endoreg_db/data/disease/hepatology.yaml +5 -0
  64. endoreg_db/data/disease/misc.yaml +5 -0
  65. endoreg_db/data/disease/renal.yaml +5 -0
  66. endoreg_db/data/disease_classification/chronic_kidney_disease.yaml +6 -0
  67. endoreg_db/data/disease_classification/coronary_vessel_disease.yaml +6 -0
  68. endoreg_db/data/disease_classification_choice/chronic_kidney_disease.yaml +41 -0
  69. endoreg_db/data/disease_classification_choice/coronary_vessel_disease.yaml +20 -0
  70. endoreg_db/data/distribution/date/patient.yaml +7 -0
  71. endoreg_db/data/distribution/multiple_categorical/.init +0 -0
  72. endoreg_db/data/distribution/numeric/data.yaml +14 -0
  73. endoreg_db/data/distribution/single_categorical/patient.yaml +7 -0
  74. endoreg_db/data/emission_factor/green_endoscopy_dashboard_EmissionFactor.yaml +132 -0
  75. endoreg_db/data/endoscope/data.yaml +93 -0
  76. endoreg_db/data/endoscope_type/data.yaml +11 -0
  77. endoreg_db/data/endoscopy_processor/data.yaml +50 -0
  78. endoreg_db/data/event/cardiology.yaml +15 -0
  79. endoreg_db/data/event/neurology.yaml +14 -0
  80. endoreg_db/data/event/surgery.yaml +13 -0
  81. endoreg_db/data/event/thrombembolism.yaml +20 -0
  82. endoreg_db/data/event_classification/data.yaml +4 -0
  83. endoreg_db/data/event_classification_choice/data.yaml +9 -0
  84. endoreg_db/data/examination/examinations/data.yaml +172 -0
  85. endoreg_db/data/examination/time/data.yaml +48 -0
  86. endoreg_db/data/examination/time-type/data.yaml +5 -0
  87. endoreg_db/data/examination/type/data.yaml +17 -0
  88. endoreg_db/data/examination_indication/endoscopy.yaml +359 -0
  89. endoreg_db/data/examination_indication_classification/endoscopy.yaml +90 -0
  90. endoreg_db/data/examination_indication_classification_choice/endoscopy.yaml +97 -0
  91. endoreg_db/data/examination_requirement_set/colonoscopy.yaml +15 -0
  92. endoreg_db/data/finding/00_generic.yaml +35 -0
  93. endoreg_db/data/finding/00_generic_complication.yaml +9 -0
  94. endoreg_db/data/finding/01_gastroscopy_baseline.yaml +88 -0
  95. endoreg_db/data/finding/01_gastroscopy_observation.yaml +113 -0
  96. endoreg_db/data/finding/02_colonoscopy_baseline.yaml +53 -0
  97. endoreg_db/data/finding/02_colonoscopy_hidden.yaml +119 -0
  98. endoreg_db/data/finding/02_colonoscopy_observation.yaml +152 -0
  99. endoreg_db/data/finding_classification/00_generic.yaml +44 -0
  100. endoreg_db/data/finding_classification/00_generic_histology.yaml +28 -0
  101. endoreg_db/data/finding_classification/00_generic_lesion.yaml +52 -0
  102. endoreg_db/data/finding_classification/02_colonoscopy_baseline.yaml +83 -0
  103. endoreg_db/data/finding_classification/02_colonoscopy_histology.yaml +13 -0
  104. endoreg_db/data/finding_classification/02_colonoscopy_other.yaml +12 -0
  105. endoreg_db/data/finding_classification/02_colonoscopy_polyp.yaml +101 -0
  106. endoreg_db/data/finding_classification_choice/00_generic.yaml +15 -0
  107. endoreg_db/data/finding_classification_choice/00_generic_baseline.yaml +23 -0
  108. endoreg_db/data/finding_classification_choice/00_generic_complication.yaml +15 -0
  109. endoreg_db/data/finding_classification_choice/00_generic_histology.yaml +21 -0
  110. endoreg_db/data/finding_classification_choice/00_generic_lesion.yaml +158 -0
  111. endoreg_db/data/finding_classification_choice/02_colonoscopy_bowel_preparation.yaml +49 -0
  112. endoreg_db/data/finding_classification_choice/02_colonoscopy_generic.yaml +19 -0
  113. endoreg_db/data/finding_classification_choice/02_colonoscopy_histology.yaml +20 -0
  114. endoreg_db/data/finding_classification_choice/02_colonoscopy_location.yaml +248 -0
  115. endoreg_db/data/finding_classification_choice/02_colonoscopy_other.yaml +34 -0
  116. endoreg_db/data/finding_classification_choice/02_colonoscopy_polyp_advanced_imaging.yaml +76 -0
  117. endoreg_db/data/finding_classification_choice/02_colonoscopy_polyp_morphology.yaml +75 -0
  118. endoreg_db/data/finding_classification_choice/02_colonoscopy_size.yaml +27 -0
  119. endoreg_db/data/finding_classification_type/00_generic.yaml +53 -0
  120. endoreg_db/data/finding_classification_type/02_colonoscopy.yaml +9 -0
  121. endoreg_db/data/finding_intervention/00_generic_endoscopy.yaml +59 -0
  122. endoreg_db/data/finding_intervention/00_generic_endoscopy_ablation.yaml +44 -0
  123. endoreg_db/data/finding_intervention/00_generic_endoscopy_bleeding.yaml +55 -0
  124. endoreg_db/data/finding_intervention/00_generic_endoscopy_resection.yaml +85 -0
  125. endoreg_db/data/finding_intervention/00_generic_endoscopy_stenosis.yaml +17 -0
  126. endoreg_db/data/finding_intervention/00_generic_endoscopy_stent.yaml +9 -0
  127. endoreg_db/data/finding_intervention/01_gastroscopy.yaml +19 -0
  128. endoreg_db/data/finding_intervention/04_eus.yaml +39 -0
  129. endoreg_db/data/finding_intervention/05_ercp.yaml +3 -0
  130. endoreg_db/data/finding_intervention_type/endoscopy.yaml +15 -0
  131. endoreg_db/data/finding_type/data.yaml +39 -0
  132. endoreg_db/data/gender/data.yaml +42 -0
  133. endoreg_db/data/information_source/annotation.yaml +6 -0
  134. endoreg_db/data/information_source/data.yaml +30 -0
  135. endoreg_db/data/information_source/endoscopy_guidelines.yaml +7 -0
  136. endoreg_db/data/information_source/medication.yaml +6 -0
  137. endoreg_db/data/information_source/prediction.yaml +7 -0
  138. endoreg_db/data/information_source_type/data.yaml +8 -0
  139. endoreg_db/data/lab_value/cardiac_enzymes.yaml +37 -0
  140. endoreg_db/data/lab_value/coagulation.yaml +54 -0
  141. endoreg_db/data/lab_value/electrolytes.yaml +228 -0
  142. endoreg_db/data/lab_value/gastrointestinal_function.yaml +133 -0
  143. endoreg_db/data/lab_value/hematology.yaml +184 -0
  144. endoreg_db/data/lab_value/hormones.yaml +59 -0
  145. endoreg_db/data/lab_value/lipids.yaml +53 -0
  146. endoreg_db/data/lab_value/misc.yaml +76 -0
  147. endoreg_db/data/lab_value/renal_function.yaml +12 -0
  148. endoreg_db/data/log_type/data.yaml +57 -0
  149. endoreg_db/data/lx_client_tag/base.yaml +54 -0
  150. endoreg_db/data/lx_client_type/base.yaml +30 -0
  151. endoreg_db/data/lx_permission/base.yaml +24 -0
  152. endoreg_db/data/lx_permission/endoreg.yaml +52 -0
  153. endoreg_db/data/material/material.yaml +91 -0
  154. endoreg_db/data/medication/anticoagulation.yaml +65 -0
  155. endoreg_db/data/medication/tah.yaml +70 -0
  156. endoreg_db/data/medication_indication/anticoagulation.yaml +115 -0
  157. endoreg_db/data/medication_indication_type/data.yaml +11 -0
  158. endoreg_db/data/medication_indication_type/thrombembolism.yaml +41 -0
  159. endoreg_db/data/medication_intake_time/base.yaml +31 -0
  160. endoreg_db/data/medication_schedule/apixaban.yaml +95 -0
  161. endoreg_db/data/medication_schedule/ass.yaml +12 -0
  162. endoreg_db/data/medication_schedule/enoxaparin.yaml +26 -0
  163. endoreg_db/data/names_first/first_names.yaml +54 -0
  164. endoreg_db/data/names_last/last_names.yaml +51 -0
  165. endoreg_db/data/network_device/data.yaml +59 -0
  166. endoreg_db/data/network_device_type/data.yaml +12 -0
  167. endoreg_db/data/organ/data.yaml +29 -0
  168. endoreg_db/data/patient_lab_sample_type/generic.yaml +6 -0
  169. endoreg_db/data/pdf_type/data.yaml +46 -0
  170. endoreg_db/data/product/green_endoscopy_dashboard_Product.yaml +66 -0
  171. endoreg_db/data/product_group/green_endoscopy_dashboard_ProductGroup.yaml +33 -0
  172. endoreg_db/data/product_material/green_endoscopy_dashboard_ProductMaterial.yaml +308 -0
  173. endoreg_db/data/product_weight/green_endoscopy_dashboard_ProductWeight.yaml +88 -0
  174. endoreg_db/data/profession/data.yaml +70 -0
  175. endoreg_db/data/qualification/endoscopy.yaml +36 -0
  176. endoreg_db/data/qualification/m2.yaml +39 -0
  177. endoreg_db/data/qualification/outpatient_clinic.yaml +35 -0
  178. endoreg_db/data/qualification/sonography.yaml +36 -0
  179. endoreg_db/data/qualification_type/base.yaml +29 -0
  180. endoreg_db/data/reference_product/green_endoscopy_dashboard_ReferenceProduct.yaml +55 -0
  181. endoreg_db/data/report_reader_flag/rkh-histology-generic.yaml +10 -0
  182. endoreg_db/data/report_reader_flag/ukw-examination-generic.yaml +30 -0
  183. endoreg_db/data/report_reader_flag/ukw-histology-generic.yaml +24 -0
  184. endoreg_db/data/requirement/01_patient_data.yaml +93 -0
  185. endoreg_db/data/requirement/old/colon_polyp_intervention.yaml +49 -0
  186. endoreg_db/data/requirement/old/colonoscopy_baseline_austria.yaml +45 -0
  187. endoreg_db/data/requirement/old/coloreg_colon_polyp.yaml +49 -0
  188. endoreg_db/data/requirement/old/disease_cardiovascular.yaml +79 -0
  189. endoreg_db/data/requirement/old/disease_classification_choice_cardiovascular.yaml +41 -0
  190. endoreg_db/data/requirement/old/disease_hepatology.yaml +12 -0
  191. endoreg_db/data/requirement/old/disease_misc.yaml +12 -0
  192. endoreg_db/data/requirement/old/disease_renal.yaml +96 -0
  193. endoreg_db/data/requirement/old/endoscopy_bleeding_risk.yaml +59 -0
  194. endoreg_db/data/requirement/old/event_cardiology.yaml +251 -0
  195. endoreg_db/data/requirement/old/event_requirements.yaml +145 -0
  196. endoreg_db/data/requirement/old/finding_colon_polyp.yaml +50 -0
  197. endoreg_db/data/requirement/old/gender.yaml +0 -0
  198. endoreg_db/data/requirement/old/lab_value.yaml +441 -0
  199. endoreg_db/data/requirement/old/medication.yaml +93 -0
  200. endoreg_db/data/requirement_operator/_old/age.yaml +13 -0
  201. endoreg_db/data/requirement_operator/_old/lab_operators.yaml +129 -0
  202. endoreg_db/data/requirement_operator/_old/model_operators.yaml +96 -0
  203. endoreg_db/data/requirement_operator/new_operators.yaml +36 -0
  204. endoreg_db/data/requirement_set/01_endoscopy_generic.yaml +65 -0
  205. endoreg_db/data/requirement_set/01_laboratory.yaml +13 -0
  206. endoreg_db/data/requirement_set/02_endoscopy_bleeding_risk.yaml +46 -0
  207. endoreg_db/data/requirement_set/90_coloreg.yaml +190 -0
  208. endoreg_db/data/requirement_set/_old_ +109 -0
  209. endoreg_db/data/requirement_set/colonoscopy_austria_screening.yaml +57 -0
  210. endoreg_db/data/requirement_set_type/data.yaml +41 -0
  211. endoreg_db/data/requirement_type/requirement_types.yaml +165 -0
  212. endoreg_db/data/resource/green_endoscopy_dashboard_Resource.yaml +15 -0
  213. endoreg_db/data/risk/bleeding.yaml +26 -0
  214. endoreg_db/data/risk/thrombosis.yaml +37 -0
  215. endoreg_db/data/risk_type/data.yaml +27 -0
  216. endoreg_db/data/setup_config.yaml +38 -0
  217. endoreg_db/data/shift/endoscopy.yaml +21 -0
  218. endoreg_db/data/shift/m2.yaml +0 -0
  219. endoreg_db/data/shift_type/base.yaml +35 -0
  220. endoreg_db/data/tag/requirement_set_tags.yaml +32 -0
  221. endoreg_db/data/tmp/chronic_kidney_disease.yaml +0 -0
  222. endoreg_db/data/tmp/congestive_heart_failure.yaml +0 -0
  223. endoreg_db/data/transport_route/green_endoscopy_dashboard_TransportRoute.yaml +12 -0
  224. endoreg_db/data/unit/concentration.yaml +115 -0
  225. endoreg_db/data/unit/data.yaml +17 -0
  226. endoreg_db/data/unit/length.yaml +31 -0
  227. endoreg_db/data/unit/misc.yaml +20 -0
  228. endoreg_db/data/unit/rate.yaml +6 -0
  229. endoreg_db/data/unit/time.yaml +48 -0
  230. endoreg_db/data/unit/volume.yaml +35 -0
  231. endoreg_db/data/unit/weight.yaml +38 -0
  232. endoreg_db/data/waste/data.yaml +12 -0
  233. endoreg_db/exceptions.py +24 -0
  234. endoreg_db/export/frames/export.py +6 -0
  235. endoreg_db/export/frames/export_frames_with_labels.py +616 -0
  236. endoreg_db/factories/__init__.py +0 -0
  237. endoreg_db/forms/__init__.py +4 -0
  238. endoreg_db/forms/examination_form.py +12 -0
  239. endoreg_db/forms/patient_finding_intervention_form.py +40 -0
  240. endoreg_db/forms/patient_form.py +23 -0
  241. endoreg_db/forms/questionnaires/__init__.py +1 -0
  242. endoreg_db/forms/questionnaires/tto_questionnaire.py +23 -0
  243. endoreg_db/forms/settings/__init__.py +11 -0
  244. endoreg_db/forms/unit.py +7 -0
  245. endoreg_db/helpers/__init__.py +0 -0
  246. endoreg_db/helpers/count_db.py +48 -0
  247. endoreg_db/helpers/data_loader.py +280 -0
  248. endoreg_db/helpers/default_objects.py +414 -0
  249. endoreg_db/helpers/download_segmentation_model.py +32 -0
  250. endoreg_db/helpers/interact.py +1 -0
  251. endoreg_db/helpers/test_video_helper.py +127 -0
  252. endoreg_db/import_files/__init__.py +27 -0
  253. endoreg_db/import_files/context/__init__.py +7 -0
  254. endoreg_db/import_files/context/default_sensitive_meta.py +83 -0
  255. endoreg_db/import_files/context/ensure_center.py +17 -0
  256. endoreg_db/import_files/context/file_lock.py +66 -0
  257. endoreg_db/import_files/context/import_context.py +42 -0
  258. endoreg_db/import_files/context/validate_directories.py +57 -0
  259. endoreg_db/import_files/file_storage/__init__.py +15 -0
  260. endoreg_db/import_files/file_storage/create_report_file.py +99 -0
  261. endoreg_db/import_files/file_storage/create_video_file.py +104 -0
  262. endoreg_db/import_files/file_storage/sensitive_meta_storage.py +42 -0
  263. endoreg_db/import_files/file_storage/state_management.py +463 -0
  264. endoreg_db/import_files/file_storage/storage.py +42 -0
  265. endoreg_db/import_files/import_service.md +26 -0
  266. endoreg_db/import_files/processing/__init__.py +11 -0
  267. endoreg_db/import_files/processing/report_processing/report_anonymization.py +99 -0
  268. endoreg_db/import_files/processing/sensitive_meta_adapter.py +51 -0
  269. endoreg_db/import_files/processing/video_processing/video_anonymization.py +107 -0
  270. endoreg_db/import_files/pseudonymization/__init__.py +0 -0
  271. endoreg_db/import_files/pseudonymization/fake.py +52 -0
  272. endoreg_db/import_files/pseudonymization/k_anonymity.py +181 -0
  273. endoreg_db/import_files/pseudonymization/k_pseudonymity.py +139 -0
  274. endoreg_db/import_files/pseudonymization/pseudonymize.py +0 -0
  275. endoreg_db/import_files/report_import_service.py +147 -0
  276. endoreg_db/import_files/video_import_service.py +154 -0
  277. endoreg_db/logger_conf.py +156 -0
  278. endoreg_db/management/__init__.py +1 -0
  279. endoreg_db/management/commands/__init__.py +1 -0
  280. endoreg_db/management/commands/anonymize_video.py +0 -0
  281. endoreg_db/management/commands/check_auth.py +132 -0
  282. endoreg_db/management/commands/create_model_meta_from_huggingface.py +177 -0
  283. endoreg_db/management/commands/create_multilabel_model_meta.py +419 -0
  284. endoreg_db/management/commands/export_frame_annot.py +196 -0
  285. endoreg_db/management/commands/fix_missing_patient_data.py +206 -0
  286. endoreg_db/management/commands/fix_video_paths.py +186 -0
  287. endoreg_db/management/commands/import_report.py +361 -0
  288. endoreg_db/management/commands/list_routes.py +20 -0
  289. endoreg_db/management/commands/load_ai_model_data.py +83 -0
  290. endoreg_db/management/commands/load_ai_model_label_data.py +60 -0
  291. endoreg_db/management/commands/load_base_db_data.py +63 -0
  292. endoreg_db/management/commands/load_center_data.py +68 -0
  293. endoreg_db/management/commands/load_contraindication_data.py +39 -0
  294. endoreg_db/management/commands/load_disease_classification_choices_data.py +38 -0
  295. endoreg_db/management/commands/load_disease_classification_data.py +38 -0
  296. endoreg_db/management/commands/load_disease_data.py +59 -0
  297. endoreg_db/management/commands/load_distribution_data.py +63 -0
  298. endoreg_db/management/commands/load_endoscope_data.py +58 -0
  299. endoreg_db/management/commands/load_event_data.py +39 -0
  300. endoreg_db/management/commands/load_examination_data.py +78 -0
  301. endoreg_db/management/commands/load_examination_indication_data.py +85 -0
  302. endoreg_db/management/commands/load_finding_data.py +115 -0
  303. endoreg_db/management/commands/load_gender_data.py +37 -0
  304. endoreg_db/management/commands/load_green_endoscopy_wuerzburg_data.py +142 -0
  305. endoreg_db/management/commands/load_information_source.py +46 -0
  306. endoreg_db/management/commands/load_lab_value_data.py +52 -0
  307. endoreg_db/management/commands/load_legacy_data.py +303 -0
  308. endoreg_db/management/commands/load_medication_data.py +104 -0
  309. endoreg_db/management/commands/load_name_data.py +36 -0
  310. endoreg_db/management/commands/load_organ_data.py +39 -0
  311. endoreg_db/management/commands/load_pdf_type_data.py +58 -0
  312. endoreg_db/management/commands/load_profession_data.py +40 -0
  313. endoreg_db/management/commands/load_qualification_data.py +56 -0
  314. endoreg_db/management/commands/load_report_reader_flag_data.py +40 -0
  315. endoreg_db/management/commands/load_requirement_data.py +207 -0
  316. endoreg_db/management/commands/load_requirement_set_tags.py +95 -0
  317. endoreg_db/management/commands/load_risk_data.py +57 -0
  318. endoreg_db/management/commands/load_shift_data.py +57 -0
  319. endoreg_db/management/commands/load_tag_data.py +54 -0
  320. endoreg_db/management/commands/load_unit_data.py +40 -0
  321. endoreg_db/management/commands/load_user_groups.py +26 -0
  322. endoreg_db/management/commands/model_input.py +169 -0
  323. endoreg_db/management/commands/register_ai_model.py +70 -0
  324. endoreg_db/management/commands/setup_endoreg_db.py +459 -0
  325. endoreg_db/management/commands/start_filewatcher.py +115 -0
  326. endoreg_db/management/commands/storage_management.py +622 -0
  327. endoreg_db/management/commands/summarize_db_content.py +280 -0
  328. endoreg_db/management/commands/train_image_multilabel_model.py +144 -0
  329. endoreg_db/management/commands/validate_video_files.py +189 -0
  330. endoreg_db/management/commands/video_validation.py +20 -0
  331. endoreg_db/mermaid/Overall_flow_patient_finding_intervention.md +10 -0
  332. endoreg_db/mermaid/anonymized_image_annotation.md +20 -0
  333. endoreg_db/mermaid/binary_classification_annotation.md +50 -0
  334. endoreg_db/mermaid/classification.md +8 -0
  335. endoreg_db/mermaid/examination.md +8 -0
  336. endoreg_db/mermaid/findings.md +7 -0
  337. endoreg_db/mermaid/image_classification.md +28 -0
  338. endoreg_db/mermaid/interventions.md +8 -0
  339. endoreg_db/mermaid/morphology.md +8 -0
  340. endoreg_db/mermaid/patient_creation.md +14 -0
  341. endoreg_db/mermaid/video_segmentation_annotation.md +17 -0
  342. endoreg_db/migrations/0001_initial.py +1953 -0
  343. endoreg_db/migrations/__init__.py +0 -0
  344. endoreg_db/models/__init__.py +322 -0
  345. endoreg_db/models/administration/__init__.py +95 -0
  346. endoreg_db/models/administration/ai/__init__.py +9 -0
  347. endoreg_db/models/administration/ai/active_model.py +35 -0
  348. endoreg_db/models/administration/ai/ai_model.py +180 -0
  349. endoreg_db/models/administration/ai/model_type.py +42 -0
  350. endoreg_db/models/administration/case/__init__.py +5 -0
  351. endoreg_db/models/administration/case/case.py +114 -0
  352. endoreg_db/models/administration/case/case_template/__init__.py +3 -0
  353. endoreg_db/models/administration/case/case_template/case_template.py +3 -0
  354. endoreg_db/models/administration/case/case_template/case_template_rule.py +3 -0
  355. endoreg_db/models/administration/case/case_template/case_template_rule_value.py +3 -0
  356. endoreg_db/models/administration/case/case_template/case_template_type.py +3 -0
  357. endoreg_db/models/administration/center/__init__.py +13 -0
  358. endoreg_db/models/administration/center/center.py +85 -0
  359. endoreg_db/models/administration/center/center_product.py +67 -0
  360. endoreg_db/models/administration/center/center_resource.py +69 -0
  361. endoreg_db/models/administration/center/center_shift.py +94 -0
  362. endoreg_db/models/administration/center/center_waste.py +42 -0
  363. endoreg_db/models/administration/person/__init__.py +26 -0
  364. endoreg_db/models/administration/person/employee/__init__.py +3 -0
  365. endoreg_db/models/administration/person/employee/employee.py +40 -0
  366. endoreg_db/models/administration/person/employee/employee_qualification.py +44 -0
  367. endoreg_db/models/administration/person/employee/employee_type.py +50 -0
  368. endoreg_db/models/administration/person/examiner/__init__.py +4 -0
  369. endoreg_db/models/administration/person/examiner/examiner.py +64 -0
  370. endoreg_db/models/administration/person/names/__init__.py +0 -0
  371. endoreg_db/models/administration/person/names/first_name.py +20 -0
  372. endoreg_db/models/administration/person/names/last_name.py +20 -0
  373. endoreg_db/models/administration/person/patient/__init__.py +7 -0
  374. endoreg_db/models/administration/person/patient/patient.py +488 -0
  375. endoreg_db/models/administration/person/patient/patient_external_id.py +36 -0
  376. endoreg_db/models/administration/person/person.py +35 -0
  377. endoreg_db/models/administration/person/profession/__init__.py +28 -0
  378. endoreg_db/models/administration/person/user/__init__.py +5 -0
  379. endoreg_db/models/administration/person/user/portal_user_information.py +41 -0
  380. endoreg_db/models/administration/product/__init__.py +15 -0
  381. endoreg_db/models/administration/product/product.py +106 -0
  382. endoreg_db/models/administration/product/product_group.py +41 -0
  383. endoreg_db/models/administration/product/product_material.py +60 -0
  384. endoreg_db/models/administration/product/product_weight.py +51 -0
  385. endoreg_db/models/administration/product/reference_product.py +147 -0
  386. endoreg_db/models/administration/qualification/__init__.py +7 -0
  387. endoreg_db/models/administration/qualification/qualification.py +43 -0
  388. endoreg_db/models/administration/qualification/qualification_type.py +39 -0
  389. endoreg_db/models/administration/shift/__init__.py +9 -0
  390. endoreg_db/models/administration/shift/scheduled_days.py +72 -0
  391. endoreg_db/models/administration/shift/shift.py +57 -0
  392. endoreg_db/models/administration/shift/shift_type.py +108 -0
  393. endoreg_db/models/aidataset/__init__.py +5 -0
  394. endoreg_db/models/aidataset/aidataset.py +193 -0
  395. endoreg_db/models/label/__init__.py +23 -0
  396. endoreg_db/models/label/annotation/__init__.py +12 -0
  397. endoreg_db/models/label/annotation/image_classification.py +85 -0
  398. endoreg_db/models/label/annotation/video_segmentation_annotation.py +61 -0
  399. endoreg_db/models/label/label.py +91 -0
  400. endoreg_db/models/label/label_set.py +68 -0
  401. endoreg_db/models/label/label_type.py +29 -0
  402. endoreg_db/models/label/label_video_segment/__init__.py +3 -0
  403. endoreg_db/models/label/label_video_segment/_create_from_video.py +42 -0
  404. endoreg_db/models/label/label_video_segment/label_video_segment.py +611 -0
  405. endoreg_db/models/label/video_segmentation_label.py +35 -0
  406. endoreg_db/models/label/video_segmentation_labelset.py +28 -0
  407. endoreg_db/models/media/__init__.py +23 -0
  408. endoreg_db/models/media/frame/__init__.py +3 -0
  409. endoreg_db/models/media/frame/frame.py +137 -0
  410. endoreg_db/models/media/pdf/__init__.py +12 -0
  411. endoreg_db/models/media/pdf/raw_pdf.py +764 -0
  412. endoreg_db/models/media/pdf/report_file.py +162 -0
  413. endoreg_db/models/media/pdf/report_reader/__init__.py +7 -0
  414. endoreg_db/models/media/pdf/report_reader/report_reader_config.py +85 -0
  415. endoreg_db/models/media/pdf/report_reader/report_reader_flag.py +46 -0
  416. endoreg_db/models/media/video/__init__.py +9 -0
  417. endoreg_db/models/media/video/create_from_file.py +402 -0
  418. endoreg_db/models/media/video/pipe_1.py +258 -0
  419. endoreg_db/models/media/video/pipe_2.py +129 -0
  420. endoreg_db/models/media/video/video_file.py +907 -0
  421. endoreg_db/models/media/video/video_file_ai.py +828 -0
  422. endoreg_db/models/media/video/video_file_anonymize.py +524 -0
  423. endoreg_db/models/media/video/video_file_frames/__init__.py +49 -0
  424. endoreg_db/models/media/video/video_file_frames/_bulk_create_frames.py +25 -0
  425. endoreg_db/models/media/video/video_file_frames/_create_frame_object.py +23 -0
  426. endoreg_db/models/media/video/video_file_frames/_delete_frames.py +126 -0
  427. endoreg_db/models/media/video/video_file_frames/_extract_frames.py +233 -0
  428. endoreg_db/models/media/video/video_file_frames/_get_frame.py +36 -0
  429. endoreg_db/models/media/video/video_file_frames/_get_frame_number.py +13 -0
  430. endoreg_db/models/media/video/video_file_frames/_get_frame_path.py +24 -0
  431. endoreg_db/models/media/video/video_file_frames/_get_frame_paths.py +40 -0
  432. endoreg_db/models/media/video/video_file_frames/_get_frame_range.py +44 -0
  433. endoreg_db/models/media/video/video_file_frames/_get_frames.py +30 -0
  434. endoreg_db/models/media/video/video_file_frames/_initialize_frames.py +205 -0
  435. endoreg_db/models/media/video/video_file_frames/_manage_frame_range.py +228 -0
  436. endoreg_db/models/media/video/video_file_frames/_mark_frames_extracted_status.py +107 -0
  437. endoreg_db/models/media/video/video_file_io.py +272 -0
  438. endoreg_db/models/media/video/video_file_meta/__init__.py +22 -0
  439. endoreg_db/models/media/video/video_file_meta/get_crop_template.py +58 -0
  440. endoreg_db/models/media/video/video_file_meta/get_endo_roi.py +62 -0
  441. endoreg_db/models/media/video/video_file_meta/get_fps.py +183 -0
  442. endoreg_db/models/media/video/video_file_meta/initialize_video_specs.py +198 -0
  443. endoreg_db/models/media/video/video_file_meta/text_meta.py +178 -0
  444. endoreg_db/models/media/video/video_file_meta/video_meta.py +105 -0
  445. endoreg_db/models/media/video/video_file_segments.py +317 -0
  446. endoreg_db/models/media/video/video_metadata.py +67 -0
  447. endoreg_db/models/media/video/video_processing.py +192 -0
  448. endoreg_db/models/medical/__init__.py +136 -0
  449. endoreg_db/models/medical/contraindication/README.md +1 -0
  450. endoreg_db/models/medical/contraindication/__init__.py +29 -0
  451. endoreg_db/models/medical/disease.py +174 -0
  452. endoreg_db/models/medical/event.py +154 -0
  453. endoreg_db/models/medical/examination/__init__.py +20 -0
  454. endoreg_db/models/medical/examination/examination.py +183 -0
  455. endoreg_db/models/medical/examination/examination_indication.py +229 -0
  456. endoreg_db/models/medical/examination/examination_time.py +68 -0
  457. endoreg_db/models/medical/examination/examination_time_type.py +44 -0
  458. endoreg_db/models/medical/examination/examination_type.py +47 -0
  459. endoreg_db/models/medical/finding/__init__.py +20 -0
  460. endoreg_db/models/medical/finding/finding.py +113 -0
  461. endoreg_db/models/medical/finding/finding_classification.py +131 -0
  462. endoreg_db/models/medical/finding/finding_intervention.py +68 -0
  463. endoreg_db/models/medical/finding/finding_type.py +38 -0
  464. endoreg_db/models/medical/hardware/__init__.py +8 -0
  465. endoreg_db/models/medical/hardware/endoscope.py +77 -0
  466. endoreg_db/models/medical/hardware/endoscopy_processor.py +182 -0
  467. endoreg_db/models/medical/laboratory/__init__.py +5 -0
  468. endoreg_db/models/medical/laboratory/lab_value.py +490 -0
  469. endoreg_db/models/medical/medication/__init__.py +23 -0
  470. endoreg_db/models/medical/medication/medication.py +45 -0
  471. endoreg_db/models/medical/medication/medication_indication.py +78 -0
  472. endoreg_db/models/medical/medication/medication_indication_type.py +58 -0
  473. endoreg_db/models/medical/medication/medication_intake_time.py +58 -0
  474. endoreg_db/models/medical/medication/medication_schedule.py +58 -0
  475. endoreg_db/models/medical/organ/__init__.py +38 -0
  476. endoreg_db/models/medical/patient/__init__.py +48 -0
  477. endoreg_db/models/medical/patient/medication_examples.py +56 -0
  478. endoreg_db/models/medical/patient/patient_disease.py +72 -0
  479. endoreg_db/models/medical/patient/patient_event.py +80 -0
  480. endoreg_db/models/medical/patient/patient_examination.py +280 -0
  481. endoreg_db/models/medical/patient/patient_examination_indication.py +57 -0
  482. endoreg_db/models/medical/patient/patient_finding.py +416 -0
  483. endoreg_db/models/medical/patient/patient_finding_classification.py +231 -0
  484. endoreg_db/models/medical/patient/patient_finding_intervention.py +37 -0
  485. endoreg_db/models/medical/patient/patient_lab_sample.py +157 -0
  486. endoreg_db/models/medical/patient/patient_lab_value.py +247 -0
  487. endoreg_db/models/medical/patient/patient_medication.py +111 -0
  488. endoreg_db/models/medical/patient/patient_medication_schedule.py +152 -0
  489. endoreg_db/models/medical/risk/__init__.py +7 -0
  490. endoreg_db/models/medical/risk/risk.py +73 -0
  491. endoreg_db/models/medical/risk/risk_type.py +54 -0
  492. endoreg_db/models/metadata/__init__.py +19 -0
  493. endoreg_db/models/metadata/model_meta.py +266 -0
  494. endoreg_db/models/metadata/model_meta_logic.py +485 -0
  495. endoreg_db/models/metadata/pdf_meta.py +96 -0
  496. endoreg_db/models/metadata/sensitive_meta.py +345 -0
  497. endoreg_db/models/metadata/sensitive_meta_logic.py +1161 -0
  498. endoreg_db/models/metadata/video_meta.py +459 -0
  499. endoreg_db/models/metadata/video_prediction_logic.py +232 -0
  500. endoreg_db/models/metadata/video_prediction_meta.py +319 -0
  501. endoreg_db/models/operation_log.py +63 -0
  502. endoreg_db/models/other/__init__.py +40 -0
  503. endoreg_db/models/other/distribution/__init__.py +46 -0
  504. endoreg_db/models/other/distribution/base_value_distribution.py +22 -0
  505. endoreg_db/models/other/distribution/date_value_distribution.py +163 -0
  506. endoreg_db/models/other/distribution/multiple_categorical_value_distribution.py +50 -0
  507. endoreg_db/models/other/distribution/numeric_value_distribution.py +211 -0
  508. endoreg_db/models/other/distribution/single_categorical_value_distribution.py +23 -0
  509. endoreg_db/models/other/emission/__init__.py +5 -0
  510. endoreg_db/models/other/emission/emission_factor.py +110 -0
  511. endoreg_db/models/other/gender.py +32 -0
  512. endoreg_db/models/other/information_source.py +190 -0
  513. endoreg_db/models/other/material.py +34 -0
  514. endoreg_db/models/other/resource.py +24 -0
  515. endoreg_db/models/other/tag.py +32 -0
  516. endoreg_db/models/other/transport_route.py +40 -0
  517. endoreg_db/models/other/unit.py +40 -0
  518. endoreg_db/models/other/waste.py +28 -0
  519. endoreg_db/models/report/__init__.py +0 -0
  520. endoreg_db/models/report/images.py +0 -0
  521. endoreg_db/models/report/report.py +5 -0
  522. endoreg_db/models/requirement/__init__.py +11 -0
  523. endoreg_db/models/requirement/requirement.py +792 -0
  524. endoreg_db/models/requirement/requirement_error.py +84 -0
  525. endoreg_db/models/requirement/requirement_evaluation/__init__.py +6 -0
  526. endoreg_db/models/requirement/requirement_evaluation/evaluate_with_dependencies.py +268 -0
  527. endoreg_db/models/requirement/requirement_evaluation/get_values.py +40 -0
  528. endoreg_db/models/requirement/requirement_evaluation/operator_evaluation_models.py +6 -0
  529. endoreg_db/models/requirement/requirement_evaluation/requirement_type_parser.py +137 -0
  530. endoreg_db/models/requirement/requirement_operator.py +187 -0
  531. endoreg_db/models/requirement/requirement_set.py +327 -0
  532. endoreg_db/models/state/__init__.py +13 -0
  533. endoreg_db/models/state/abstract.py +11 -0
  534. endoreg_db/models/state/anonymization.py +30 -0
  535. endoreg_db/models/state/audit_ledger.py +155 -0
  536. endoreg_db/models/state/label_video_segment.py +31 -0
  537. endoreg_db/models/state/processing_history/__init__.py +3 -0
  538. endoreg_db/models/state/processing_history/processing_history.py +136 -0
  539. endoreg_db/models/state/raw_pdf.py +219 -0
  540. endoreg_db/models/state/sensitive_meta.py +50 -0
  541. endoreg_db/models/state/video.py +251 -0
  542. endoreg_db/models/upload_job.py +100 -0
  543. endoreg_db/models/utils.py +138 -0
  544. endoreg_db/queries/__init__.py +3 -0
  545. endoreg_db/queries/annotations/__init__.py +1 -0
  546. endoreg_db/queries/annotations/legacy.py +169 -0
  547. endoreg_db/queries/sanity/__init_.py +0 -0
  548. endoreg_db/root_urls.py +27 -0
  549. endoreg_db/schemas/__init__.py +0 -0
  550. endoreg_db/schemas/examination_evaluation.py +30 -0
  551. endoreg_db/serializers/Frames_NICE_and_PARIS_classifications.py +861 -0
  552. endoreg_db/serializers/__init__.py +104 -0
  553. endoreg_db/serializers/administration/__init__.py +13 -0
  554. endoreg_db/serializers/administration/ai/__init__.py +9 -0
  555. endoreg_db/serializers/administration/ai/active_model.py +12 -0
  556. endoreg_db/serializers/administration/ai/ai_model.py +20 -0
  557. endoreg_db/serializers/administration/ai/model_type.py +12 -0
  558. endoreg_db/serializers/administration/center.py +14 -0
  559. endoreg_db/serializers/administration/gender.py +11 -0
  560. endoreg_db/serializers/anonymization.py +77 -0
  561. endoreg_db/serializers/evaluation/examination_evaluation.py +0 -0
  562. endoreg_db/serializers/examination/__init__.py +10 -0
  563. endoreg_db/serializers/examination/base.py +45 -0
  564. endoreg_db/serializers/examination/dropdown.py +20 -0
  565. endoreg_db/serializers/examination_serializer.py +9 -0
  566. endoreg_db/serializers/finding/__init__.py +5 -0
  567. endoreg_db/serializers/finding/finding.py +61 -0
  568. endoreg_db/serializers/finding_classification/__init__.py +7 -0
  569. endoreg_db/serializers/finding_classification/choice.py +19 -0
  570. endoreg_db/serializers/finding_classification/classification.py +11 -0
  571. endoreg_db/serializers/label_video_segment/__init__.py +9 -0
  572. endoreg_db/serializers/label_video_segment/image_classification_annotation.py +62 -0
  573. endoreg_db/serializers/label_video_segment/label/__init__.py +6 -0
  574. endoreg_db/serializers/label_video_segment/label/label.py +15 -0
  575. endoreg_db/serializers/label_video_segment/label_video_segment.py +427 -0
  576. endoreg_db/serializers/meta/__init__.py +13 -0
  577. endoreg_db/serializers/meta/sensitive_meta_detail.py +122 -0
  578. endoreg_db/serializers/meta/sensitive_meta_update.py +153 -0
  579. endoreg_db/serializers/meta/sensitive_meta_verification.py +62 -0
  580. endoreg_db/serializers/meta/video_meta.py +39 -0
  581. endoreg_db/serializers/misc/__init__.py +14 -0
  582. endoreg_db/serializers/misc/file_overview.py +72 -0
  583. endoreg_db/serializers/misc/sensitive_patient_data.py +144 -0
  584. endoreg_db/serializers/misc/stats.py +35 -0
  585. endoreg_db/serializers/misc/translatable_field_mix_in.py +44 -0
  586. endoreg_db/serializers/misc/upload_job.py +74 -0
  587. endoreg_db/serializers/patient/__init__.py +12 -0
  588. endoreg_db/serializers/patient/patient.py +103 -0
  589. endoreg_db/serializers/patient/patient_dropdown.py +35 -0
  590. endoreg_db/serializers/patient_examination/__init__.py +7 -0
  591. endoreg_db/serializers/patient_examination/patient_examination.py +168 -0
  592. endoreg_db/serializers/patient_finding/__init__.py +15 -0
  593. endoreg_db/serializers/patient_finding/patient_finding.py +32 -0
  594. endoreg_db/serializers/patient_finding/patient_finding_classification.py +47 -0
  595. endoreg_db/serializers/patient_finding/patient_finding_detail.py +62 -0
  596. endoreg_db/serializers/patient_finding/patient_finding_intervention.py +28 -0
  597. endoreg_db/serializers/patient_finding/patient_finding_list.py +40 -0
  598. endoreg_db/serializers/patient_finding/patient_finding_write.py +135 -0
  599. endoreg_db/serializers/pdf/__init__.py +3 -0
  600. endoreg_db/serializers/pdf/anony_text_validation.py +101 -0
  601. endoreg_db/serializers/requirements/requirement_schema.py +20 -0
  602. endoreg_db/serializers/requirements/requirement_sets.py +99 -0
  603. endoreg_db/serializers/sensitive_meta_serializer.py +301 -0
  604. endoreg_db/serializers/video/__init__.py +7 -0
  605. endoreg_db/serializers/video/video_file.py +283 -0
  606. endoreg_db/serializers/video/video_file_brief.py +14 -0
  607. endoreg_db/serializers/video/video_file_detail.py +96 -0
  608. endoreg_db/serializers/video/video_file_list.py +100 -0
  609. endoreg_db/serializers/video/video_processing_history.py +172 -0
  610. endoreg_db/serializers/video_examination.py +198 -0
  611. endoreg_db/services/__init__.py +5 -0
  612. endoreg_db/services/anonymization.py +274 -0
  613. endoreg_db/services/examination_evaluation.py +172 -0
  614. endoreg_db/services/finding_description_service.py +0 -0
  615. endoreg_db/services/lookup_service.py +424 -0
  616. endoreg_db/services/lookup_store.py +266 -0
  617. endoreg_db/services/model_meta_from_hf.py +76 -0
  618. endoreg_db/services/pdf_import.py +0 -0
  619. endoreg_db/services/polling_coordinator.py +319 -0
  620. endoreg_db/services/pseudonym_service.py +94 -0
  621. endoreg_db/services/report_import.py +13 -0
  622. endoreg_db/services/segment_sync.py +171 -0
  623. endoreg_db/services/video_import.py +9 -0
  624. endoreg_db/templates/admin/patient_finding_intervention.html +253 -0
  625. endoreg_db/templates/admin/start_examination.html +12 -0
  626. endoreg_db/templates/timeline.html +176 -0
  627. endoreg_db/urls/__init__.py +56 -0
  628. endoreg_db/urls/ai.py +14 -0
  629. endoreg_db/urls/anonymization.py +78 -0
  630. endoreg_db/urls/auth.py +16 -0
  631. endoreg_db/urls/classification.py +34 -0
  632. endoreg_db/urls/examination.py +63 -0
  633. endoreg_db/urls/media.py +251 -0
  634. endoreg_db/urls/patient.py +23 -0
  635. endoreg_db/urls/requirements.py +15 -0
  636. endoreg_db/urls/root_urls.py +28 -0
  637. endoreg_db/urls/stats.py +54 -0
  638. endoreg_db/urls/upload.py +12 -0
  639. endoreg_db/urls.py +9 -0
  640. endoreg_db/utils/__init__.py +97 -0
  641. endoreg_db/utils/ai/__init__.py +9 -0
  642. endoreg_db/utils/ai/data_loader_for_model_input.py +262 -0
  643. endoreg_db/utils/ai/data_loader_for_model_training.py +262 -0
  644. endoreg_db/utils/ai/get.py +6 -0
  645. endoreg_db/utils/ai/inference_dataset.py +51 -0
  646. endoreg_db/utils/ai/model_training/config.py +117 -0
  647. endoreg_db/utils/ai/model_training/dataset.py +74 -0
  648. endoreg_db/utils/ai/model_training/losses.py +68 -0
  649. endoreg_db/utils/ai/model_training/metrics.py +78 -0
  650. endoreg_db/utils/ai/model_training/model_backbones.py +155 -0
  651. endoreg_db/utils/ai/model_training/model_gastronet_resnet.py +118 -0
  652. endoreg_db/utils/ai/model_training/trainer_gastronet_multilabel.py +771 -0
  653. endoreg_db/utils/ai/multilabel_classification_net.py +270 -0
  654. endoreg_db/utils/ai/postprocess.py +63 -0
  655. endoreg_db/utils/ai/predict.py +293 -0
  656. endoreg_db/utils/ai/preprocess.py +76 -0
  657. endoreg_db/utils/calc_duration_seconds.py +24 -0
  658. endoreg_db/utils/case_generator/__init__.py +3 -0
  659. endoreg_db/utils/case_generator/lab_sample_factory.py +32 -0
  660. endoreg_db/utils/check_video_files.py +175 -0
  661. endoreg_db/utils/cropping.py +30 -0
  662. endoreg_db/utils/dataloader.py +285 -0
  663. endoreg_db/utils/dates.py +59 -0
  664. endoreg_db/utils/defaults/set_default_center.py +33 -0
  665. endoreg_db/utils/env.py +37 -0
  666. endoreg_db/utils/extract_specific_frames.py +87 -0
  667. endoreg_db/utils/file_operations.py +70 -0
  668. endoreg_db/utils/fix_video_path_direct.py +157 -0
  669. endoreg_db/utils/frame_anonymization_utils.py +463 -0
  670. endoreg_db/utils/hashs.py +138 -0
  671. endoreg_db/utils/links/__init__.py +0 -0
  672. endoreg_db/utils/links/requirement_link.py +237 -0
  673. endoreg_db/utils/mime_types.py +0 -0
  674. endoreg_db/utils/names.py +82 -0
  675. endoreg_db/utils/ocr.py +195 -0
  676. endoreg_db/utils/operation_log.py +87 -0
  677. endoreg_db/utils/parse_and_generate_yaml.py +45 -0
  678. endoreg_db/utils/paths.py +159 -0
  679. endoreg_db/utils/permissions.py +160 -0
  680. endoreg_db/utils/pipelines/Readme.md +235 -0
  681. endoreg_db/utils/pipelines/__init__.py +0 -0
  682. endoreg_db/utils/pipelines/process_video_dir.py +144 -0
  683. endoreg_db/utils/product/__init__.py +0 -0
  684. endoreg_db/utils/product/sum_emissions.py +22 -0
  685. endoreg_db/utils/product/sum_weights.py +20 -0
  686. endoreg_db/utils/pydantic_models/__init__.py +5 -0
  687. endoreg_db/utils/pydantic_models/db_config.py +57 -0
  688. endoreg_db/utils/requirement_helpers.py +0 -0
  689. endoreg_db/utils/requirement_operator_logic/__init__.py +0 -0
  690. endoreg_db/utils/requirement_operator_logic/_old/lab_value_operators.py +678 -0
  691. endoreg_db/utils/requirement_operator_logic/_old/model_evaluators.py +842 -0
  692. endoreg_db/utils/requirement_operator_logic/new_operator_logic.py +114 -0
  693. endoreg_db/utils/setup_config.py +196 -0
  694. endoreg_db/utils/storage.py +117 -0
  695. endoreg_db/utils/translation.py +31 -0
  696. endoreg_db/utils/uuid.py +5 -0
  697. endoreg_db/utils/validate_endo_roi.py +33 -0
  698. endoreg_db/utils/validate_subcategory_dict.py +93 -0
  699. endoreg_db/utils/validate_video_detailed.py +415 -0
  700. endoreg_db/utils/video/__init__.py +30 -0
  701. endoreg_db/utils/video/extract_frames.py +100 -0
  702. endoreg_db/utils/video/ffmpeg_wrapper.py +996 -0
  703. endoreg_db/utils/video/names.py +47 -0
  704. endoreg_db/utils/video/streaming_processor.py +386 -0
  705. endoreg_db/utils/video/video_splitter.py +105 -0
  706. endoreg_db/versioning.md +79 -0
  707. endoreg_db/views/Frames_NICE_and_PARIS_classifications_views.py +247 -0
  708. endoreg_db/views/__init__.py +157 -0
  709. endoreg_db/views/anonymization/__init__.py +31 -0
  710. endoreg_db/views/anonymization/media_management.py +486 -0
  711. endoreg_db/views/anonymization/overview.py +307 -0
  712. endoreg_db/views/anonymization/validate.py +310 -0
  713. endoreg_db/views/auth/__init__.py +13 -0
  714. endoreg_db/views/auth/keycloak.py +146 -0
  715. endoreg_db/views/examination/__init__.py +30 -0
  716. endoreg_db/views/examination/examination.py +37 -0
  717. endoreg_db/views/examination/examination_manifest_cache.py +26 -0
  718. endoreg_db/views/examination/get_finding_classification_choices.py +62 -0
  719. endoreg_db/views/examination/get_finding_classifications.py +38 -0
  720. endoreg_db/views/examination/get_findings.py +39 -0
  721. endoreg_db/views/examination/get_instruments.py +19 -0
  722. endoreg_db/views/examination/get_interventions.py +14 -0
  723. endoreg_db/views/finding/__init__.py +9 -0
  724. endoreg_db/views/finding/finding.py +116 -0
  725. endoreg_db/views/finding/get_classifications.py +14 -0
  726. endoreg_db/views/finding/get_interventions.py +17 -0
  727. endoreg_db/views/finding_classification/__init__.py +13 -0
  728. endoreg_db/views/finding_classification/base.py +0 -0
  729. endoreg_db/views/finding_classification/finding_classification.py +41 -0
  730. endoreg_db/views/finding_classification/get_classification_choices.py +54 -0
  731. endoreg_db/views/media/__init__.py +32 -0
  732. endoreg_db/views/media/pdf_media.py +411 -0
  733. endoreg_db/views/media/sensitive_metadata.py +372 -0
  734. endoreg_db/views/media/video_media.py +275 -0
  735. endoreg_db/views/meta/__init__.py +7 -0
  736. endoreg_db/views/meta/sensitive_meta_list.py +102 -0
  737. endoreg_db/views/meta/sensitive_meta_verification.py +74 -0
  738. endoreg_db/views/misc/__init__.py +29 -0
  739. endoreg_db/views/misc/center.py +14 -0
  740. endoreg_db/views/misc/csrf.py +8 -0
  741. endoreg_db/views/misc/gender.py +15 -0
  742. endoreg_db/views/misc/stats.py +255 -0
  743. endoreg_db/views/misc/upload_views.py +241 -0
  744. endoreg_db/views/patient/__init__.py +3 -0
  745. endoreg_db/views/patient/patient.py +253 -0
  746. endoreg_db/views/patient_examination/__init__.py +11 -0
  747. endoreg_db/views/patient_examination/patient_examination.py +141 -0
  748. endoreg_db/views/patient_examination/patient_examination_create.py +58 -0
  749. endoreg_db/views/patient_examination/patient_examination_detail.py +63 -0
  750. endoreg_db/views/patient_examination/patient_examination_list.py +72 -0
  751. endoreg_db/views/patient_examination/video.py +228 -0
  752. endoreg_db/views/patient_finding/__init__.py +7 -0
  753. endoreg_db/views/patient_finding/base.py +0 -0
  754. endoreg_db/views/patient_finding/patient_finding.py +71 -0
  755. endoreg_db/views/patient_finding/patient_finding_optimized.py +291 -0
  756. endoreg_db/views/patient_finding_classification/__init__.py +5 -0
  757. endoreg_db/views/patient_finding_classification/pfc_create.py +75 -0
  758. endoreg_db/views/report/__init__.py +7 -0
  759. endoreg_db/views/report/reimport.py +177 -0
  760. endoreg_db/views/report/report_stream.py +191 -0
  761. endoreg_db/views/requirement/__init__.py +11 -0
  762. endoreg_db/views/requirement/evaluate.py +278 -0
  763. endoreg_db/views/requirement/lookup.py +380 -0
  764. endoreg_db/views/requirement/lookup_store.py +183 -0
  765. endoreg_db/views/requirement/requirement_utils.py +87 -0
  766. endoreg_db/views/requirement_lookup/lookup.py +0 -0
  767. endoreg_db/views/requirement_lookup/lookup_store.py +0 -0
  768. endoreg_db/views/stats/__init__.py +13 -0
  769. endoreg_db/views/stats/stats_views.py +266 -0
  770. endoreg_db/views/video/__init__.py +49 -0
  771. endoreg_db/views/video/ai/__init__.py +8 -0
  772. endoreg_db/views/video/ai/label.py +159 -0
  773. endoreg_db/views/video/correction.py +529 -0
  774. endoreg_db/views/video/reimport.py +230 -0
  775. endoreg_db/views/video/segments_crud.py +709 -0
  776. endoreg_db/views/video/video_apply_mask.py +49 -0
  777. endoreg_db/views/video/video_correction.py +22 -0
  778. endoreg_db/views/video/video_download_processed.py +58 -0
  779. endoreg_db/views/video/video_examination_viewset.py +242 -0
  780. endoreg_db/views/video/video_metadata.py +101 -0
  781. endoreg_db/views/video/video_processing_history.py +25 -0
  782. endoreg_db/views/video/video_remove_frames.py +49 -0
  783. endoreg_db/views/video/video_stream.py +334 -0
  784. endoreg_db-0.8.9.32.dist-info/METADATA +404 -0
  785. endoreg_db-0.8.9.32.dist-info/RECORD +787 -0
  786. endoreg_db-0.8.9.32.dist-info/WHEEL +4 -0
  787. endoreg_db-0.8.9.32.dist-info/licenses/LICENSE +674 -0
endoreg_db/data/requirement/old/disease_classification_choice_cardiovascular.yaml ADDED
@@ -0,0 +1,41 @@
1
+ - model: endoreg_db.requirement
2
+ fields:
3
+ name: "disease_classification_choice_is_coronary_artery_disease_1_vessel"
4
+ name_de: "Koronare Gefäßerkrankung (1-Gefäß-Erkrankung)"
5
+ name_en: "Coronary artery disease (1-vessel disease)"
6
+ description: "Coronary artery disease (1-vessel disease)"
7
+ requirement_types:
8
+ - "patient"
9
+ - "patient_disease"
10
+ operators:
11
+ - models_match_all
12
+ disease_classification_choices:
13
+ - "khk_1_ge"
14
+
15
+ - model: endoreg_db.requirement
16
+ fields:
17
+ name: "disease_classification_choice_is_coronary_artery_disease_2_vessel"
18
+ name_de: "Koronare Gefäßerkrankung (2-Gefäß-Erkrankung)"
19
+ name_en: "Coronary artery disease (2-vessel disease)"
20
+ description: "Coronary artery disease (2-vessel disease)"
21
+ requirement_types:
22
+ - "patient"
23
+ - "patient_disease"
24
+ operators:
25
+ - models_match_all
26
+ disease_classification_choices:
27
+ - "khk_2_ge"
28
+
29
+ - model: endoreg_db.requirement
30
+ fields:
31
+ name: "disease_classification_choice_is_coronary_artery_disease_3_vessel"
32
+ name_de: "Koronare Gefäßerkrankung (3-Gefäß-Erkrankung)"
33
+ name_en: "Coronary artery disease (3-vessel disease)"
34
+ description: "Coronary artery disease (3-vessel disease)"
35
+ requirement_types:
36
+ - "patient"
37
+ - "patient_disease"
38
+ operators:
39
+ - models_match_all
40
+ disease_classification_choices:
41
+ - "khk_3_ge"
endoreg_db/data/requirement/old/disease_hepatology.yaml ADDED
@@ -0,0 +1,12 @@
1
+ - model: endoreg_db.requirement
2
+ fields:
3
+ name: "disease_is_liver_cirrhosis"
4
+ name_de: "Erkrankung Leberzirrhose"
5
+ name_en: "Disease Liver Cirrhosis"
6
+ description: "Disease Liver Cirrhosis"
7
+ requirement_types:
8
+ - "patient"
9
+ operators:
10
+ - models_match_all
11
+ diseases:
12
+ - "liver_cirrhosis"
endoreg_db/data/requirement/old/disease_misc.yaml ADDED
@@ -0,0 +1,12 @@
1
+ - model: endoreg_db.requirement
2
+ fields:
3
+ name: "disease_is_malignoma_unspecified"
4
+ name_de: "Malignom, nicht näher bezeichnet"
5
+ name_en: "Malignoma, unspecified"
6
+ description: "Malignoma, unspecified"
7
+ requirement_types:
8
+ - "patient"
9
+ operators:
10
+ - models_match_all
11
+ diseases:
12
+ - "disease_is_malignoma_unspecified"
endoreg_db/data/requirement/old/disease_renal.yaml ADDED
@@ -0,0 +1,96 @@
1
+ - model: endoreg_db.requirement
2
+ fields:
3
+ name: "disease_is_chronic_kidney_disease"
4
+ name_de: "Erkrankung chronische Nierenerkrankung"
5
+ name_en: "Disease Chronic Kidney Disease"
6
+ description: "Disease Chronic Kidney Disease"
7
+ requirement_types:
8
+ - "patient"
9
+ operators:
10
+ - models_match_all
11
+ diseases:
12
+ - "chronic_kidney_disease"
13
+
14
+ - model: endoreg_db.requirement
15
+ fields:
16
+ name: "disease_classification_choice_is_ckd_kdigo_1"
17
+ name_de: "Erkrankung Klassifikation chronische Nierenerkrankung (KDIGO) (Stadium 1)"
18
+ name_en: "Disease Classification Chronic Kidney Disease (KDIGO) (Stage 1)"
19
+ description: "Disease Classification Chronic Kidney Disease (KDIGO) (Stage 1)"
20
+ requirement_types:
21
+ - "patient_disease"
22
+ - "patient"
23
+ operators:
24
+ - models_match_all
25
+ disease_classification_choices:
26
+ - "ckd_kdigo_1"
27
+
28
+ - model: endoreg_db.requirement
29
+ fields:
30
+ name: "disease_classification_choice_is_ckd_kdigo_2"
31
+ name_de: "Erkrankung Klassifikation chronische Nierenerkrankung (KDIGO) (Stadium 2)"
32
+ name_en: "Disease Classification Chronic Kidney Disease (KDIGO) (Stage 2)"
33
+ description: "Disease Classification Chronic Kidney Disease (KDIGO) (Stage 2)"
34
+ requirement_types:
35
+ - "patient_disease"
36
+ - "patient"
37
+ operators:
38
+ - models_match_all
39
+ disease_classification_choices:
40
+ - "ckd_kdigo_2"
41
+
42
+ - model: endoreg_db.requirement
43
+ fields:
44
+ name: "disease_classification_choice_is_ckd_kdigo_3a"
45
+ name_de: "Erkrankung Klassifikation chronische Nierenerkrankung (KDIGO) (Stadium 3a)"
46
+ name_en: "Disease Classification Chronic Kidney Disease (KDIGO) (Stage 3a)"
47
+ description: "Disease Classification Chronic Kidney Disease (KDIGO) (Stage 3a)"
48
+ requirement_types:
49
+ - "patient_disease"
50
+ - "patient"
51
+ operators:
52
+ - models_match_all
53
+ disease_classification_choices:
54
+ - "ckd_kdigo_3a"
55
+
56
+ - model: endoreg_db.requirement
57
+ fields:
58
+ name: "disease_classification_choice_is_ckd_kdigo_3b"
59
+ name_de: "Erkrankung Klassifikation chronische Nierenerkrankung (KDIGO) (Stadium 3b)"
60
+ name_en: "Disease Classification Chronic Kidney Disease (KDIGO) (Stage 3b)"
61
+ description: "Disease Classification Chronic Kidney Disease (KDIGO) (Stage 3b)"
62
+ requirement_types:
63
+ - "patient_disease"
64
+ - "patient"
65
+ operators:
66
+ - models_match_all
67
+ disease_classification_choices:
68
+ - "ckd_kdigo_3b"
69
+
70
+ - model: endoreg_db.requirement
71
+ fields:
72
+ name: "disease_classification_choice_is_ckd_kdigo_4"
73
+ name_de: "Erkrankung Klassifikation chronische Nierenerkrankung (KDIGO) (Stadium 4)"
74
+ name_en: "Disease Classification Chronic Kidney Disease (KDIGO) (Stage 4)"
75
+ description: "Disease Classification Chronic Kidney Disease (KDIGO) (Stage 4)"
76
+ requirement_types:
77
+ - "patient_disease"
78
+ - "patient"
79
+ operators:
80
+ - models_match_all
81
+ disease_classification_choices:
82
+ - "ckd_kdigo_4"
83
+
84
+ - model: endoreg_db.requirement
85
+ fields:
86
+ name: "disease_classification_choice_is_ckd_kdigo_5"
87
+ name_de: "Erkrankung Klassifikation chronische Nierenerkrankung (KDIGO) (Stadium 5)"
88
+ name_en: "Disease Classification Chronic Kidney Disease (KDIGO) (Stage 5)"
89
+ description: "Disease Classification Chronic Kidney Disease (KDIGO) (Stage 5)"
90
+ requirement_types:
91
+ - "patient_disease"
92
+ - "patient"
93
+ operators:
94
+ - models_match_all
95
+ disease_classification_choices:
96
+ - "ckd_kdigo_5"
endoreg_db/data/requirement/old/endoscopy_bleeding_risk.yaml ADDED
@@ -0,0 +1,59 @@
1
+ - model: endoreg_db.requirement
2
+ fields:
3
+ name: "endoscopy_intervention_bleeding_risk_high"
4
+ name_de: "Endoskopische Intervention - Blutungsrisiko: hoch"
5
+ name_en: "Endoscopy Intervention - Bleeding Risk: High"
6
+ description: "Endoskopische Intervention - Blutungsrisiko: hoch"
7
+ requirement_types:
8
+ - "examination_indication"
9
+ operators:
10
+ - "models_match_any"
11
+ finding_interventions:
12
+ - "egd_lesion_polypectomy_cold_snare"
13
+ - "egd_lesion_polypectomy_hot_snare"
14
+ - "colon_lesion_polypectomy_cold_snare"
15
+ - "colon_lesion_polypectomy_hot_snare"
16
+ - "colon_lesion_emr"
17
+ - "colon_lesion_esd"
18
+ - "colon_lesion_eftr"
19
+ - "egd_lesion_emr"
20
+ - "egd_lesion_esd"
21
+ - "egd_poem"
22
+ - "ercp_sphincterotomy"
23
+ - "egd_varice_band_ligation"
24
+ - "egd_varice_sclerotherapy"
25
+ - "egd_percutaneous_gastroenterostomy"
26
+ - "percutaneous_transhepatic_cholangiography"
27
+ - "percutaneous_transhepatic_biliary_drainage"
28
+ - "ercp_radiofrequency_ablation"
29
+
30
+ - model: endoreg_db.requirement
31
+ fields:
32
+ name: "endoscopy_intervention_bleeding_risk_low"
33
+ name_de: "Endoskopische Intervention - Blutungsrisiko: niedrig"
34
+ name_en: "Endoscopy Intervention - Bleeding Risk: Low"
35
+ description: "Endoskopische Intervention - Blutungsrisiko: niedrig"
36
+ requirement_types:
37
+ - "examination_indication"
38
+ operators:
39
+ - "models_match_any"
40
+ finding_interventions:
41
+ - "egd_lesion_biopsy"
42
+ - "colon_lesion_biopsy"
43
+ - "ercp"
44
+ - "egd_argon_plasma_coagulation"
45
+
46
+ - model: endoreg_db.requirement
47
+ fields:
48
+ name: "indication_is_colon_emr"
49
+ name_de: "Indikation Kolon EMR"
50
+ name_en: "Indication colon EMR"
51
+ description: "This functions evaluates whether the input ()"
52
+ requirement_types:
53
+ - "examination_indication"
54
+ operators:
55
+ - "models_match_any"
56
+ # when creating a requirement involving other models,
57
+ # we need to create the relationship here:
58
+ examination_indications:
59
+ - "colonoscopy_lesion_removal_emr"
endoreg_db/data/requirement/old/event_cardiology.yaml ADDED
@@ -0,0 +1,251 @@
1
+ - model: endoreg_db.requirement
2
+ fields:
3
+ name: "event_had_coro_des_implantation"
4
+ name_de: "Ereignis: Koronarstent-Implantation (DES) durchgeführt"
5
+ name_en: "Event: Coronary Stent Implantation (DES) performed"
6
+ description: "Ereignis: Koronarstent-Implantation (DES) durchgeführt"
7
+ operators:
8
+ - "models_match_any"
9
+ events:
10
+ - "coro_des_implantation"
11
+ requirement_types:
12
+ - "patient"
13
+
14
+ - model: endoreg_db.requirement
15
+ fields:
16
+ name: "event_had_coro_des_implantation_count_between_1_and_3 (exclusive)"
17
+ name_de: "Ereignis: Koronarstent-Implantation (DES) durchgeführt zwischen 1 und 3 (exklusive)"
18
+ name_en: "Event: Coronary Stent Implantation (DES) performed between 1 and 3 (exclusive)"
19
+ description: "Ereignis: Koronarstent-Implantation (DES) durchgeführt zwischen 1 und 3 (exklusive)"
20
+ operators:
21
+ - "models_match_count_in_range"
22
+ events:
23
+ - "coro_des_implantation"
24
+ numeric_value_min: 1
25
+ numeric_value_max: 3
26
+ requirement_types:
27
+ - "patient"
28
+
29
+ - model: endoreg_db.requirement
30
+ fields:
31
+ name: "event_had_coro_des_implantation_count_greater_than_3"
32
+ name_de: "Ereignis: Koronarstent-Implantation (DES) durchgeführt mehr als 3"
33
+ name_en: "Event: Coronary Stent Implantation (DES) performed more than 3"
34
+ description: "Ereignis: Koronarstent-Implantation (DES) durchgeführt mehr als 3"
35
+ operators:
36
+ - "models_match_n_or_more"
37
+ events:
38
+ - "coro_des_implantation"
39
+ numeric_value: 3
40
+ requirement_types:
41
+ - "patient"
42
+
43
+ - model: endoreg_db.requirement
44
+ fields:
45
+ name: "event_had_coro_bms_implantation"
46
+ name_de: "Ereignis: Koronarstent-Implantation (BMS) durchgeführt"
47
+ name_en: "Event: Coronary Stent Implantation (BMS) performed"
48
+ description: "Ereignis: Koronarstent-Implantation (BMS) durchgeführt"
49
+ operators:
50
+ - "models_match_any"
51
+ events:
52
+ - "coro_bms_implantation"
53
+ requirement_types:
54
+ - "patient"
55
+
56
+ - model: endoreg_db.requirement
57
+ fields:
58
+ name: "event_had_complication_coro_stent_thrombosis"
59
+ name_de: "Ereignis: Komplikation Koronar Stent Thrombose"
60
+ name_en: "Event: Complication Coronary Stent Thrombosis"
61
+ description: "Ereignis: Komplikation Koronar Stent Thrombose"
62
+ operators:
63
+ - "models_match_any"
64
+ events:
65
+ - "complication_coro_stent_thrombosis"
66
+ requirement_types:
67
+ - "patient"
68
+
69
+ - model: endoreg_db.requirement
70
+ fields:
71
+ name: "event_had_pulmonary_embolism"
72
+ name_de: "Ereignis: Lungenembolie"
73
+ name_en: "Event: Pulmonary Embolism"
74
+ description: "Ereignis: Lungenembolie"
75
+ operators:
76
+ - "models_match_any"
77
+ events:
78
+ - "pulmonary_embolism"
79
+ requirement_types:
80
+ - "patient"
81
+
82
+ - model: endoreg_db.requirement
83
+ fields:
84
+ name: "event_had_deep_vein_thrombosis"
85
+ name_de: "Ereignis: Tiefe Beinvenenthrombose"
86
+ name_en: "Event: Deep Vein Thrombosis"
87
+ description: "Ereignis: Tiefe Beinvenenthrombose"
88
+ operators:
89
+ - "models_match_any"
90
+ events:
91
+ - "deep_vein_thrombosis"
92
+ requirement_types:
93
+ - "patient"
94
+
95
+ - model: endoreg_db.requirement
96
+ fields:
97
+ name: "event_had_deep_vein_thrombosis_10_d"
98
+ name_de: "Ereignis: Tiefe Beinvenenthrombose innerhalb 10 Tage"
99
+ name_en: "Event: Deep Vein Thrombosis within 10 days"
100
+ description: "Ereignis: Tiefe Beinvenenthrombose innerhalb 10 Tage"
101
+ operators:
102
+ - "models_match_any_in_timeframe"
103
+ events:
104
+ - "deep_vein_thrombosis"
105
+ numeric_value_min: -10
106
+ numeric_value_max: 0
107
+ unit: "days"
108
+ requirement_types:
109
+ - "patient"
110
+
111
+ - model: endoreg_db.requirement
112
+ fields:
113
+ name: "event_had_more_than_1_deep_vein_thrombosis"
114
+ name_de: "Ereignis: Mehr als 1 Tiefe Beinvenenthrombose"
115
+ name_en: "Event: More than 1 Deep Vein Thrombosis"
116
+ description: "Ereignis: Mehr als 1 Tiefe Beinvenenthrombose"
117
+ operators:
118
+ - "models_match_n_or_more"
119
+ events:
120
+ - "deep_vein_thrombosis"
121
+ numeric_value: 1
122
+ requirement_types:
123
+ - "patient"
124
+
125
+ - model: endoreg_db.requirement
126
+ fields:
127
+ name: "event_had_coro_des_stent_implantation_30_d"
128
+ name_de: "Ereignis: Koronarstent-Implantation (DES) durchgeführt innerhalb 30 Tage"
129
+ name_en: "Event: Coronary Stent Implantation (DES) performed within 30 days"
130
+ description: "Ereignis: Koronarstent-Implantation (DES) durchgeführt innerhalb 30 Tage"
131
+ operators:
132
+ - "models_match_any_in_timeframe"
133
+ events:
134
+ - "coro_des_implantation"
135
+ numeric_value_min: -30
136
+ numeric_value_max: 0
137
+ unit: "days"
138
+ requirement_types:
139
+ - "patient"
140
+
141
+ - model: endoreg_db.requirement
142
+ fields:
143
+ name: "event_had_coro_des_stent_implantation_6_w"
144
+ name_de: "Ereignis: Koronarstent-Implantation (DES) durchgeführt innerhalb 6 Wochen"
145
+ name_en: "Event: Coronary Stent Implantation (DES) performed within 6 weeks"
146
+ description: "Ereignis: Koronarstent-Implantation (DES) durchgeführt innerhalb 6 Wochen"
147
+ operators:
148
+ - "models_match_any_in_timeframe"
149
+ events:
150
+ - "coro_des_implantation"
151
+ numeric_value_min: -6
152
+ numeric_value_max: 0
153
+ unit: "weeks"
154
+ requirement_types:
155
+ - "patient"
156
+
157
+ - model: endoreg_db.requirement
158
+ fields:
159
+ name: "event_had_coro_des_stent_implantation_6_m"
160
+ name_de: "Ereignis: Koronarstent-Implantation (DES) durchgeführt innerhalb 6 Monate"
161
+ name_en: "Event: Coronary Stent Implantation (DES) performed within 6 months"
162
+ description: "Ereignis: Koronarstent-Implantation (DES) durchgeführt innerhalb 6 Monate"
163
+ operators:
164
+ - "models_match_any_in_timeframe"
165
+ events:
166
+ - "coro_des_implantation"
167
+ numeric_value_min: -6
168
+ numeric_value_max: 0
169
+ unit: "months"
170
+ requirement_types:
171
+ - "patient"
172
+
173
+ - model: endoreg_db.requirement
174
+ fields:
175
+ name: "event_had_coro_des_stent_implantation_1_y"
176
+ name_de: "Ereignis: Koronarstent-Implantation (DES) durchgeführt innerhalb 1 Jahr"
177
+ name_en: "Event: Coronary Stent Implantation (DES) performed within 1 year"
178
+ description: "Ereignis: Koronarstent-Implantation (DES) durchgeführt innerhalb 1 Jahr"
179
+ operators:
180
+ - "models_match_any_in_timeframe"
181
+ events:
182
+ - "coro_des_implantation"
183
+ numeric_value_min: -1
184
+ numeric_value_max: 0
185
+ unit: "years"
186
+ requirement_types:
187
+ - "patient"
188
+
189
+ - model: endoreg_db.requirement
190
+ fields:
191
+ name: "event_had_coro_bms_stent_implantation_30_d"
192
+ name_de: "Ereignis: Koronarstent-Implantation (BMS) durchgeführt innerhalb 30 Tage"
193
+ name_en: "Event: Coronary Stent Implantation (BMS) performed within 30 days"
194
+ description: "Ereignis: Koronarstent-Implantation (BMS) durchgeführt innerhalb 30 Tage"
195
+ operators:
196
+ - "models_match_any_in_timeframe"
197
+ events:
198
+ - "coro_bms_implantation"
199
+ numeric_value_min: -30
200
+ numeric_value_max: 0
201
+ unit: "days"
202
+ requirement_types:
203
+ - "patient"
204
+
205
+ - model: endoreg_db.requirement
206
+ fields:
207
+ name: "event_had_coro_bms_stent_implantation_6_w"
208
+ name_de: "Ereignis: Koronarstent-Implantation (BMS) durchgeführt innerhalb 6 Wochen"
209
+ name_en: "Event: Coronary Stent Implantation (BMS) performed within 6 weeks"
210
+ description: "Ereignis: Koronarstent-Implantation (BMS) durchgeführt innerhalb 6 Wochen"
211
+ operators:
212
+ - "models_match_any_in_timeframe"
213
+ events:
214
+ - "coro_bms_implantation"
215
+ numeric_value_min: -6
216
+ numeric_value_max: 0
217
+ unit: "weeks"
218
+ requirement_types:
219
+ - "patient"
220
+
221
+ - model: endoreg_db.requirement
222
+ fields:
223
+ name: "event_had_coro_bms_stent_implantation_6_m"
224
+ name_de: "Ereignis: Koronarstent-Implantation (BMS) durchgeführt innerhalb 6 Monate"
225
+ name_en: "Event: Coronary Stent Implantation (BMS) performed within 6 months"
226
+ description: "Ereignis: Koronarstent-Implantation (BMS) durchgeführt innerhalb 6 Monate"
227
+ operators:
228
+ - "models_match_any_in_timeframe"
229
+ events:
230
+ - "coro_bms_implantation"
231
+ numeric_value_min: -6
232
+ numeric_value_max: 0
233
+ unit: "months"
234
+ requirement_types:
235
+ - "patient"
236
+
237
+ - model: endoreg_db.requirement
238
+ fields:
239
+ name: "event_had_coro_bms_stent_implantation_1_y"
240
+ name_de: "Ereignis: Koronarstent-Implantation (BMS) durchgeführt innerhalb 1 Jahr"
241
+ name_en: "Event: Coronary Stent Implantation (BMS) performed within 1 year"
242
+ description: "Ereignis: Koronarstent-Implantation (BMS) durchgeführt innerhalb 1 Jahr"
243
+ operators:
244
+ - "models_match_any_in_timeframe"
245
+ events:
246
+ - "coro_bms_implantation"
247
+ numeric_value_min: -1
248
+ numeric_value_max: 0
249
+ unit: "years"
250
+ requirement_types:
251
+ - "patient"
endoreg_db/data/requirement/old/event_requirements.yaml ADDED
@@ -0,0 +1,145 @@
1
+ # /home/admin/dev/endo-ai/endoreg-db/endoreg_db/data/requirement/event_requirements.yaml
2
+ - model: endoreg_db.requirement
3
+ fields:
4
+ name: "event_coro_des_implantation_exists"
5
+ name_de: "Ereignis Koronarstent-Implantation (DES) vorhanden"
6
+ name_en: "Event Coronary Stent Implantation (DES) exists"
7
+ description: "Checks if a 'coro_des_implantation' event exists for the patient."
8
+ requirement_types:
9
+ - "patient"
10
+ - "patient_event" # Added patient_event
11
+ operators:
12
+ - models_match_any
13
+ events:
14
+ - "coro_des_implantation"
15
+
16
+ - model: endoreg_db.requirement
17
+ fields:
18
+ name: "event_coro_bms_implantation_exists"
19
+ name_de: "Ereignis Koronarstent-Implantation (BMS) vorhanden"
20
+ name_en: "Event Coronary Stent Implantation (BMS) exists"
21
+ description: "Checks if a 'coro_bms_implantation' event exists for the patient."
22
+ requirement_types:
23
+ - "patient"
24
+ - "patient_event" # Added patient_event
25
+ operators:
26
+ - models_match_any
27
+ events:
28
+ - "coro_bms_implantation"
29
+
30
+ - model: endoreg_db.requirement
31
+ fields:
32
+ name: "event_pulmonary_embolism_exists"
33
+ name_de: "Ereignis Lungenembolie vorhanden"
34
+ name_en: "Event Pulmonary Embolism exists"
35
+ description: "Checks if a 'pulmonary_embolism' event exists for the patient."
36
+ requirement_types:
37
+ - "patient"
38
+ - "patient_event" # Added patient_event
39
+ operators:
40
+ - models_match_any
41
+ events:
42
+ - "pulmonary_embolism"
43
+
44
+ - model: endoreg_db.requirement
45
+ fields:
46
+ name: "event_deep_vein_thrombosis_exists"
47
+ name_de: "Ereignis Tiefe Beinvenenthrombose vorhanden"
48
+ name_en: "Event Deep Vein Thrombosis exists"
49
+ description: "Checks if a 'deep_vein_thrombosis' event exists for the patient."
50
+ requirement_types:
51
+ - "patient"
52
+ - "patient_event" # Added patient_event
53
+ operators:
54
+ - models_match_any
55
+ events:
56
+ - "deep_vein_thrombosis"
57
+
58
+ - model: endoreg_db.requirement
59
+ fields:
60
+ name: "event_stroke_exists"
61
+ name_de: "Ereignis Schlaganfall vorhanden"
62
+ name_en: "Event Stroke exists"
63
+ description: "Checks if a 'stroke' event exists for the patient."
64
+ requirement_types:
65
+ - "patient"
66
+ - "patient_event" # Added patient_event
67
+ operators:
68
+ - models_match_any
69
+ events:
70
+ - "stroke"
71
+
72
+ - model: endoreg_db.requirement
73
+ fields:
74
+ name: "event_transient_ischemic_attack_exists"
75
+ name_de: "Ereignis Transitorische ischämische Attacke vorhanden"
76
+ name_en: "Event Transient Ischemic Attack exists"
77
+ description: "Checks if a 'transient_ischemic_attack' event exists for the patient."
78
+ requirement_types:
79
+ - "patient"
80
+ - "patient_event" # Added patient_event
81
+ operators:
82
+ - models_match_any
83
+ events:
84
+ - "transient_ischemic_attack"
85
+
86
+ - model: endoreg_db.requirement
87
+ fields:
88
+ name: "event_hip_replacement_surgery_exists"
89
+ name_de: "Ereignis Hüft-TEP Operation vorhanden"
90
+ name_en: "Event Hip replacement surgery exists"
91
+ description: "Checks if a 'hip_replacement_surgery' event exists for the patient."
92
+ requirement_types:
93
+ - "patient"
94
+ - "patient_event" # Added patient_event
95
+ operators:
96
+ - models_match_any
97
+ events:
98
+ - "hip_replacement_surgery"
99
+
100
+ - model: endoreg_db.requirement
101
+ fields:
102
+ name: "event_knee_replacement_surgery_exists"
103
+ name_de: "Ereignis Knie-TEP Operation vorhanden"
104
+ name_en: "Event Knee replacement surgery exists"
105
+ description: "Checks if a 'knee_replacement_surgery' event exists for the patient."
106
+ requirement_types:
107
+ - "patient"
108
+ - "patient_event" # Added patient_event
109
+ operators:
110
+ - models_match_any
111
+ events:
112
+ - "knee_replacement_surgery"
113
+
114
+ - model: endoreg_db.requirement
115
+ fields:
116
+ name: "event_recurrent_thrombembolism_exists"
117
+ name_de: "Ereignis Rezidivierende Thrombembolien vorhanden"
118
+ name_en: "Event Recurrent Thrombembolism exists"
119
+ description: "Checks if a 'recurrent_thrombembolism' event exists for the patient."
120
+ requirement_types:
121
+ - "patient"
122
+ - "patient_event" # Added patient_event
123
+ operators:
124
+ - models_match_any
125
+ events:
126
+ - "recurrent_thrombembolism"
127
+
128
+ # Example for models_match_any_in_timeframe
129
+ - model: endoreg_db.requirement
130
+ fields:
131
+ name: "event_stroke_in_last_30_days"
132
+ name_de: "Ereignis Schlaganfall in den letzten 30 Tagen"
133
+ name_en: "Event Stroke in the last 30 days"
134
+ description: "Checks if a 'stroke' event occurred for the patient in the last 30 days."
135
+ requirement_types: # Defines which input models are expected by Requirement.evaluate()
136
+ - "patient"
137
+ - "patient_event" # This tells the system to look for PatientEvent models in the input
138
+ operators:
139
+ - models_match_any_in_timeframe
140
+ events: # This links the Requirement to specific Event models (e.g. "stroke")
141
+ - "stroke"
142
+ # Timeframe definition for the operator:
143
+ numeric_value_min: -30 # Start of timeframe (days ago)
144
+ numeric_value_max: 0 # End of timeframe (days ago, i.e., today)
145
+ unit: "days" # Unit for the timeframe
endoreg_db/data/requirement/old/finding_colon_polyp.yaml ADDED
@@ -0,0 +1,50 @@
1
+ - model: endoreg_db.requirement
2
+ fields:
3
+ name: "colon_austria_screening_polyp_size"
4
+ requirement_types:
5
+ - "patient_examination"
6
+ - "patient_finding"
7
+ operators:
8
+ - "models_match_any"
9
+ finding_classifications:
10
+ - "colon_lesion_size_mm"
11
+ - "colon_lesion_size_austria_categorical"
12
+
13
+ - model: endoreg_db.requirement
14
+ fields:
15
+ name: "colonoscopy_austria_screening_polyp_location"
16
+ requirement_types:
17
+ - "patient_examination"
18
+ - "patient_finding"
19
+ operators:
20
+ - "models_match_any"
21
+ finding_classifications:
22
+ - "colonoscopy_austria_screening_location"
23
+ - "colonoscopy_location_default"
24
+
25
+ - model: endoreg_db.requirement
26
+ fields:
27
+ name: "colonoscopy_austria_screening_polyp_morphology"
28
+ operators:
29
+ - "models_match_any"
30
+ requirement_types:
31
+ - "patient_examination"
32
+ - "patient_finding"
33
+ finding_classifications:
34
+ - "colon_lesion_paris"
35
+ - "colon_lesion_lst"
36
+ - "colon_lesion_planarity_default"
37
+
38
+ - model: endoreg_db.requirement
39
+ fields:
40
+ name: "colonoscopy_austria_screening_polyp_histology"
41
+ requirement_types:
42
+ - "patient_finding"
43
+ - "patient_examination"
44
+ operators:
45
+ - "models_match_all"
46
+ finding_classifications:
47
+ - "colonoscopy_polyp_histology"
48
+ - "colonoscopy_polyp_histology_dysplasia"
49
+ - "colonoscopy_histology_dignity"
50
+
endoreg_db/data/requirement/old/gender.yaml ADDED
File without changes