endoreg-db 0.6.4__py3-none-any.whl → 0.8.1__py3-none-any.whl

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  1. endoreg_db/admin.py +26 -26
  2. endoreg_db/api_urls.py +4 -0
  3. endoreg_db/apps.py +12 -0
  4. endoreg_db/assets/dummy_model.ckpt +1 -0
  5. endoreg_db/codemods/readme.md +88 -0
  6. endoreg_db/codemods/rename_datetime_fields.py +92 -0
  7. endoreg_db/config/env.py +101 -0
  8. endoreg_db/data/__init__.py +12 -0
  9. endoreg_db/data/ai_model/data.yaml +1 -1
  10. endoreg_db/data/ai_model_label/label/polyp_classification.yaml +52 -0
  11. endoreg_db/data/ai_model_label/label-set/data.yaml +20 -1
  12. endoreg_db/data/ai_model_label/label-set/polyp_classifications.yaml +25 -0
  13. endoreg_db/data/center/data.yaml +13 -12
  14. endoreg_db/data/center_shift/ukw.yaml +9 -0
  15. endoreg_db/data/db_summary.csv +58 -0
  16. endoreg_db/data/db_summary.xlsx +0 -0
  17. endoreg_db/data/disease/misc.yaml +1 -2
  18. endoreg_db/data/endoscopy_processor/data.yaml +3 -0
  19. endoreg_db/data/event/cardiology.yaml +0 -13
  20. endoreg_db/data/examination/examinations/data.yaml +14 -9
  21. endoreg_db/data/examination_indication/endoscopy.yaml +30 -30
  22. endoreg_db/data/examination_indication_classification/endoscopy.yaml +11 -11
  23. endoreg_db/data/examination_requirement_set/colonoscopy.yaml +15 -0
  24. endoreg_db/data/finding/anatomy_colon.yaml +128 -0
  25. endoreg_db/data/finding/colonoscopy.yaml +40 -0
  26. endoreg_db/data/finding/colonoscopy_bowel_prep.yaml +56 -0
  27. endoreg_db/data/finding/complication.yaml +16 -0
  28. endoreg_db/data/finding/data.yaml +3 -46
  29. endoreg_db/data/finding/examination_setting.yaml +16 -0
  30. endoreg_db/data/finding/medication_related.yaml +18 -0
  31. endoreg_db/data/finding/outcome.yaml +12 -0
  32. endoreg_db/data/finding_classification/colonoscopy_bowel_preparation.yaml +95 -0
  33. endoreg_db/data/finding_classification/colonoscopy_jnet.yaml +22 -0
  34. endoreg_db/data/finding_classification/colonoscopy_kudo.yaml +25 -0
  35. endoreg_db/data/finding_classification/colonoscopy_lesion_circularity.yaml +20 -0
  36. endoreg_db/data/finding_classification/colonoscopy_lesion_planarity.yaml +24 -0
  37. endoreg_db/data/finding_classification/colonoscopy_lesion_size.yaml +68 -0
  38. endoreg_db/data/finding_classification/colonoscopy_lesion_surface.yaml +20 -0
  39. endoreg_db/data/finding_classification/colonoscopy_location.yaml +80 -0
  40. endoreg_db/data/finding_classification/colonoscopy_lst.yaml +21 -0
  41. endoreg_db/data/finding_classification/colonoscopy_nice.yaml +20 -0
  42. endoreg_db/data/finding_classification/colonoscopy_paris.yaml +26 -0
  43. endoreg_db/data/finding_classification/colonoscopy_sano.yaml +22 -0
  44. endoreg_db/data/finding_classification/colonoscopy_summary.yaml +53 -0
  45. endoreg_db/data/finding_classification/complication_generic.yaml +25 -0
  46. endoreg_db/data/finding_classification/examination_setting_generic.yaml +40 -0
  47. endoreg_db/data/finding_classification/histology_colo.yaml +51 -0
  48. endoreg_db/data/finding_classification/intervention_required.yaml +26 -0
  49. endoreg_db/data/finding_classification/medication_related.yaml +23 -0
  50. endoreg_db/data/finding_classification/visualized.yaml +33 -0
  51. endoreg_db/data/finding_classification_choice/bowel_preparation.yaml +78 -0
  52. endoreg_db/data/{finding_morphology_classification_choice → finding_classification_choice}/colon_lesion_circularity_default.yaml +0 -2
  53. endoreg_db/data/finding_classification_choice/colon_lesion_jnet.yaml +15 -0
  54. endoreg_db/data/finding_classification_choice/colon_lesion_kudo.yaml +23 -0
  55. endoreg_db/data/finding_classification_choice/colon_lesion_lst.yaml +15 -0
  56. endoreg_db/data/{finding_morphology_classification_choice → finding_classification_choice}/colon_lesion_nice.yaml +4 -7
  57. endoreg_db/data/{finding_morphology_classification_choice → finding_classification_choice}/colon_lesion_paris.yaml +0 -8
  58. endoreg_db/data/{finding_morphology_classification_choice → finding_classification_choice}/colon_lesion_planarity_default.yaml +6 -13
  59. endoreg_db/data/finding_classification_choice/colon_lesion_sano.yaml +14 -0
  60. endoreg_db/data/{finding_morphology_classification_choice → finding_classification_choice}/colon_lesion_surface_intact_default.yaml +3 -6
  61. endoreg_db/data/{finding_location_classification_choice/colonoscopy.yaml → finding_classification_choice/colonoscopy_location.yaml} +11 -22
  62. endoreg_db/data/finding_classification_choice/colonoscopy_not_complete_reason.yaml +19 -0
  63. endoreg_db/data/finding_classification_choice/colonoscopy_size.yaml +82 -0
  64. endoreg_db/data/finding_classification_choice/colonoscopy_summary_worst_finding.yaml +15 -0
  65. endoreg_db/data/finding_classification_choice/complication_generic_types.yaml +15 -0
  66. endoreg_db/data/finding_classification_choice/examination_setting_generic_types.yaml +15 -0
  67. endoreg_db/data/finding_classification_choice/histology.yaml +24 -0
  68. endoreg_db/data/finding_classification_choice/histology_polyp.yaml +20 -0
  69. endoreg_db/data/finding_classification_choice/outcome.yaml +19 -0
  70. endoreg_db/data/finding_classification_choice/yes_no_na.yaml +11 -0
  71. endoreg_db/data/finding_classification_type/colonoscopy_basic.yaml +48 -0
  72. endoreg_db/data/finding_intervention/endoscopy_colonoscopy.yaml +8 -3
  73. endoreg_db/data/finding_morphology_classification_type/colonoscopy.yaml +6 -6
  74. endoreg_db/data/finding_type/data.yaml +23 -10
  75. endoreg_db/data/gender/data.yaml +8 -1
  76. endoreg_db/data/information_source/annotation.yaml +6 -0
  77. endoreg_db/data/information_source/prediction.yaml +7 -0
  78. endoreg_db/data/information_source_type/data.yaml +8 -0
  79. endoreg_db/data/lab_value/misc.yaml +43 -0
  80. endoreg_db/data/medication/anticoagulation.yaml +5 -5
  81. endoreg_db/data/medication/tah.yaml +5 -5
  82. endoreg_db/data/medication_intake_time/base.yaml +4 -4
  83. endoreg_db/data/names_first/first_names.yaml +3 -0
  84. endoreg_db/data/pdf_type/data.yaml +26 -2
  85. endoreg_db/data/qualification/endoscopy.yaml +36 -0
  86. endoreg_db/data/qualification/m2.yaml +39 -0
  87. endoreg_db/data/qualification/outpatient_clinic.yaml +35 -0
  88. endoreg_db/data/qualification/sonography.yaml +36 -0
  89. endoreg_db/data/qualification_type/base.yaml +29 -0
  90. endoreg_db/data/report_reader_flag/rkh-histology-generic.yaml +10 -0
  91. endoreg_db/data/report_reader_flag/ukw-histology-generic.yaml +5 -0
  92. endoreg_db/data/requirement/age.yaml +26 -0
  93. endoreg_db/data/requirement/colonoscopy_baseline_austria.yaml +45 -0
  94. endoreg_db/data/requirement/disease_cardiovascular.yaml +6 -6
  95. endoreg_db/data/requirement/disease_classification_choice_cardiovascular.yaml +9 -6
  96. endoreg_db/data/requirement/disease_hepatology.yaml +1 -1
  97. endoreg_db/data/requirement/disease_misc.yaml +3 -3
  98. endoreg_db/data/requirement/disease_renal.yaml +18 -2
  99. endoreg_db/data/requirement/{colonoscopy_indications.yaml → endoscopy_bleeding_risk.yaml} +6 -3
  100. endoreg_db/data/requirement/event_cardiology.yaml +17 -17
  101. endoreg_db/data/requirement/event_requirements.yaml +145 -0
  102. endoreg_db/data/requirement/finding_colon_polyp.yaml +50 -0
  103. endoreg_db/data/requirement/gender.yaml +25 -0
  104. endoreg_db/data/requirement/lab_value.yaml +352 -31
  105. endoreg_db/data/requirement/medication.yaml +93 -0
  106. endoreg_db/data/requirement_operator/age.yaml +13 -0
  107. endoreg_db/data/requirement_operator/lab_operators.yaml +36 -35
  108. endoreg_db/data/requirement_operator/model_operators.yaml +13 -7
  109. endoreg_db/data/requirement_set/01_endoscopy_generic.yaml +48 -0
  110. endoreg_db/data/requirement_set/colonoscopy_austria_screening.yaml +57 -0
  111. endoreg_db/data/requirement_set/endoscopy_bleeding_risk.yaml +42 -2
  112. endoreg_db/data/requirement_type/requirement_types.yaml +82 -0
  113. endoreg_db/data/shift/endoscopy.yaml +21 -0
  114. endoreg_db/data/shift_type/base.yaml +35 -0
  115. endoreg_db/data/tag/requirement_set_tags.yaml +11 -0
  116. endoreg_db/data/unit/concentration.yaml +23 -0
  117. endoreg_db/exceptions.py +19 -0
  118. endoreg_db/forms/patient_finding_intervention_form.py +4 -5
  119. endoreg_db/forms/patient_form.py +7 -6
  120. endoreg_db/forms/questionnaires/__init__.py +1 -1
  121. endoreg_db/forms/questionnaires/tto_questionnaire.py +19 -19
  122. endoreg_db/helpers/count_db.py +45 -0
  123. endoreg_db/helpers/data_loader.py +208 -0
  124. endoreg_db/helpers/default_objects.py +359 -0
  125. endoreg_db/helpers/interact.py +6 -0
  126. endoreg_db/helpers/test_video_helper.py +119 -0
  127. endoreg_db/logger_conf.py +140 -0
  128. endoreg_db/management/__init__.py +1 -0
  129. endoreg_db/management/commands/__init__.py +1 -0
  130. endoreg_db/management/commands/anonymize_video.py +0 -0
  131. endoreg_db/management/commands/check_auth.py +125 -0
  132. endoreg_db/management/commands/create_multilabel_model_meta.py +214 -0
  133. endoreg_db/management/commands/fix_missing_patient_data.py +172 -0
  134. endoreg_db/management/commands/fix_video_paths.py +165 -0
  135. endoreg_db/management/commands/import_fallback_video.py +203 -0
  136. endoreg_db/management/commands/import_report.py +298 -0
  137. endoreg_db/management/commands/import_video.py +422 -0
  138. endoreg_db/management/commands/import_video_with_classification.py +367 -0
  139. endoreg_db/management/commands/init_default_ai_model.py +112 -0
  140. endoreg_db/management/commands/load_ai_model_data.py +2 -7
  141. endoreg_db/management/commands/load_base_db_data.py +1 -0
  142. endoreg_db/management/commands/load_endoscope_data.py +2 -2
  143. endoreg_db/management/commands/load_examination_indication_data.py +2 -3
  144. endoreg_db/management/commands/load_finding_data.py +49 -92
  145. endoreg_db/management/commands/load_green_endoscopy_wuerzburg_data.py +0 -1
  146. endoreg_db/management/commands/load_information_source.py +13 -7
  147. endoreg_db/management/commands/load_name_data.py +37 -0
  148. endoreg_db/management/commands/load_qualification_data.py +59 -0
  149. endoreg_db/management/commands/load_requirement_data.py +30 -6
  150. endoreg_db/management/commands/load_shift_data.py +60 -0
  151. endoreg_db/management/commands/load_tag_data.py +57 -0
  152. endoreg_db/management/commands/register_ai_model.py +1 -1
  153. endoreg_db/management/commands/start_filewatcher.py +106 -0
  154. endoreg_db/management/commands/storage_management.py +548 -0
  155. endoreg_db/management/commands/summarize_db_content.py +189 -0
  156. endoreg_db/management/commands/validate_video.py +204 -0
  157. endoreg_db/management/commands/validate_video_files.py +161 -0
  158. endoreg_db/management/commands/video_validation.py +22 -0
  159. endoreg_db/migrations/0001_initial.py +625 -813
  160. endoreg_db/migrations/0002_add_video_correction_models.py +52 -0
  161. endoreg_db/models/__init__.py +270 -307
  162. endoreg_db/models/administration/__init__.py +116 -0
  163. endoreg_db/models/{ai_model → administration/ai}/__init__.py +6 -1
  164. endoreg_db/models/administration/ai/active_model.py +35 -0
  165. endoreg_db/models/administration/ai/ai_model.py +156 -0
  166. endoreg_db/models/{ai_model → administration/ai}/model_type.py +6 -1
  167. endoreg_db/models/administration/case/__init__.py +19 -0
  168. endoreg_db/models/administration/case/case.py +114 -0
  169. endoreg_db/models/{case_template → administration/case/case_template}/case_template.py +3 -3
  170. endoreg_db/models/{case_template → administration/case/case_template}/case_template_rule.py +3 -10
  171. endoreg_db/models/{case_template → administration/case/case_template}/case_template_rule_value.py +2 -4
  172. endoreg_db/models/{case_template → administration/case/case_template}/case_template_type.py +1 -3
  173. endoreg_db/models/{center → administration/center}/__init__.py +3 -1
  174. endoreg_db/models/administration/center/center.py +61 -0
  175. endoreg_db/models/administration/center/center_product.py +64 -0
  176. endoreg_db/models/{center → administration/center}/center_resource.py +19 -3
  177. endoreg_db/models/administration/center/center_shift.py +88 -0
  178. endoreg_db/models/administration/center/center_waste.py +30 -0
  179. endoreg_db/models/administration/permissions/__init__.py +44 -0
  180. endoreg_db/models/administration/person/__init__.py +24 -0
  181. endoreg_db/models/administration/person/employee/__init__.py +3 -0
  182. endoreg_db/models/administration/person/employee/employee.py +35 -0
  183. endoreg_db/models/administration/person/employee/employee_qualification.py +39 -0
  184. endoreg_db/models/administration/person/employee/employee_type.py +42 -0
  185. endoreg_db/models/administration/person/examiner/__init__.py +4 -0
  186. endoreg_db/models/administration/person/examiner/examiner.py +54 -0
  187. endoreg_db/models/administration/person/names/__init__.py +0 -0
  188. endoreg_db/models/{persons → administration/person/names}/first_name.py +1 -1
  189. endoreg_db/models/{persons → administration/person/names}/last_name.py +2 -3
  190. endoreg_db/models/administration/person/patient/__init__.py +5 -0
  191. endoreg_db/models/administration/person/patient/patient.py +460 -0
  192. endoreg_db/models/administration/person/profession/__init__.py +24 -0
  193. endoreg_db/models/administration/person/user/__init__.py +5 -0
  194. endoreg_db/models/administration/person/user/portal_user_information.py +37 -0
  195. endoreg_db/models/administration/product/product.py +97 -0
  196. endoreg_db/models/administration/product/product_group.py +39 -0
  197. endoreg_db/models/administration/product/product_material.py +54 -0
  198. endoreg_db/models/{product → administration/product}/product_weight.py +9 -0
  199. endoreg_db/models/{product → administration/product}/reference_product.py +26 -11
  200. endoreg_db/models/administration/qualification/__init__.py +7 -0
  201. endoreg_db/models/administration/qualification/qualification.py +37 -0
  202. endoreg_db/models/administration/qualification/qualification_type.py +35 -0
  203. endoreg_db/models/administration/shift/__init__.py +9 -0
  204. endoreg_db/models/administration/shift/scheduled_days.py +69 -0
  205. endoreg_db/models/administration/shift/shift.py +51 -0
  206. endoreg_db/models/administration/shift/shift_type.py +108 -0
  207. endoreg_db/models/label/__init__.py +24 -1
  208. endoreg_db/models/label/annotation/__init__.py +12 -0
  209. endoreg_db/models/label/annotation/image_classification.py +84 -0
  210. endoreg_db/models/label/annotation/video_segmentation_annotation.py +66 -0
  211. endoreg_db/models/label/label.py +45 -74
  212. endoreg_db/models/label/label_set.py +53 -0
  213. endoreg_db/models/label/label_type.py +29 -0
  214. endoreg_db/models/label/label_video_segment/__init__.py +3 -0
  215. endoreg_db/models/label/label_video_segment/_create_from_video.py +41 -0
  216. endoreg_db/models/label/label_video_segment/label_video_segment.py +511 -0
  217. endoreg_db/models/label/video_segmentation_label.py +31 -0
  218. endoreg_db/models/{annotation → label}/video_segmentation_labelset.py +7 -0
  219. endoreg_db/models/media/__init__.py +14 -0
  220. endoreg_db/models/media/frame/__init__.py +3 -0
  221. endoreg_db/models/media/frame/frame.py +111 -0
  222. endoreg_db/models/media/pdf/__init__.py +11 -0
  223. endoreg_db/models/media/pdf/raw_pdf.py +608 -0
  224. endoreg_db/models/media/pdf/report_file.py +162 -0
  225. endoreg_db/models/media/pdf/report_reader/report_reader_config.py +77 -0
  226. endoreg_db/models/media/video/__init__.py +4 -0
  227. endoreg_db/models/media/video/create_from_file.py +336 -0
  228. endoreg_db/models/media/video/pipe_1.py +195 -0
  229. endoreg_db/models/media/video/pipe_2.py +105 -0
  230. endoreg_db/models/media/video/refactor_plan.md +0 -0
  231. endoreg_db/models/media/video/video_file.py +680 -0
  232. endoreg_db/models/media/video/video_file_ai.py +443 -0
  233. endoreg_db/models/media/video/video_file_anonymize.py +348 -0
  234. endoreg_db/models/media/video/video_file_frames/__init__.py +47 -0
  235. endoreg_db/models/media/video/video_file_frames/_bulk_create_frames.py +22 -0
  236. endoreg_db/models/media/video/video_file_frames/_create_frame_object.py +23 -0
  237. endoreg_db/models/media/video/video_file_frames/_delete_frames.py +104 -0
  238. endoreg_db/models/media/video/video_file_frames/_extract_frames.py +174 -0
  239. endoreg_db/models/media/video/video_file_frames/_get_frame.py +28 -0
  240. endoreg_db/models/media/video/video_file_frames/_get_frame_number.py +27 -0
  241. endoreg_db/models/media/video/video_file_frames/_get_frame_path.py +20 -0
  242. endoreg_db/models/media/video/video_file_frames/_get_frame_paths.py +27 -0
  243. endoreg_db/models/media/video/video_file_frames/_get_frame_range.py +34 -0
  244. endoreg_db/models/media/video/video_file_frames/_get_frames.py +27 -0
  245. endoreg_db/models/media/video/video_file_frames/_initialize_frames.py +129 -0
  246. endoreg_db/models/media/video/video_file_frames/_manage_frame_range.py +129 -0
  247. endoreg_db/models/media/video/video_file_frames/_mark_frames_extracted_status.py +65 -0
  248. endoreg_db/models/media/video/video_file_frames.py +0 -0
  249. endoreg_db/models/media/video/video_file_io.py +166 -0
  250. endoreg_db/models/media/video/video_file_meta/__init__.py +22 -0
  251. endoreg_db/models/media/video/video_file_meta/get_crop_template.py +45 -0
  252. endoreg_db/models/media/video/video_file_meta/get_endo_roi.py +39 -0
  253. endoreg_db/models/media/video/video_file_meta/get_fps.py +147 -0
  254. endoreg_db/models/media/video/video_file_meta/initialize_video_specs.py +143 -0
  255. endoreg_db/models/media/video/video_file_meta/text_meta.py +134 -0
  256. endoreg_db/models/media/video/video_file_meta/video_meta.py +70 -0
  257. endoreg_db/models/media/video/video_file_meta.py +11 -0
  258. endoreg_db/models/media/video/video_file_segments.py +209 -0
  259. endoreg_db/models/medical/__init__.py +146 -0
  260. endoreg_db/models/{contraindication → medical/contraindication}/__init__.py +1 -5
  261. endoreg_db/models/{disease.py → medical/disease.py} +60 -52
  262. endoreg_db/models/{event.py → medical/event.py} +31 -54
  263. endoreg_db/models/{examination → medical/examination}/__init__.py +1 -1
  264. endoreg_db/models/medical/examination/examination.py +148 -0
  265. endoreg_db/models/{examination → medical/examination}/examination_indication.py +64 -35
  266. endoreg_db/models/{examination → medical/examination}/examination_time.py +0 -4
  267. endoreg_db/models/{examination → medical/examination}/examination_time_type.py +1 -8
  268. endoreg_db/models/{examination → medical/examination}/examination_type.py +1 -7
  269. endoreg_db/models/medical/finding/__init__.py +18 -0
  270. endoreg_db/models/medical/finding/finding.py +96 -0
  271. endoreg_db/models/medical/finding/finding_classification.py +142 -0
  272. endoreg_db/models/{finding → medical/finding}/finding_intervention.py +2 -10
  273. endoreg_db/models/medical/finding/finding_type.py +35 -0
  274. endoreg_db/models/medical/hardware/__init__.py +8 -0
  275. endoreg_db/models/{hardware → medical/hardware}/endoscope.py +28 -23
  276. endoreg_db/models/medical/laboratory/__init__.py +5 -0
  277. endoreg_db/models/medical/laboratory/lab_value.py +419 -0
  278. endoreg_db/models/{medication → medical/medication}/medication.py +1 -3
  279. endoreg_db/models/{medication → medical/medication}/medication_indication_type.py +8 -3
  280. endoreg_db/models/{medication → medical/medication}/medication_intake_time.py +21 -3
  281. endoreg_db/models/{medication → medical/medication}/medication_schedule.py +13 -5
  282. endoreg_db/models/{organ → medical/organ}/__init__.py +3 -6
  283. endoreg_db/models/medical/patient/__init__.py +56 -0
  284. endoreg_db/models/medical/patient/medication_examples.py +38 -0
  285. endoreg_db/models/medical/patient/patient_disease.py +63 -0
  286. endoreg_db/models/medical/patient/patient_event.py +75 -0
  287. endoreg_db/models/medical/patient/patient_examination.py +249 -0
  288. endoreg_db/models/{persons → medical}/patient/patient_examination_indication.py +21 -9
  289. endoreg_db/models/medical/patient/patient_finding.py +357 -0
  290. endoreg_db/models/medical/patient/patient_finding_classification.py +207 -0
  291. endoreg_db/models/{patient → medical/patient}/patient_finding_intervention.py +15 -1
  292. endoreg_db/models/medical/patient/patient_lab_sample.py +148 -0
  293. endoreg_db/models/{persons → medical}/patient/patient_lab_value.py +40 -15
  294. endoreg_db/models/medical/patient/patient_medication.py +104 -0
  295. endoreg_db/models/medical/patient/patient_medication_schedule.py +136 -0
  296. endoreg_db/models/{risk → medical/risk}/risk_type.py +0 -4
  297. endoreg_db/models/{data_file/metadata → metadata}/__init__.py +6 -0
  298. endoreg_db/models/metadata/frame_ocr_result.py +0 -0
  299. endoreg_db/models/metadata/model_meta.py +193 -0
  300. endoreg_db/models/metadata/model_meta_logic.py +236 -0
  301. endoreg_db/models/{data_file/metadata → metadata}/pdf_meta.py +28 -13
  302. endoreg_db/models/metadata/sensitive_meta.py +288 -0
  303. endoreg_db/models/metadata/sensitive_meta_logic.py +643 -0
  304. endoreg_db/models/metadata/video_meta.py +332 -0
  305. endoreg_db/models/metadata/video_prediction_logic.py +190 -0
  306. endoreg_db/models/metadata/video_prediction_meta.py +270 -0
  307. endoreg_db/models/other/__init__.py +17 -0
  308. endoreg_db/models/other/distribution/date_value_distribution.py +0 -2
  309. endoreg_db/models/other/distribution/numeric_value_distribution.py +30 -2
  310. endoreg_db/models/{emission → other/emission}/emission_factor.py +15 -6
  311. endoreg_db/models/{persons → other}/gender.py +8 -3
  312. endoreg_db/models/other/information_source.py +159 -0
  313. endoreg_db/models/other/material.py +10 -2
  314. endoreg_db/models/other/resource.py +6 -2
  315. endoreg_db/models/other/tag.py +27 -0
  316. endoreg_db/models/other/transport_route.py +13 -2
  317. endoreg_db/models/{unit.py → other/unit.py} +16 -6
  318. endoreg_db/models/other/waste.py +10 -3
  319. endoreg_db/models/requirement/requirement.py +556 -114
  320. endoreg_db/models/requirement/requirement_evaluation/__init__.py +4 -132
  321. endoreg_db/models/requirement/requirement_evaluation/get_values.py +40 -0
  322. endoreg_db/models/requirement/requirement_evaluation/operator_evaluation_models.py +9 -0
  323. endoreg_db/models/requirement/requirement_evaluation/requirement_type_parser.py +80 -87
  324. endoreg_db/models/requirement/requirement_operator.py +132 -14
  325. endoreg_db/models/requirement/requirement_set.py +181 -21
  326. endoreg_db/models/rule/__init__.py +13 -0
  327. endoreg_db/models/{rules → rule}/rule.py +6 -3
  328. endoreg_db/models/{rules → rule}/rule_attribute_dtype.py +0 -2
  329. endoreg_db/models/{rules → rule}/rule_type.py +0 -2
  330. endoreg_db/models/{rules → rule}/ruleset.py +0 -2
  331. endoreg_db/models/state/__init__.py +12 -0
  332. endoreg_db/models/state/abstract.py +11 -0
  333. endoreg_db/models/state/audit_ledger.py +150 -0
  334. endoreg_db/models/state/label_video_segment.py +22 -0
  335. endoreg_db/models/state/raw_pdf.py +187 -0
  336. endoreg_db/models/state/sensitive_meta.py +46 -0
  337. endoreg_db/models/state/video.py +232 -0
  338. endoreg_db/models/upload_job.py +99 -0
  339. endoreg_db/models/utils.py +135 -0
  340. endoreg_db/models/video_metadata.py +66 -0
  341. endoreg_db/models/video_processing.py +153 -0
  342. endoreg_db/renames.yml +8 -0
  343. endoreg_db/root_urls.py +9 -0
  344. endoreg_db/schemas/__init__.py +0 -0
  345. endoreg_db/schemas/examination_evaluation.py +27 -0
  346. endoreg_db/serializers/Frames_NICE_and_PARIS_classifications.py +775 -0
  347. endoreg_db/serializers/__init__.py +147 -10
  348. endoreg_db/serializers/{raw_pdf_meta_validation.py → _old/raw_pdf_meta_validation.py} +3 -3
  349. endoreg_db/serializers/{raw_video_meta_validation.py → _old/raw_video_meta_validation.py} +18 -14
  350. endoreg_db/serializers/_old/video.py +71 -0
  351. endoreg_db/serializers/administration/__init__.py +14 -0
  352. endoreg_db/serializers/administration/ai/__init__.py +10 -0
  353. endoreg_db/serializers/administration/ai/active_model.py +10 -0
  354. endoreg_db/serializers/administration/ai/ai_model.py +18 -0
  355. endoreg_db/serializers/administration/ai/model_type.py +10 -0
  356. endoreg_db/serializers/administration/center.py +9 -0
  357. endoreg_db/serializers/administration/gender.py +9 -0
  358. endoreg_db/serializers/anonymization.py +66 -0
  359. endoreg_db/serializers/evaluation/examination_evaluation.py +1 -0
  360. endoreg_db/serializers/examination/__init__.py +10 -0
  361. endoreg_db/serializers/examination/base.py +46 -0
  362. endoreg_db/serializers/examination/dropdown.py +21 -0
  363. endoreg_db/serializers/examination_serializer.py +12 -0
  364. endoreg_db/serializers/finding/__init__.py +5 -0
  365. endoreg_db/serializers/finding/finding.py +54 -0
  366. endoreg_db/serializers/finding_classification/__init__.py +7 -0
  367. endoreg_db/serializers/finding_classification/choice.py +19 -0
  368. endoreg_db/serializers/finding_classification/classification.py +13 -0
  369. endoreg_db/serializers/label/__init__.py +7 -0
  370. endoreg_db/serializers/label/image_classification_annotation.py +62 -0
  371. endoreg_db/serializers/label/label.py +15 -0
  372. endoreg_db/serializers/label_video_segment/__init__.py +7 -0
  373. endoreg_db/serializers/label_video_segment/_lvs_create.py +149 -0
  374. endoreg_db/serializers/label_video_segment/_lvs_update.py +138 -0
  375. endoreg_db/serializers/label_video_segment/_lvs_validate.py +149 -0
  376. endoreg_db/serializers/label_video_segment/label_video_segment.py +344 -0
  377. endoreg_db/serializers/label_video_segment/label_video_segment_annotation.py +99 -0
  378. endoreg_db/serializers/label_video_segment/label_video_segment_update.py +163 -0
  379. endoreg_db/serializers/meta/__init__.py +19 -0
  380. endoreg_db/serializers/meta/pdf_file_meta_extraction.py +115 -0
  381. endoreg_db/serializers/meta/report_meta.py +53 -0
  382. endoreg_db/serializers/meta/sensitive_meta_detail.py +162 -0
  383. endoreg_db/serializers/meta/sensitive_meta_update.py +148 -0
  384. endoreg_db/serializers/meta/sensitive_meta_verification.py +59 -0
  385. endoreg_db/serializers/meta/video_meta.py +39 -0
  386. endoreg_db/serializers/misc/__init__.py +14 -0
  387. endoreg_db/serializers/misc/file_overview.py +152 -0
  388. endoreg_db/serializers/misc/stats.py +33 -0
  389. endoreg_db/serializers/misc/translatable_field_mix_in.py +44 -0
  390. endoreg_db/serializers/misc/upload_job.py +71 -0
  391. endoreg_db/serializers/misc/vop_patient_data.py +120 -0
  392. endoreg_db/serializers/patient/__init__.py +11 -0
  393. endoreg_db/serializers/patient/patient.py +86 -0
  394. endoreg_db/serializers/patient/patient_dropdown.py +27 -0
  395. endoreg_db/serializers/patient_examination/__init__.py +7 -0
  396. endoreg_db/serializers/patient_examination/patient_examination.py +141 -0
  397. endoreg_db/serializers/patient_finding/__init__.py +15 -0
  398. endoreg_db/serializers/patient_finding/patient_finding.py +31 -0
  399. endoreg_db/serializers/patient_finding/patient_finding_classification.py +39 -0
  400. endoreg_db/serializers/patient_finding/patient_finding_detail.py +53 -0
  401. endoreg_db/serializers/patient_finding/patient_finding_intervention.py +26 -0
  402. endoreg_db/serializers/patient_finding/patient_finding_list.py +41 -0
  403. endoreg_db/serializers/patient_finding/patient_finding_write.py +126 -0
  404. endoreg_db/serializers/pdf/__init__.py +5 -0
  405. endoreg_db/serializers/pdf/anony_text_validation.py +85 -0
  406. endoreg_db/serializers/report/__init__.py +9 -0
  407. endoreg_db/serializers/report/mixins.py +45 -0
  408. endoreg_db/serializers/report/report.py +105 -0
  409. endoreg_db/serializers/report/report_list.py +22 -0
  410. endoreg_db/serializers/report/secure_file_url.py +26 -0
  411. endoreg_db/serializers/requirements/requirement_schema.py +25 -0
  412. endoreg_db/serializers/requirements/requirement_sets.py +29 -0
  413. endoreg_db/serializers/sensitive_meta_serializer.py +282 -0
  414. endoreg_db/serializers/video/__init__.py +7 -0
  415. endoreg_db/serializers/video/segmentation.py +263 -0
  416. endoreg_db/serializers/video/video_file_brief.py +10 -0
  417. endoreg_db/serializers/video/video_file_detail.py +83 -0
  418. endoreg_db/serializers/video/video_file_list.py +67 -0
  419. endoreg_db/serializers/video/video_metadata.py +105 -0
  420. endoreg_db/serializers/video/video_processing_history.py +153 -0
  421. endoreg_db/services/__init__.py +5 -0
  422. endoreg_db/services/anonymization.py +223 -0
  423. endoreg_db/services/examination_evaluation.py +149 -0
  424. endoreg_db/services/finding_description_service.py +0 -0
  425. endoreg_db/services/lookup_service.py +241 -0
  426. endoreg_db/services/lookup_store.py +122 -0
  427. endoreg_db/services/ollama_api_docs.py +1528 -0
  428. endoreg_db/services/pdf_import.py +993 -0
  429. endoreg_db/services/polling_coordinator.py +288 -0
  430. endoreg_db/services/pseudonym_service.py +89 -0
  431. endoreg_db/services/requirements_object.py +147 -0
  432. endoreg_db/services/segment_sync.py +155 -0
  433. endoreg_db/services/storage_aware_video_processor.py +344 -0
  434. endoreg_db/services/video_import.py +915 -0
  435. endoreg_db/tasks/upload_tasks.py +207 -0
  436. endoreg_db/tasks/video_ingest.py +157 -0
  437. endoreg_db/tasks/video_processing_tasks.py +327 -0
  438. endoreg_db/urls/__init__.py +72 -0
  439. endoreg_db/urls/anonymization.py +32 -0
  440. endoreg_db/urls/auth.py +16 -0
  441. endoreg_db/urls/classification.py +39 -0
  442. endoreg_db/urls/examination.py +54 -0
  443. endoreg_db/urls/files.py +6 -0
  444. endoreg_db/urls/label_video_segment_validate.py +33 -0
  445. endoreg_db/urls/label_video_segments.py +44 -0
  446. endoreg_db/urls/media.py +32 -0
  447. endoreg_db/urls/patient.py +19 -0
  448. endoreg_db/urls/pdf.py +0 -0
  449. endoreg_db/urls/report.py +78 -0
  450. endoreg_db/urls/requirements.py +13 -0
  451. endoreg_db/urls/sensitive_meta.py +36 -0
  452. endoreg_db/urls/stats.py +46 -0
  453. endoreg_db/urls/upload.py +20 -0
  454. endoreg_db/urls/video.py +119 -0
  455. endoreg_db/urls.py +6 -283
  456. endoreg_db/utils/__init__.py +66 -57
  457. endoreg_db/utils/ai/__init__.py +9 -0
  458. endoreg_db/{models/ai_model/utils.py → utils/ai/get.py} +1 -4
  459. endoreg_db/{models/ai_model/lightning → utils/ai}/inference_dataset.py +0 -1
  460. endoreg_db/{models/ai_model/lightning → utils/ai}/multilabel_classification_net.py +14 -10
  461. endoreg_db/{models/ai_model/lightning → utils/ai}/postprocess.py +15 -5
  462. endoreg_db/utils/ai/predict.py +291 -0
  463. endoreg_db/{models/ai_model/lightning → utils/ai}/preprocess.py +1 -1
  464. endoreg_db/utils/calc_duration_seconds.py +24 -0
  465. endoreg_db/utils/case_generator/__init__.py +0 -0
  466. endoreg_db/utils/check_video_files.py +148 -0
  467. endoreg_db/utils/dataloader.py +50 -12
  468. endoreg_db/utils/dates.py +21 -0
  469. endoreg_db/utils/env.py +33 -0
  470. endoreg_db/utils/extract_specific_frames.py +72 -0
  471. endoreg_db/utils/file_operations.py +29 -1
  472. endoreg_db/utils/fix_video_path_direct.py +141 -0
  473. endoreg_db/utils/frame_anonymization_utils.py +463 -0
  474. endoreg_db/utils/links/__init__.py +0 -0
  475. endoreg_db/utils/links/requirement_link.py +193 -0
  476. endoreg_db/utils/mime_types.py +0 -0
  477. endoreg_db/utils/names.py +2 -0
  478. endoreg_db/utils/paths.py +100 -82
  479. endoreg_db/utils/permissions.py +143 -0
  480. endoreg_db/utils/pipelines/Readme.md +235 -0
  481. endoreg_db/utils/pipelines/__init__.py +0 -0
  482. endoreg_db/utils/pipelines/process_video_dir.py +120 -0
  483. endoreg_db/utils/product/__init__.py +0 -0
  484. endoreg_db/utils/product/sum_emissions.py +20 -0
  485. endoreg_db/utils/product/sum_weights.py +18 -0
  486. endoreg_db/utils/pydantic_models/db_config.py +1 -1
  487. endoreg_db/utils/requirement_helpers.py +0 -0
  488. endoreg_db/utils/requirement_operator_logic/__init__.py +0 -0
  489. endoreg_db/utils/requirement_operator_logic/lab_value_operators.py +578 -0
  490. endoreg_db/utils/requirement_operator_logic/model_evaluators.py +368 -0
  491. endoreg_db/utils/translation.py +27 -0
  492. endoreg_db/utils/validate_video_detailed.py +357 -0
  493. endoreg_db/utils/video/__init__.py +19 -6
  494. endoreg_db/utils/video/extract_frames.py +37 -70
  495. endoreg_db/utils/video/ffmpeg_wrapper.py +772 -0
  496. endoreg_db/utils/video/names.py +42 -0
  497. endoreg_db/utils/video/streaming_processor.py +312 -0
  498. endoreg_db/utils/video/video_splitter.py +94 -0
  499. endoreg_db/views/Frames_NICE_and_PARIS_classifications_views.py +238 -0
  500. endoreg_db/views/__init__.py +282 -2
  501. endoreg_db/views/anonymization/__init__.py +27 -0
  502. endoreg_db/views/anonymization/media_management.py +454 -0
  503. endoreg_db/views/anonymization/overview.py +216 -0
  504. endoreg_db/views/anonymization/validate.py +63 -0
  505. endoreg_db/views/auth/__init__.py +13 -0
  506. endoreg_db/views/{views.py → auth/keycloak.py} +19 -13
  507. endoreg_db/views/examination/__init__.py +33 -0
  508. endoreg_db/views/examination/examination.py +37 -0
  509. endoreg_db/views/examination/examination_manifest_cache.py +26 -0
  510. endoreg_db/views/examination/get_finding_classification_choices.py +59 -0
  511. endoreg_db/views/examination/get_finding_classifications.py +36 -0
  512. endoreg_db/views/examination/get_findings.py +41 -0
  513. endoreg_db/views/examination/get_instruments.py +18 -0
  514. endoreg_db/views/examination/get_interventions.py +14 -0
  515. endoreg_db/views/finding/__init__.py +9 -0
  516. endoreg_db/views/finding/finding.py +112 -0
  517. endoreg_db/views/finding/get_classifications.py +14 -0
  518. endoreg_db/views/finding/get_interventions.py +17 -0
  519. endoreg_db/views/finding_classification/__init__.py +13 -0
  520. endoreg_db/views/finding_classification/base.py +0 -0
  521. endoreg_db/views/finding_classification/finding_classification.py +42 -0
  522. endoreg_db/views/finding_classification/get_classification_choices.py +55 -0
  523. endoreg_db/views/label/__init__.py +5 -0
  524. endoreg_db/views/label/label.py +15 -0
  525. endoreg_db/views/label_video_segment/__init__.py +16 -0
  526. endoreg_db/views/label_video_segment/create_lvs_from_annotation.py +44 -0
  527. endoreg_db/views/label_video_segment/get_lvs_by_name_and_video.py +50 -0
  528. endoreg_db/views/label_video_segment/label_video_segment.py +77 -0
  529. endoreg_db/views/label_video_segment/label_video_segment_by_label.py +174 -0
  530. endoreg_db/views/label_video_segment/label_video_segment_detail.py +73 -0
  531. endoreg_db/views/label_video_segment/update_lvs_from_annotation.py +46 -0
  532. endoreg_db/views/label_video_segment/validate.py +226 -0
  533. endoreg_db/views/media/__init__.py +9 -0
  534. endoreg_db/views/media/pdf_media.py +386 -0
  535. endoreg_db/views/media/video_media.py +272 -0
  536. endoreg_db/views/meta/__init__.py +15 -0
  537. endoreg_db/views/meta/available_files_list.py +146 -0
  538. endoreg_db/views/meta/report_meta.py +53 -0
  539. endoreg_db/views/meta/sensitive_meta_detail.py +148 -0
  540. endoreg_db/views/meta/sensitive_meta_list.py +104 -0
  541. endoreg_db/views/meta/sensitive_meta_verification.py +71 -0
  542. endoreg_db/views/misc/__init__.py +63 -0
  543. endoreg_db/views/misc/center.py +13 -0
  544. endoreg_db/views/misc/gender.py +14 -0
  545. endoreg_db/views/misc/secure_file_serving_view.py +80 -0
  546. endoreg_db/views/misc/secure_file_url_view.py +84 -0
  547. endoreg_db/views/misc/secure_url_validate.py +79 -0
  548. endoreg_db/views/misc/stats.py +220 -0
  549. endoreg_db/views/misc/translation.py +182 -0
  550. endoreg_db/views/misc/upload_views.py +240 -0
  551. endoreg_db/views/patient/__init__.py +5 -0
  552. endoreg_db/views/patient/patient.py +210 -0
  553. endoreg_db/views/patient_examination/DEPRECATED_video_backup.py +164 -0
  554. endoreg_db/views/patient_examination/__init__.py +11 -0
  555. endoreg_db/views/patient_examination/patient_examination.py +140 -0
  556. endoreg_db/views/patient_examination/patient_examination_create.py +63 -0
  557. endoreg_db/views/patient_examination/patient_examination_detail.py +66 -0
  558. endoreg_db/views/patient_examination/patient_examination_list.py +68 -0
  559. endoreg_db/views/patient_examination/video.py +194 -0
  560. endoreg_db/views/patient_finding/__init__.py +7 -0
  561. endoreg_db/views/patient_finding/base.py +0 -0
  562. endoreg_db/views/patient_finding/patient_finding.py +64 -0
  563. endoreg_db/views/patient_finding/patient_finding_optimized.py +259 -0
  564. endoreg_db/views/patient_finding_classification/__init__.py +5 -0
  565. endoreg_db/views/patient_finding_classification/pfc_create.py +67 -0
  566. endoreg_db/views/patient_finding_location/__init__.py +5 -0
  567. endoreg_db/views/patient_finding_location/pfl_create.py +70 -0
  568. endoreg_db/views/patient_finding_morphology/__init__.py +5 -0
  569. endoreg_db/views/patient_finding_morphology/pfm_create.py +70 -0
  570. endoreg_db/views/pdf/__init__.py +11 -0
  571. endoreg_db/views/pdf/pdf_media.py +239 -0
  572. endoreg_db/views/pdf/pdf_stream_views.py +127 -0
  573. endoreg_db/views/pdf/reimport.py +151 -0
  574. endoreg_db/views/report/__init__.py +9 -0
  575. endoreg_db/views/report/report_list.py +112 -0
  576. endoreg_db/views/report/report_with_secure_url.py +28 -0
  577. endoreg_db/views/report/start_examination.py +7 -0
  578. endoreg_db/views/requirement/__init__.py +10 -0
  579. endoreg_db/views/requirement/evaluate.py +279 -0
  580. endoreg_db/views/requirement/lookup.py +483 -0
  581. endoreg_db/views/requirement/lookup_store.py +252 -0
  582. endoreg_db/views/requirement_lookup/lookup.py +0 -0
  583. endoreg_db/views/requirement_lookup/lookup_store.py +0 -0
  584. endoreg_db/views/stats/__init__.py +13 -0
  585. endoreg_db/views/stats/stats_views.py +229 -0
  586. endoreg_db/views/video/__init__.py +72 -0
  587. endoreg_db/views/video/correction.py +672 -0
  588. endoreg_db/views/video/media/__init__.py +23 -0
  589. endoreg_db/views/video/media/task_status.py +49 -0
  590. endoreg_db/views/video/media/video_analyze.py +52 -0
  591. endoreg_db/views/video/media/video_apply_mask.py +48 -0
  592. endoreg_db/views/video/media/video_correction.py +21 -0
  593. endoreg_db/views/video/media/video_download_processed.py +58 -0
  594. endoreg_db/views/video/media/video_media.py +158 -0
  595. endoreg_db/views/video/media/video_meta.py +29 -0
  596. endoreg_db/views/video/media/video_processing_history.py +24 -0
  597. endoreg_db/views/video/media/video_remove_frames.py +48 -0
  598. endoreg_db/views/video/media/video_reprocess.py +40 -0
  599. endoreg_db/views/video/reimport.py +192 -0
  600. endoreg_db/views/video/segmentation.py +274 -0
  601. endoreg_db/views/{views_for_timeline.py → video/timeline.py} +3 -3
  602. endoreg_db/views/video/video_examination_viewset.py +329 -0
  603. endoreg_db/views/video/video_stream.py +188 -0
  604. endoreg_db-0.8.1.dist-info/METADATA +384 -0
  605. endoreg_db-0.8.1.dist-info/RECORD +789 -0
  606. endoreg_db/data/agl_service/data.yaml +0 -19
  607. endoreg_db/data/finding_location_classification/colonoscopy.yaml +0 -46
  608. endoreg_db/data/finding_morphology_classification/colonoscopy.yaml +0 -48
  609. endoreg_db/data/finding_morphology_classification_choice/colonoscopy_size.yaml +0 -57
  610. endoreg_db/management/commands/_load_model_template.py +0 -41
  611. endoreg_db/management/commands/delete_all.py +0 -18
  612. endoreg_db/management/commands/fetch_legacy_image_dataset.py +0 -32
  613. endoreg_db/management/commands/fix_auth_permission.py +0 -20
  614. endoreg_db/management/commands/load_active_model_data.py +0 -45
  615. endoreg_db/management/commands/load_g_play_data.py +0 -113
  616. endoreg_db/management/commands/load_logging_data.py +0 -39
  617. endoreg_db/management/commands/load_lx_data.py +0 -64
  618. endoreg_db/management/commands/load_medication_indication_data.py +0 -63
  619. endoreg_db/management/commands/load_medication_indication_type_data.py +0 -41
  620. endoreg_db/management/commands/load_medication_intake_time_data.py +0 -41
  621. endoreg_db/management/commands/load_medication_schedule_data.py +0 -55
  622. endoreg_db/management/commands/load_network_data.py +0 -57
  623. endoreg_db/migrations/0002_alter_frame_image_alter_rawframe_image.py +0 -23
  624. endoreg_db/migrations/0003_alter_frame_image_alter_rawframe_image.py +0 -23
  625. endoreg_db/migrations/0004_alter_rawvideofile_file_alter_video_file.py +0 -25
  626. endoreg_db/migrations/0005_rawvideofile_frame_count_and_more.py +0 -33
  627. endoreg_db/migrations/0006_frame_extracted_rawframe_extracted.py +0 -23
  628. endoreg_db/migrations/0007_rename_pseudo_patient_video_patient_and_more.py +0 -24
  629. endoreg_db/migrations/0008_remove_reportfile_patient_examination_and_more.py +0 -48
  630. endoreg_db/migrations/0009_requirementoperator_requirementsettype_and_more.py +0 -154
  631. endoreg_db/models/ai_model/active_model.py +0 -9
  632. endoreg_db/models/ai_model/ai_model.py +0 -90
  633. endoreg_db/models/ai_model/lightning/__init__.py +0 -3
  634. endoreg_db/models/ai_model/lightning/predict.py +0 -172
  635. endoreg_db/models/ai_model/lightning/prediction_visualizer.py +0 -55
  636. endoreg_db/models/ai_model/lightning/run_visualizer.py +0 -21
  637. endoreg_db/models/ai_model/model_meta.py +0 -240
  638. endoreg_db/models/annotation/__init__.py +0 -32
  639. endoreg_db/models/annotation/anonymized_image_annotation.py +0 -115
  640. endoreg_db/models/annotation/binary_classification_annotation_task.py +0 -117
  641. endoreg_db/models/annotation/image_classification.py +0 -86
  642. endoreg_db/models/annotation/video_segmentation_annotation.py +0 -52
  643. endoreg_db/models/case/__init__.py +0 -1
  644. endoreg_db/models/case/case.py +0 -34
  645. endoreg_db/models/center/center.py +0 -51
  646. endoreg_db/models/center/center_product.py +0 -33
  647. endoreg_db/models/center/center_waste.py +0 -16
  648. endoreg_db/models/data_file/__init__.py +0 -39
  649. endoreg_db/models/data_file/base_classes/__init__.py +0 -7
  650. endoreg_db/models/data_file/base_classes/abstract_frame.py +0 -98
  651. endoreg_db/models/data_file/base_classes/abstract_pdf.py +0 -127
  652. endoreg_db/models/data_file/base_classes/abstract_video.py +0 -806
  653. endoreg_db/models/data_file/base_classes/frame_helpers.py +0 -17
  654. endoreg_db/models/data_file/base_classes/prepare_bulk_frames.py +0 -19
  655. endoreg_db/models/data_file/base_classes/utils.py +0 -58
  656. endoreg_db/models/data_file/frame.py +0 -29
  657. endoreg_db/models/data_file/import_classes/__init__.py +0 -18
  658. endoreg_db/models/data_file/import_classes/processing_functions/__init__.py +0 -35
  659. endoreg_db/models/data_file/import_classes/processing_functions/pdf.py +0 -28
  660. endoreg_db/models/data_file/import_classes/processing_functions/video.py +0 -260
  661. endoreg_db/models/data_file/import_classes/raw_pdf.py +0 -254
  662. endoreg_db/models/data_file/import_classes/raw_video.py +0 -290
  663. endoreg_db/models/data_file/metadata/sensitive_meta.py +0 -290
  664. endoreg_db/models/data_file/metadata/video_meta.py +0 -199
  665. endoreg_db/models/data_file/report_file.py +0 -56
  666. endoreg_db/models/data_file/video/__init__.py +0 -11
  667. endoreg_db/models/data_file/video/import_meta.py +0 -25
  668. endoreg_db/models/data_file/video/video.py +0 -196
  669. endoreg_db/models/data_file/video_segment.py +0 -214
  670. endoreg_db/models/examination/examination.py +0 -67
  671. endoreg_db/models/finding/__init__.py +0 -11
  672. endoreg_db/models/finding/finding.py +0 -75
  673. endoreg_db/models/finding/finding_location_classification.py +0 -94
  674. endoreg_db/models/finding/finding_morphology_classification.py +0 -89
  675. endoreg_db/models/finding/finding_type.py +0 -22
  676. endoreg_db/models/hardware/__init__.py +0 -2
  677. endoreg_db/models/information_source.py +0 -65
  678. endoreg_db/models/laboratory/__init__.py +0 -1
  679. endoreg_db/models/laboratory/lab_value.py +0 -162
  680. endoreg_db/models/logging/__init__.py +0 -11
  681. endoreg_db/models/logging/agl_service.py +0 -19
  682. endoreg_db/models/logging/base.py +0 -22
  683. endoreg_db/models/logging/log_type.py +0 -23
  684. endoreg_db/models/logging/network_device.py +0 -27
  685. endoreg_db/models/lx/__init__.py +0 -4
  686. endoreg_db/models/lx/client.py +0 -57
  687. endoreg_db/models/lx/identity.py +0 -34
  688. endoreg_db/models/lx/permission.py +0 -18
  689. endoreg_db/models/lx/user.py +0 -16
  690. endoreg_db/models/network/__init__.py +0 -9
  691. endoreg_db/models/network/agl_service.py +0 -38
  692. endoreg_db/models/network/network_device.py +0 -58
  693. endoreg_db/models/network/network_device_type.py +0 -23
  694. endoreg_db/models/other/distribution.py +0 -5
  695. endoreg_db/models/patient/__init__.py +0 -24
  696. endoreg_db/models/patient/patient_examination.py +0 -182
  697. endoreg_db/models/patient/patient_finding.py +0 -143
  698. endoreg_db/models/patient/patient_finding_location.py +0 -120
  699. endoreg_db/models/patient/patient_finding_morphology.py +0 -166
  700. endoreg_db/models/permissions/__init__.py +0 -44
  701. endoreg_db/models/persons/__init__.py +0 -34
  702. endoreg_db/models/persons/examiner/__init__.py +0 -2
  703. endoreg_db/models/persons/examiner/examiner.py +0 -60
  704. endoreg_db/models/persons/examiner/examiner_type.py +0 -2
  705. endoreg_db/models/persons/patient/__init__.py +0 -8
  706. endoreg_db/models/persons/patient/patient.py +0 -389
  707. endoreg_db/models/persons/patient/patient_disease.py +0 -22
  708. endoreg_db/models/persons/patient/patient_event.py +0 -52
  709. endoreg_db/models/persons/patient/patient_lab_sample.py +0 -108
  710. endoreg_db/models/persons/patient/patient_medication.py +0 -59
  711. endoreg_db/models/persons/patient/patient_medication_schedule.py +0 -88
  712. endoreg_db/models/persons/portal_user_information.py +0 -27
  713. endoreg_db/models/prediction/__init__.py +0 -8
  714. endoreg_db/models/prediction/image_classification.py +0 -51
  715. endoreg_db/models/prediction/video_prediction_meta.py +0 -306
  716. endoreg_db/models/product/product.py +0 -110
  717. endoreg_db/models/product/product_group.py +0 -27
  718. endoreg_db/models/product/product_material.py +0 -28
  719. endoreg_db/models/questionnaires/__init__.py +0 -114
  720. endoreg_db/models/quiz/__init__.py +0 -9
  721. endoreg_db/models/quiz/quiz_answer.py +0 -41
  722. endoreg_db/models/quiz/quiz_question.py +0 -54
  723. endoreg_db/models/report_reader/report_reader_config.py +0 -53
  724. endoreg_db/models/rules/__init__.py +0 -5
  725. endoreg_db/queries/get/__init__.py +0 -6
  726. endoreg_db/queries/get/center.py +0 -42
  727. endoreg_db/queries/get/model.py +0 -13
  728. endoreg_db/queries/get/patient.py +0 -14
  729. endoreg_db/queries/get/patient_examination.py +0 -20
  730. endoreg_db/queries/get/report_file.py +0 -33
  731. endoreg_db/queries/get/video.py +0 -31
  732. endoreg_db/serializers/ai_model.py +0 -19
  733. endoreg_db/serializers/annotation.py +0 -14
  734. endoreg_db/serializers/center.py +0 -11
  735. endoreg_db/serializers/examination.py +0 -33
  736. endoreg_db/serializers/frame.py +0 -9
  737. endoreg_db/serializers/hardware.py +0 -21
  738. endoreg_db/serializers/label.py +0 -22
  739. endoreg_db/serializers/patient.py +0 -33
  740. endoreg_db/serializers/prediction.py +0 -10
  741. endoreg_db/serializers/raw_pdf_anony_text_validation.py +0 -137
  742. endoreg_db/serializers/report_file.py +0 -7
  743. endoreg_db/serializers/video.py +0 -20
  744. endoreg_db/serializers/video_segmentation.py +0 -574
  745. endoreg_db/tests.py +0 -3
  746. endoreg_db/utils/legacy_ocr.py +0 -201
  747. endoreg_db/utils/video/transcode_videofile.py +0 -111
  748. endoreg_db/views/patient_views.py +0 -90
  749. endoreg_db/views/raw_pdf_anony_text_validation_views.py +0 -95
  750. endoreg_db/views/raw_pdf_meta_validation_views.py +0 -111
  751. endoreg_db/views/raw_video_meta_validation_views.py +0 -148
  752. endoreg_db/views/report_views.py +0 -96
  753. endoreg_db/views/video_segmentation_views.py +0 -166
  754. endoreg_db-0.6.4.dist-info/METADATA +0 -161
  755. endoreg_db-0.6.4.dist-info/RECORD +0 -470
  756. /endoreg_db/{case_generator/__init__.py → api/serializers/finding_descriptions.py} +0 -0
  757. /endoreg_db/{queries/get/annotation.py → api/views/finding_descriptions.py} +0 -0
  758. /endoreg_db/{queries/get/prediction.py → data/shift/m2.yaml} +0 -0
  759. /endoreg_db/{queries/get/video_import_meta.py → factories/__init__.py} +0 -0
  760. /endoreg_db/{queries/get/video_prediction_meta.py → helpers/__init__.py} +0 -0
  761. /endoreg_db/models/{case_template → administration/case/case_template}/__init__.py +0 -0
  762. /endoreg_db/models/{persons → administration/person}/person.py +0 -0
  763. /endoreg_db/models/{product → administration/product}/__init__.py +0 -0
  764. /endoreg_db/models/{report_reader → media/pdf/report_reader}/__init__.py +0 -0
  765. /endoreg_db/models/{report_reader → media/pdf/report_reader}/report_reader_flag.py +0 -0
  766. /endoreg_db/models/{hardware → medical/hardware}/endoscopy_processor.py +0 -0
  767. /endoreg_db/models/{medication → medical/medication}/__init__.py +0 -0
  768. /endoreg_db/models/{medication → medical/medication}/medication_indication.py +0 -0
  769. /endoreg_db/models/{risk → medical/risk}/__init__.py +0 -0
  770. /endoreg_db/models/{risk → medical/risk}/risk.py +0 -0
  771. /endoreg_db/models/{emission → other/emission}/__init__.py +0 -0
  772. /endoreg_db/models/{rules → rule}/rule_applicator.py +0 -0
  773. /endoreg_db/{case_generator → utils/case_generator}/case_generator.py +0 -0
  774. /endoreg_db/{case_generator → utils/case_generator}/lab_sample_factory.py +0 -0
  775. /endoreg_db/{case_generator → utils/case_generator}/utils.py +0 -0
  776. /endoreg_db/views/{csrf.py → misc/csrf.py} +0 -0
  777. {endoreg_db-0.6.4.dist-info → endoreg_db-0.8.1.dist-info}/WHEEL +0 -0
  778. {endoreg_db-0.6.4.dist-info → endoreg_db-0.8.1.dist-info}/licenses/LICENSE +0 -0
endoreg_db/data/{finding_location_classification_choice/colonoscopy.yaml → finding_classification_choice/colonoscopy_location.yaml} RENAMED
@@ -1,9 +1,8 @@
1
- - model: endoreg_db.finding_location_classification_choice
1
+ - model: endoreg_db.finding_classification_choice
2
2
  fields:
3
3
  name: "terminal_ileum"
4
4
  name_de: "terminales Ileum"
5
5
  name_en: "Terminal Ileum"
6
- organs: ["ileum"]
7
6
  subcategories:
8
7
  description: {
9
8
  choices: ["unspecified"],
@@ -17,12 +16,11 @@
17
16
  description: "Insertion depth of the colonoscope in cm (rectified)"
18
17
  required: false
19
18
 
20
- - model: endoreg_db.finding_location_classification_choice
19
+ - model: endoreg_db.finding_classification_choice
21
20
  fields:
22
21
  name: "cecum"
23
22
  name_de: "Caecum"
24
23
  name_en: "Cecum"
25
- organs: ["colon"]
26
24
  subcategories:
27
25
  description:
28
26
  choices: ["unspecified", "ileocecal-valve", "peri-appendicular"]
@@ -40,12 +38,11 @@
40
38
  description: "Insertion depth of the colonoscope in cm (rectified)"
41
39
  required: false
42
40
 
43
- - model: endoreg_db.finding_location_classification_choice
41
+ - model: endoreg_db.finding_classification_choice
44
42
  fields:
45
43
  name: "ascending_colon"
46
44
  name_de: "Colon ascendens"
47
45
  name_en: "Ascending Colon"
48
- organs: ["colon"]
49
46
  subcategories:
50
47
  description:
51
48
  choices: ["unspecified", "proximal", "distal"]
@@ -61,12 +58,11 @@
61
58
  description: "Insertion depth of the colonoscope in cm (rectified)"
62
59
  required: false
63
60
 
64
- - model: endoreg_db.finding_location_classification_choice
61
+ - model: endoreg_db.finding_classification_choice
65
62
  fields:
66
63
  name: "right_flexure"
67
64
  name_de: "Rechte Flexur"
68
65
  name_en: "Right Flexure"
69
- organs: ["colon"]
70
66
  subcategories:
71
67
  description:
72
68
  choices: ["unspecified", "proximal", "distal"]
@@ -84,12 +80,11 @@
84
80
  description: "Insertion depth of the colonoscope in cm (rectified)"
85
81
  required: false
86
82
 
87
- - model: endoreg_db.finding_location_classification_choice
83
+ - model: endoreg_db.finding_classification_choice
88
84
  fields:
89
85
  name: "transverse_colon"
90
86
  name_de: "Colon transversum"
91
87
  name_en: "Transverse Colon"
92
- organs: ["colon"]
93
88
  subcategories:
94
89
  description:
95
90
  choices: ["unspecified", "proximal", "distal"]
@@ -107,12 +102,11 @@
107
102
  description: "Insertion depth of the colonoscope in cm (rectified)"
108
103
  required: false
109
104
 
110
- - model: endoreg_db.finding_location_classification_choice
105
+ - model: endoreg_db.finding_classification_choice
111
106
  fields:
112
107
  name: "descending_colon"
113
108
  name_de: "Colon descendens"
114
109
  name_en: "Descending Colon"
115
- organs: ["colon"]
116
110
  subcategories:
117
111
  description:
118
112
  choices: ["unspecified", "proximal", "distal"]
@@ -130,12 +124,11 @@
130
124
  description: "Insertion depth of the colonoscope in cm (rectified)"
131
125
  required: false
132
126
 
133
- - model: endoreg_db.finding_location_classification_choice
127
+ - model: endoreg_db.finding_classification_choice
134
128
  fields:
135
129
  name: "sigmoid_colon"
136
130
  name_de: "Colon sigmoideum"
137
131
  name_en: "Sigmoid Colon"
138
- organs: ["colon"]
139
132
  subcategories:
140
133
  description:
141
134
  choices: ["unspecified", "proximal", "distal"]
@@ -150,12 +143,11 @@
150
143
  description: "Insertion depth of the colonoscope in cm (rectified)"
151
144
  required: true
152
145
 
153
- - model: endoreg_db.finding_location_classification_choice
146
+ - model: endoreg_db.finding_classification_choice
154
147
  fields:
155
148
  name: "rectum"
156
149
  name_de: "Rektum"
157
150
  name_en: "Rectum"
158
- organs: ["rectum"]
159
151
  subcategories:
160
152
  description:
161
153
  choices: ["1/3", "2/3", "3/3"]
@@ -170,12 +162,11 @@
170
162
  description: "Insertion depth of the colonoscope in cm (rectified)"
171
163
  required: true
172
164
 
173
- - model: endoreg_db.finding_location_classification_choice
165
+ - model: endoreg_db.finding_classification_choice
174
166
  fields:
175
167
  name: "anal_canal"
176
168
  name_de: "Analkanal"
177
169
  name_en: "Anal Canal"
178
- organs: ["rectum"]
179
170
  subcategories:
180
171
  description:
181
172
  choices: ["unspecified", "proximal", "distal"]
@@ -193,12 +184,11 @@
193
184
  description: "Insertion depth of the colonoscope in cm (rectified)"
194
185
  required: true
195
186
 
196
- - model: endoreg_db.finding_location_classification_choice
187
+ - model: endoreg_db.finding_classification_choice
197
188
  fields:
198
189
  name: "left_colon"
199
190
  name_de: "linkes Kolon"
200
191
  name_en: "Left Colon"
201
- organs: ["colon"]
202
192
  subcategories:
203
193
  description:
204
194
  choices: ["unspecified", "proximal", "distal"]
@@ -216,12 +206,11 @@
216
206
  description: "Insertion depth of the colonoscope in cm (rectified)"
217
207
  required: false
218
208
 
219
- - model: endoreg_db.finding_location_classification_choice
209
+ - model: endoreg_db.finding_classification_choice
220
210
  fields:
221
211
  name: "right_colon"
222
212
  name_de: "rechtes Kolon"
223
213
  name_en: "Right Colon"
224
- organs: ["colon"]
225
214
  subcategories:
226
215
  description:
227
216
  choices: ["unspecified", "proximal", "distal"]
endoreg_db/data/finding_classification_choice/colonoscopy_not_complete_reason.yaml ADDED
@@ -0,0 +1,19 @@
1
+ - model: endoreg_db.finding_classification_choice
2
+ fields:
3
+ name: "colonoscopy_incomplete_insufficient_preparation"
4
+
5
+ - model: endoreg_db.finding_classification_choice
6
+ fields:
7
+ name: "colonoscopy_incomplete_complication"
8
+
9
+ - model: endoreg_db.finding_classification_choice
10
+ fields:
11
+ name: "colonoscopy_incomplete_pain"
12
+
13
+ - model: endoreg_db.finding_classification_choice
14
+ fields:
15
+ name: "colonoscopy_incomplete_stenosis"
16
+
17
+ - model: endoreg_db.finding_classification_choice
18
+ fields:
19
+ name: "colonoscopy_incomplete_other"
endoreg_db/data/finding_classification_choice/colonoscopy_size.yaml ADDED
@@ -0,0 +1,82 @@
1
+ - model: endoreg_db.finding_classification_choice
2
+ fields:
3
+ name: "colon_lesion_size_categorical_diminutive"
4
+ name_de: "Größenklassifikation Kolonläsion (kategorisch)"
5
+ name_en: "Colon Lesion Size Classification (categorical)"
6
+ description: "Diminutive (< 6 mm)"
7
+
8
+ - model: endoreg_db.finding_classification_choice
9
+ fields:
10
+ name: "colon_lesion_size_categorical_small"
11
+ name_de: "Größenklassifikation Kolonläsion (kategorisch)"
12
+ name_en: "Colon Lesion Size Classification (categorical)"
13
+ description: "Small (6 - 9 mm)"
14
+
15
+ - model: endoreg_db.finding_classification_choice
16
+ fields:
17
+ name: "colon_lesion_size_categorical_medium"
18
+ name_de: "Größenklassifikation Kolonläsion (kategorisch)"
19
+ name_en: "Colon Lesion Size Classification (categorical)"
20
+ description: "Medium (10 - 19 mm)"
21
+
22
+ - model: endoreg_db.finding_classification_choice
23
+ fields:
24
+ name: "colon_lesion_size_categorical_large"
25
+ name_de: "Größenklassifikation Kolonläsion (kategorisch)"
26
+ name_en: "Colon Lesion Size Classification (categorical)"
27
+ description: "Large (> 19 mm)"
28
+
29
+ ##########
30
+
31
+ - model: endoreg_db.finding_classification_choice
32
+ fields:
33
+ name: "colon_lesion_size_oval_mm"
34
+ name_de: "Formklassifikation Kolonläsion (kategorisch)"
35
+ name_en: "Colon Lesion Shape Classification (categorical)"
36
+ description: "oval lesions"
37
+ numerical_descriptors:
38
+ largest_diameter_mm:
39
+ unit: "mm"
40
+ min: 0
41
+ max: 35
42
+ distribution: "normal"
43
+ mean: 5
44
+ std: 3
45
+ description: "Largest diameter of the lesion in mm"
46
+ required: true
47
+ perpendicular_diameter_mm:
48
+ unit: "mm"
49
+ min: 0
50
+ max: 35
51
+ description: "Perpendicular diameter of the lesion in mm"
52
+ required: false
53
+
54
+ # Austria Screening Quality Assurance
55
+ # "colon_lesion_size_austria_categorical_0_5",
56
+ # "colon_lesion_size_austria_categorical_6_9",
57
+ # "colon_lesion_size_austria_categorical_10_20",
58
+ # "colon_lesion_size_austria_categorical_21_x"
59
+ - model: endoreg_db.finding_classification_choice
60
+ fields:
61
+ name: "colon_lesion_size_austria_categorical_0_5"
62
+ name_de: "Größenklassifikation Kolonläsion (kategorisch)"
63
+ name_en: "Colon Lesion Size Classification (categorical)"
64
+ description: "0 - 5 mm"
65
+ - model: endoreg_db.finding_classification_choice
66
+ fields:
67
+ name: "colon_lesion_size_austria_categorical_6_9"
68
+ name_de: "Größenklassifikation Kolonläsion (kategorisch)"
69
+ name_en: "Colon Lesion Size Classification (categorical)"
70
+ description: "6 - 9 mm"
71
+ - model: endoreg_db.finding_classification_choice
72
+ fields:
73
+ name: "colon_lesion_size_austria_categorical_10_20"
74
+ name_de: "Größenklassifikation Kolonläsion (kategorisch)"
75
+ name_en: "Colon Lesion Size Classification (categorical)"
76
+ description: "10 - 20 mm"
77
+ - model: endoreg_db.finding_classification_choice
78
+ fields:
79
+ name: "colon_lesion_size_austria_categorical_21_x"
80
+ name_de: "Größenklassifikation Kolonläsion (kategorisch)"
81
+ name_en: "Colon Lesion Size Classification (categorical)"
82
+ description: "> 20 mm"
endoreg_db/data/finding_classification_choice/colonoscopy_summary_worst_finding.yaml ADDED
@@ -0,0 +1,15 @@
1
+ - model: endoreg_db.finding_classification_choice
2
+ fields:
3
+ name: "colonoscopy_worst_finding_polyp"
4
+
5
+ - model: endoreg_db.finding_classification_choice
6
+ fields:
7
+ name: "colonoscopy_worst_finding_rectum_cancer"
8
+
9
+ - model: endoreg_db.finding_classification_choice
10
+ fields:
11
+ name: "colonoscopy_worst_finding_colon_cancer"
12
+
13
+ - model: endoreg_db.finding_classification_choice
14
+ fields:
15
+ name: "colonoscopy_worst_finding_other"
endoreg_db/data/finding_classification_choice/complication_generic_types.yaml ADDED
@@ -0,0 +1,15 @@
1
+ - model: endoreg_db.finding_classification_choice
2
+ fields:
3
+ name: "complication_generic_type_cardiorespiratory"
4
+
5
+ - model: endoreg_db.finding_classification_choice
6
+ fields:
7
+ name: "complication_generic_type_bleeding"
8
+
9
+ - model: endoreg_db.finding_classification_choice
10
+ fields:
11
+ name: "complication_generic_type_perforation"
12
+
13
+ - model: endoreg_db.finding_classification_choice
14
+ fields:
15
+ name: "complication_generic_type_other"
endoreg_db/data/finding_classification_choice/examination_setting_generic_types.yaml ADDED
@@ -0,0 +1,15 @@
1
+ - model: endoreg_db.finding_classification_choice
2
+ fields:
3
+ name: "examination_setting_generic_location_inpatient"
4
+
5
+ - model: endoreg_db.finding_classification_choice
6
+ fields:
7
+ name: "examination_setting_generic_location_outpatient"
8
+
9
+ - model: endoreg_db.finding_classification_choice
10
+ fields:
11
+ name: "examination_setting_operative"
12
+
13
+ - model: endoreg_db.finding_classification_choice
14
+ fields:
15
+ name: "examination_setting_conservative"
endoreg_db/data/finding_classification_choice/histology.yaml ADDED
@@ -0,0 +1,24 @@
1
+ # "histology_dysplasia_none",
2
+ # "histology_dysplasia_low_grade",
3
+ # "histology_dysplasia_high_grade",
4
+ - model: endoreg_db.finding_classification_choice
5
+ fields:
6
+ name: "histology_dysplasia_none"
7
+ description: "Histology: No dysplasia"
8
+ - model: endoreg_db.finding_classification_choice
9
+ fields:
10
+ name: "histology_dysplasia_low_grade"
11
+ description: "Histology: Low-grade dysplasia"
12
+ - model: endoreg_db.finding_classification_choice
13
+ fields:
14
+ name: "histology_dysplasia_high_grade"
15
+ description: "Histology: High-grade dysplasia"
16
+
17
+ - model: endoreg_db.finding_classification_choice
18
+ fields:
19
+ name: "histology_dignity_benign"
20
+ description: "Histology: Benign"
21
+ - model: endoreg_db.finding_classification_choice
22
+ fields:
23
+ name: "histology_dignity_malign"
24
+ description: "Histology: Malign"
endoreg_db/data/finding_classification_choice/histology_polyp.yaml ADDED
@@ -0,0 +1,20 @@
1
+ - model: endoreg_db.finding_classification_choice
2
+ fields:
3
+ name: "histology_polyp_hyperplastic"
4
+ description: "Histology: Hyperplastic polyp"
5
+ - model: endoreg_db.finding_classification_choice
6
+ fields:
7
+ name: "histology_polyp_adenoma_tubular"
8
+ description: "Histology: Tubular adenoma"
9
+ - model: endoreg_db.finding_classification_choice
10
+ fields:
11
+ name: "histology_polyp_adenoma_tubulovillous"
12
+ description: "Histology: Tubulovillous adenoma"
13
+ - model: endoreg_db.finding_classification_choice
14
+ fields:
15
+ name: "histology_polyp_adenoma_villous"
16
+ description: "Histology: Villous adenoma"
17
+ - model: endoreg_db.finding_classification_choice
18
+ fields:
19
+ name: "histology_polyp_sessile_serrated_lesion"
20
+ description: "Histology: Sessile serrated lesion"
endoreg_db/data/finding_classification_choice/outcome.yaml ADDED
@@ -0,0 +1,19 @@
1
+ - model: endoreg_db.finding_classification_choice
2
+ fields:
3
+ name: "outcome_restitutio_ad_integrum"
4
+ description: "Outcome: Restitutio ad integrum"
5
+
6
+ - model: endoreg_db.finding_classification_choice
7
+ fields:
8
+ name: "outcome_death"
9
+ description: "Outcome: Death"
10
+
11
+ - model: endoreg_db.finding_classification_choice
12
+ fields:
13
+ name: "outcome_unknown"
14
+ description: "Outcome: Unknown"
15
+
16
+ - model: endoreg_db.finding_classification_choice
17
+ fields:
18
+ name: "outcome_lasting_disability"
19
+ description: "Outcome: Lasting disability"
endoreg_db/data/finding_classification_choice/yes_no_na.yaml ADDED
@@ -0,0 +1,11 @@
1
+ - model: endoreg_db.finding_classification_choice
2
+ fields:
3
+ name: "yes"
4
+
5
+ - model: endoreg_db.finding_classification_choice
6
+ fields:
7
+ name: "no"
8
+
9
+ - model: endoreg_db.finding_classification_choice
10
+ fields:
11
+ name: "na"
endoreg_db/data/finding_classification_type/colonoscopy_basic.yaml ADDED
@@ -0,0 +1,48 @@
1
+ #####
2
+ # Base types for distinguishing morphology and location
3
+ # Related Fields
4
+ - model: endoreg_db.finding_classification_type
5
+ fields:
6
+ name: "location"
7
+ name_de: "Lokalisation"
8
+ name_en: "Location"
9
+
10
+ - model: endoreg_db.finding_classification_type
11
+ fields:
12
+ name: "morphology"
13
+ name_de: "Morphologie"
14
+ name_en: "Morphology"
15
+
16
+ #####
17
+
18
+ - model: endoreg_db.finding_classification_type
19
+ fields:
20
+ name: "bowel_prep"
21
+
22
+ - model: endoreg_db.finding_classification_type
23
+ fields:
24
+ name: "colon_lesion_size"
25
+
26
+ - model: endoreg_db.finding_classification_type
27
+ fields:
28
+ name: "colon_lesion_surface_intact"
29
+
30
+ - model: endoreg_db.finding_classification_type
31
+ fields:
32
+ name: "colon_lesion_planarity"
33
+
34
+ - model: endoreg_db.finding_classification_type
35
+ fields:
36
+ name: "colon_lesion_circularity"
37
+
38
+ - model: endoreg_db.finding_classification_type
39
+ fields:
40
+ name: "colon_lesion_advanced_imaging"
41
+
42
+ - model: endoreg_db.finding_classification_type
43
+ fields:
44
+ name: "colon_lesion_shape"
45
+
46
+ - model: endoreg_db.finding_classification_type
47
+ fields:
48
+ name: "colon_lesion_capillary_pattern"
endoreg_db/data/finding_intervention/endoscopy_colonoscopy.yaml CHANGED
@@ -152,12 +152,17 @@
152
152
  contraindications: []
153
153
  - model: endoreg_db.finding_intervention
154
154
  fields:
155
- name: colon_eftr
155
+ name: colon_lesion_eftr
156
156
  description:
157
157
  Endoscopic full-thickness resection (EFTR) is a technique used to
158
158
  remove lesions in the colon.
159
159
  intervention_types:
160
160
  - therapeutic
161
161
  - invasive
162
- required_lab_values: []
163
- contraindications: []
162
+ required_lab_values:
163
+ - hemoglobin
164
+ - platelets
165
+ - international_normalized_ratio
166
+ contraindications:
167
+ - anticoagulation-therapeutic
168
+ - thrombocytopenia-severe
endoreg_db/data/finding_morphology_classification_type/colonoscopy.yaml CHANGED
@@ -1,4 +1,4 @@
1
- - model: endoreg_db.finding_morphology_classification_type
1
+ - model: endoreg_db.finding_classification_type
2
2
  fields:
3
3
  name: "colon_lesion_size"
4
4
  name_de: "Größenklassifikation Kolonläsion"
@@ -11,7 +11,7 @@
11
11
  "tumor"
12
12
  ]
13
13
 
14
- - model: endoreg_db.finding_morphology_classification_type
14
+ - model: endoreg_db.finding_classification_type
15
15
  fields:
16
16
  name: "colon_lesion_shape"
17
17
  name_de: "Formklassifikation Kolonläsion"
@@ -24,7 +24,7 @@
24
24
  "tumor"
25
25
  ]
26
26
 
27
- - model: endoreg_db.finding_morphology_classification_type
27
+ - model: endoreg_db.finding_classification_type
28
28
  fields:
29
29
  name: "colon_lesion_surface_intact"
30
30
  name_de: "Oberflächenklassifikation Kolonläsion"
@@ -37,7 +37,7 @@
37
37
  "tumor"
38
38
  ]
39
39
 
40
- - model: endoreg_db.finding_morphology_classification_type
40
+ - model: endoreg_db.finding_classification_type
41
41
  fields:
42
42
  name: "colon_lesion_planarity"
43
43
  name_de: "Planaritätsklassifikation Kolonläsion"
@@ -51,7 +51,7 @@
51
51
  ]
52
52
 
53
53
  # Circularity
54
- - model: endoreg_db.finding_morphology_classification_type
54
+ - model: endoreg_db.finding_classification_type
55
55
  fields:
56
56
  name: "colon_lesion_circularity"
57
57
  name_de: "Kolonläsion - Zirkularität"
@@ -65,7 +65,7 @@
65
65
  ]
66
66
 
67
67
  # colon_lesion_advanced_imaging
68
- - model: endoreg_db.finding_morphology_classification_type
68
+ - model: endoreg_db.finding_classification_type
69
69
  fields:
70
70
  name: "colon_lesion_advanced_imaging"
71
71
  name_de: "Kolonläsion - Advanced Imaging"
endoreg_db/data/finding_type/data.yaml CHANGED
@@ -1,30 +1,43 @@
1
1
  - model: endoreg_db.finding_type
2
2
  fields:
3
3
  name: "macroscopic"
4
- name_de: "Makroskopisch"
5
- name_en: "Macroscopic"
6
4
 
7
5
  - model: endoreg_db.finding_type
8
6
  fields:
9
7
  name: "iatrogenic"
10
- name_de: "Iatrogen"
11
- name_en: "Iatrogenic"
12
8
 
13
9
  - model: endoreg_db.finding_type
14
10
  fields:
15
11
  name: "postinterventional_immediate"
16
- name_de: "Postinterventionell unmittelbar"
17
- name_en: "Postinterventional Immediate"
18
12
 
19
13
  - model: endoreg_db.finding_type
20
14
  fields:
21
15
  name: "postinterventional_delayed"
22
- name_de: "Postinterventionell verzögert"
23
- name_en: "Postinterventional Delayed"
24
16
 
25
17
  - model: endoreg_db.finding_type
26
18
  fields:
27
19
  name: "bleeding"
28
- name_de: "Blutung"
29
- name_en: "Bleeding"
30
20
 
21
+ - model: endoreg_db.finding_type
22
+ fields:
23
+ name: "endoscopy_baseline"
24
+
25
+ - model: endoreg_db.finding_type
26
+ fields:
27
+ name: "medication_related"
28
+
29
+ - model: endoreg_db.finding_type
30
+ fields:
31
+ name: "anatomy"
32
+
33
+ - model: endoreg_db.finding_type
34
+ fields:
35
+ name: "anatomy_colon"
36
+
37
+ - model: endoreg_db.finding_type
38
+ fields:
39
+ name: "summary"
40
+
41
+ - model: endoreg_db.finding_type
42
+ fields:
43
+ name: "complication"
endoreg_db/data/gender/data.yaml CHANGED
@@ -17,7 +17,7 @@
17
17
  abbreviation: "f"
18
18
  - model: endoreg_db.gender
19
19
  fields:
20
- name: "mostly_femaly"
20
+ name: "mostly_female"
21
21
  name_de: "überwiegend weiblich"
22
22
  name_en: "mostly female"
23
23
  abbreviation: "mf"
@@ -33,3 +33,10 @@
33
33
  name_de: "andere"
34
34
  name_en: "other"
35
35
  abbreviation: "x"
36
+ - model: endoreg_db.gender
37
+ fields:
38
+ name: "unknown"
39
+ name_de: "unbekannt"
40
+ name_en: "unknown"
41
+ abbreviation: "?"
42
+
endoreg_db/data/information_source/annotation.yaml ADDED
@@ -0,0 +1,6 @@
1
+ - model: endoreg_db.InformationSource
2
+ fields:
3
+ name: "default_annotation"
4
+ information_source_types: [
5
+ "annotation"
6
+ ]
endoreg_db/data/information_source/prediction.yaml ADDED
@@ -0,0 +1,7 @@
1
+ - model: endoreg_db.InformationSource
2
+ fields:
3
+ name: "default_prediction"
4
+ information_source_types: [
5
+ "prediction"
6
+ ]
7
+
endoreg_db/data/information_source_type/data.yaml ADDED
@@ -0,0 +1,8 @@
1
+ - model: endoreg_db.InformationSourceType
2
+ fields:
3
+ name: "annotation"
4
+
5
+ - model: endoreg_db.InformationSourceType
6
+ fields:
7
+ name: "prediction"
8
+
endoreg_db/data/lab_value/misc.yaml CHANGED
@@ -31,3 +31,46 @@
31
31
  default_unit: "units per liter"
32
32
  default_normal_range: {"min": 60, "max": 160}
33
33
  default_numerical_value_distribution: "uniform_default"
34
+
35
+ # Categorical Lab Values
36
+ - model: endoreg_db.lab_value
37
+ fields:
38
+ name: "blood_group"
39
+ name_de: "Blutgruppe"
40
+ name_en: "Blood Group"
41
+ abbreviation: "BG"
42
+
43
+ - model: endoreg_db.lab_value
44
+ fields:
45
+ name: "urine_bacteria_culture"
46
+ name_de: "Urinbakterienkultur"
47
+ name_en: "Urine Bacteria Culture"
48
+ abbreviation: "UBC"
49
+
50
+ - model: endoreg_db.lab_value
51
+ fields:
52
+ name: "microbiology_pathogen_report"
53
+ name_de: "Mikrobiologie Erregerbericht"
54
+ name_en: "Microbiology Pathogen Report"
55
+ abbreviation: "MPR"
56
+
57
+ - model: endoreg_db.lab_value
58
+ fields:
59
+ name: "drug_screening_urine"
60
+ name_de: "Drogenscreening Urin"
61
+ name_en: "Drug Screening Urine"
62
+ abbreviation: "DSU"
63
+
64
+ - model: endoreg_db.lab_value
65
+ fields:
66
+ name: "antibiotic_resistance_report"
67
+ name_de: "Antibiotikaresistenzbericht"
68
+ name_en: "Antibiotic Resistance Report"
69
+ abbreviation: "ARR"
70
+
71
+ - model: endoreg_db.lab_value
72
+ fields:
73
+ name: "cytology_report"
74
+ name_de: "Zytologiebericht"
75
+ name_en: "Cytology Report"
76
+ abbreviation: "CR"