endoreg-db 0.8.6.4__py3-none-any.whl

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  1. endoreg_db/__init__.py +0 -0
  2. endoreg_db/admin.py +92 -0
  3. endoreg_db/api/serializers/finding_descriptions.py +0 -0
  4. endoreg_db/api/views/finding_descriptions.py +0 -0
  5. endoreg_db/api_urls.py +4 -0
  6. endoreg_db/apps.py +18 -0
  7. endoreg_db/assets/dummy_model.ckpt +1 -0
  8. endoreg_db/codemods/readme.md +88 -0
  9. endoreg_db/codemods/rename_datetime_fields.py +92 -0
  10. endoreg_db/config/__init__.py +0 -0
  11. endoreg_db/config/env.py +101 -0
  12. endoreg_db/data/__init__.py +144 -0
  13. endoreg_db/data/ai_model/data.yaml +7 -0
  14. endoreg_db/data/ai_model_label/label/data.yaml +88 -0
  15. endoreg_db/data/ai_model_label/label/polyp_classification.yaml +52 -0
  16. endoreg_db/data/ai_model_label/label-set/data.yaml +40 -0
  17. endoreg_db/data/ai_model_label/label-set/polyp_classifications.yaml +25 -0
  18. endoreg_db/data/ai_model_label/label-type/data.yaml +7 -0
  19. endoreg_db/data/ai_model_meta/default_multilabel_classification.yaml +27 -0
  20. endoreg_db/data/ai_model_type/data.yaml +7 -0
  21. endoreg_db/data/ai_model_video_segmentation_label/base_segmentation.yaml +176 -0
  22. endoreg_db/data/ai_model_video_segmentation_labelset/data.yaml +20 -0
  23. endoreg_db/data/case_template/rule/00_patient_lab_sample_add_default_value.yaml +167 -0
  24. endoreg_db/data/case_template/rule/01_patient-set-age.yaml +8 -0
  25. endoreg_db/data/case_template/rule/01_patient-set-gender.yaml +9 -0
  26. endoreg_db/data/case_template/rule/11_create_patient_lab_sample.yaml +23 -0
  27. endoreg_db/data/case_template/rule/12_create-patient_medication-anticoagulation.yaml +19 -0
  28. endoreg_db/data/case_template/rule/13_create-patient_medication_schedule-anticoagulation.yaml +19 -0
  29. endoreg_db/data/case_template/rule/19_create_patient.yaml +17 -0
  30. endoreg_db/data/case_template/rule_type/base_types.yaml +35 -0
  31. endoreg_db/data/case_template/rule_value/.init +0 -0
  32. endoreg_db/data/case_template/rule_value_type/base_types.yaml +59 -0
  33. endoreg_db/data/case_template/template/base.yaml +8 -0
  34. endoreg_db/data/case_template/template_type/pre_endoscopy.yaml +3 -0
  35. endoreg_db/data/case_template/tmp/_rule_value +13 -0
  36. endoreg_db/data/case_template/tmp/rule/01_atrial_fibrillation.yaml +21 -0
  37. endoreg_db/data/case_template/tmp/rule/02_create_object.yaml +10 -0
  38. endoreg_db/data/case_template/tmp/template/atrial_fibrillation_low_risk.yaml +7 -0
  39. endoreg_db/data/center/data.yaml +91 -0
  40. endoreg_db/data/center_resource/green_endoscopy_dashboard_CenterResource.yaml +144 -0
  41. endoreg_db/data/center_shift/ukw.yaml +9 -0
  42. endoreg_db/data/center_waste/green_endoscopy_dashboard_CenterWaste.yaml +48 -0
  43. endoreg_db/data/contraindication/bleeding.yaml +11 -0
  44. endoreg_db/data/db_summary.csv +58 -0
  45. endoreg_db/data/db_summary.xlsx +0 -0
  46. endoreg_db/data/disease/cardiovascular.yaml +37 -0
  47. endoreg_db/data/disease/hepatology.yaml +5 -0
  48. endoreg_db/data/disease/misc.yaml +5 -0
  49. endoreg_db/data/disease/renal.yaml +5 -0
  50. endoreg_db/data/disease_classification/chronic_kidney_disease.yaml +6 -0
  51. endoreg_db/data/disease_classification/coronary_vessel_disease.yaml +6 -0
  52. endoreg_db/data/disease_classification_choice/chronic_kidney_disease.yaml +41 -0
  53. endoreg_db/data/disease_classification_choice/coronary_vessel_disease.yaml +20 -0
  54. endoreg_db/data/distribution/date/patient.yaml +7 -0
  55. endoreg_db/data/distribution/multiple_categorical/.init +0 -0
  56. endoreg_db/data/distribution/numeric/data.yaml +14 -0
  57. endoreg_db/data/distribution/single_categorical/patient.yaml +7 -0
  58. endoreg_db/data/emission_factor/green_endoscopy_dashboard_EmissionFactor.yaml +132 -0
  59. endoreg_db/data/endoscope/data.yaml +93 -0
  60. endoreg_db/data/endoscope_type/data.yaml +11 -0
  61. endoreg_db/data/endoscopy_processor/data.yaml +50 -0
  62. endoreg_db/data/event/cardiology.yaml +15 -0
  63. endoreg_db/data/event/neurology.yaml +14 -0
  64. endoreg_db/data/event/surgery.yaml +13 -0
  65. endoreg_db/data/event/thrombembolism.yaml +20 -0
  66. endoreg_db/data/examination/examinations/data.yaml +72 -0
  67. endoreg_db/data/examination/time/data.yaml +48 -0
  68. endoreg_db/data/examination/time-type/data.yaml +8 -0
  69. endoreg_db/data/examination/type/data.yaml +17 -0
  70. endoreg_db/data/examination_indication/endoscopy.yaml +424 -0
  71. endoreg_db/data/examination_indication_classification/endoscopy.yaml +160 -0
  72. endoreg_db/data/examination_indication_classification_choice/endoscopy.yaml +101 -0
  73. endoreg_db/data/examination_requirement_set/colonoscopy.yaml +15 -0
  74. endoreg_db/data/finding/anatomy_colon.yaml +128 -0
  75. endoreg_db/data/finding/colonoscopy.yaml +40 -0
  76. endoreg_db/data/finding/colonoscopy_bowel_prep.yaml +56 -0
  77. endoreg_db/data/finding/complication.yaml +16 -0
  78. endoreg_db/data/finding/data.yaml +105 -0
  79. endoreg_db/data/finding/examination_setting.yaml +16 -0
  80. endoreg_db/data/finding/medication_related.yaml +18 -0
  81. endoreg_db/data/finding/outcome.yaml +12 -0
  82. endoreg_db/data/finding_classification/colonoscopy_bowel_preparation.yaml +95 -0
  83. endoreg_db/data/finding_classification/colonoscopy_jnet.yaml +22 -0
  84. endoreg_db/data/finding_classification/colonoscopy_kudo.yaml +25 -0
  85. endoreg_db/data/finding_classification/colonoscopy_lesion_circularity.yaml +20 -0
  86. endoreg_db/data/finding_classification/colonoscopy_lesion_planarity.yaml +24 -0
  87. endoreg_db/data/finding_classification/colonoscopy_lesion_size.yaml +68 -0
  88. endoreg_db/data/finding_classification/colonoscopy_lesion_surface.yaml +20 -0
  89. endoreg_db/data/finding_classification/colonoscopy_location.yaml +80 -0
  90. endoreg_db/data/finding_classification/colonoscopy_lst.yaml +21 -0
  91. endoreg_db/data/finding_classification/colonoscopy_nice.yaml +20 -0
  92. endoreg_db/data/finding_classification/colonoscopy_paris.yaml +26 -0
  93. endoreg_db/data/finding_classification/colonoscopy_sano.yaml +22 -0
  94. endoreg_db/data/finding_classification/colonoscopy_summary.yaml +53 -0
  95. endoreg_db/data/finding_classification/complication_generic.yaml +25 -0
  96. endoreg_db/data/finding_classification/examination_setting_generic.yaml +40 -0
  97. endoreg_db/data/finding_classification/histology_colo.yaml +51 -0
  98. endoreg_db/data/finding_classification/intervention_required.yaml +26 -0
  99. endoreg_db/data/finding_classification/medication_related.yaml +23 -0
  100. endoreg_db/data/finding_classification/visualized.yaml +33 -0
  101. endoreg_db/data/finding_classification_choice/bowel_preparation.yaml +78 -0
  102. endoreg_db/data/finding_classification_choice/colon_lesion_circularity_default.yaml +32 -0
  103. endoreg_db/data/finding_classification_choice/colon_lesion_jnet.yaml +15 -0
  104. endoreg_db/data/finding_classification_choice/colon_lesion_kudo.yaml +23 -0
  105. endoreg_db/data/finding_classification_choice/colon_lesion_lst.yaml +15 -0
  106. endoreg_db/data/finding_classification_choice/colon_lesion_nice.yaml +17 -0
  107. endoreg_db/data/finding_classification_choice/colon_lesion_paris.yaml +57 -0
  108. endoreg_db/data/finding_classification_choice/colon_lesion_planarity_default.yaml +49 -0
  109. endoreg_db/data/finding_classification_choice/colon_lesion_sano.yaml +14 -0
  110. endoreg_db/data/finding_classification_choice/colon_lesion_surface_intact_default.yaml +36 -0
  111. endoreg_db/data/finding_classification_choice/colonoscopy_location.yaml +229 -0
  112. endoreg_db/data/finding_classification_choice/colonoscopy_not_complete_reason.yaml +19 -0
  113. endoreg_db/data/finding_classification_choice/colonoscopy_size.yaml +82 -0
  114. endoreg_db/data/finding_classification_choice/colonoscopy_summary_worst_finding.yaml +15 -0
  115. endoreg_db/data/finding_classification_choice/complication_generic_types.yaml +15 -0
  116. endoreg_db/data/finding_classification_choice/examination_setting_generic_types.yaml +15 -0
  117. endoreg_db/data/finding_classification_choice/histology.yaml +24 -0
  118. endoreg_db/data/finding_classification_choice/histology_polyp.yaml +20 -0
  119. endoreg_db/data/finding_classification_choice/outcome.yaml +19 -0
  120. endoreg_db/data/finding_classification_choice/yes_no_na.yaml +11 -0
  121. endoreg_db/data/finding_classification_type/colonoscopy_basic.yaml +48 -0
  122. endoreg_db/data/finding_intervention/endoscopy.yaml +43 -0
  123. endoreg_db/data/finding_intervention/endoscopy_colonoscopy.yaml +168 -0
  124. endoreg_db/data/finding_intervention/endoscopy_egd.yaml +128 -0
  125. endoreg_db/data/finding_intervention/endoscopy_ercp.yaml +32 -0
  126. endoreg_db/data/finding_intervention/endoscopy_eus_lower.yaml +9 -0
  127. endoreg_db/data/finding_intervention/endoscopy_eus_upper.yaml +36 -0
  128. endoreg_db/data/finding_intervention_type/endoscopy.yaml +15 -0
  129. endoreg_db/data/finding_morphology_classification_type/colonoscopy.yaml +79 -0
  130. endoreg_db/data/finding_type/data.yaml +43 -0
  131. endoreg_db/data/gender/data.yaml +42 -0
  132. endoreg_db/data/information_source/annotation.yaml +6 -0
  133. endoreg_db/data/information_source/data.yaml +30 -0
  134. endoreg_db/data/information_source/endoscopy_guidelines.yaml +7 -0
  135. endoreg_db/data/information_source/medication.yaml +6 -0
  136. endoreg_db/data/information_source/prediction.yaml +7 -0
  137. endoreg_db/data/information_source_type/data.yaml +8 -0
  138. endoreg_db/data/lab_value/cardiac_enzymes.yaml +37 -0
  139. endoreg_db/data/lab_value/coagulation.yaml +54 -0
  140. endoreg_db/data/lab_value/electrolytes.yaml +228 -0
  141. endoreg_db/data/lab_value/gastrointestinal_function.yaml +133 -0
  142. endoreg_db/data/lab_value/hematology.yaml +184 -0
  143. endoreg_db/data/lab_value/hormones.yaml +59 -0
  144. endoreg_db/data/lab_value/lipids.yaml +53 -0
  145. endoreg_db/data/lab_value/misc.yaml +76 -0
  146. endoreg_db/data/lab_value/renal_function.yaml +12 -0
  147. endoreg_db/data/log_type/data.yaml +57 -0
  148. endoreg_db/data/lx_client_tag/base.yaml +54 -0
  149. endoreg_db/data/lx_client_type/base.yaml +30 -0
  150. endoreg_db/data/lx_permission/base.yaml +24 -0
  151. endoreg_db/data/lx_permission/endoreg.yaml +52 -0
  152. endoreg_db/data/material/material.yaml +91 -0
  153. endoreg_db/data/medication/anticoagulation.yaml +65 -0
  154. endoreg_db/data/medication/tah.yaml +70 -0
  155. endoreg_db/data/medication_indication/anticoagulation.yaml +115 -0
  156. endoreg_db/data/medication_indication_type/data.yaml +11 -0
  157. endoreg_db/data/medication_indication_type/thrombembolism.yaml +41 -0
  158. endoreg_db/data/medication_intake_time/base.yaml +31 -0
  159. endoreg_db/data/medication_schedule/apixaban.yaml +95 -0
  160. endoreg_db/data/medication_schedule/ass.yaml +12 -0
  161. endoreg_db/data/medication_schedule/enoxaparin.yaml +26 -0
  162. endoreg_db/data/names_first/first_names.yaml +54 -0
  163. endoreg_db/data/names_last/last_names.yaml +51 -0
  164. endoreg_db/data/network_device/data.yaml +59 -0
  165. endoreg_db/data/network_device_type/data.yaml +12 -0
  166. endoreg_db/data/organ/data.yaml +29 -0
  167. endoreg_db/data/patient_lab_sample_type/generic.yaml +6 -0
  168. endoreg_db/data/pdf_type/data.yaml +46 -0
  169. endoreg_db/data/product/green_endoscopy_dashboard_Product.yaml +66 -0
  170. endoreg_db/data/product_group/green_endoscopy_dashboard_ProductGroup.yaml +33 -0
  171. endoreg_db/data/product_material/green_endoscopy_dashboard_ProductMaterial.yaml +308 -0
  172. endoreg_db/data/product_weight/green_endoscopy_dashboard_ProductWeight.yaml +88 -0
  173. endoreg_db/data/profession/data.yaml +70 -0
  174. endoreg_db/data/qualification/endoscopy.yaml +36 -0
  175. endoreg_db/data/qualification/m2.yaml +39 -0
  176. endoreg_db/data/qualification/outpatient_clinic.yaml +35 -0
  177. endoreg_db/data/qualification/sonography.yaml +36 -0
  178. endoreg_db/data/qualification_type/base.yaml +29 -0
  179. endoreg_db/data/reference_product/green_endoscopy_dashboard_ReferenceProduct.yaml +55 -0
  180. endoreg_db/data/report_reader_flag/rkh-histology-generic.yaml +10 -0
  181. endoreg_db/data/report_reader_flag/ukw-examination-generic.yaml +30 -0
  182. endoreg_db/data/report_reader_flag/ukw-histology-generic.yaml +24 -0
  183. endoreg_db/data/requirement/age.yaml +26 -0
  184. endoreg_db/data/requirement/colonoscopy_baseline_austria.yaml +45 -0
  185. endoreg_db/data/requirement/disease_cardiovascular.yaml +79 -0
  186. endoreg_db/data/requirement/disease_classification_choice_cardiovascular.yaml +41 -0
  187. endoreg_db/data/requirement/disease_hepatology.yaml +12 -0
  188. endoreg_db/data/requirement/disease_misc.yaml +12 -0
  189. endoreg_db/data/requirement/disease_renal.yaml +96 -0
  190. endoreg_db/data/requirement/endoscopy_bleeding_risk.yaml +59 -0
  191. endoreg_db/data/requirement/event_cardiology.yaml +251 -0
  192. endoreg_db/data/requirement/event_requirements.yaml +145 -0
  193. endoreg_db/data/requirement/finding_colon_polyp.yaml +50 -0
  194. endoreg_db/data/requirement/gender.yaml +25 -0
  195. endoreg_db/data/requirement/lab_value.yaml +441 -0
  196. endoreg_db/data/requirement/medication.yaml +93 -0
  197. endoreg_db/data/requirement_operator/age.yaml +13 -0
  198. endoreg_db/data/requirement_operator/lab_operators.yaml +129 -0
  199. endoreg_db/data/requirement_operator/model_operators.yaml +96 -0
  200. endoreg_db/data/requirement_set/01_endoscopy_generic.yaml +48 -0
  201. endoreg_db/data/requirement_set/colonoscopy_austria_screening.yaml +57 -0
  202. endoreg_db/data/requirement_set/endoscopy_bleeding_risk.yaml +52 -0
  203. endoreg_db/data/requirement_set_type/data.yaml +20 -0
  204. endoreg_db/data/requirement_type/requirement_types.yaml +165 -0
  205. endoreg_db/data/resource/green_endoscopy_dashboard_Resource.yaml +15 -0
  206. endoreg_db/data/risk/bleeding.yaml +26 -0
  207. endoreg_db/data/risk/thrombosis.yaml +37 -0
  208. endoreg_db/data/risk_type/data.yaml +27 -0
  209. endoreg_db/data/setup_config.yaml +38 -0
  210. endoreg_db/data/shift/endoscopy.yaml +21 -0
  211. endoreg_db/data/shift/m2.yaml +0 -0
  212. endoreg_db/data/shift_type/base.yaml +35 -0
  213. endoreg_db/data/tag/requirement_set_tags.yaml +11 -0
  214. endoreg_db/data/tmp/chronic_kidney_disease.yaml +0 -0
  215. endoreg_db/data/tmp/congestive_heart_failure.yaml +0 -0
  216. endoreg_db/data/transport_route/green_endoscopy_dashboard_TransportRoute.yaml +12 -0
  217. endoreg_db/data/unit/concentration.yaml +115 -0
  218. endoreg_db/data/unit/data.yaml +17 -0
  219. endoreg_db/data/unit/length.yaml +31 -0
  220. endoreg_db/data/unit/misc.yaml +20 -0
  221. endoreg_db/data/unit/rate.yaml +6 -0
  222. endoreg_db/data/unit/time.yaml +48 -0
  223. endoreg_db/data/unit/volume.yaml +35 -0
  224. endoreg_db/data/unit/weight.yaml +38 -0
  225. endoreg_db/data/waste/data.yaml +12 -0
  226. endoreg_db/exceptions.py +19 -0
  227. endoreg_db/factories/__init__.py +0 -0
  228. endoreg_db/forms/__init__.py +5 -0
  229. endoreg_db/forms/examination_form.py +11 -0
  230. endoreg_db/forms/patient_finding_intervention_form.py +18 -0
  231. endoreg_db/forms/patient_form.py +27 -0
  232. endoreg_db/forms/questionnaires/__init__.py +1 -0
  233. endoreg_db/forms/questionnaires/tto_questionnaire.py +23 -0
  234. endoreg_db/forms/settings/__init__.py +8 -0
  235. endoreg_db/forms/unit.py +6 -0
  236. endoreg_db/helpers/__init__.py +0 -0
  237. endoreg_db/helpers/count_db.py +45 -0
  238. endoreg_db/helpers/data_loader.py +208 -0
  239. endoreg_db/helpers/default_objects.py +378 -0
  240. endoreg_db/helpers/download_segmentation_model.py +31 -0
  241. endoreg_db/helpers/interact.py +6 -0
  242. endoreg_db/helpers/test_video_helper.py +119 -0
  243. endoreg_db/logger_conf.py +140 -0
  244. endoreg_db/management/__init__.py +1 -0
  245. endoreg_db/management/commands/__init__.py +1 -0
  246. endoreg_db/management/commands/anonymize_video.py +0 -0
  247. endoreg_db/management/commands/check_auth.py +125 -0
  248. endoreg_db/management/commands/create_model_meta_from_huggingface.py +115 -0
  249. endoreg_db/management/commands/create_multilabel_model_meta.py +214 -0
  250. endoreg_db/management/commands/fix_missing_patient_data.py +172 -0
  251. endoreg_db/management/commands/fix_video_paths.py +165 -0
  252. endoreg_db/management/commands/import_fallback_video.py +203 -0
  253. endoreg_db/management/commands/import_report.py +298 -0
  254. endoreg_db/management/commands/import_video.py +423 -0
  255. endoreg_db/management/commands/import_video_with_classification.py +367 -0
  256. endoreg_db/management/commands/init_default_ai_model.py +112 -0
  257. endoreg_db/management/commands/load_ai_model_data.py +77 -0
  258. endoreg_db/management/commands/load_ai_model_label_data.py +59 -0
  259. endoreg_db/management/commands/load_base_db_data.py +192 -0
  260. endoreg_db/management/commands/load_center_data.py +68 -0
  261. endoreg_db/management/commands/load_contraindication_data.py +41 -0
  262. endoreg_db/management/commands/load_disease_classification_choices_data.py +41 -0
  263. endoreg_db/management/commands/load_disease_classification_data.py +41 -0
  264. endoreg_db/management/commands/load_disease_data.py +62 -0
  265. endoreg_db/management/commands/load_distribution_data.py +66 -0
  266. endoreg_db/management/commands/load_endoscope_data.py +68 -0
  267. endoreg_db/management/commands/load_event_data.py +41 -0
  268. endoreg_db/management/commands/load_examination_data.py +75 -0
  269. endoreg_db/management/commands/load_examination_indication_data.py +86 -0
  270. endoreg_db/management/commands/load_finding_data.py +128 -0
  271. endoreg_db/management/commands/load_gender_data.py +44 -0
  272. endoreg_db/management/commands/load_green_endoscopy_wuerzburg_data.py +132 -0
  273. endoreg_db/management/commands/load_information_source.py +51 -0
  274. endoreg_db/management/commands/load_lab_value_data.py +50 -0
  275. endoreg_db/management/commands/load_medication_data.py +103 -0
  276. endoreg_db/management/commands/load_name_data.py +37 -0
  277. endoreg_db/management/commands/load_organ_data.py +43 -0
  278. endoreg_db/management/commands/load_pdf_type_data.py +61 -0
  279. endoreg_db/management/commands/load_profession_data.py +44 -0
  280. endoreg_db/management/commands/load_qualification_data.py +59 -0
  281. endoreg_db/management/commands/load_report_reader_flag_data.py +46 -0
  282. endoreg_db/management/commands/load_requirement_data.py +180 -0
  283. endoreg_db/management/commands/load_risk_data.py +56 -0
  284. endoreg_db/management/commands/load_shift_data.py +60 -0
  285. endoreg_db/management/commands/load_tag_data.py +57 -0
  286. endoreg_db/management/commands/load_unit_data.py +46 -0
  287. endoreg_db/management/commands/load_user_groups.py +28 -0
  288. endoreg_db/management/commands/register_ai_model.py +64 -0
  289. endoreg_db/management/commands/reset_celery_schedule.py +9 -0
  290. endoreg_db/management/commands/setup_endoreg_db.py +381 -0
  291. endoreg_db/management/commands/start_filewatcher.py +106 -0
  292. endoreg_db/management/commands/storage_management.py +548 -0
  293. endoreg_db/management/commands/summarize_db_content.py +189 -0
  294. endoreg_db/management/commands/validate_video.py +204 -0
  295. endoreg_db/management/commands/validate_video_files.py +161 -0
  296. endoreg_db/management/commands/video_validation.py +22 -0
  297. endoreg_db/mermaid/Overall_flow_patient_finding_intervention.md +10 -0
  298. endoreg_db/mermaid/anonymized_image_annotation.md +20 -0
  299. endoreg_db/mermaid/binary_classification_annotation.md +50 -0
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  607. endoreg_db/tasks/video_ingest.py +157 -0
  608. endoreg_db/tasks/video_processing_tasks.py +327 -0
  609. endoreg_db/templates/admin/patient_finding_intervention.html +253 -0
  610. endoreg_db/templates/admin/start_examination.html +12 -0
  611. endoreg_db/templates/timeline.html +176 -0
  612. endoreg_db/urls/__init__.py +83 -0
  613. endoreg_db/urls/anonymization.py +32 -0
  614. endoreg_db/urls/auth.py +16 -0
  615. endoreg_db/urls/classification.py +39 -0
  616. endoreg_db/urls/examination.py +54 -0
  617. endoreg_db/urls/files.py +6 -0
  618. endoreg_db/urls/label_video_segment_validate.py +33 -0
  619. endoreg_db/urls/label_video_segments.py +46 -0
  620. endoreg_db/urls/media.py +227 -0
  621. endoreg_db/urls/patient.py +19 -0
  622. endoreg_db/urls/report.py +48 -0
  623. endoreg_db/urls/requirements.py +13 -0
  624. endoreg_db/urls/sensitive_meta.py +0 -0
  625. endoreg_db/urls/stats.py +46 -0
  626. endoreg_db/urls/upload.py +20 -0
  627. endoreg_db/urls/video.py +61 -0
  628. endoreg_db/urls.py +9 -0
  629. endoreg_db/utils/__init__.py +88 -0
  630. endoreg_db/utils/ai/__init__.py +9 -0
  631. endoreg_db/utils/ai/get.py +5 -0
  632. endoreg_db/utils/ai/inference_dataset.py +52 -0
  633. endoreg_db/utils/ai/multilabel_classification_net.py +159 -0
  634. endoreg_db/utils/ai/postprocess.py +63 -0
  635. endoreg_db/utils/ai/predict.py +291 -0
  636. endoreg_db/utils/ai/preprocess.py +68 -0
  637. endoreg_db/utils/calc_duration_seconds.py +24 -0
  638. endoreg_db/utils/case_generator/__init__.py +0 -0
  639. endoreg_db/utils/case_generator/case_generator.py +159 -0
  640. endoreg_db/utils/case_generator/lab_sample_factory.py +33 -0
  641. endoreg_db/utils/case_generator/utils.py +30 -0
  642. endoreg_db/utils/check_video_files.py +148 -0
  643. endoreg_db/utils/cropping.py +29 -0
  644. endoreg_db/utils/dataloader.py +175 -0
  645. endoreg_db/utils/dates.py +60 -0
  646. endoreg_db/utils/env.py +33 -0
  647. endoreg_db/utils/extract_specific_frames.py +72 -0
  648. endoreg_db/utils/file_operations.py +58 -0
  649. endoreg_db/utils/fix_video_path_direct.py +141 -0
  650. endoreg_db/utils/frame_anonymization_utils.py +463 -0
  651. endoreg_db/utils/hashs.py +153 -0
  652. endoreg_db/utils/links/__init__.py +0 -0
  653. endoreg_db/utils/links/requirement_link.py +193 -0
  654. endoreg_db/utils/mime_types.py +0 -0
  655. endoreg_db/utils/names.py +76 -0
  656. endoreg_db/utils/ocr.py +190 -0
  657. endoreg_db/utils/parse_and_generate_yaml.py +46 -0
  658. endoreg_db/utils/paths.py +95 -0
  659. endoreg_db/utils/permissions.py +143 -0
  660. endoreg_db/utils/pipelines/Readme.md +235 -0
  661. endoreg_db/utils/pipelines/__init__.py +0 -0
  662. endoreg_db/utils/pipelines/process_video_dir.py +120 -0
  663. endoreg_db/utils/product/__init__.py +0 -0
  664. endoreg_db/utils/product/sum_emissions.py +20 -0
  665. endoreg_db/utils/product/sum_weights.py +18 -0
  666. endoreg_db/utils/pydantic_models/__init__.py +6 -0
  667. endoreg_db/utils/pydantic_models/db_config.py +57 -0
  668. endoreg_db/utils/requirement_helpers.py +0 -0
  669. endoreg_db/utils/requirement_operator_logic/__init__.py +0 -0
  670. endoreg_db/utils/requirement_operator_logic/lab_value_operators.py +578 -0
  671. endoreg_db/utils/requirement_operator_logic/model_evaluators.py +368 -0
  672. endoreg_db/utils/setup_config.py +177 -0
  673. endoreg_db/utils/translation.py +27 -0
  674. endoreg_db/utils/uuid.py +4 -0
  675. endoreg_db/utils/validate_endo_roi.py +19 -0
  676. endoreg_db/utils/validate_subcategory_dict.py +91 -0
  677. endoreg_db/utils/validate_video_detailed.py +357 -0
  678. endoreg_db/utils/video/__init__.py +26 -0
  679. endoreg_db/utils/video/extract_frames.py +88 -0
  680. endoreg_db/utils/video/ffmpeg_wrapper.py +835 -0
  681. endoreg_db/utils/video/names.py +42 -0
  682. endoreg_db/utils/video/streaming_processor.py +312 -0
  683. endoreg_db/utils/video/video_splitter.py +94 -0
  684. endoreg_db/views/Frames_NICE_and_PARIS_classifications_views.py +238 -0
  685. endoreg_db/views/__init__.py +274 -0
  686. endoreg_db/views/anonymization/__init__.py +27 -0
  687. endoreg_db/views/anonymization/media_management.py +454 -0
  688. endoreg_db/views/anonymization/overview.py +216 -0
  689. endoreg_db/views/anonymization/validate.py +107 -0
  690. endoreg_db/views/auth/__init__.py +13 -0
  691. endoreg_db/views/auth/keycloak.py +113 -0
  692. endoreg_db/views/examination/__init__.py +33 -0
  693. endoreg_db/views/examination/examination.py +37 -0
  694. endoreg_db/views/examination/examination_manifest_cache.py +26 -0
  695. endoreg_db/views/examination/get_finding_classification_choices.py +59 -0
  696. endoreg_db/views/examination/get_finding_classifications.py +36 -0
  697. endoreg_db/views/examination/get_findings.py +41 -0
  698. endoreg_db/views/examination/get_instruments.py +18 -0
  699. endoreg_db/views/examination/get_interventions.py +14 -0
  700. endoreg_db/views/finding/__init__.py +9 -0
  701. endoreg_db/views/finding/finding.py +112 -0
  702. endoreg_db/views/finding/get_classifications.py +14 -0
  703. endoreg_db/views/finding/get_interventions.py +17 -0
  704. endoreg_db/views/finding_classification/__init__.py +13 -0
  705. endoreg_db/views/finding_classification/base.py +0 -0
  706. endoreg_db/views/finding_classification/finding_classification.py +42 -0
  707. endoreg_db/views/finding_classification/get_classification_choices.py +55 -0
  708. endoreg_db/views/label/__init__.py +5 -0
  709. endoreg_db/views/label/label.py +15 -0
  710. endoreg_db/views/label_video_segment/__init__.py +16 -0
  711. endoreg_db/views/label_video_segment/create_lvs_from_annotation.py +44 -0
  712. endoreg_db/views/label_video_segment/get_lvs_by_name_and_video.py +50 -0
  713. endoreg_db/views/label_video_segment/label_video_segment.py +77 -0
  714. endoreg_db/views/label_video_segment/label_video_segment_by_label.py +174 -0
  715. endoreg_db/views/label_video_segment/label_video_segment_detail.py +73 -0
  716. endoreg_db/views/label_video_segment/update_lvs_from_annotation.py +46 -0
  717. endoreg_db/views/label_video_segment/validate.py +226 -0
  718. endoreg_db/views/media/__init__.py +45 -0
  719. endoreg_db/views/media/pdf_media.py +388 -0
  720. endoreg_db/views/media/segments.py +71 -0
  721. endoreg_db/views/media/sensitive_metadata.py +314 -0
  722. endoreg_db/views/media/video_media.py +272 -0
  723. endoreg_db/views/media/video_segments.py +524 -0
  724. endoreg_db/views/meta/__init__.py +15 -0
  725. endoreg_db/views/meta/available_files_list.py +146 -0
  726. endoreg_db/views/meta/report_meta.py +53 -0
  727. endoreg_db/views/meta/sensitive_meta_detail.py +148 -0
  728. endoreg_db/views/meta/sensitive_meta_list.py +104 -0
  729. endoreg_db/views/meta/sensitive_meta_verification.py +71 -0
  730. endoreg_db/views/misc/__init__.py +63 -0
  731. endoreg_db/views/misc/center.py +13 -0
  732. endoreg_db/views/misc/csrf.py +7 -0
  733. endoreg_db/views/misc/gender.py +14 -0
  734. endoreg_db/views/misc/secure_file_serving_view.py +80 -0
  735. endoreg_db/views/misc/secure_file_url_view.py +84 -0
  736. endoreg_db/views/misc/secure_url_validate.py +79 -0
  737. endoreg_db/views/misc/stats.py +220 -0
  738. endoreg_db/views/misc/translation.py +182 -0
  739. endoreg_db/views/misc/upload_views.py +240 -0
  740. endoreg_db/views/patient/__init__.py +5 -0
  741. endoreg_db/views/patient/patient.py +210 -0
  742. endoreg_db/views/patient_examination/DEPRECATED_video_backup.py +164 -0
  743. endoreg_db/views/patient_examination/__init__.py +11 -0
  744. endoreg_db/views/patient_examination/patient_examination.py +140 -0
  745. endoreg_db/views/patient_examination/patient_examination_create.py +63 -0
  746. endoreg_db/views/patient_examination/patient_examination_detail.py +66 -0
  747. endoreg_db/views/patient_examination/patient_examination_list.py +68 -0
  748. endoreg_db/views/patient_examination/video.py +194 -0
  749. endoreg_db/views/patient_finding/__init__.py +7 -0
  750. endoreg_db/views/patient_finding/base.py +0 -0
  751. endoreg_db/views/patient_finding/patient_finding.py +64 -0
  752. endoreg_db/views/patient_finding/patient_finding_optimized.py +259 -0
  753. endoreg_db/views/patient_finding_classification/__init__.py +5 -0
  754. endoreg_db/views/patient_finding_classification/pfc_create.py +67 -0
  755. endoreg_db/views/patient_finding_location/__init__.py +5 -0
  756. endoreg_db/views/patient_finding_location/pfl_create.py +70 -0
  757. endoreg_db/views/patient_finding_morphology/__init__.py +5 -0
  758. endoreg_db/views/patient_finding_morphology/pfm_create.py +70 -0
  759. endoreg_db/views/pdf/__init__.py +8 -0
  760. endoreg_db/views/pdf/pdf_stream.py +186 -0
  761. endoreg_db/views/pdf/reimport.py +177 -0
  762. endoreg_db/views/report/__init__.py +9 -0
  763. endoreg_db/views/report/report_list.py +112 -0
  764. endoreg_db/views/report/report_with_secure_url.py +28 -0
  765. endoreg_db/views/report/start_examination.py +7 -0
  766. endoreg_db/views/requirement/__init__.py +10 -0
  767. endoreg_db/views/requirement/evaluate.py +279 -0
  768. endoreg_db/views/requirement/lookup.py +367 -0
  769. endoreg_db/views/requirement/lookup_store.py +252 -0
  770. endoreg_db/views/requirement_lookup/lookup.py +0 -0
  771. endoreg_db/views/requirement_lookup/lookup_store.py +0 -0
  772. endoreg_db/views/stats/__init__.py +13 -0
  773. endoreg_db/views/stats/stats_views.py +229 -0
  774. endoreg_db/views/video/__init__.py +59 -0
  775. endoreg_db/views/video/correction.py +530 -0
  776. endoreg_db/views/video/reimport.py +195 -0
  777. endoreg_db/views/video/segmentation.py +274 -0
  778. endoreg_db/views/video/task_status.py +49 -0
  779. endoreg_db/views/video/timeline.py +46 -0
  780. endoreg_db/views/video/video_analyze.py +52 -0
  781. endoreg_db/views/video/video_apply_mask.py +48 -0
  782. endoreg_db/views/video/video_correction.py +21 -0
  783. endoreg_db/views/video/video_download_processed.py +58 -0
  784. endoreg_db/views/video/video_examination_viewset.py +242 -0
  785. endoreg_db/views/video/video_meta.py +29 -0
  786. endoreg_db/views/video/video_processing_history.py +24 -0
  787. endoreg_db/views/video/video_remove_frames.py +48 -0
  788. endoreg_db/views/video/video_stream.py +306 -0
  789. endoreg_db/views.py +0 -0
  790. endoreg_db-0.8.6.4.dist-info/METADATA +383 -0
  791. endoreg_db-0.8.6.4.dist-info/RECORD +793 -0
  792. endoreg_db-0.8.6.4.dist-info/WHEEL +4 -0
  793. endoreg_db-0.8.6.4.dist-info/licenses/LICENSE +674 -0
endoreg_db/data/requirement/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/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/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/gender.yaml ADDED
@@ -0,0 +1,25 @@
1
+ - model: endoreg_db.requirement
2
+ fields:
3
+ name: "patient_gender_is_male"
4
+ name_de: "Patient ist männlich"
5
+ name_en: "Patient is male"
6
+ description: "Checks if the patient is male."
7
+ requirement_types:
8
+ - "patient"
9
+ operators:
10
+ - models_match_all
11
+ genders:
12
+ - "male"
13
+
14
+ - model: endoreg_db.requirement
15
+ fields:
16
+ name: "patient_gender_is_female"
17
+ name_de: "Patient ist weiblich"
18
+ name_en: "Patient is female"
19
+ description: "Checks if the patient is female."
20
+ requirement_types:
21
+ - "patient"
22
+ operators:
23
+ - models_match_all
24
+ genders:
25
+ - "female"